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Schuster, Matthias; Deluigi, Mattia; Pantić, Milica; Vacca, Santiago; Baumann, Christian; Scott, Daniel J; Plückthun, Andreas; Zerbe, Oliver (2020). Optimizing the α1B-adrenergic receptor for solution NMR studies. BBA Biomembranes, 1862(10):183354.

Gray, Alison C; Bradbury, Andrew R M; Knappik, Achim; Plückthun, Andreas; Borrebaeck, Carl A K; Dübel, Stefan (2020). Animal-derived-antibody generation faces strict reform in accordance with European Union policy on animal use. Nature Methods, 17(8):755-756.

Pinto, Paola H; Kroupova, Alena; Schleiffer, Alexander; Mechtler, Karl; Jinek, Martin; Weitzer, Stefan; Martinez, Javier (2020). ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity. Science, 369(6503):524-530.

Brücher, Dominik; Franc, Vojtech; Smith, Sheena N; Heck, Albert J R; Plückthun, Andreas (2020). Malignant tissues produce divergent antibody glycosylation of relevance for cancer gene therapy effectiveness. mAbs, 12(1):1792084.

Chabloz, Antoine; Schaefer, Jonas V; Kozieradzki, Ivona; Cronin, Shane J F; Strebinger, Daniel; Macaluso, Francesca; Wald, Jiri; Rabbitts, Terence H; Plückthun, Andreas; Marlovits, Thomas C; Penninger, Josef M (2020). Salmonella-based platform for efficient delivery of functional binding proteins to the cytosol. Communications Biology, 3(1):342.

Persson, B David; Lenman, Annasara; Frängsmyr, Lars; Schmid, Markus; Ahlm, Clas; Plückthun, Andreas; Jenssen, Håvard; Arnberg, Niklas (2020). Lactoferrin-hexon interactions mediate CAR-independent adenovirus infection of human respiratory cells. Journal of Virology, 94(14):e00542-20.

Zosel, Franziska; Soranno, Andrea; Buholzer, Karin J; Nettels, Daniel; Schuler, Benjamin (2020). Depletion interactions modulate the binding between disordered proteins in crowded environments. Proceedings of the National Academy of Sciences of the United States of America, 117(24):13480-13489.

Wrona, Dominik; Pastukhov, Oleksandr; Pritchard, Robert S; Raimondi, Federica; Tchinda, Joëlle; Jinek, Martin; Siler, Ulrich; Reichenbach, Janine (2020). CRISPR-Directed Therapeutic Correction at the NCF1 Locus Is Challenged by Frequent Incidence of Chromosomal Deletions. Molecular Therapy - Methods & Clinical Development, 17:936-943.

Drożdżyk, Katarzyna; Sawicka, Marta; Bahamonde-Santos, Maria-Isabel; Jonas, Zaugg; Deneka, Dawid; Albrecht, Christiane; Dutzler, Raimund (2020). Cryo-EM structures and functional properties of CALHM channels of the human placenta. eLife, 9:e55853.

Bedi, Rajiv K; Huang, Danzhi; Eberle, Stefanie A; Wiedmer, Lars; Śledź, Pawel; Caflisch, Amedeo (2020). Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer. ChemMedChem, 15(9):744-748.

Gray, Alison C; Bradbury, Andrew; Dübel, Stefan; Knappik, Achim; Plückthun, Andreas; Borrebaeck, Carl A K (2020). Reproducibility: bypass animals for antibody production. Nature, 581(7808):262.

Pretze, Marc; Neuber, Christin; Kinski, Elisa; Belter, Birgit; Köckerling, Martin; Caflisch, Amedeo; Steinbach, Jörg; Pietzsch, Jens; Mamat, Constantin (2020). Synthesis, radiolabelling and initial biological characterisation of $^{18}$F-labelled xanthine derivatives for PET imaging of Eph receptors. Organic & Biomolecular Chemistry, 18(16):3104-3116.

Andres, Fabio; Schwill, Martin; Boersma, Ykelien L; Plückthun, Andreas (2020). High-Throughput Generation of Bispecific Binding Proteins by Sortase A-Mediated Coupling for Direct Functional Screening in Cell Culture. Molecular Cancer Therapeutics, 19(4):1080-1088.

Arnold, Fabian M; Weber, Miriam S; Gonda, Imre; Gallenito, Marc J; Adenau, Sophia; Egloff, Pascal; Zimmermann, Iwan; Hutter, Cedric A J; Hürlimann, Lea M; Peters, Eike E; Piel, Jörn; Meloni, Gabriele; Medalia, Ohad; Seeger, Markus A (2020). The ABC exporter IrtAB imports and reduces mycobacterial siderophores. Nature, 580(7803):413-417.

Davies, Kevin; Jínek, Martin (2020). The CRISPR-RNA World: An Interview with Martin Jínek. The CRISPR journal, 3(2):68-72.

Bertrand, Anne T; Brull, Astrid; Azibani, Feriel; Benarroch, Louise; Chikhaoui, Khadija; Stewart, Colin L; Medalia, Ohad; Ben Yaou, Rabah; Bonne, Gisèle (2020). Lamin A/C Assembly Defects in LMNA-Congenital Muscular Dystrophy Is Responsible for the Increased Severity of the Disease Compared with Emery-Dreifuss Muscular Dystrophy. Cells, 9(4):844-861.

Garcia-Doval, Carmela; Schwede, Frank; Berk, Christian; Rostøl, Jakob T; Niewoehner, Ole; Tejero, Oliver; Hall, Jonathan; Marraffini, Luciano A; Jinek, Martin (2020). Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6. Nature Communications, 11:1596.

Bedi, Rajiv Kumar; Huang, Danzhi; Wiedmer, Lars; Li, Yaozong; Dolbois, Aymeric; Wojdyla, Justyna Aleksandra; Sharpe, May Elizabeth; Caflisch, Amedeo; Sledz, Pawel (2020). Selectively Disrupting m$^{6}$A-Dependent Protein-RNA Interactions with Fragments. ACS Chemical Biology, 15(3):618-625.

Petrenčáková, Martina; Filandr, František; Hovan, Andrej; Yassaghi, Ghazaleh; Man, Petr; Kožár, Tibor; Schwer, Marc-Simon; Jancura, Daniel; Plückthun, Andreas; Novák, Petr; Miškovský, Pavol; Bánó, Gregor; Sedlák, Erik (2020). Photoinduced damage of AsLOV2 domain is accompanied by increased singlet oxygen production due to flavin dissociation. Scientific Reports, 10:4119.

Quesada, Roberto; Dutzler, Raimund (2020). Alternative chloride transport pathways as pharmacological targets for the treatment of cystic fibrosis. Journal of Cystic Fibrosis, 19 Suppl:S37-S41.

Ernst, Patrick; Zosel, Franziska; Reichen, Christian; Nettels, Daniel; Schuler, Benjamin; Plückthun, Andreas (2020). Structure-Guided Design of a Peptide Lock for Modular Peptide Binders. ACS Chemical Biology, 15(2):457-468.

Mittl, Peer Re; Ernst, Patrick; Plückthun, Andreas (2020). Chaperone-assisted structure elucidation with DARPins. Current Opinion in Structural Biology, 60:93-100.

Gosavi, Shachi; Schuler, Benjamin (2020). Editorial overview: Molecular interactions that drive folding and binding: new challenges and opportunities. Current Opinion in Structural Biology, 60:iii-iv.

Kast, Florian. Engineering Biparatopic Antibodies and Their Mechanisms of Action. 2020, University of Zurich, Faculty of Science.

Caflisch, Amedeo (2020). Kinetic Control of Amyloidogenesis Calls for Unconventional Drugs To Fight Alzheimer's Disease. ACS Chemical Neuroscience, 11(2):103-104.

Salutari, Ilaria; Martin, Roland; Caflisch, Amedeo (2020). The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins, 88(1):31-46.

Horev, Melanie B; Zabary, Yishaia; Zarka, Revital; Sorrentino, Simona; Medalia, Ohad; Zaritsky, Assaf; Geiger, Benjamin (2020). Differential dynamics of early stages of platelet adhesion and spreading on collagen IV- and fibrinogen-coated surfaces. F1000Research, 9:ISF-449.


Schuler, Benjamin; Borgia, Alessandro; Borgia, Madeleine B; Heidarsson, Pétur O; Holmstrom, Erik D; Nettels, Daniel; Sottini, Andrea (2019). Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Current Opinion in Structural Biology, 60:66-76.

Assenza, Salvatore; Sassi, Alberto Stefano; Kellner, Ruth; Schuler, Benjamin; De Los Rios, Paolo; Barducci, Alessandro (2019). Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones. eLife, 8:e48491.

Balakrishnan, Ashwini; Rajan, Anusha; Salter, Alexander I; Kosasih, Paula L; Wu, Qian; Voutsinas, Jenna; Jensen, Michael C; Plückthun, Andreas; Riddell, Stanley R (2019). Multispecific Targeting with Synthetic Ankyrin Repeat Motif Chimeric Antigen Receptors. Clinical Cancer Research, 25(24):7506-7516.

Li, Yaozong; Bedi, Rajiv Kumar; Wiedmer, Lars; Huang, Danzhi; Śledź, Pawel; Caflisch, Amedeo (2019). Flexible binding of m$^{6}$A reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation, 15(12):7004-7014.

Chernyavska, M; Schmid, M; Freitag, P C; Palacio-Castañeda, V; Piruska, A; Huck, W T S; Plückthun, Andreas; Verdurmen, W P R (2019). Unravelling receptor and RGD motif dependence of retargeted adenoviral vectors using advanced tumor model systems. Scientific Reports, 9(1):18568.

Manatschal, Cristina; Pujol-Giménez, Jonai; Poirier, Marion; Reymond, Jean-Louis; Hediger, Matthias A; Dutzler, Raimund (2019). Mechanistic basis of the inhibition of SLC11/NRAMP-mediated metal ion transport by bis-isothiourea substituted compounds. eLife, 8:e51913.

Allain, Frédéric H-T; Jinek, Martin (2019). Editorial overview: Protein-nucleic acid interactions - cryo-EM, what else? Current Opinion in Structural Biology, 59:vi-viii.

Dumeau, Charles-Etienne; Monfort, Asun; Kissling, Lucas; Swarts, Daan C; Jinek, Martin; Wutz, Anton (2019). Introducing gene deletions by mouse zygote electroporation of Cas12a/Cpf1. Transgenic research, 28(5-6):525-535.

Kumar, Ananthanarayanan; Clerici, Marcello; Muckenfuss, Lena M; Passmore, Lori A; Jinek, Martin (2019). Mechanistic insights into mRNA 3'-end processing. Current Opinion in Structural Biology, 59:143-150.

Ehrenmann, Janosch; Schöppe, Jendrik; Klenk, Christoph; Plückthun, Andreas (2019). New views into class B GPCRs from the crystal structure of PTH1R. FEBS Journal, 286(24):4852-4860.

Jinek, Martin (2019). Uncut but primed for change. The CRISPR journal, 2(6):352-354.

Ernst, Patrick; Honegger, Annemarie; van der Valk, Floor; Ewald, Christina; Mittl, Peer R E; Plückthun, Andreas (2019). Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts. Scientific Reports, 9:16162.

Boneberg, Franziska M; Brandmann, Tobias; Kobel, Lena; van den Heuvel, Jasmin; Bargsten, Katja; Bammert, Lukas; Kutay, Ulrike; Jinek, Martin (2019). Corrigendum: Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA, 25(11):1576.

Dunne, Matthew; Rupf, Beatrice; Tala, Marc; Qabrati, Xhem; Ernst, Patrick; Shen, Yang; Sumrall, Eric; Heeb, Laura; Plückthun, Andreas; Loessner, Martin J; Kilcher, Samuel (2019). Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Reports, 29(5):1336-1350.e4.

Ernst, Patrick; Plückthun, Andreas; Mittl, Peer R E (2019). Structural analysis of biological targets by host:guest crystal lattice engineering. Scientific Reports, 9:15199.

Renko, Miha; Fiedler, Marc; Rutherford, Trevor J; Schaefer, Jonas V; Plückthun, Andreas; Bienz, Mariann (2019). Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome. Proceedings of the National Academy of Sciences of the United States of America, 116(42):20977-20983.

Karoutas, Adam; Szymanski, Witold; Rausch, Tobias; Guhathakurta, Sukanya; Rog-Zielinska, Eva A; Peyronnet, Remi; Seyfferth, Janine; Chen, Hui-Ru; de Leeuw, Rebecca; Herquel, Benjamin; Kimura, Hiroshi; Mittler, Gerhard; Kohl, Peter; Medalia, Ohad; Korbel, Jan O; Akhtar, Asifa (2019). The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nature Cell Biology, 21(10):1248-1260.

Boneberg, Franziska M. Molecular Mechanisms of DExH/D-Box RNA Helicases Involved in Eukaryotic Ribosome Assembly. 2019, University of Zurich, Faculty of Science.

Brandl, Fabian; Merten, Hannes; Zimmermann, Martina; Béhé, Martin; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2019). Influence of size and charge of unstructured polypeptides on pharmacokinetics and biodistribution of targeted fusion proteins. Journal of Controlled Release, 307:379-392.

Wiedmer, Lars; Schärer, Claude; Spiliotopoulos, Dimitrios; Hürzeler, Marianne; Śledź, Paweł; Caflisch, Amedeo (2019). Ligand retargeting by binding site analogy. European journal of medicinal chemistry, 175:107-113.

Lorenzer, Cornelia; Streußnig, Sonja; Tot, Emilia; Winkler, Anna-Maria; Merten, Hannes; Brandl, Fabian; Sayers, Edward J; Watson, Peter; Jones, Arwyn T; Zangemeister-Wittke, Uwe; Plückthun, Andreas; Winkler, Johannes (2019). Targeted delivery and endosomal cellular uptake of DARPin-siRNA bioconjugates: Influence of linker stability on gene silencing. European Journal of Pharmaceutics and Biopharmaceutics, 141:37-50.

Bunzel, H Adrian; Kries, Hajo; Marchetti, Luca; Zeymer, Cathleen; Mittl, Peer R E; Mulholland, Adrian J; Hilvert, Donald (2019). Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme. Journal of the American Chemical Society, 141(30):11745-11748.

Walter, Justin D; Sawicka, Marta; Dutzler, Raimund (2019). Cryo-EM structures and functional characterization of murine Slc26a9 reveal mechanism of uncoupled chloride transport. eLife, 8:e46986.

Radom, Filip; Paci, Emanuele; Plückthun, Andreas (2019). Computational Modeling of Designed Ankyrin Repeat Protein Complexes with Their Targets. Journal of Molecular Biology, 431(15):2852-2868.

Radom, Filip. Computational Modeling of Protein–Protein Complexes with Therapeutic Binding Proteins. 2019, University of Zurich, Faculty of Science.

Wiedmer, Lars. New Strategies for Virtual Screening and Assay Development. 2019, University of Zurich, Faculty of Science.

Sorrentino, Simona. Structural Analysis of Platelets Using Cryo-Electron Tomography. 2019, University of Zurich, Faculty of Science.

Stüber, Jakob C; Kast, Florian; Plückthun, Andreas (2019). High-Throughput Quantification of Surface Protein Internalization and Degradation. ACS Chemical Biology, 14(6):1154-1163.

Hegge, Jorrit W; Swarts, Daan C; Chandradoss, Stanley D; Cui, Tao Ju; Kneppers, Jeroen; Jinek, Martin; Joo, Chirlmin; van der Oost, John (2019). DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Research, 47(11):5809-5821.

Walter, Justin. On the Boundary Between Channels and Transporters – Studies of Slc26a9. 2019, University of Zurich, Faculty of Science.

Holmstrom, Erik D; Liu, Zhaowei; Nettels, Daniel; Best, Robert B; Schuler, Benjamin (2019). Disordered RNA chaperones can enhance nucleic acid folding via local charge screening. Nature Communications, 10:2453.

Boneberg, Franziska M; Brandmann, Tobias; Kobel, Lena; van den Heuvel, Jasmin; Bargsten, Katja; Bammert, Lukas; Kutay, Ulrike; Jinek, Martin (2019). Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA, 25(6):685-701.

Campanacci, Valérie; Urvoas, Agathe; Cantos-Fernandes, Soraya; Aumont-Nicaise, Magali; Arteni, Ana-Andreea; Velours, Christophe; Valerio-Lepiniec, Marie; Dreier, Birgit; Plückthun, Andreas; Pilon, Antoine; Poüs, Christian; Minard, Philippe; Gigant, Benoît (2019). Insight into microtubule nucleation from tubulin-capping proteins. Proceedings of the National Academy of Sciences of the United States of America, 116(20):9859-9864.

Andres, Fabio; Iamele, Luisa; Meyer, Timo; Stüber, Jakob C; Kast, Florian; Gherardi, Ermanno; Niemann, Hartmut H; Plückthun, Andreas (2019). Inhibition of the MET Kinase Activity and Cell Growth in MET-Addicted Cancer Cells by Bi-Paratopic Linking. Journal of Molecular Biology, 431(10):2020-2039.

Qi, Chao; Sorrentino, Simona; Medalia, Ohad; Korkhov, Volodymyr M (2019). The structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein. Science, 364(6438):389-394.

Ricci, Clarisse G; Chen, Janice S; Miao, Yinglong; Jinek, Martin; Doudna, Jennifer A; McCammon, J Andrew; Palermo, Giulia (2019). Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Central Science, 5(4):651-662.

Meksiriporn, Bunyarit; Ludwicki, Morgan B; Stephens, Erin A; Jiang, Allen; Lee, Hyeon-Cheol; Waraho-Zhmayev, Dujduan; Kummer, Lutz; Brandl, Fabian; Plückthun, Andreas; DeLisa, Matthew P (2019). A survival selection strategy for engineering synthetic binding proteins that specifically recognize post-translationally phosphorylated proteins. Nature Communications, 10:1830.

Deprey, Kirsten; Becker, Lukas; Kritzer, Joshua; Plückthun, Andreas (2019). Trapped! A Critical Evaluation of Methods for Measuring Total Cellular Uptake versus Cytosolic Localization. Bioconjugate Chemistry, 30(4):1006-1027.

Garolini, Davide; Vitalis, Andreas; Caflisch, Amedeo (2019). Unsupervised identification of states from voltage recordings of neural networks. Journal of Neuroscience Methods, 318:104-117.

Ilie, Ioana M; Caflisch, Amedeo (2019). Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chemical Reviews, 119(12):6956-6993.

Buholzer, Karin. Interactions of Intrinsically Disordered Proteins Studied with Single-Molecule Spectroscopy. 2019, University of Zurich, Faculty of Science.

Heine, P; Witt, G; Gilardi, A; Gribbon, P; Kummer, L; Plückthun, Andreas (2019). High-Throughput Fluorescence Polarization Assay to Identify Ligands Using Purified G Protein-Coupled Receptor. SLAS Discovery:2472555219837344.

Gall, Flavio M; Hohl, Deborah; Frasson, David; Wermelinger, Tobias; Mittl, Peer R E; Sievers, Martin; Riedl, Rainer (2019). Drug Design Inspired by Nature: Crystallographic Detection of an Auto-Tailored Protease Inhibitor Template. Angewandte Chemie Internationale Edition, 58(12):4051-4055.

Bacci, Marco; Caflisch, Amedeo; Vitalis, Andreas (2019). On the removal of initial state bias from simulation data. Journal of Chemical Physics, 150(10):104105.

Michel, Erich; Plückthun, Andreas; Zerbe, Oliver (2019). Peptide binding affinity redistributes preassembled repeat protein fragments. Biological Chemistry, 400(3):395-404.

Tomatis, Pablo Emiliano; Schütz, Marco; Umudumov, Elina; Plückthun, Andreas (2019). Mutations in sigma 70 transcription factor improves expression of functional eukaryotic membrane proteins in Escherichia coli. Scientific Reports, 9(1):2483.

Kalienkova, Valeria; Clerico Mosina, Vanessa; Bryner, Laura; Oostergetel, Gert T; Dutzler, Raimund; Paulino, Cristina (2019). Stepwise activation mechanism of the scramblase nhTMEM16 revealed by cryo-EM. eLife, 8:e44364.

Alvadia, Carolina; Lim, Novandy K; Clerico Mosina, Vanessa; Oostergetel, Gert T; Dutzler, Raimund; Paulino, Cristina (2019). Cryo-EM structures and functional characterization of the murine lipid scramblase TMEM16F. eLife, 8:e44365.

Wiedmer, Lars; Eberle, Stefanie Alexandra; Bedi, Rajiv Kumar; Śledź, Paweł; Caflisch, Amedeo (2019). A Reader-Based Assay for mA Writers and Erasers. Analytical Chemistry, 91(4):3078-3084.

Swarts, Daan C; Jinek, Martin (2019). Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. Molecular Cell, 73(3):589-600.e4.

Gay, Jamie C; Eckenroth, Brian E; Evans, Chiara M; Langini, Cassiano; Carlson, Samuel; Lloyd, Jonathan T; Caflisch, Amedeo; Glass, Karen C (2019). Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins, 87(2):157-167.

Kroupova, Alena; Ivaşcu, Anastasia; Reimão-Pinto, Madalena M; Ameres, Stefan L; Jinek, Martin (2019). Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Research, 47(2):1030-1042.

Schwill, Martin; Tamaskovic, Rastislav; Gajadhar, Aaron S; Kast, Florian; White, Forest M; Plückthun, Andreas (2019). Systemic analysis of tyrosine kinase signaling reveals a common adaptive response program in a HER2-positive breast cancer. Science Signaling, 12(565):1-23.

Weber, Miriam Sarah; Wojtynek, Matthias; Medalia, Ohad (2019). Cellular and Structural Studies of Eukaryotic Cells by Cryo-Electron Tomography. Cells, 8(1):57.

Savić, Nataša; Ringnalda, Femke Cas; Berk, Christian; Bargsten, Katja; Hall, Jonathan; Jinek, Martin; Schwank, Gerald (2019). In vitro Generation of CRISPR-Cas9 Complexes with Covalently Bound Repair Templates for Genome Editing in Mammalian Cells. Bio-protocol, 9(1):1-48.

Schöppe, Jendrik; Ehrenmann, Janosch; Klenk, Christoph; Rucktooa, Prakash; Schütz, Marco; Doré, Andrew S; Plückthun, Andreas (2019). Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Nature Communications, 10(1):17.

Davey, Norman E; Babu, M Madan; Blackledge, Martin; Bridge, Alan; Capella-Gutierrez, Salvador; Dosztanyi, Zsuzsanna; Drysdale, Rachel; Edwards, Richard J; Elofsson, Arne; Felli, Isabella C; Gibson, Toby J; Gutmanas, Aleksandras; Hancock, John M; Harrow, Jen; Higgins, Desmond; Jeffries, Cy M; Le Mercier, Philippe; Mészáros, Balint; Necci, Marco; Notredame, Cedric; Orchard, Sandra; Ouzounis, Christos A; Pancsa, Rita; Papaleo, Elena; Pierattelli, Roberta; Piovesan, Damiano; Promponas, Vasilis J; Ruch, Patrick; Rustici, Gabriella; Romero, Pedro; et al (2019). An intrinsically disordered proteins community for ELIXIR. F1000Research, 8:1753.

Ernst, Patrick. Design and characterization of Armadillo repeat proteins and novel crystallization chaperones. 2019, University of Zurich, Faculty of Science.

Merten, Hannes; Schaefer, Jonas V; Brandl, Fabian; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2019). Facile Site-Specific Multiconjugation Strategies in Recombinant Proteins Produced in Bacteria. In: Massa, Sam; Devoogdt, Nick. Bioconjugation : Methods and Protocols. New York: Springer, 253-273.

Kumar, Abhinav; Plückthun, Andreas (2019). In vivo assembly and large-scale purification of a GPCR - Gα fusion with Gβγ, and characterization of the active complex. PLoS ONE, 14(1):e0210131.

Stüber, Jakob C; Plückthun, Andreas (2019). Labeling surface proteins with high specificity: Intrinsic limitations of phosphopantetheinyl transferase systems. PLoS ONE, 14(12):e0226579.

Kissling, Lucas; Monfort, Asun; Swarts, Daan C; Wutz, Anton; Jinek, Martin (2019). Preparation and electroporation of Cas12a/Cpf1-guide RNA complexes for introducing large gene deletions in mouse embryonic stem cells. In: Pyle, A M; Christianson, D W. Methods in Enzymology. Cambridge MA: Elsevier, 241-263.

Schöppe, Jendrik. Protein engineering and structural biology of G protein-coupled receptors. 2019, University of Zurich, Faculty of Science.

Zhang, Yi; Auger, Shelby; Schaefer, Jonas V; Plückthun, Andreas; Distefano, Mark D (2019). Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. In: Massa, Sam; Devoogdt, Nick. Bioconjugation : Methods and Protocols. New York: Springer, 207-219.

Kalienkova, Valeriia. Structural prespective on lipid scrambling by TMEM16 proteins. 2019, University of Zurich, Faculty of Science.

Chen, Tse-Hsiang. Therapeutic potential of bromodomain inhibitors for the treatment of tumor necrosis factor-α-compromised bone regeneration. 2019, University of Zurich, Faculty of Science.


Studer, Sabine; Hansen, Douglas A; Pianowski, Zbigniew L; Mittl, Peer R E; Debon, Aaron; Guffy, Sharon L; Der, Bryan S; Kuhlman, Brian; Hilvert, Donald (2018). Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science, 362(6420):1285-1288.

Nishimura, Tamiko; Fakim, Hana; Brandmann, Tobias; Youn, Ji-Young; Gingras, Anne-Claude; Jinek, Martin; Fabian, Marc R (2018). Human MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs. Nucleic Acids Research, 46(22):12008-12021.

Vigano, M Alessandra; Bieli, Dimitri; Schaefer, Jonas V; Jakob, Roman P; Matsuda, Shinya; Maier, Timm; Plückthun, Andreas; Affolter, Markus (2018). Correction: DARPins recognizing mTFP1 as novel reagents for and protein manipulations (doi:10.1242/bio.036749). Biology Open, 7(12):1.

Schuler, Benjamin; Szabo, Attila; Wolynes, Peter G (2018). Tribute to William A. Eaton. Journal of Physical Chemistry B, 122(49):10971-10973.

Ernst, Patrick. Design of Armadillo Repeat Proteins and Novel Crystallization Chaperones. 2018, University of Zurich, Faculty of Science.

Gutte, B; Klauser, S (2018). Design of catalytic polypeptides and proteins. Protein Engineering, Design & Selection, 31(12):457-470.

Ehrenmann, Janosch; Schöppe, Jendrik; Klenk, Christoph; Rappas, Mathieu; Kummer, Lutz; Doré, Andrew S; Plückthun, Andreas (2018). High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. Nature Structural & Molecular Biology, 25(12):1086-1092.

Śledź, Pawel; Caflisch, Amedeo (2018). Protein structure-based drug design: from docking to molecular dynamics. Current Opinion in Structural Biology, 48:93-102.

Rezaei-Ghaleh, Nasrollah; Parigi, Giacomo; Soranno, Andrea; Holla, Andrea; Becker, Stefan; Schuler, Benjamin; Luchinat, Claudio; Zweckstetter, Markus (2018). Local and Global Dynamics in Intrinsically Disordered Synuclein. Angewandte Chemie Internationale Edition, 57(46):15262-15266.

Sturzenegger, Flurin; Zosel, Franziska; Holmstrom, Erik D; Buholzer, Karin J; Makarov, Dmitrii E; Nettels, Daniel; Schuler, Benjamin (2018). Transition path times of coupled folding and binding reveal the formation of an encounter complex. Nature Communications, 9:4708.

Saponara, Enrica; Visentin, Michele; Baschieri, Francesco; Seleznik, Gitta; Martinelli, Paola; Esposito, Irene; Buschmann, Johanna; Chen, Rong; Parrotta, Rossella; Borgeaud, Nathalie; Bombardo, Marta; Malagola, Ermanno; Caflisch, Amedeo; Farhan, Hesso; Graf, Rolf; Sonda, Sabrina (2018). Serotonin uptake is required for Rac1 activation in Kras-induced acinar-to-ductal metaplasia in the pancreas. Journal of Pathology, 246(3):352-365.

Hellenkamp, Björn; Schmid, Sonja; et al; Nettels, Daniel; Schuler, Benjamin (2018). Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature Methods, 15(11):984.

Esposito, Carmen; Vitalis, Andreas (2018). Precise estimation of transfer free energies for ionic species between similar media. Physical Chemistry Chemical Physics (PCCP), 20(42):27003-27010.

Vigano, M Alessandra; Bieli, Dimitri; Schaefer, Jonas V; Jakob, Roman P; Matsuda, Shinya; Maier, Timm; Plückthun, Andreas; Affolter, Markus (2018). DARPins recognize mTFP1 as novel reagents for and protein manipulations. Biology Open, 7(11):036749.

Esposito, C; Wiedmer, L; Caflisch, A (2018). In Silico Identification of JMJD3 Demethylase Inhibitors. Journal of Chemical Information and Modeling, 58(10):2151-2163.

Grotz, Kara K; Nueesch, Mark F; Holmstrom, Erik D; Heinz, Marcel; Stelzl, Lukas S; Schuler, Benjamin; Hummer, Gerhard (2018). Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. Journal of Physical Chemistry B, 122:11626-11639.

Lam, Andy K M; Dutzler, Raimund (2018). Calcium-dependent electrostatic control of anion access to the pore of the calcium-activated chloride channel TMEM16A. eLife, 7:39122.

Zheng, Wenwei; Hofmann, Hagen; Schuler, Benjamin; Best, Robert B (2018). Origin of Internal Friction in Disordered Proteins Depends on Solvent Quality. Journal of Physical Chemistry B, 122:11478-11487.

Dahan, Idit; Sorrentino, Simona; Boujemaa-Paterski, Rajaa; Medalia, Ohad (2018). Tiopronin-Protected Gold Nanoparticles as a Potential Marker for Cryo-EM and Tomography. Structure, 26(10):1408-1413.e3.

Hartmann, Jessica; Münch, Robert C; Freiling, Ruth-Therese; Schneider, Irene C; Dreier, Birgit; Samukange, Washington; Koch, Joachim; Seeger, Markus A; Plückthun, Andreas; Buchholz, Christian J (2018). A Library-Based Screening Strategy for the Identification of DARPins as Ligands for Receptor-Targeted AAV and Lentiviral Vectors. Molecular Therapy - Methods & Clinical Development, 10:128-143.

ElGamacy, Mohammad; Coles, Murray; Ernst, Patrick; Zhu, Hongbo; Hartmann, Marcus D; Plückthun, Andreas; Lupas, Andrei N (2018). An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture. ACS Synthetic Biology, 7(9):2226-2235.

Marino, Jacopo; Buholzer, Karin J; Zosel, Franziska; Nettels, Daniel; Schuler, Benjamin (2018). Charge Interactions Can Dominate Coupled Folding and Binding on the Ribosome. Biophysical Journal, 115(6):996-1006.

Dingfelder, Fabian. Microfluidic Devices for Probing Protein Dynamics with Single-Molecule Spectroscopy. 2018, University of Zurich, Faculty of Science.

Zhu, Jian; Dong, Jing; Batiste, Laurent; Unzue, Andrea; Dolbois, Aymeric; Pascanu, Vlad; Śledź, Paweł; Nevado, Cristina; Caflisch, Amedeo (2018). Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules. ACS Medicinal Chemistry Letters, 9(9):929-934.

Dingfelder, Fabian; Benke, Stephan; Nettels, Daniel; Schuler, Benjamin (2018). Mapping an Equilibrium Folding Intermediate of the Cytolytic Pore Toxin ClyA with Single-Molecule FRET. Journal of Physical Chemistry B, 122:11251-11261.

Hellenkamp, Björn; Schmid, Sonja; et al; Nettels, Daniel; Schuler, Benjamin (2018). Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature Methods, 15(9):669-676.

Best, Robert B; Zheng, Wenwei; Borgia, Alessandro; Buholzer, Karin; Borgia, Madeleine B; Hofmann, Hagen; Soranno, Andrea; Nettels, Daniel; Gast, Klaus; Grishaev, Alexander; Schuler, Benjamin (2018). Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water". Science, 361(6405):eaar7101.

Kumar, Abhinav. G Protein-Coupled Receptor-Gα Fusion Proteins: A Tool for Investigating the GPCR – G protein Interactions. 2018, University of Zurich, Faculty of Science.

Esposito, Carmen. In silico screening for demethylase inhibitors and simulations of proteins in the denatured state. 2018, University of Zurich, Faculty of Science.

Zosel, Franziska; Mercadante, Davide; Nettels, Daniel; Schuler, Benjamin (2018). A proline switch explains kinetic heterogeneity in a coupled folding and binding reaction. Nature Communications, 9:3332.

Stüber, Jakob C. Molecular Mechanisms of ErbB Receptor Targeting. 2018, University of Zurich, Faculty of Science.

Mikula, Kornelia M; Krumwiede, Luisa; Plückthun, Andreas; Iwaï, Hideo (2018). Segmental isotopic labeling by asparaginyl endopeptidase-mediated protein ligation. Journal of Biomolecular NMR, 71(4):225-235.

Dalle Vedove, Andrea; Spiliotopoulos, Dimitrios; D'Agostino, Vito G; Marchand, Jean-Rémy; Unzue, Andrea; Nevado, Cristina; Lolli, Graziano; Caflisch, Amedeo (2018). Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains. ChemMedChem, 13(14):1479-1487.

Ilie, Ioana M; Caflisch, Amedeo (2018). Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. Journal of Physical Chemistry B, 122:11072-11082.

Marchand, Jean-Rémy; Caflisch, Amedeo (2018). In silico fragment-based drug design with SEED. European journal of medicinal chemistry, 156:907-917.

Zhu, Jian; Zhou, Chunxian; Caflisch, Amedeo (2018). Structure-based discovery of selective BRPF1 bromodomain inhibitors. European journal of medicinal chemistry, 155:337-352.

Schuler, Benjamin (2018). Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET. Journal of Chemical Physics, 149(1):010901.

Wu, Yufan; Honegger, Annemarie; Batyuk, Alexander; Mittl, Peer R E; Plückthun, Andreas (2018). Structural Basis for the Selective Inhibition of c-Jun N-Terminal Kinase 1 Determined by Rigid DARPin-DARPin Fusions. Journal of Molecular Biology, 430(14):2128-2138.

Yen, Hsin-Yung; Hoi, Kin Kuan; Liko, Idlir; Hedger, George; Horrell, Michael R; Song, Wanling; Wu, Di; Heine, Philipp; Warne, Tony; Lee, Yang; Carpenter, Byron; Plückthun, Andreas; Tate, Christopher G; Sansom, Mark S P; Robinson, Carol V (2018). PtdIns(4,5)P stabilizes active states of GPCRs and enhances selectivity of G-protein coupling. Nature, 559(7714):423-427.

Brandmann, Tobias. Structural and Biochemical Studies of Proteins Involved in RNA-Targeting Innate Immunity and mRNA turnover. 2018, University of Zurich, Faculty of Science.

Heine, Philipp. In vitro Ligand Screening with a Peptide-Binding G Protein-Coupled Recepto. 2018, University of Zurich, Faculty of Science.

Radom, Filip; Plückthun, Andreas; Paci, Emanuele (2018). Assessment of ab initio models of protein complexes by molecular dynamics. PLoS Computational Biology, 14(6):e1006182.

Swainston, Neil; Baici, Antonio; Bakker, Barbara M; Cornish-Bowden, Athel; Fitzpatrick, Paul F; Halling, Peter; Leyh, Thomas S; O'Donovan, Claire; Raushel, Frank M; Reschel, Udo; Rohwer, Johann M; Schnell, Santiago; Schomburg, Dietmar; Tipton, Keith F; Tsai, Ming-Daw; Westerhoff, Hans V; Wittig, Ulrike; Wohlgemuth, Roland; Kettner, Carsten (2018). STRENDA DB: enabling the validation and sharing of enzyme kinetics data. FEBS Journal, 285(12):2193-2204.

Deneka, Dawid; Sawicka, Marta; Lam, Andy K M; Paulino, Cristina; Dutzler, Raimund (2018). Structure of a volume-regulated anion channel of the LRRC8 family. Nature, 558(7709):254-259.

Savic, Natasa; Ringnalda, Femke Cas; Lindsay, Helen; Berk, Christian; Bargsten, Katja; Li, Yizhou; Neri, Dario; Robinson, Mark D; Ciaudo, Constance; Hall, Jonathan; Jinek, Martin; Schwank, Gerald (2018). Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. eLife, 7:33761.

Swarts, Daan C; Jinek, Martin (2018). Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing. Wiley Interdisciplinary Reviews. RNA, 9:e1481.

Tatli, Meltem; Medalia, Ohad (2018). Insight into the functional organization of nuclear lamins in health and disease. Current Opinion in Cell Biology, 54:72-79.

Stritt, Simon; Birkholz, Inga; Beck, Sarah; Sorrentino, Simona; Sapra, K Tanuj; Viaud, Julien; Heck, Johannes; Gaits-Iacovoni, Frédérique; Schulze, Harald; Du, Xiaoping; Hartwig, John H; Braun, Attila; Bender, Markus; Medalia, Ohad; Nieswandt, Bernhard (2018). Profilin 1-mediated cytoskeletal rearrangements regulate integrin function in mouse platelets. Blood advances, 2(9):1040-1045.

Schaefer, Jonas V; Sedlák, Erik; Kast, Florian; Nemergut, Michal; Plückthun, Andreas (2018). Modification of the kinetic stability of immunoglobulin G by solvent additives. mAbs, 10(4):607-623.

Unzue, A; Cribiú, R; Hoffman, M M; Knehans, T; Lafleur, K; Caflisch, A; Nevado, C (2018). Iriomoteolides: novel chemical tools to study actin dynamics. Chemical Science, 9(15):3793-3802.

Yong, Kelvin J; Vaid, Tasneem M; Shilling, Patrick J; Wu, Feng-Jie; Williams, Lisa M; Deluigi, Mattia; Plückthun, Andreas; Bathgate, Ross A D; Gooley, Paul R; Scott, Daniel J (2018). Determinants of Ligand Subtype-Selectivity at α-Adrenoceptor Revealed Using Saturation Transfer Difference (STD) NMR. ACS Chemical Biology, 13(4):1090-1102.

Brandmann, Tobias; Fakim, Hana; Padamsi, Zoya; Youn, Ji-Young; Gingras, Anne-Claude; Fabian, Marc R; Jinek, Martin (2018). Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. EMBO Journal Online, 37(7):e97869.

Lickert, Sebastian; Sorrentino, Simona; Studt, Jan-Dirk; Medalia, Ohad; Vogel, Viola; Schoen, Ingmar (2018). Morphometric analysis of spread platelets identifies integrin αβ-specific contractile phenotype. Scientific Reports, 8(1):5428.

Clerici, Marcello; Faini, Marco; Muckenfuss, Lena M; Aebersold, Ruedi; Jinek, Martin (2018). Author Correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nature Structural & Molecular Biology, 25(4):355.

Schmid, Markus. Development of an Adenoviral Gene Vector with Designed Shield and Adapter for Paracrine Delivery of Therapeutics. 2018, University of Zurich, Faculty of Science.

Makarov, Dmitrii E; Schuler, Benjamin (2018). Preface: Special Topic on Single-Molecule Biophysics. Journal of Chemical Physics, 148(12):123001.

Masliah, Gregoire; Maris, Christophe; König, Sebastian L B; Yulikov, Maxim; Aeschimann, Florian; Malinowska, Anna L; Mabille, Julie; Weiler, Jan; Holla, Andrea; Hunziker, Juerg; Meisner-Kober, Nicole; Schuler, Benjamin; Jeschke, Gunnar; Allain, Frederic H-T (2018). Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains. EMBO Journal Online, 37(6):e97089.

Härmä, Harri; Tong-Ochoa, Natalia; van Adrichem, Arjan J; Jelesarov, Ilian; Wennerberg, Krister; Kopra, Kari (2018). Toward universal protein post-translational modification detection in high throughput format. Chemical Communications, 54(23):2910-2913.

Stichling, Nicole; Suomalainen, Maarit; Flatt, Justin W; Schmid, Markus; Pacesa, Martin; Hemmi, Silvio; Jungraithmayr, Wolfgang; Maler, Mareike D; Freudenberg, Marina A; Plückthun, Andreas; May, Tobias; Köster, Mario; Fejer, György; Greber, Urs F (2018). Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor. PLoS Pathogens, 14(3):e1006914.

Borgia, Alessandro; Borgia, Madeleine B; Bugge, Katrine; Kissling, Vera M; Heidarsson, Pétur O; Fernandes, Catarina B; Sottini, Andrea; Soranno, Andrea; Buholzer, Karin J; Nettels, Daniel; Kragelund, Birthe B; Best, Robert B; Schuler, Benjamin (2018). Extreme disorder in an ultrahigh-affinity protein complex. Nature, 555(7694):61-66.

Morger, Damien; Zosel, Franziska; Bühlmann, Martin; Züger, Sara; Mittelviefhaus, Maximilian; Schuler, Benjamin; Luban, Jeremy; Grütter, Markus G (2018). The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5α. Journal of Virology, 92(5):e01541-17.

Batiste, Laurent; Unzue, Andrea; Dolbois, Aymeric; Hassler, Fabrice; Wang, Xuan; Deerain, Nicholas; Zhu, Jian; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo (2018). Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). ACS Central Science, 4(2):180-188.

Chorev, Dror S; Volberg, Tova; Livne, Ariel; Eisenstein, Miriam; Martins, Bruno; Kam, Zvi; Jockusch, Brigitte M; Medalia, Ohad; Sharon, Michal; Geiger, Benny (2018). Conformational states during vinculin unlocking differentially regulate focal adhesion properties. Scientific Reports, 8(1):2693.

Hansen, Simon; Ernst, Patrick; König, Sebastian L B; Reichen, Christian; Ewald, Christina; Nettels, Daniel; Mittl, Peer R E; Schuler, Benjamin; Plückthun, Andreas (2018). Curvature of designed armadillo repeat proteins allows modular peptide binding. Journal of Structural Biology, 201(2):108-117.

Caflisch, Amedeo; Gianni, Stefano (2018). Editorial overview: Folding and binding: In silico, in vitro and in cellula. Current Opinion in Structural Biology, 48:iv-vii.

Tamás, Markus J; Fauvet, Bruno; Christen, Philipp; Goloubinoff, Pierre (2018). Misfolding and aggregation of nascent proteins: a novel mode of toxic cadmium action in vivo. Current Genetics, 64(1):177-181.

Clerici, Marcello; Faini, Marco; Muckenfuss, Lena M; Aebersold, Ruedi; Jinek, Martin (2018). Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nature Structural & Molecular Biology, 25(2):135-138.

Pott, Moritz; Hayashi, Takahiro; Mori, Takahiro; Mittl, Peer R E; Green, Anthony P; Hilvert, Donald (2018). A noncanonical proximal heme ligand affords an efficient peroxidase in a globin fold. Journal of the American Chemical Society, 140(4):1535-1543.

Schmid, Markus; Ernst, Patrick; Honegger, Annemarie; Suomalainen, Maarit; Zimmermann, Martina; Braun, Lukas; Stauffer, Sarah; Thom, Cristian; Dreier, Birgit; Eibauer, Matthias; Kipar, Anja; Vogel, Viola; Greber, Urs F; Medalia, Ohad; Plückthun, Andreas (2018). Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control. Nature Communications, 9(1):450.

Vlot, Marnix; Houkes, Joep; Lochs, Silke J A; Swarts, Daan C; Zheng, Peiyuan; Kunne, Tim; Mohanraju, Prarthana; Anders, Carolin; Jinek, Martin; van der Oost, John; Dickman, Mark J; Brouns, Stan J J (2018). Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes. Nucleic Acids Research, 46(2):873-885.

de Leeuw, Rebecca; Gruenbaum, Yosef; Medalia, Ohad (2018). Nuclear lamins: thin filaments with major functions. Trends in Cell Biology, 28(1):34-45.

Holmstrom, Erik D; Holla, Andrea; Zheng, Wenwei; Nettels, Daniel; Best, Robert B; Schuler, Benjamin (2018). Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. Methods in Enzymology, 611:287-325.

Dolbois, Aymeric. Bromodomain chemical probes : diving into underexplored epigenetic readers. 2018, University of Zurich, Faculty of Science.

Holmstrom, Erik D; Nettels, Daniel; Schuler, Benjamin (2018). Conformational plasticity of hepatitis C virus core protein enables RNA-induced formation of nucleocapsid-like particles. Journal of Molecular Biology, 430(16):2453-2467.

Kumar, Abhinav. Evaluation of G protein coupled receptor-Gα fusions for the structural characterization of a GPCR-G protein complex. 2018, University of Zurich, Faculty of Science.

Zhu, Jian. Fragment-based drug design of bromodomain ligands. 2018, University of Zurich, Faculty of Science.

Heine, Philipp Christian Johannes. In vitro ligand screening with a peptide-binding G protein-coupled receptor. 2018, University of Zurich, Faculty of Science.

Zheng, Wenwei; Zerze, Gül H; Borgia, Alessandro; Mittal, Jeetain; Schuler, Benjamin; Best, Robert B (2018). Inferring properties of disordered chains from FRET transfer efficiencies. Journal of Chemical Physics, 148(12):123329.

Palermo, Giulia; Chen, Janice S; Ricci, Clarisse G; Rivalta, Ivan; Jinek, Martin; Batista, Victor S; Doudna, Jennifer A; McCammon, J Andrew (2018). Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly reviews of biophysics, 51:e91.

Michel, Erich; Plückthun, Andreas; Zerbe, Oliver (2018). Peptide-guided assembly of repeat protein fragments. Angewandte Chemie Internationale Edition, 57(17):4576-4579.

Dreier, Birgit; Plückthun, Andreas (2018). Rapid Selection of High-Affinity Antibody scFv Fragments Using Ribosome Display. In: Nevoltris, Damien; Chames, Patrick. Antibody Engineering. Heidelberg: Springer, 235-268.

Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T; Jacob, Christoph R; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander (2018). Simulation of FRET dyes allows quantitative comparison against experimental data. Journal of Chemical Physics, 148(12):123321.

Hutter, Cedric. Structural and mechanistic insights into the transport cycle of the heterodimeric ABC exporter TM287/288. 2018, University of Zurich, Faculty of Science.

Niewöhner, Ole. Structural and mechanistic insights into type II and type III CRISPR-Cas systems. 2018, University of Zurich, Faculty of Science.


Clerici, Marcello; Faini, Marco; Aebersold, Ruedi; Jinek, Martin (2017). Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex. eLife, 6:e33111.

Paulino, Cristina; Kalienkova, Valeria; Lam, Andy K M; Neldner, Yvonne; Dutzler, Raimund (2017). Activation mechanism of the calcium-activated chloride channel TMEM16A revealed by cryo-EM. Nature, 552(7685):421-425.

Schwer, Marc-Simon. Heading for Light-Switchable Designed Ankyrin Repeat Proteins. 2017, University of Zurich, Faculty of Science.

Niewoehner, Ole. Type III CRISPR-Cas systems regulate the ribonuclease activity of Csm6 via cyclic oligoadenylate second messengers. 2017, University of Zurich, Faculty of Science.

Hansen, Simon; Stüber, Jakob C; Ernst, Patrick; Koch, Alexander; Bojar, Daniel; Batyuk, Alexander; Plückthun, Andreas (2017). Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity. Scientific Reports, 7(1):16292.

Marchand, Jean-Rémy. Computational Drug Discovery: Methods Development and Applications to Bromodomains. 2017, University of Zurich, Faculty of Science.

Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas (2017). Focused conformational sampling in proteins. Journal of Chemical Physics, 147(19):195102.

Langini, Cassiano; Caflisch, Amedeo; Vitalis, Andreas (2017). Correction to: The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(46):19121.

Garcia-Doval, Carmela; Jinek, Martin (2017). Molecular architectures and mechanisms of Class 2 CRISPR-associated nucleases. Current Opinion in Structural Biology, 47:157-166.

Nemergut, Michal; Žoldák, Gabriel; Schaefer, Jonas V; Kast, Florian; Miškovský, Pavol; Plückthun, Andreas; Sedlák, Erik (2017). Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering. Protein Science, 26(11):2229-2239.

Abplanalp, Jeannette; Leutert, Mario; Frugier, Emilie; Nowak, Kathrin; Feurer, Roxane; Kato, Jiro; Kistemaker, Hans V A; Filippov, Dmitri V; Moss, Joel; Caflisch, Amedeo; Hottiger, Michael O (2017). Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nature Communications, 8(1):2055.

Santoro, Alice; Ewa Wezynfeld, Nina; Vašák, Milan; Bal, Wojciech; Faller, Peter (2017). Cysteine and glutathione trigger the Cu-Zn swap between Cu(ii)-amyloid-β4-16 peptide and Zn7-metallothionein-3. Chemical Communications, 53(85):11634-11637.

Marchand, Jean-Rémy; Dalle Vedove, Andrea; Lolli, Graziano; Caflisch, Amedeo (2017). Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Journal of Chemical Information and Modeling, 57(10):2584-2597.

Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin (2017). Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein. Journal of Chemical Physics, 147(15):152708.

Spiliotopoulos, Dimitrios; Wamhoff, Eike-Christian; Lolli, Graziano; Rademacher, Christoph; Caflisch, Amedeo (2017). Discovery of BAZ2A bromodomain ligands. European journal of medicinal chemistry, 139:564-572.

Henning, Andrea. Selection and Characterization of Designed Armadillo Repeat Proteins for Modular Peptide Recognition. 2017, University of Zurich, Faculty of Science.

Verdurmen, Wouter P R; Mazlami, Marigona; Plückthun, Andreas (2017). A quantitative comparison of cytosolic delivery via different protein uptake systems. Scientific Reports, 7(1):13194.

Bacci, Marco; Vymětal, Jiří; Mihajlovic, Maja; Caflisch, Amedeo; Vitalis, Andreas (2017). Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. Journal of Chemical Theory and Computation, 13(10):5117-5130.

Langini, Cassiano; Caflisch, Amedeo; Vitalis, Andreas (2017). The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(40):16734-16745.

Hansen, Simon; Kiefer, Jonathan D; Madhurantakam, Chaithanya; Mittl, Peer R E; Plückthun, Andreas (2017). Structures of designed armadillo repeat proteins binding to peptides fused to globular domains. Protein Science, 26(10):1942-1952.

Andres, Fabio. Modulating RTK Interactions with DARPins for Cancer Cell Targeting and Characterization. 2017, University of Zurich, Faculty of Science.

Peón, Antonio; Robles, Adrián; Blanco, Beatriz; Convertino, Marino; Thompson, Paul; Hawkins, Alastair R; Caflisch, Amedeo; González-Bello, Concepción (2017). Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem, 12(18):1512-1524.

Niewoehner, Ole; Jinek, Martin (2017). Specialized weaponry: how a type III-A CRISPR-cas system excels at combating phages. Cell Host & Microbe, 22(3):258-259.

Wu, Yufan; Batyuk, Alexander; Honegger, Annemarie; Brandl, Fabian; Mittl, Peer R E; Plückthun, Andreas (2017). Rigidly connected multispecific artificial binders with adjustable geometries. Scientific Reports, 7(1):11217.

Jost, Christian; Stüber, Jakob C; Honegger, Annemarie; Wu, Yufan; Batyuk, Alexander; Plückthun, Andreas (2017). Rigidity of the extracellular part of HER2: evidence from engineering subdomain interfaces and shared-helix DARPin-DARPin fusions. Protein Science, 26(9):1796-1806.

Niewoehner, Ole; Garcia-Doval, Carmela; Rostøl, Jakob T; Berk, Christian; Schwede, Frank; Bigler, Laurent; Hall, Jonathan; Marraffini, Luciano A; Jinek, Martin (2017). Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. Nature, 548(7669):543-548.

Schenck, Stephan; Kunz, Laura; Sahlender, Daniela; Pardon, Els; Geertsma, Eric R; Savtchouk, Iaroslav; Suzuki, Toshiharu; Neldner, Yvonne; Štefanić, Saša; Steyaert, Jan; Volterra, Andrea; Dutzler, Raimund (2017). Generation and characterization of Anti-VGLUT nanobodies acting as inhibitors of transport. Biochemistry, 56(30):3962-3971.

Plitzko, Jürgen M; Schuler, Benjamin; Selenko, Philipp (2017). Structural biology outside the box-inside the cell. Current Opinion in Structural Biology, 46:110-121.

Hofer, René. Identification and Structural Characterisation of a Prokaryotic Bestrophin Homologue. 2017, University of Zurich, Faculty of Science.

Palermo, Giulia; Miao, Yinglong; Walker, Ross C; Jinek, Martin; McCammon, J Andrew (2017). CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proceedings of the National Academy of Sciences of the United States of America, 114(28):7260-7265.

Koenig, Ivo. Single-Molecule FRET Spectroscopy of Intrinsically Disordered Proteins in Crowded Solutions and in Living Mammalian Cells. 2017, University of Zurich, Faculty of Science.

Afroz, Tariq; Hock, Eva-Maria; Ernst, Patrick; Foglieni, Chiara; Jambeau, Melanie; Gilhespy, Larissa A B; Laferriere, Florent; Maniecka, Zuzanna; Plückthun, Andreas; Mittl, Peer; Paganetti, Paolo; Allain, Frédéric H T; Polymenidou, Magdalini (2017). Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Nature Communications, 8:45.

Turgay, Y; Medalia, O (2017). The structure of lamin filaments in somatic cells as revealed by cryo-electron tomography. Nucleus, 8(5):475-481.

Parren, Paul W H I; Carter, Paul J; Plückthun, Andreas (2017). Changes to International Nonproprietary Names for antibody therapeutics 2017 and beyond: of mice, men and more. mAbs, 9(6):898-906.

Zijlstra, Niels; Dingfelder, Fabian; Wunderlich, Bengt; Zosel, Franziska; Benke, Stephan; Nettels, Daniel; Schuler, Benjamin (2017). Rapid microfluidic dilution for single-molecule spectroscopy of low-affinity biomolecular complexes. Angewandte Chemie Internationale Edition, 56(25):7126-7129.

Skegro, Darko; Stutz, Cian; Ollier, Romain; Svensson, Emelie; Wassmann, Paul; Bourquin, Florence; Monney, Thierry; Gn, Sunitha; Blein, Stanislas (2017). Immunoglobulin domain interface exchange as a platform technology for the generation of Fc heterodimers and bispecific antibodies. Journal of Biological Chemistry, 292(23):9745-9759.

Samatanga, Brighton; Cléry, Antoine; Barraud, Pierre; Allain, Frédéric H-T; Jelesarov, Ilian (2017). Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs. Nucleic Acids Research, 45(10):6037-6050.

Spiliotopoulos, Dimitrios; Zhu, Jian; Wamhoff, Eike-Christian; Deerain, Nicholas; Marchand, Jean-Rémy; Aretz, Jonas; Rademacher, Christoph; Caflisch, Amedeo (2017). Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain. Bioorganic & Medicinal Chemistry Letters, 27(11):2472-2478.

Paulino, Cristina; Neldner, Yvonne; Lam, Andy K M; Kalienkova, Valeria; Brunner, Janine Denise; Schenck, Stephan; Dutzler, Raimund (2017). Structural basis for anion conduction in the calcium-activated chloride channel TMEM16A. eLife, 6:26232.

Vašák, Milan; Meloni, Gabriele (2017). Mammalian metallothionein-3: new functional and structural insights. International Journal of Molecular Sciences, 18(6):1117.

Anders, Carolin. Structural Framework for Cas9-mediated DNA Recognition and Cleavage. 2017, University of Zurich, Faculty of Science.

Dingfelder, Fabian; Wunderlich, Bengt; Benke, Stephan; Zosel, Franziska; Zijlstra, Niels; Nettels, Daniel; Schuler, Benjamin (2017). Rapid microfluidic double-jump mixing device for single-molecule spectroscopy. Journal of the American Chemical Society, 139(17):6062-6065.

Ruggeri, Francesca; Zosel, Franziska; Mutter, Natalie; Różycka, Mirosława; Wojtas, Magdalena; Ożyhar, Andrzej; Schuler, Benjamin; Krishnan, Madhavi (2017). Single-molecule electrometry. Nature Nanotechnology, 12(5):488-495.

Swarts, Daan C; van der Oost, John; Jinek, Martin (2017). Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a. Molecular Cell, 66(2):221-233.e4.

Harapin, Jan. Structural Characterization of Macromolecular Complexes Within Thick Specimens. 2017, University of Zurich, Faculty of Science.

Hansen, Simon. Functional and Structural Characterization of Modular Peptide-binding by Designed Armadillo Repeat Proteins. 2017, University of Zurich, Faculty of Science.

Ranganathan, Anirudh; Heine, Philipp; Rudling, Axel; Plückthun, Andreas; Kummer, Lutz; Carlsson, Jens (2017). Ligand discovery for a peptide-binding GPCR by Structure-based screening of fragment- and lead-like chemical libraries. ACS Chemical Biology, 12(3):735-745.

Benke, Stephan; Nettels, Daniel; Hofmann, Hagen; Schuler, Benjamin (2017). Quantifying kinetics from time series of single-molecule Förster resonance energy transfer efficiency histograms. Nanotechnology, 28(11):114002.

Malka-Gibor, Eti; Kornreich, Micha; Laser-Azogui, Adi; Doron, Ofer; Zingerman-Koladko, Irena; Harapin, Jan; Medalia, Ohad; Beck, Roy (2017). Phosphorylation-Induced Mechanical Regulation of Intrinsically Disordered Neurofilament Proteins. Biophysical Journal, 112(5):892-900.

Turgay, Yagmur; Eibauer, Matthias; Goldman, Anne E; Shimi, Takeshi; Khayat, Maayan; Ben-Harush, Kfir; Dubrovsky-Gaupp, Anna; Sapra, K Tanuj; Goldman, Robert D; Medalia, Ohad (2017). The molecular architecture of lamins in somatic cells. Nature, 543(7644):261-264.

Soranno, Andrea; Holla, Andrea; Dingfelder, Fabian; Nettels, Daniel; Makarov, Dmitrii E; Schuler, Benjamin (2017). Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations. Proceedings of the National Academy of Sciences of the United States of America, 114(10):E1833-E1839.

Anders, Ulrike; Schaefer, Jonas V; Hibti, Fatima-Ezzahra; Frydman, Chiraz; Suckau, Detlev; Plückthun, Andreas; Zenobi, Renato (2017). SPRi-MALDI MS: characterization and identification of a kinase from cell lysate by specific interaction with different designed ankyrin repeat proteins. Analytical and Bioanalytical Chemistry, 409(7):1827-1836.

Schwill, Martin. Biparatopic DARPins for Anti-ErbB2 Therapy: Intermolecular Trapping of ErbB2/HER2 Receptor Induces pan-ErbB Inhibition and Overcomes the Signaling Robustness in ErbB2-Dependent Cancers. 2017, University of Zurich, Faculty of Science.

Ghayor, Chafik; Gjoksi, Bebeka; Dong, Jing; Siegenthaler, Barbara; Caflisch, Amedeo; Weber, Franz E (2017). N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment. Scientific Reports, 7:42108.

Wu, Yufan. Adapting DARPin-Based Rigid Fusions for Crystallography. 2017, University of Zurich, Faculty of Science.

Ehrnstorfer, Ines A; Manatschal, Cristina; Arnold, Fabian M; Laederach, Juerg; Dutzler, Raimund (2017). Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family. Nature Communications, 8:14033.

Syafrizayanti; Lueong, Smiths S; Di, Cuixia; Schaefer, Jonas V; Plückthun, Andreas; Hoheisel, Jörg D (2017). Personalised proteome analysis by means of protein microarrays made from individual patient samples. Scientific Reports, 7:39756.

Ernst, Patrick; Plückthun, Andreas (2017). Advances in the design and engineering of peptide-binding repeat proteins. Biological Chemistry, 398(1):23-29.

Nasr, Mahmoud L; Baptista, Diego; Strauss, Mike; Sun, Zhen-Yu J; Grigoriu, Simina; Huser, Sonja; Plückthun, Andreas; Hagn, Franz; Walz, Thomas; Hogle, James M; Wagner, Gerhard (2017). Covalently circularized nanodiscs for studying membrane proteins and viral entry. Nature Methods, 14(1):49-52.

Obexer, Richard; Godina, Alexei; Garrabou, Xavier; Mittl, Peer R E; Baker, David; Griffiths, Andrew D; Hilvert, Donald (2017). Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nature Chemistry, 9(1):50-56.

Verdurmen, Wouter P R; Mazlami, Marigona; Plückthun, Andreas (2017). A Biotin Ligase-Based Assay for the Quantification of the Cytosolic Delivery of Therapeutic Proteins. Methods in Molecular Biology, 1575:223-236.

Marino, Jacopo; Holzhüter, Katharina; Kuhn, Benedikt; Geertsma, Eric R (2017). Efficient Screening and Optimization of Membrane Protein Production in Escherichia coli. Methods in Enzymology, 594:139-164.

Kramer, Lovro; Renko, Miha; Završnik, Janja; Turk, Dušan; Seeger, Markus A; Vasiljeva, Olga; Grütter, Markus G; Turk, Vito; Turk, Boris (2017). Non-invasive in vivo imaging of tumour-associated cathepsin B by a highly selective inhibitory DARPin. Theranostics, 7(11):2806-2821.

Huber, Sylwia; Casagrande, Fabio; Hug, Melanie N; Wang, Lisha; Heine, Philipp; Kummer, Lutz; Plückthun, Andreas; Hennig, Michael (2017). SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands. PLoS ONE, 12(5):e0175842.


Lim, Novandy. Structural and functional characterization of TMEM16 family members. 2016, University of Zurich, Faculty of Science.

Schiller, Christian B; Braciak, Todd A; Fenn, Nadja C; Seidel, Ursula J E; Roskopf, Claudia C; Wildenhain, Sarah; Honegger, Annemarie; Schubert, Ingo A; Schele, Alexandra; Lämmermann, Kerstin; Fey, Georg H; Jacob, Uwe; Lang, Peter; Hopfner, Karl-Peter; Oduncu, Fuat S (2016). CD19-specific triplebody SPM-1 engages NK and γδ T cells for rapid and efficient lysis of malignant B-lymphoid cells. OncoTarget, 7(50):83392-83408.

Zosel, Franziska. Dynamics and interactions of intrinsically disordered proteins studied with single-molecule spectroscopy. 2016, University of Zurich, Faculty of Science.

Reimão-Pinto, Madalena M; Manzenreither, Raphael A; Burkard, Thomas R; Sledz, Pawel; Jinek, Martin; Mechtler, Karl; Ameres, Stefan L (2016). Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila. EMBO Journal Online, 35(22):2417-2434.

Marchand, Jean-Rémy; Lolli, Graziano; Caflisch, Amedeo (2016). Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation. Journal of Medicinal Chemistry, 59(21):9919-9927.

Börmel, Mandy. Structural analysis of zipping during dorsal closure in drosophila melanogaster embryogenesis. 2016, University of Zurich, Faculty of Science.

Borgia, Alessandro; Zheng, Wenwei; Buholzer, Karin; Borgia, Madeleine B; Schüler, Anja; Hofmann, Hagen; Soranno, Andrea; Nettels, Daniel; Gast, Klaus; Grishaev, Alexander; Best, Robert B; Schuler, Benjamin (2016). Consistent view of polypeptide chain expansion in chemical denaturants from multiple experimental methods. Journal of the American Chemical Society, 138(36):11714-11726.

Zheng, Wenwei; Borgia, Alessandro; Buholzer, Karin; Grishaev, Alexander; Schuler, Benjamin; Best, Robert B (2016). Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. Journal of the American Chemical Society, 138(36):11702-11713.

Aznauryan, Mikayel; Delgado, Leonildo; Soranno, Andrea; Nettels, Daniel; Huang, Jie-Rong; Labhardt, Alexander M; Grzesiek, Stephan; Schuler, Benjamin (2016). Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS. Proceedings of the National Academy of Sciences of the United States of America, 113(37):E5389-E5398.

Green, Anthony P; Hayashi, Takahiro; Mittl, Peer R E; Hilvert, Donald (2016). A chemically programmed proximal ligand enhances the catalytic properties of a heme enzyme. Journal of the American Chemical Society, 138(35):11344-11352.

Sorrentino, Simona; Studt, Jan-Dirk; Horev, Melanie Bokstad; Medalia, Ohad; Sapra, K Tanuj (2016). Toward correlating structure and mechanics of platelets. Cell Adhesion & Migration, 10(5):568-575.

Engeler, Sibylle. Structural and functional analysis of prokaryotic pentameric ligand-gated ion channels. 2016, University of Zurich, Faculty of Science.

Lindsay, Helen; Burger, Alexa; Biyong, Berthin; Felker, Anastasia; Hess, Christopher; Zaugg, Jonas; Chiavacci, Elena; Anders, Carolin; Jinek, Martin; Mosimann, Christian; Robinson, Mark D (2016). CrispRVariants charts the mutation spectrum of genome engineering experiments. Nature Biotechnology, 34(7):701-702.

Schuler, Benjamin; Soranno, Andrea; Hofmann, Hagen; Nettels, Daniel (2016). Single-molecule FRET spectroscopy and the polymer physics of unfolded and intrinsically disordered proteins. Annual review of biophysics, 45:207-231.

Goricanec, David; Stehle, Ralf; Egloff, Pascal; Grigoriu, Simina; Plückthun, Andreas; Wagner, Gerhard; Hagn, Franz (2016). Conformational dynamics of a G-protein α subunit is tightly regulated by nucleotide binding. Proceedings of the National Academy of Sciences of the United States of America, 113(26):E3629-E3638.

Brunner, Janine D; Schenck, Stephan; Dutzler, Raimund (2016). Structural basis for phospholipid scrambling in the TMEM16 family. Current Opinion in Structural Biology, 39:61-70.

Zhu, Jian; Caflisch, Amedeo (2016). Twenty crystal structures of bromodomain and PHD finger containing protein 1 (BRPF1)/ligand complexes reveal conserved binding motifs and rare interactions. Journal of Medicinal Chemistry, 59(11):5555-5561.

Zingerman-Koladko, Irena; Khayat, Maayan; Harapin, Jan; Shoseyov, Oded; Gruenbaum, Yosef; Salman, Ahmad; Medalia, Ohad; Ben-Harush, Kfir (2016). The assembly of C. elegans lamins into macroscopic fibers. Journal of the Mechanical Behavior of Biomedical Materials, 63:35-43.

Burger, Alexa; Lindsay, Helen; Felker, Anastasia; Hess, Christopher; Anders, Carolin; Chiavacci, Elena; Zaugg, Jonas; Weber, Lukas M; Catena, Raul; Jinek, Martin; Robinson, Mark D; Mosimann, Christian (2016). Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development, 143(11):2025-2037.

Bender, Ruben R; Muth, Anke; Schneider, Irene C; Friedel, Thorsten; Hartmann, Jessica; Plückthun, Andreas; Maisner, Andrea; Buchholz, Christian J (2016). Receptor-targeted nipah virus glycoproteins improve cell-type selective gene delivery and reveal a preference for membrane-proximal cell attachment. PLoS Pathogens, 12(6):e1005641.

Geertsma, Eric R; Chang, Yung-Ning; Shaik, Farooque R; Neldner, Yvonne; Pardon, Els; Steyaert, Jan; Dutzler, Raimund (2016). Corrigendum: Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family. Nature Structural & Molecular Biology, 23(5):462.

Spalinger, Marianne R; Kasper, Stephanie; Gottier, Claudia; Lang, Silvia; Atrott, Kirstin; Vavricka, Stephan R; Scharl, Sylvie; Gutte, Petrus M; Grütter, Markus G; Beer, Hans-Dietmar; Contassot, Emmanuel; Chan, Andrew C; Dai, Xuezhi; Rawlings, David J; Mair, Florian; Becher, Burkhard; Falk, Werner; Fried, Michael; Rogler, Gerhard; Scharl, Michael (2016). NLRP3 tyrosine phosphorylation is controlled by protein tyrosine phosphatase PTPN22. Journal of Clinical Investigation, 126(5):1783-1800.

Zuela, Noam; Zwerger, Monika; Levin, Tal; Medalia, Ohad; Gruenbaum, Yosef (2016). Impaired mechanical response of an EDMD mutation leads to motility phenotypes that are repaired by loss of prenylation. Journal of Cell Science, 129(9):1781-1791.

Batyuk, Alexander; Wu, Yufan; Honegger, Annemarie; Heberling, Matthew M; Plückthun, Andreas (2016). DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography. Journal of Molecular Biology, 428(8):1574-1588.

Schütz, Marco; Batyuk, Alexander; Klenk, Christoph; Kummer, Lutz; de Picciotto, Seymour; Gülbakan, Basri; Wu, Yufan; Newby, Gregory A; Zosel, Franziska; Schöppe, Jendrik; Sedlák, Erik; Mittl, Peer R E; Zenobi, Renato; Wittrup, K Dane; Plückthun, Andreas (2016). Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools. Journal of Molecular Biology, 428(6):1272-1289.

Lolli, Graziano; Caflisch, Amedeo (2016). High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography. ACS Chemical Biology, 11(3):800-807.

Anders, Carolin; Bargsten, Katja; Jinek, Martin (2016). Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Molecular Cell, 61(6):895-902.

Hansen, Simon; Tremmel, Dirk; Madhurantakam, Chaithanya; Reichen, Christian; Mittl, Peer R E; Plückthun, Andreas (2016). Structure and Energetic Contributions of a Designed Modular Peptide-Binding Protein with Picomolar Affinity. Journal of the American Chemical Society, 138(10):3526-3532.

Roderer, Daniel; Benke, Stephan; Schuler, Benjamin; Glockshuber, Rudi (2016). Soluble oligomers of the pore-forming toxin cytolysin a from escherichia coli are off-pathway products of pore assembly. Journal of Biological Chemistry, 291(11):5652-5663.

Xu, Min; Caflisch, Amedeo; Hamm, Peter (2016). Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates. Journal of Chemical Theory and Computation, 12(3):1393-1399.

Ben Halima, Saoussen; Mishra, Sabyashachi; Raja, K Muruga Poopathi; Willem, Michael; Baici, Antonio; Simons, Kai; Brüstle, Oliver; Koch, Philipp; Haass, Christian; Caflisch, Amedeo; Rajendran, Lawrence (2016). Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein. Cell Reports, 14(9):2127-2141.

Olieric, Vincent; Weinert, Tobias; Finke, Aaron D; Anders, Carolin; Li, Dianfan; Olieric, Natacha; Borca, Camelia N; Steinmetz, Michel O; Caffrey, Martin; Jinek, Martin; Wang, Meitian (2016). Data-collection strategy for challenging native SAD phasing. Acta Crystallographica. Section D: Structural Biology, 72(Pt 3):421-429.

Zwerger, Monika; Eibauer, Matthias; Medalia, Ohad (2016). Insights into the gate of the nuclear pore complex. Nucleus, 7(1):1-7.

Bertozzi, Carlo; Zimmermann, Iwan; Engeler, Sibylle; Hilf, Ricarda J C; Dutzler, Raimund (2016). Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels. PLoS Biology, 14(3):e1002393.

Niewoehner, Ole; Jinek, Martin (2016). Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA, 22(3):318-329.

Tamir, Adi; Sorrentino, Simona; Motahedeh, Sarah; Shai, Ela; Dubrovsky, Anna; Dahan, Idit; Eibauer, Matthias; Studt, Jan-Dirk; Sapra, K Tanuj; Varon, David; Medalia, Ohad (2016). The macromolecular architecture of platelet-derived microparticles. Journal of Structural Biology, 193(3):181-187.

Dubey, Gyanendra P; Malli Mohan, Ganesh Babu; Dubrovsky, Anna; Amen, Triana; Tsipshtein, Shai; Rouvinski, Alex; Rosenberg, Alex; Kaganovich, Daniel; Sherman, Eilon; Medalia, Ohad; Ben-Yehuda, Sigal (2016). Architecture and Characteristics of Bacterial Nanotubes. Developmental Cell, 36(4):453-61.

Irobalieva, Rossitza N; Martins, Bruno; Medalia, Ohad (2016). Cellular structural biology as revealed by cryo-electron tomography. Journal of Cell Science, 129(3):469-476.

Jones, Tim D; Carter, Paul J; Plückthun, Andreas; et al (2016). The INNs and outs of antibody nonproprietary names. mAbs, 8(1):1-9.

Reichen, Christian; Madhurantakam, Chaithanya; Hansen, Simon; Grütter, Markus G; Plückthun, Andreas; Mittl, Peer R E (2016). Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects. Acta Crystallographica. Section D: Structural Biology, 72(Pt 1):168-175.

Roos, Martina; Pradère, Ugo; Ngondo, Richard P; Behera, Alok; Allegrini, Sara; Civenni, Gianluca; Zagalak, Julian A; Marchand, Jean-Rémy; Menzi, Mirjam; Towbin, Harry; Scheuermann, Jörg; Neri, Dario; Caflisch, Amedeo; Catapano, Carlo V; Ciaudo, Constance; Hall, Jonathan (2016). A Small-Molecule Inhibitor of Lin28. ACS Chemical Biology, 11(10):2773-2781.

Klenk, Christoph; Ehrenmann, Janosch; Schütz, Marco; Plückthun, Andreas (2016). A generic selection system for improved expression and thermostability of G protein-coupled receptors by directed evolution. Scientific Reports, 6:21294.

Reichen, Christian; Hansen, Simon; Forzani, Cristina; Honegger, Annemarie; Fleishman, Sarel J; Zhou, Ting; Parmeggiani, Fabio; Ernst, Patrick; Madhurantakam, Chaithanya; Ewald, Christina; Mittl, Peer R E; Zerbe, Oliver; Baker, David; Caflisch, Amedeo; Plückthun, Andreas (2016). Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. Journal of Molecular Biology, 428(22):4467-4489.

Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H (2016). Correction to concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry, 55(39):5647.

Spalinger, Marianne R; Kasper, Stephanie; Gottier, Claudia; Lang, Silvia; Atrott, Kirstin; Vavricka, Stephan R; Scharl, Sylvie; Raselli, Tina; Frey-Wagner, Isabelle; Gutte, Petrus M; Grütter, Markus G; Beer, Hans-Dietmar; Contassot, Emmanuel; Chan, Andrew C; Dai, Xuezhi; Rawlings, David J; Mair, Florian; Becher, Burkhard; Falk, Werner; Fried, Michael; Rogler, Gerhard; Scharl, Michael (2016). Corrigendum - NLRP3 tyrosine phosphorylation is controlled by protein tyrosine phosphatase PTPN22. Journal of Clinical Investigation, 126(11):4388.

Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Christopher Fromme, J; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7:10882.

Ahmad, Shoeb; Pecqueur, Ludovic; Dreier, Birgit; Hamdane, Djemel; Aumont-Nicaise, Magali; Plückthun, Andreas; Knossow, Marcel; Gigant, Benoît (2016). Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Scientific Reports, 6:28922.

Schütz, Marco; Schöppe, Jendrik; Sedlák, Erik; Hillenbrand, Matthias; Nagy-Davidescu, Gabriela; Ehrenmann, Janosch; Klenk, Christoph; Egloff, Pascal; Kummer, Lutz; Plückthun, Andreas (2016). Directed evolution of G protein-coupled receptors in yeast for higher functional production in eukaryotic expression hosts. Scientific Reports, 6:21508.

Arnon, Zohar A; Vitalis, Andreas; Levin, Aviad; Michaels, Thomas C T; Caflisch, Amedeo; Knowles, Tuomas P J; Adler-Abramovich, Lihi; Gazit, Ehud (2016). Dynamic microfluidic control of supramolecular peptide self-assembly. Nature Communications, 7:13190.

Hanauer, Jan Rh; Gottschlich, Lisa; Riehl, Dennis; Rusch, Tillmann; Koch, Vivian; Friedrich, Katrin; Hutzler, Stefan; Prüfer, Steffen; Friedel, Thorsten; Hanschmann, Kay-Martin; Münch, Robert C; Jost, Christian; Plückthun, Andreas; Cichutek, Klaus; Buchholz, Christian J; Mühlebach, Michael D (2016). Enhanced lysis by bispecific oncolytic measles viruses simultaneously using HER2/neu or EpCAM as target receptors. Molecular Therapy - Oncolytics, 3:16003.

Benke, Stephan; Roderer, Daniel; Wunderlich, Bengt; Nettels, Daniel; Glockshuber, Rudi; Schuler, Benjamin (2016). Erratum: The assembly dynamics of the cytolytic pore toxin ClyA. Nature Communications, 7:10650.

Unzue, Andrea; Xu, Ming; Dong, Jing; Wiedmer, Lars; Spiliotopoulos, Dimitrios; Caflisch, Amedeo; Nevado, Cristina (2016). Fragment-based design of selective nanomolar ligands of the crebbp bromodomain. Journal of Medicinal Chemistry, 59(4):1350-1356.

Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2016). Fragment-based in silico screening of bromodomain ligands. Drug Discovery Today: Technologies, 19:81-90.

Bode, Heiko; Bourquin, Florence; Suriyanarayanan, Saranya; Wei, Yu; Alecu, Irina; Othman, Alaa; von Eckardstein, Arnold; Hornemann, Thorsten (2016). HSAN1 mutations in serine palmitoyltransferase reveal a close structure-function-phenotype relationship. Human Molecular Genetics, 25(5):853-865.

Lim, Novandy K; Lam, Andy K M; Dutzler, Raimund (2016). Independent activation of ion conduction pores in the double-barreled calcium-activated chloride channel TMEM16A. Journal of General Physiology, 148(5):375-392.

Tamaskovic, Rastislav; Schwill, Martin; Nagy-Davidescu, Gabriela; Jost, Christian; Schaefer, Dagmar C; Verdurmen, Wouter P R; Schaefer, Jonas V; Honegger, Annemarie; Plückthun, Andreas (2016). Intermolecular biparatopic trapping of ErbB2 prevents compensatory activation of PI3K/AKT via RAS-p110 crosstalk. Nature Communications, 7:11672.

Vašák, Milan; Schnabl, Joachim (2016). Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Metal Ions in Life Sciences, 16:259-290.

Palermo, Giulia; Miao, Yinglong; Walker, Ross C; Jinek, Martin; McCammon, J Andrew (2016). Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. ACS Central Science, 2(10):756-763.

Śledź, Paweł; Jinek, Martin (2016). Structural insights into the molecular mechanism of the m(6)A writer complex. eLife, 5:1-16.

Unzue, Andrea; Zhao, Hongtao; Lolli, Graziano; Dong, Jing; Zhu, Jian; Zechner, Melanie; Dolbois, Aymeric; Caflisch, Amedeo; Nevado, Cristina (2016). The “Gatekeeper” residue influences the mode of binding of acetyl indoles to bromodomains. Journal of Medicinal Chemistry, 59(7):3087-3097.

Unzue, Andrea; Lafleur, Karine; Zhao, Hongtao; Zhou, Ting; Dong, Jing; Kolb, Peter; Liebl, Johanna; Zahler, Stefan; Caflisch, Amedeo; Nevado, Cristina (2016). Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation. European journal of medicinal chemistry, 112:347-366.


Nettels, Daniel; Haenni, Dominik; Maillot, Sacha; Gueye, Moussa; Barth, Anders; Hirschfeld, Verena; Hübner, Christian G; Léonard, Jérémie; Schuler, Benjamin (2015). Excited-state annihilation reduces power dependence of single-molecule FRET experiments. Physical Chemistry Chemical Physics (PCCP), 17(48):32304-32315.

Merten, Hannes; Brandl, Fabian; Plückthun, Andreas; Zangemeister-Wittke, Uwe (2015). Antibody-drug conjugates for tumor targeting-novel conjugation chemistries and the promise of non-igg binding proteins. Bioconjugate Chemistry, 26(11):2176-2185.

Zheng, Wenwei; Borgia, Alessandro; Borgia, Madeleine B; Schuler, Benjamin; Best, Robert B (2015). Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations. Journal of Chemical Theory and Computation, 11(11):5543-5553.

Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas (2015). Weighted distance functions improve analysis of high-dimensional data: application to molecular dynamics simulations. Journal of Chemical Theory and Computation, 11(11):5481-5492.

Huang, Danzhi; Caflisch, Amedeo (2015). The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion, 9(6):412-419.

Xu, Min. Molecular Dynamics Simulations of Protein-Ligand Complex Systems and Applications to Drug Design. 2015, University of Zurich, Faculty of Science.

Zwerger, Monika; Roschitzki-Voser, Heidi; Zbinden, Reto; Denais, Celine; Herrmann, Harald; Lammerding, Jan; Grütter, Markus G; Medalia, Ohad (2015). Altering lamina assembly reveals lamina-dependent and -independent functions for A-type lamins. Journal of Cell Science, 128(19):3607-3620.

Schuler, Benjamin D; Smith, Janet L (2015). Editorial overview: Biophysical and molecular biological methods: Structure, dynamics, and single molecules. Current Opinion in Structural Biology, 34:iv-vi.

Bradbury, Andrew R M; Plückthun, Andreas (2015). Getting to reproducible antibodies: the rationale for sequenced recombinant characterized reagents. Protein Engineering, Design & Selection, 28(10):303-305.

Geertsma, Eric R; Chang, Yung-Ning; Shaik, Farooque R; Neldner, Yvonne; Pardon, Els; Steyaert, Jan; Dutzler, Raimund (2015). Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family. Nature Structural & Molecular Biology, 22(10):803-808.

Dubrovsky, Anna; Sorrentino, Simona; Harapin, Jan; Sapra, K Tanuj; Medalia, Ohad (2015). Developments in cryo-electron tomography for in situ structural analysis. Archives of Biochemistry and Biophysics, 581:78-85.

Benke, Stephan. The Cytolytic Pore Toxin ClyA Studied With Single-Molecule Spectroscopy. 2015, University of Zurich, Faculty of Science.

Herrmann, Uli S; Schütz, Anne K; Shirani, Hamid; Huang, Danzhi; Saban, Dino; Nuvolone, Mario; Li, Bei; Ballmer, Boris; Åslund, Andreas K O; Mason, Jeffrey J; Rushing, Elisabeth; Budka, Herbert; Nystrom, Sofie; Hammarstrom, Per; Böckmann, Anja; Caflisch, Amedeo; Meier, Beat H; Nilsson, K Peter R; Hornemann, Simone; Aguzzi, Adriano (2015). Structure-based drug design identifies polythiophenes as antiprion compounds. Science Translational Medicine, 7(299):299ra123.

Czar, Martin F; Zosel, Franziska; König, Iwo; Nettels, Daniel; Wunderlich, Bengt; Schuler, Benjamin; Zarrine-Afsar, Arash; Jockusch, Rebecca A (2015). Gas-Phase FRET Efficiency Measurements To Probe the Conformation of Mass-Selected Proteins. Analytical Chemistry, 87(15):7559-7565.

Marchand, Jean-Rémy; Caflisch, Amedeo (2015). Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem, 10(8):1327-1333.

Fleishman, Sarel J; Plückthun, Andreas (2015). Editorial overview: Protein design and evolution-new protein architectures, evolutionary fine-tuning and analysis. Current Opinion in Structural Biology, 33:v-vi.

Baici, Antonio (2015). Kinetics of Enzyme-Modifier Interactions. Heidelberg: Springer.

König, Iwo; Zarrine-Afsar, Arash; Aznauryan, Mikayel; Soranno, Andrea; Wunderlich, Bengt; Dingfelder, Fabian; Stüber, Jakob C; Plückthun, Andreas; Nettels, Daniel; Schuler, Benjamin (2015). Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nature Methods, 12(8):773-779.

Knehans, Tim. Atomistic simulations of cavitands, cytochrome P450, and natural product binding to actin. 2015, University of Zurich, Faculty of Science.

Brunner, Janine. Insight into Ca2+ Dependent Lipid Scrambling from the Crystal Structure of a TMEM16 Family Member. 2015, University of Zurich, Faculty of Science.

Sedlák, Erik; Schaefer, Jonas V; Marek, Jozef; Gimeson, Peter; Plückthun, Andreas (2015). Advanced analyses of kinetic stabilities of iggs modified by mutations and glycosylation. Protein Science, 24(7):1100-1113.

Harapin, Jan; Börmel, Mandy; Sapra, K Tanuj; Brunner, Damian; Kaech, Andres; Medalia, Ohad (2015). Structural analysis of multicellular organisms with cryo-electron tomography. Nature Methods, 12(7):634-636.

Schütz, Marco. Directed Evolution of G Protein-Coupled Receptors in Yeast for Higher Functional Production in Eukaryotic Expression Hosts. 2015, University of Zurich, Faculty of Science.

Best, Robert B; Hofmann, Hagen; Nettels, Daniel; Schuler, Benjamin (2015). Quantitative interpretation of FRET experiments via molecular simulation: force field and validation. Biophysical Journal, 108(11):2721-2731.

Zhao, Hongtao; Caflisch, Amedeo (2015). Current kinase inhibitors cover a tiny fraction of fragment space. Bioorganic & Medicinal Chemistry Letters, 25(11):2372-2376.

Blöchliger, Nicolas. Analysis and Visualisation of the Metastable States and Pathways Sampled in Molecular Dynamics Simulations. 2015, University of Zurich, Faculty of Science.

Bukowska, Magdalena A; Hohl, Michael; Geertsma, Eric R; Hürlimann, Lea M; Grütter, Markus G; Seeger, Markus A (2015). A Transporter Motor Taken Apart: Flexibility in the Nucleotide Binding Domains of a Heterodimeric ABC Exporter. Biochemistry, 54(19):3086-3099.

Kellner, Ruth. Single-molecule Fluorescence Spectroscopy of the Interaction of Proteins with the DnaK-DnaJ-Chaperone System. 2015, University of Zurich, Faculty of Science.

Blöchliger, Nicolas; Xu, Min; Caflisch, Amedeo (2015). Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophysical Journal, 108(9):2362-2370.

Bacci, Marco; Vitalis, Andreas; Caflisch, Amedeo (2015). A molecular simulation protocol to avoid sampling redundancy and discover new states. BBA - Biochimica et Biophysica Acta, 1850(5):889-902.

Ewald, Christina; Christen, Martin T; Watson, Randall P; Mihajlovic, Maja; Zhou, Ting; Honegger, Annemarie; Plückthun, Andreas; Caflisch, Amedeo; Zerbe, Oliver (2015). A combined NMR and computational approach to investigate peptide binding to a designed armadillo repeat protein. Journal of Molecular Biology, 427(10):1916-1933.

Brandmann, Tobias; Jinek, Martin (2015). Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3. Proteins, 83(5):997-1002.

Feuerstacke, Christian. Role of Skeletal Muscle Transport Systems in Statin-Induced Myotoxicity. 2015, University of Zurich, Faculty of Science.

Bradbury, Andrew M; Plückthun, Andreas (2015). Antibodies: validate recombinants once. Nature, 520(7547):295.

Baltimore, David; Berg, Paul; Botchan, Michael; Carroll, Dana; Charo, R Alta; Church, George; Corn, Jacob E; Daley, George Q; Doudna, Jennifer A; Fenner, Marsha; Greely, Henry T; Jinek, Martin; Martin, G Steven; Penhoet, Edward; Puck, Jennifer; Sternberg, Samuel H; Weissman, Jonathan S; Yamamoto, Keith R (2015). Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science, 348(6230):36-38.

Egloff, Pascal; Deluigi, Mattia; Heine, Philipp; Balada, Stefanie; Plückthun, Andreas (2015). A cleavable ligand column for the rapid isolation of large quantities of homogeneous and functional neurotensin receptor 1 variants from E. coli. Protein Expression and Purification, 108:106-114.

Friedel, Thorsten; Hanisch, Lydia J; Muth, Anke; Honegger, Annemarie; Abken, Hinrich; Plückthun, Andreas; Buchholz, Christian J; Schneider, Irene C (2015). Receptor-targeted lentiviral vectors are exceptionally sensitive toward the biophysical properties of the displayed single-chain Fv. Protein Engineering, Design & Selection, 28(4):93-106.

Sorrentino, Simona; Studt, Jan-Dirk; Medalia, Ohad; Tanuj Sapra, K (2015). Roll, adhere, spread and contract: structural mechanics of platelet function. European Journal of Cell Biology, 94(3-4):129-138.

Oude Blenke, Erik; Klaasse, Gruson; Merten, Hannes; Plückthun, Andreas; Mastrobattista, Enrico; Martin, Nathaniel I (2015). Liposome functionalization with copper-free "click chemistry". Journal of Controlled Release, 202:14-20.

Hillenbrand, Matthias; Schori, Christian; Schöppe, Jendrik; Plückthun, Andreas (2015). Comprehensive analysis of heterotrimeric G-protein complex diversity and their interactions with GPCRs in solution. Proceedings of the National Academy of Sciences of the United States of America, 112(11):E1181-E1190.

Yuan, Haifeng; Gaiduk, Alexander; Siekierzycka, Joanna R; Fujiyoshi, Satoru; Matsushita, Michio; Nettels, Daniel; Schuler, Benjamin; Seidel, Claus A M; Orrit, Michel (2015). Temperature-cycle microscopy reveals single-molecule conformational heterogeneity. Physical Chemistry Chemical Physics (PCCP), 17(9):6532-6544.

Huang, Danzhi; Caflisch, Amedeo (2015). Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. Journal of the American Chemical Society, 137(8):2948-2957.

Holehouse, Alex S; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V (2015). Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. Journal of the American Chemical Society, 137(8):2984-2995.

Hillenbrand, Matthias. Heterotrimeric G-Proteins & G-Protein-Coupled Receptors - A Complex Story. 2015, University of Zurich, Faculty of Science.

Verdurmen, Wouter P R; Luginbühl, Manuel; Honegger, Annemarie; Plückthun, Andreas (2015). Efficient cell-specific uptake of binding proteins into the cytoplasm through engineered modular transport systems. Journal of Controlled Release, 200:13-22.

Gruenbaum, Yosef; Medalia, Ohad (2015). Lamins: the structure and protein complexes. Current Opinion in Cell Biology, 32C:7-12.

Bradbury, Andrew; Plückthun, Andreas (2015). Reproducibility: Standardize antibodies used in research. Nature, 518(7537):27-29.

Ehrnstorfer, Ines A. The Structural Basis for Ion Selectivity in Transition Metal Ion Transporters of the SLC11/NRAMP Family. 2015, University of Zurich, Faculty of Science.

Goldstein, Robert; Sosabowski, Jane; Livanos, Maria; Leyton, Julius; Vigor, Kim; Bhavsar, Gaurav; Nagy-Davidescu, Gabriela; Rashid, Mohammed; Miranda, Enrique; Yeung, Jenny; Tolner, Berend; Plückthun, Andreas; Mather, Stephen; Meyer, Tim; Chester, Kerry (2015). Development of the designed ankyrin repeat protein (DARPin) G3 for HER2 molecular imaging. European Journal of Nuclear Medicine and Molecular Imaging, 42(2):288-301.

Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H (2015). Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry, 54(3):711-721.

Salvati Manni, Livia; Zabara, Alexandru; Osornio, Yazmin M; Schöppe, Jendrik; Batyuk, Alexander; Plückthun, Andreas; Siegel, Jay S; Mezzenga, Raffaele; Landau, Ehud M (2015). Phase behavior of a designed cyclopropyl analogue of monoolein: implications for low-temperature membrane protein crystallization. Angewandte Chemie Internationale Edition, 54(3):1027-1031.

Dong, Jing; Zhao, Hongtao; Zhou, Ting; Spiliotopoulos, Dimitrios; Rajendran, Chitra; Li, Xiao-Dan; Huang, Danzhi; Caflisch, Amedeo (2015). Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases. ACS Medicinal Chemistry Letters, 6(1):79-83.

Zou, Jun; Tran, Diana; Baalbaki, Mai; Tang, Ling Fung; Poon, Annie; Pelonero, Angelo; Titus, Erron W; Yuan, Christiana; Shi, Chenxu; Patchava, Shruthi; Halper, Elizabeth; Garg, Jasmine; Movsesyan, Irina; Yin, Chaoying; Wu, Roland; Wilsbacher, Lisa D; Liu, Jiandong; Hager, Ronald L; Coughlin, Shaun R; Jinek, Martin; Pullinger, Clive R; Kane, John P; Hart, Daniel O; Kwok, Pui-Yan; Deo, Rahul C (2015). An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish. eLife, 4:e09406.

Marino, Jacopo; Hohl, Michael; Seeger, Markus A; Zerbe, Oliver; Geertsma, Eric (2015). Bicistronic mRNAs to enhance membrane protein overexpression. Journal of Molecular Biology, 427:943-953.

Weinert, Christopher; Morger, Damien; Djekic, Aleksandra; Grütter, Markus G; Mittl, Peer R E (2015). Crystal structure of TRIM20 C-terminal coiled-coil/B30.2 fragment: implications for the recognition of higher order oligomers. Scientific Reports, 5:10819.

Plückthun, Andreas (2015). Designed ankyrin repeat proteins (DARPins): binding proteins for research, diagnostics, and therapy. Annual Review of Pharmacology and Toxicology, 55:489-511.

Xu, Min; Unzue, Andrea; Dong, Jing; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo (2015). Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics. Journal of Medicinal Chemistry:2487-2491.

Anders, Carolin; Niewoehner, Ole; Jinek, Martin (2015). In Vitro Reconstitution and Crystallization of Cas9 Endonuclease Bound to a Guide RNA and a DNA Target. Methods in Enzymology, 558:515-537.

Zhao, Hongtao; Caflisch, Amedeo (2015). Molecular dynamics in drug design. European journal of medicinal chemistry, 91:4-14.

Münch, Robert C; Muth, Anke; Muik, Alexander; Friedel, Thorsten; Schmatz, Julia; Dreier, Birgit; Trkola, Alexandra; Plückthun, Andreas; Büning, Hildegard; Buchholz, Christian J (2015). Off-target-free gene delivery by affinity-purified receptor-targeted viral vectors. Nature Communications, 6:6246.

Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur; Dubrovsky, Anna; Wild, Annik; Medalia, Ohad (2015). Structure and gating of the nuclear pore complex. Nature Communications, 6:7532.

Benke, Stephan; Roderer, Daniel; Wunderlich, Bengt; Nettels, Daniel; Glockshuber, Rudi; Schuler, Benjamin (2015). The assembly dynamics of the cytolytic pore toxin ClyA. Nature Communications, 6:6198.

Borgia, Alessandro; Kemplen, Katherine R; Borgia, Madeleine B; Soranno, Andrea; Shammas, Sarah; Wunderlich, Bengt; Nettels, Daniel; Best, Robert B; Clarke, Jane; Schuler, Benjamin (2015). Transient misfolding dominates multidomain protein folding. Nature Communications, 6(8861):online.


Stefan, Nikolas; Zimmermann, Martina; Simon, Manuel; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2014). Novel prodrug-like fusion toxin with protease-sensitive bioorthogonal PEGylation for tumor targeting. Bioconjugate Chemistry, 25(12):2144-2156.

Hofmann, Hagen; Hillger, Frank; Delley, Cyrille; Hoffmann, Armin; Pfeil, Shawn H; Nettels, Daniel; Lipman, Everett A; Schuler, Benjamin (2014). Role of denatured-state properties in chaperonin action probed by single-molecule spectroscopy. Biophysical Journal, 107(12):2882-2893.

Brunner, Janine D; Lim, Novandy K; Schenck, Stephan; Duerst, Alessia; Dutzler, Raimund (2014). X-ray structure of a calcium-activated TMEM16 lipid scramblase. Nature, 516(7530):207-212.

Reichen, Christian. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. 2014, University of Zurich, Faculty of Science.

Ehrnstorfer, Ines A; Geertsma, Eric R; Pardon, Els; Steyaert, Jan; Dutzler, Raimund (2014). Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport. Nature Structural & Molecular Biology, 21(11):990-996.

Reichen, Christian; Madhurantakam, Chaithanya; Plückthun, Andreas; Mittl, Peer R E (2014). Crystal structures of designed armadillo repeat proteins: Implications of construct design and crystallization conditions on overall structure. Protein Science, 23(11):1572-1583.

Schmitz, Mark. Seeking truly novel proteins in a fully random library by bacterial Tat-dependent selections for folding. 2014, University of Zurich, Faculty of Science.

Roderer, Daniel; Benke, Stephan; Müller, Marcus; Fäh-Rechsteiner, Helene; Ban, Nenad; Schuler, Benjamin; Glockshuber, Rudi (2014). Characterization of variants of the pore-forming toxin ClyA from Escherichia coli controlled by a redox switch. Biochemistry, 53(40):6357-6369.

Larrick, James W; Parren, Paul Whi; Huston, James S; Plückthun, Andreas; Bradbury, Andrew; Tomlinson, Ian M; Chester, Kerry A; Burton, Dennis R; Adams, Gregory P; Weiner, Louis M; Scott, Jamie K; Alfenito, Mark R; Veldman, Trudi; Reichert, Janice M (2014). Antibody engineering and therapeutics conference. mAbs, 6(5):1115-1123.

Frugier, Emilie. Computational design and experimental validation of selective inhibitors of enzymes regulating post-translational modifications. 2014, University of Zurich, Faculty of Science.

Szydelko, Adrian. Structural and functional investigation of cytoplasmic dopmains in cic proteins. 2014, University of Zurich, Faculty of Science.

Sonderegger, Peter; Matsumoto-Miyai, Kazumasa (2014). Activity-controlled proteolytic cleavage at the synapse. Trends in Neurosciences, 37(8):413-423.

Hohl, Michael; Hürlimann, Lea M; Böhm, Simon; Schöppe, Jendrik; Grütter, Markus G; Bordignon, Enrica; Seeger, Markus A (2014). Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter. Proceedings of the National Academy of Sciences of the United States of America, 111(30):11025-11030.

Egloff, Pascal. Structure determination of neurotensin receptor 1 variants functionally expressed in e. coli. 2014, University of Zurich, Faculty of Science.

Ster, Jeanne; Steuble, Martin; Orlando, Clara; Diep, Tu-My; Akhmedov, Alexander; Raineteau, Olivier; Pernet, Vincent; Sonderegger, Peter; Gerber, Urs (2014). Calsyntenin-1 regulates targeting of dendritic NMDA receptors and dendritic spine maturation in CA1 hippocampal pyramidal cells during postnatal development. Journal of Neuroscience, 34(26):8716-8727.

Bertozzi, Carlo. Mechanistic insight into gating and open channel block in prokaryotic pLGICs. 2014, University of Zurich, Faculty of Science.

Wunderlich, Bengt. Microfluidics for single-molecule spectroscopy. 2014, University of Zurich, Faculty of Science.

Morger, Damian. Pattern recognition of the HIV-1 capsid by the innate immune receptor TRIM5. 2014, University of Zurich, Faculty of Science.

Novinec, Marko; Korenč, Matevž; Caflisch, Amedeo; Ranganathan, Rama; Lenarčič, Brigita; Baici, Antonio (2014). A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nature Communications, 5:3287.

Yan, Junhong; Gu, Gucci Jijuan; Jost, Christian; Hammond, Maria; Plückthun, Andreas; Landegren, Ulf; Kamali-Moghaddam, Masood (2014). A universal approach to prepare reagents for DNA-assisted protein analysis. PLoS ONE, 9(9):e108061.

Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea (2014). ALMOST: an all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry, 35(14):1101-1105.

Hanenberg, Michael; McAfoose, Jordan; Kulic, Luka; Welt, Tobias; Wirth, Fabian; Parizek, Petra; Strobel, Lisa; Cattepoel, Susann; Späni, Claudia; Derungs, Rebecca; Maier, Marcel; Plückthun, Andreas; Nitsch, Roger M (2014). Amyloid-β peptide-specific DARPins as a novel class of potential therapeutics for Alzheimer disease. Journal of Biological Chemistry, 289(39):27080-27089.

Schilling, Johannes; Schöppe, Jendrik; Sauer, Evelyn; Plückthun, Andreas (2014). Co-crystallization with conformation-specific designed ankyrin repeat proteins explains the conformational flexibility of BCL-W. Journal of Molecular Biology, 426(12):2346-2362.

Flütsch, Andreas; Ackermann, Rafael; Schroeder, Thilo; Lukarska, Maria; Hausammann, Georg J; Weinert, Christopher; Briand, Christophe; Grütter, Markus G (2014). Combined inhibition of caspase 3 and caspase 7 by two highly selective DARPins slows down cellular demise. Biochemical Journal, 461(2):279-290.

Weisenburger, Siegfried; Jing, Bo; Hänni, Dominik; Reymond, Luc; Schuler, Benjamin; Renn, Alois; Sandoghdar, Vahid (2014). Cryogenic colocalization microscopy for nanometer-distance measurements. ChemPhysChem, 15(4):763-770.

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490):62-67.

Zhao, Hongtao; Gartenmann, Lisa; Dong, Jing; Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2014). Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorganic & Medicinal Chemistry Letters, 24(11):2493-2496.

Zhao, Hongtao; Caflisch, Amedeo (2014). Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorganic & Medicinal Chemistry Letters, 24(6):1523-1527.

Jost, Christian; Plückthun, Andreas (2014). Engineered proteins with desired specificity: DARPins, other alternative scaffolds and bispecific IgGs. Current Opinion in Structural Biology, 27:102-112.

Vitalis, Andreas; Caflisch, Amedeo (2014). Equilibrium sampling approach to the interpretation of electron density maps. Structure, 22(1):156-167.

Niewoehner, Ole; Jinek, Martin; Doudna, Jennifer A (2014). Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Research, 42(2):1341-1353.

Pochorovski, Igor; Knehans, Tim; Nettels, Daniel; Müller, Astrid M; Schweizer, W Bernd; Caflisch, Amedeo; Schuler, Benjamin; Diederich, François (2014). Experimental and computational study of BODIPY dye-labeled cavitand dynamics. Journal of the American Chemical Society, 136(6):2441-2449.

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee (2014). Fragment-based docking: Development of the CHARMMing web user interface as a platform for computer-aided drug design. Journal of Chemical Information and Modeling, 54(9):2612-2620.

Schilling, Johannes; Schöppe, Jendrik; Plückthun, Andreas (2014). From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display. Journal of Molecular Biology, 426(3):691-721.

Scholz, Oliver; Hansen, Simon; Plückthun, Andreas (2014). G-quadruplexes are specifically recognized and distinguished by selected designed ankyrin repeat proteins. Nucleic Acids Research, 42(14):9182-9194.

Tamás, Markus J; Sharma, Sandeep K; Ibstedt, Sebastian; Jacobson, Therese; Christen, Philipp (2014). Heavy metals and metalloids as a cause for protein misfolding and aggregation. Biomolecules, 4(1):252-267.

Blöchliger, Nicolas; Vitalis, Andreas; Caflisch, Amedeo (2014). High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Scientific Reports, 4(6264):online.

Bischofberger, I; Calzolari, D C E; De Los Rios, P; Jelezarov, I; Trappe, V (2014). Hydrophobic hydration of poly-N-isopropyl acrylamide: a matter of the mean energetic state of water. Scientific Reports, 4:4377.

Scott, Daniel J; Kummer, Lutz; Egloff, Pascal; Bathgate, Ross A D; Plückthun, Andreas (2014). Improving the apo-state detergent stability of NTS1 with CHESS for pharmacological and structural studies. BBA - Biochimica et Biophysica Acta, 1838(11):2817-2824.

Anders, Carolin; Jinek, Martin (2014). In vitro enzymology of cas9. Methods in Enzymology, 546:1-20.

Simon, Manuel; Stefan, Nikolas; Borsig, Lubor; Plückthun, Andreas; Zangemeister-Wittke, Uwe (2014). Increasing the antitumor effect of an EpCAM-targeting fusion toxin by facile click PEGylation. Molecular Cancer Therapeutics, 13(2):375-385.

Reichen, Christian; Hansen, Simon; Plückthun, Andreas (2014). Modular peptide binding: from a comparison of natural binders to designed armadillo repeat proteins. Journal of Structural Biology, 185(2):147-162.

Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2014). Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine. Israel Journal of Chemistry, 54(8-9):1084-1092.

Novinec, Marko; Lenarčič, Brigita; Baici, Antonio (2014). Probing the activity modification space of the cysteine peptidase cathepsin K with novel allosteric modifiers. PLoS ONE, 9(9):e106642.

Brauchle, Michael; Hansen, Simon; Caussinus, Emmanuel; Lenard, Anna; Ochoa-Espinosa, Amanda; Scholz, Oliver; Sprecher, Simon G; Plückthun, Andreas; Affolter, Markus (2014). Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry. Biology Open, 3(12):1252-1261.

Unzue, Andrea; Dong, Jing; Lafleur, Karine; Zhao, Hongtao; Frugier, Emilie; Caflisch, Amedeo; Nevado, Cristina (2014). Pyrrolo[3,2-b]quinoxaline derivatives as types I1/2 and II Eph tyrosine kinase inhibitors: structure-based design, synthesis, and in vivo validation. Journal of Medicinal Chemistry, 57(15):6834-6844.

Beyer, Christian; Christen, Philipp; Jelesarov, Ilian; Fröhlich, Jürg (2014). Real-time assessment of possible electromagnetic-field-induced changes in protein conformation and thermal stability. Bioelectromagnetics, 35(7):470-478.

Kellner, Ruth; Hofmann, Hagen; Barducci, Alessandro; Wunderlich, Bengt; Nettels, Daniel; Schuler, Benjamin (2014). Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein. Proceedings of the National Academy of Sciences of the United States of America, 111(37):13355-13360.

Soranno, Andrea; Koenig, Iwo; Borgia, Madeleine B; Hofmann, Hagen; Zosel, Franziska; Nettels, Daniel; Schuler, Benjamin (2014). Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proceedings of the National Academy of Sciences of the United States of America, 111(13):4874-4879.

Brucale, Marco; Schuler, Benjamin; Samorì, Bruno (2014). Single-molecule studies of intrinsically disordered proteins. Chemical Reviews, 114(6):3281-3317.

Flütsch, Andreas; Schroeder, Thilo; Barandun, Jonas; Ackermann, Rafael; Bühlmann, Martin; Grütter, Markus G (2014). Specific targeting of human caspases using designed ankyrin repeat proteins. Biological Chemistry, 395(10):1243-1252.

Zhou, T; Georgeon, S; Moser, R; Moore, D J; Caflisch, A; Hantschel, O (2014). Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia, 28(2):404-407.

Watson, Randall P; Christen, Martin T; Ewald, Christina; Bumbak, Fabian; Reichen, Christian; Mihajlovic, Maja; Schmidt, Elena; Güntert, Peter; Caflisch, Amedeo; Plückthun, Andreas; Zerbe, Oliver (2014). Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure, 22(7):985-995.

Anders, Carolin; Niewoehner, Ole; Duerst, Alessia; Jinek, Martin (2014). Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature, 513:569-573.

Egloff, Pascal; Hillenbrand, Matthias; Klenk, Christoph; Batyuk, Alexander; Heine, Philipp; Balada, Stefanie; Schlinkmann, Karola M; Scott, Daniel J; Schütz, Marco; Plückthun, Andreas (2014). Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 111(6):E655-E662.

Jinek, Martin; Jiang, Fuguo; Taylor, David W; Sternberg, Samuel H; Kaya, Emine; Ma, Enbo; Anders, Carolin; Hauer, Michael; Zhou, Kaihong; Lin, Steven; Kaplan, Matias; Iavarone, Anthony T; Charpentier, Emmanuelle; Nogales, Eva; Doudna, Jennifer A (2014). Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science, 343(6176):1247997.

Wunderlich, B; Nettels, D; Schuler, B (2014). Taylor dispersion and the position-to-time conversion in microfluidic mixing devices. tbd: RSC Publishing.

Wuttke, René; Hofmann, Hagen; Nettels, Daniel; Borgia, Madeleine B; Mittal, Jeetain; Best, Robert B; Schuler, Benjamin (2014). Temperature-dependent solvation modulates the dimensions of disordered proteins. Proceedings of the National Academy of Sciences of the United States of America, 111(14):5213-5218.

Kiuchi, Tai; Ortiz-Zapater, Elena; Monypenny, James; Matthews, Daniel R; Nguyen, Lan K; Barbeau, Jody; Coban, Oana; Lawler, Katherine; Burford, Brian; Rolfe, Daniel J; de Rinaldis, Emanuele; Dafou, Dimitra; Simpson, Michael A; Woodman, Natalie; Pinder, Sarah; Gillett, Cheryl E; Devauges, Viviane; Poland, Simon P; Fruhwirth, Gilbert; Marra, Pierfrancesco; Boersma, Ykelien L; Plückthun, Andreas; Gullick, William J; Yarden, Yosef; Santis, George; Winn, Martyn; Kholodenko, Boris N; Martin-Fernandez, Marisa L; Parker, Peter; Tutt, Andrew; Ameer-Beg, Simon M; Ng, Tony (2014). The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility. Science Signaling, 7(339):ra78.

Walczak, Michal J; Samatanga, Brighton; van Drogen, Frank; Peter, Matthias; Jelesarov, Ilian; Wider, Gerhard (2014). The RING domain of the scaffold protein Ste5 adopts a molten globular character with high thermal and chemical stability. Angewandte Chemie Internationale Edition, 53(5):1320-1323.

Gutte, Petrus G M; Jurt, Simon; Grütter, Markus G; Zerbe, Oliver (2014). Unusual structural features revealed by the solution NMR structure of the NLRC5 caspase recruitment domain. Biochemistry, 53(19):3106-3117.

Friedman, Ran; Caflisch, Amedeo (2014). Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: a simulation study. Proteins, 82(3):399-404.


Weinert, Christpher. Structural and functional investigations on pyrin/TRIM20, a modulator of the innate immune response. 2013, University of Zurich, Faculty of Science.

Gutte, Petrus. Biochemical and structural studies of proteins involved in inflammatory and apoptotic signaling. 2013, University of Zurich, Faculty of Science.

Schilling, Johannes. From DARPins to LoopDARPins: Engineering second generation binding proteins from non-­immunoglobulin domains. 2013, University of Zurich, Faculty of Science.

Shaik, Farooque Razvi. Structure - function studies of prokaryotic multifunctional anion exchangers. 2013, University of Zurich, Faculty of Science.

Flütsch, Andreas. Caspase-specific DARPins: from binding characterization, inhibition and modulation of apoptosis towards biomedical applications. 2013, University of Zurich, Faculty of Science.

Jost, Christian. Tumor targeting of the human epidermal growth factor receptor 2 with designed ankyrin repeat proteins. 2013, University of Zurich, Faculty of Science.

Steiner, Sandra. Binding of small peptide ligands to protein domains studied by molecular dynamics simulations. 2013, University of Zurich, Faculty of Science.

Magno, Andrea. Multiscale molecular dynamics studies of peptide aggregation and protein-ligand association. 2013, University of Zurich, Faculty of Science.

Hohl, Michael. Structural and functional investigations of prokaryotic heterodimeric ABC exporters. 2013, University of Zurich, Faculty of Science.

Stefan, Nikolas. EpCAM-specific high-affinity DARPins delivering protease-activated ETA biotoxins. 2013, University of Zurich, Faculty of Science.

Hausammann, Georg. Overcoming the low stability of hERG: functional studies on hERG and chimeric hERG channels. 2013, University of Zurich, Faculty of Science.

Bukowska, Magdalena A. Structural and biochemical studies of bacterial multidrug resistance transporters. 2013, University of Zurich, Faculty of Science.

Blöchliger, Nicolas; Vitalis, Andreas; Caflisch, Amedeo (2013). A scalable algorithm to order ad annotate continuous observations reveals the metastable states visited by dynamical systems. Computer Physics Communications, 184:2446-2453.

Schuler, Benjamin; Clarke, Jane (2013). Biophysics: Rough passage across a barrier. Nature, 502(7473):632-633.

Freisinger, Eva; Vasak, Milan (2013). Cadmium in metallothioneins. Metal Ions in Life Sciences, 11:339-371.

Attanasio, Francesco; Convertino, Marino; Magno, Andrea; Caflisch, Amedeo; Corazza, Alessandra; Haridas, Haritha; Esposito, Gennaro; Cataldo, Sebastiano; Pignataro, Bruno; Milardi, Danilo; Rizzarelli, Enrico (2013). Carnosine inhibits Aβ42 aggregation by perturbing the H-Bond network in and around the central Hydrophobic cluster. Chembiochem, 14(5):583-592.

Hausammann, Georg J; Grütter, Markus G (2013). Chimeric hERG channels containing a tetramerization domain are functional and stable. Biochemistry, 52(51):9237-9245.

Mann, Axel; Friedrich, Nikolas; Krarup, Anders; Weber, Jacqueline; Stiegeler, Emanuel; Dreier, Birgit; Pugach, Pavel; Robbiani, Melissa; Riedel, Tina; Moehle, Kerstin; Robinson, John A; Rusert, Peter; Plückthun, Andreas; Trkola, Alexandra (2013). Conformation-dependent recognition of HIV gp120 by designed ankyrin repeat proteins provides access to novel HIV entry inhibitors. Journal of Virology, 87(10):5868-5881.

Friedrich, Katrin; Hanauer, Jan R H; Prüfer, Steffen; Münch, Robert C; Völker, Iris; Filippis, Christodoulos; Jost, Christian; Hanschmann, Kay-Martin; Cattaneo, Roberto; Peng, Kah-Whye; Plückthun, Andreas; Buchholz, Christian J; Cichutek, Klaus; Mühlebach, Michael D (2013). DARPin-targeting of measles virus: unique bispecificity, effective oncolysis, and enhanced safety. Molecular Therapy, 21(4):849-859.

Seeger, Markus A; Zbinden, Reto; Flütsch, Andreas; Gutte, Petrus G M; Engeler, Sibylle; Roschitzki-Voser, Heidi; Grütter, Markus G (2013). Design, construction, and characterization of a second-generation DARPin library with reduced hydrophobicity. Protein Science, 22(9):1239-57.

Dreier, Birgit; Honegger, Annemarie; Hess, Christian; Nagy-Davidescu, Gabriela; Mittl, Peer R E; Grütter, Markus G; Belousova, Natalya; Mikheeva, Galina; Krasnykh, Victor; Plückthun, Andreas (2013). Development of a generic adenovirus delivery system based on structure-guided design of bispecific trimeric DARPin adapters. Proceedings of the National Academy of Sciences of the United States of America, 110(10):E869-E877.

Lavelin, Irena; Wolfenson, Haguy; Patla, Israel; Henis, Yoav I; Medalia, Ohad; Volberg, Tova; Livne, Ariel; Kam, Zvi; Geiger, Benjamin (2013). Differential effect of actomyosin relaxation on the dynamic properties of focal adhesion proteins. PLoS ONE, 8(9):e73549.

Scott, Daniel J; Plückthun, Andreas (2013). Direct molecular evolution of detergent-stable G protein-coupled receptors using polymer encapsulated cells. Journal of Molecular Biology, 425(3):662-677.

Schlinkmann, Karola M; Plückthun, Andreas (2013). Directed evolution of G-protein-coupled receptors for high functional expression and detergent stability. In: Conn, P Michael. G Protein Coupled Receptors Structure. Amsterdam: Elsevier, 67-97.

Zhao, Hongtao; Caflisch, Amedeo (2013). Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorganic & Medicinal Chemistry Letters, 23(20):5721-5726.

Steiner, Sandra; Magno, Andrea; Huang, Danzhi; Caflisch, Amedeo (2013). Does bromodomain flexibility influence histone recognition? FEBS letters, 587(14):2158-2163.

Simon, Manuel; Stefan, Nikolas; Plückthun, Andreas; Zangemeister-Wittke, Uwe (2013). Epithelial cell adhesion molecule-targeted drug delivery for cancer therapy. Expert Opinion on Drug Delivery, 10(4):451-468.

Sandler, Inga; Medalia, Ohad; Aharoni, Amir (2013). Experimental analysis of co-evolution within protein complexes: the yeast exosome as a model. Proteins, 81(11):1997-2006.

Beyer, Christian; Christen, Philipp; Jelesarov, Ilian; Fröhlich, Jürg (2013). Experimental system for real-time assessment of potential changes in protein conformation induced by electromagnetic fields. Bioelectromagnetics, 34(6):419-428.

Zwerger, Monika; Medalia, Ohad (2013). From lamins to lamina: a structural perspective. Histochemistry and Cell Biology, 140(1):3-12.

Garcia-Celma, Juan; Szydelko, Adrian; Dutzler, Raimund (2013). Functional characterization of a ClC transporter by solid-supported membrane electrophysiology. Journal of General Physiology, 141(4):479-491.

Hausammann, Georg J; Heitkamp, Thomas; Matile, Hugues; Gsell, Bernard; Thoma, Ralf; Schmid, Georg; Frasson, David; Sievers, Martin; Hennig, Michael; Grütter, Markus G (2013). Generation of an antibody toolbox to characterize hERG. Biochemical and Biophysical Research Communications, 431(1):70-75.

Zhou, Yueyang; Yu, Jing; Lei, Xiling; Wu, Jianying; Niu, Qi; Zhang, Yixuan; Liu, Hong; Christen, Philipp; Gehring, Heinz; Wu, Fang (2013). High-throughput tandem-microwell assay identifies inhibitors of the hydrogen sulfide signaling pathway. Chemical Communications, 49(100):11782-11784.

Haenni, Dominik; Zosel, Franziska; Reymond, Luc; Nettels, Daniel; Schuler, Benjamin (2013). Intramolecular distances and dynamics from the combined Photon statistics of single-molecule FRET and photoinduced electron transfer. Journal of Physical Chemistry B, 117(42):13015-13028.

Buchli, Brigitte; Waldauer, Steven A; Walser, Reto; Donten, Mateusz L; Pfister, Rolf; Blöchliger, Nicolas; Steiner, Sandra; Caflisch, Amedeo; Zerbe, Oliver; Hamm, Peter (2013). Kinetic response of a photoperturbed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America, 110(29):11725-11730.

Kummer, Lutz; Hsu, Chia-Wen; Dagliyan, Onur; Macnevin, Christopher; Kaufholz, Melanie; Zimmermann, Bastian; Dokholyan, Nikolay V; Hahn, Klaus M; Plückthun, Andreas (2013). Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chemistry & Biology, 20(6):847-856.

Rosenthal, Florian; Feijs, Karla L H; Frugier, Emilie; Bonalli, Mario; Forst, Alexandra H; Imhof, Ralph; Winkler, Hans C; Fischer, David; Caflisch, Amedeo; Hassa, Paul O; Lüscher, Bernhard; Hottiger, Michael O (2013). Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nature Structural & Molecular Biology, 20(4):502-507.

Magno, Andrea; Steiner, Sandra; Caflisch, Amedeo (2013). Mechanism ad kinetics of acetyl-lysine binding to bromodomains. Journal of Chemical Theory and Computation, 9(9):4225-4232.

Scherzer-Attali, Roni; Convertino, Marino; Pellarin, Riccardo; Gazit, Ehud; Segal, Daniel; Caflisch, Amedeo (2013). Methylations of Tryptophan-Modified Naphthoquinone affect its inhibitory potential toward Aβ aggregation. Journal of Physical Chemistry B, 117(6):1780-1789.

Wunderlich, Bengt; Nettels, Daniel; Benke, Stephan; Clark, Jennifer; Weidner, Sascha; Hofmann, Hagen; Pfeil, Shawn H; Schuler, Benjamin (2013). Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes. Nature Protocols, 8(8):1459-1474.

Zeitz, Jonas; Schmidinger, Irène; Rentsch, Katharina; Rogler, Gerhard; Vavricka, Stephan R (2013). Morbus Meulengracht. Praxis, 102(3):129-135.

Kalgin, Igor V; Caflisch, Amedeo; Chekmarev, Sergei F; Karplus, Martin (2013). New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow. Journal of Physical Chemistry B, 117(20):6092-6105.

Bukowska, Magdalena A; Grütter, Markus G (2013). New concepts and aids to facilitate crystallization. Current Opinion in Structural Biology, 23(3):409-416.

Lafleur, Karine; Dong, Jing; Huang, Danzhi; Caflisch, Amedeo; Nevado, Cristina (2013). Optimization of inhibitors of the tyrosine kinase EphB4. 2. Cellular potency improvement and binding mode validation by X-ray crystallography. Journal of Medicinal Chemistry, 56(1):84-96.

Simon, Manuel; Frey, Raphael; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2013). Orthogonal assembly of a designed ankyrin repeat protein-cytotoxin conjugate with a clickable serum albumin module for half-life extension. Bioconjugate Chemistry, 24(11):1955-1966.

Tschirren, Barbara; Andersson, Martin; Scherman, Kristin; Westerdahl, Helena; Mittl, Peer R E; Raberg, Lars (2013). Polymorphisms at the innate immune receptor TLR2 are associated with borrelia infection in a wild rodent population. Proceedings of the Royal Society of London, Series B: Biological Sciences, 280(1759):20130364.

Blomberg, Rebecca; Kries, Hajo; Pinkas, Daniel M; Mittl, Peer R E; Grütter, Markus G; Privett, Heidi K; Mayo, Stephen L; Hilvert, Donald (2013). Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature, 503(7476):418-421.

Bjelić, Saša; Jelesarov, Ilian (2013). Probing the energetic and kinetic impact of topologically conserved interactions in the SIV gp41 six-helix bundle. Biophysical Chemistry, 171:54-62.

Gu, Gucci Jijuan; Friedman, Mikaela; Jost, Christian; Johnsson, Kai; Kamali-Moghaddam, Masood; Plückthun, Andreas; Landegren, Ulf; Söderberg, Ola (2013). Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation. New biotechnology, 30(2):144-152.

Jinek, Martin; East, Alexandra; Cheng, Aaron; Lin, Steven; Ma, Enbo; Doudna, Jennifer (2013). RNA-programmed genome editing in human cells. eLife, 2:e00471.

Putty, Kalyani; Marcus, Sarah A; Mittl, Peer R E; Bogadi, Lindsey E; Hunter, Allison M; Arur, Swathi; Berg, Douglas E; Sethu, Palaniappan; Kalia, Awdhesh (2013). Robustness of Helicobacter pylori infection conferred by context-variable redundancy among cysteine-rich paralogs. PLoS ONE, 8(3):e59560.

Aznauryan, Mikayel; Nettels, Daniel; Holla, Andrea; Hofmann, Hagen; Schuler, Benjamin (2013). Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteins. Journal of the American Chemical Society, 135(38):14040-14043.

Schuler, Benjamin; Hofmann, Hagen (2013). Single-molecule spectroscopy of protein folding dynamics - expanding scope and timescales. Current Opinion in Structural Biology, 23(1):36-47.

Hofmann, Hagen; Nettels, Daniel; Schuler, Benjamin (2013). Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH. Journal of Chemical Physics, 139(12):121930.

Schroeder, Thilo; Barandun, Jonas; Flütsch, Andreas; Briand, Christophe; Mittl, Peer R E; Grütter, Markus G (2013). Specific inhibition of caspase-3 by a competitive DARPin: molecular mimicry between native and designed inhibitors. Structure, 21(2):277-289.

Scott, Daniel J; Kummer, Lutz; Tremmel, Dirk; Plückthun, Andreas (2013). Stabilizing membrane proteins through protein engineering. Current Opinion in Chemical Biology, 17(3):427-435.

Harapin, Jan; Eibauer, Matthias; Medalia, Ohad (2013). Structural analysis of supramolecular assemblies by cryo-electron tomography. Structure, 21(9):1522-1530.

Jost, Christian; Schilling, Johannes; Tamaskovic, Rastislav; Schwill, Martin; Honegger, Annemarie; Plückthun, Andreas (2013). Structural basis for eliciting a cytotoxic effect in HER2-overexpressing cancer cells via binding to the extracellular domain of HER2. Structure, 21(11):1979-1991.

Kassube, Susanne A; Jinek, Martin; Fang, Jie; Tsutakawa, Susan; Nogales, Eva (2013). Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nature Structural & Molecular Biology, 20(7):892-899.

Epa, V Chandana; Dolezal, Olan; Doughty, Larissa; Xiao, Xiaowen; Jost, Christian; Plückthun, Andreas; Adams, Timothy E (2013). Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2. PLoS ONE, 8(3):e59163.

Kebbel, Fabian; Kurz, Mareike; Arheit, Marcel; Grütter, Markus G; Stahlberg, Henning (2013). Structure and substrate-induced conformational changes of the secondary citrate/Sodium symporter CitS revealed by electron crystallography. Structure, 21(7):1243-1250.

Gigant, Benoît; Wang, Weiyi; Dreier, Birgit; Jiang, Qiyang; Pecqueur, Ludovic; Plückthun, Andreas; Wang, Chunguang; Knossow, Marcel (2013). Structure of a kinesin-tubulin complex and implications for kinesin motility. Nature Structural & Molecular Biology, 20(8):1001-1007.

Huang, Danzhi; Rossini, Emanuele; Steiner, Sandra; Caflisch, Amedeo (2013). Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem, 9(3):573-579.

Samatanga, Brighton; Dominguez, Cyril; Jelesarov, Ilian; Allain, Frédéric H-T (2013). The high kinetic stability of a G-quadruplex limits hnRNP F qRRM3 binding to G-tract RNA. Nucleic Acids Research, 41(4):2505-2516.

Elad, Nadav; Volberg, Tova; Patla, Israel; Hirschfeld-Warneken, Vera; Grashoff, Carsten; Spatz, Joachim P; Fässler, Reinhard; Geiger, Benjamin; Medalia, Ohad (2013). The role of integrin-linked kinase in the molecular architecture of focal adhesions. Journal of Cell Science, 126(18):4099-40107.

Bonnet, Mariette; Kurz, Mareike; Mesa, Socorro; Briand, Christophe; Hennecke, Hauke; Grütter, Markus G (2013). The structure of Bradyrhizobium japonicum transcription factor FixK2 unveils sites of DNA binding and oxidation. Journal of Biological Chemistry, 288(20):14238-14246.

Gisler, Claudio; Lüscher, Daniel; Schätzle, Philipp; Dürr, Stephanie; Baici, Antonio; Galliciotti, Giovanna; Reif, Raymond; Bolliger, Marc F; Kunz, Beat; Sonderegger, Peter (2013). Zymogen activation of neurotrypsin and neurotrypsin-dependent agrin cleavage on the cell surface are enhanced by glycosaminoglycans. Biochemical Journal, 453(1):83-100.


Zhao, Hongtao. Virtual screening in discovery of novel kinase inhibitors. 2012, University of Zurich, Faculty of Science.

Zimmermann, Iwan. Structural and functional studies of activation and inhibition of ELIC, a prokaryotic member of the pentameric ligand-gated ion channel family. 2012, University of Zurich, Faculty of Science.

Diep, Tu-My. The role pf Gaf-1b in intracellular trafficking and autophagy. 2012, University of Zurich, Faculty of Science.

Gisler, Claudio. Zymogen activation by neurotrypsin. 2012, University of Zurich, Faculty of Science.

Schlinkmann, Karola. Maximizing expression and detergent stability of a GPCR by exhaustive recombination and evolution. 2012, University of Zurich, Faculty of Science.

Wuttke, René. Single-molecule spectroscopy of the folding dynamics and unfolded state properties of a fast folding protein. 2012, University of Zurich, Faculty of Science.

Frei, Andreas P; Jeon, Ock-Youm; Kilcher, Samuel; Moest, Hansjoerg; Henning, Lisa M; Jost, Christian; Plückthun, Andreas; Mercer, Jason; Aebersold, Ruedi; Carreira, Erick M; Wollscheid, Bernd (2012). Direct identification of ligand-receptor interactions on living cells and tissues. Nature biotechnology, 30(10):997-1001.

Hänni, Dominik. Extending single-­molecule fluorescence spectroscopy methods to study protein conformation and dynamics of complex biological systems. 2012, University of Zurich, Faculty of Science.

Scalco, Riccardo. Markov chain methods in protein folding dynamics. 2012, University of Zurich, Faculty of Science.

Mittal, Anshumali. Structural and biochemical studies of ABC transproters using DARPin binders. 2012, University of Zurich, Faculty of Science.

Parizek, Petra. Designed ankyrin repeat proteins as specific intracellular inhibitors of prokaryotic and eukaryotic kinases. 2012, University of Zurich, Faculty of Science.

Mohr, Anja. Selection of specific binding DARPins for the adenosine receptor A2A via different phage display strategies. 2012, University of Zurich, Faculty of Science.

Rennebaum, Sandra. Actin: Computational design of novel inhibitors and study of the influence of the natural product latrunculin on conformational dynamics. 2012, University of Zurich, Faculty of Science.

Kummer, Lutz. Designed repeat proteins as novel tool for targeting intracellular signaling events. 2012, University of Zurich, Faculty of Science.

Schaefer, Jonas. Folding and aggregation of IgGs-influence of mutations and expression systems. 2012, University of Zurich, Faculty of Science.

Schärer, Martin. Protein structures and protein interfaces: Explorations in bioinformatics and structural biology. 2012, University of Zurich, Faculty of Science.

Schroeder, Thilo. Specific targeting of human caspases with DARPins. 2012, University of Zurich, Faculty of Science.

Vitalis, Andreas; Caflisch, Amedeo (2012). 50 Years of Lifson–Roig Models: Application to Molecular Simulation Data. Journal of Chemical Theory and Computation, 8(1):363-373.

Pecqueur, L; Duellberg, C; Dreier, B; Jiang, Q; Wang, C; Plückthun, A; Surrey, T; Gigant, B; Knossow, M (2012). A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 109(30):12011-12016.

Chodorge, M; Züger, S; Stirnimann, C; Briand, C; Jermutus, L; Grütter, M G; Minter, R R (2012). A series of Fas receptor agonist antibodies that demonstrate an inverse correlation between affinity and potency. Cell Death and Differentiation, 19(7):1187-1195.

Fridman, Karen; Mader, Asaf; Zwerger, Monika; Elia, Natalie; Medalia, Ohad (2012). Advances in tomography: probing the molecular architecture of cells. Nature Reviews. Molecular Cell Biology, 13(11):736-742.

Schuler, Benjamin; Müller-Späth, Sonja; Soranno, Andrea; Nettels, Daniel (2012). Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods in Molecular Biology, 896:21-45.

Mittal, Anshumali; Böhm, Simon; Grütter, Markus G; Bordignon, Enrica; Seeger, Markus A (2012). Asymmetry in the homodimeric ABC transporter MsbA recognized by a DARPin. Journal of Biological Chemistry, 287(24):20395-20406.

Schätzle, Philipp; Wuttke, René; Ziegler, Urs; Sonderegger, Peter (2012). Automated quantification of synapses by fluorescence microscopy. Journal of Neuroscience Methods, 204(1):144-149.

Rigort, Alexander; Günther, David; Hegerl, Reiner; Baum, Daniel; Weber, Britta; Prohaska, Steffen; Medalia, Ohad; Baumeister, Wolfgang; Hege, Hans-Christian (2012). Automated segmentation of electron tomograms for a quantitative description of actin filament networks. Journal of Structural Biology, 177(1):135-144.

Merz, Tobias; Heck, Tobias; Geueke, Birgit; Mittl, Peer R E; Briand, Christophe; Seebach, Dieter; Kohler, Hans-Peter E; Grütter, Markus G (2012). Autoproteolytic and Catalytic Mechanisms for the β-Aminopeptidase BapA-A Member of the Ntn Hydrolase Family. Structure, 20(11):1850-1860.

Steuble, Martin; Diep, Tu-My; Schätzle, Philipp; Ludwig, Alexander; Tagaya, Mitsuo; Kunz, Beat; Sonderegger, Peter (2012). Calsyntenin-1 shelters APP from proteolytic processing during anterograde axonal transport. Biology Open, 1(8):761-74.

Manso, Yasmina; Carrasco, Javier; Comes, Gemma; Meloni, Gabriele; Adlard, Paul A; Bush, Ashley I; Vašák, Milan; Hidalgo, Juan (2012). Characterization of the role of metallothionein-3 in an animal model of Alzheimer's disease. Cellular and Molecular Life Sciences, 69(21):3683-3700.

Novinec, Marko; Lenarčič, Brigita; Baici, Antonio (2012). Clusterin is a specific stabilizer and liberator of extracellular cathepsin K. FEBS Letters, 586(7):1062-1066.

Caflisch, A; Hamm, P (2012). Complexity in Protein Folding: Simulation Meets Experiment. Current Physical Chemistry, 2:4-11.

Nettels, Daniel; Hoffmann, Armin; Schuler, Benjamin (2012). Correction to "Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds". Journal of Physical Chemistry B, 112:6137-6146.

Schlinkmann, K M; Honegger, A; Tureci, E; Robison, K E; Lipovsek, D; Pluckthun, A (2012). Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 109(25):9810-9815.

Heck, Tobias; Merz, Tobias; Reimer, Artur; Seebach, Dieter; Rentsch, Daniel; Briand, Christophe; Grütter, Markus G; Kohler, Hans-Peter E; Geueke, Birgit (2012). Crystal Structures of BapA Complexes with β-Lactam-Derived Inhibitors Illustrate Substrate Specificity and Enantioselectivity of β-Aminopeptidases. ChemBioChem, 13(14):2137-215.

Hohl, Michael; Briand, Christophe; Grütter, Markus G; Seeger, Markus A (2012). Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation. Nature Structural and Molecular Biology, 19(4):395-402.

Mignot, I; Pecqueur, L; Dorléans, A; Karuppasamy, M; Ravelli, R B G; Dreier, B; Plückthun, A; Knossow, M; Gigant, B (2012). Design and Characterization of Modular Scaffolds for Tubulin Assembly. Journal of Biological Chemistry, 287(37):31085-31094.

Tamaskovic, Rastislav; Simon, Manuel; Stefan, Nikolas; Schwill, Martin; Plückthun, Andreas (2012). Designed Ankyrin Repeat Proteins (DARPins). Methods in Enzymology, 503:101-134.

Parizek, Petra; Kummer, Lutz; Rube, Peter; Prinz, Anke; Herberg, Friedrich W; Plückthun, Andreas (2012). Designed Ankyrin Repeat Proteins (DARPins) as Novel Isoform-Specific Intracellular Inhibitors of c-Jun N-Terminal Kinases. ACS Chemical Biology, 7(8):1356-1366.

Varadamsetty, Gautham; Tremmel, Dirk; Hansen, Simon; Parmeggiani, Fabio; Plückthun, Andreas (2012). Designed armadillo repeat proteins: library generation, characterization and selection of Peptide binders with high specificity. Journal of Molecular Biology, 424(1-2):68-87.

Vitalis, Andreas; Caflisch, Amedeo (2012). Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories. Journal of Chemical Theory and Computation, 8(3):1108-1120.

Schaefer, Jonas V; Plückthun, Andreas (2012). Engineering aggregation resistance in IgG by two independent mechanisms: lessons from comparison of Pichia pastoris and mammalian cell expression. Journal of Molecular Biology, 417(4):309-335.

Simon, Manuel; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2012). Facile Double-Functionalization of Designed Ankyrin Repeat Proteins using Click and Thiol Chemistries. Bioconjugate Chemistry, 23(2):279-286.

Grossman, Einat; Dahan, Idit; Stick, Reimer; Goldberg, Martin W; Gruenbaum, Yosef; Medalia, Ohad (2012). Filaments assembly of ectopically expressed Caenorhabditis elegans lamin within Xenopus oocytes. Journal of Structural Biology, 177(1):113-118.

Grossman, Einat; Medalia, Ohad; Zwerger, Monika (2012). Functional architecture of the nuclear pore complex. Annual Review of Biophysics, 41:557-584.

Petrera, Agnese; Amstutz, Beat; Gioia, Magda; Hähnlein, Janine; Baici, Antonio; Selchow, Petra; Ferraris, Davide M; Rizzi, Menico; Sbardella, Diego; Marini, Stefano; Coletta, Massimo; Sander, Peter (2012). Functional characterization of the Mycobacterium tuberculosis zinc metallopeptidase Zmp1 and identification of potential substrates. Biological Chemistry, 393(7):631-640.

Huang, Danzhi; Caflisch, Amedeo (2012). How Does Darunavir Prevent HIV-1 Protease Dimerization? Journal of Chemical Theory and Computation, 8(5):1786-1794.

Roschitzki-Voser, Heidi; Schroeder, Thilo; Lenherr, Esther D; Frölich, Franziska; Schweizer, Andreas; Donepudi, Mrudula; Ganesan, Rajkumar; Mittl, Peer R E; Baici, Antonio; Grütter, Markus G (2012). Human caspases in vitro: expression, purification and kinetic characterization. Protein Expression and Purification, 84(2):236-246.

Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H; Steffen, Adam T; Pappu, Rohit V (2012). Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. Journal of Physical Chemistry B, 116(23):6862-6871.

Rennebaum, Sandra; Caflisch, Amedeo (2012). Inhibition of interdomain motion in g-actin by the natural product latrunculin: a molecular dynamics study. Proteins, 80(8):1998-2008.

Zimmermann, Iwan; Marabelli, Alessandro; Bertozzi, Carlo; Sivilotti, Lucia G; Dutzler, Raimund (2012). Inhibition of the Prokaryotic Pentameric Ligand-Gated Ion Channel ELIC by Divalent Cations. PLoS Biology, 10(11):e1001429.

Bloem, Robbert; Koziol, Klemens; Waldauer, Steven A; Buchli, Brigitte; Walser, Reto; Samatanga, Brighton; Jelesarov, Ilian; Hamm, Peter (2012). Ligand Binding Studied by 2D IR Spectroscopy Using the Azidohomoalanine Label. Journal of Physical Chemistry B, 116(46):13705-13712.

Borgia, Alessandro; Wensley, Beth G; Soranno, Andrea; Nettels, Daniel; Borgia, Madeleine B; Hoffmann, Armin; Pfeil, Shawn H; Lipman, Everett A; Clarke, Jane; Schuler, Benjamin (2012). Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nature Communications, 3:1195.

Schlinkmann, Karola M; Hillenbrand, Matthias; Rittner, Alexander; Künz, Madeleine; Strohner, Ralf; Plückthun, Andreas (2012). Maximizing Detergent Stability and Functional Expression of a GPCR by Exhaustive Recombination and Evolution. Journal of Molecular Biology, 422(3):414-428.

Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo (2012). Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model. In: Dokholyan, Nikolay V. Computational Modeling of Bilogical Systems: From Molecules to Pathways. London: Springer, 191-214.

Alfarano, P; Varadamsetty, G; Ewald, C; Parmeggiani, F; Pellarin, R; Zerbe, O; Plückthun, A; Caflisch, A (2012). Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science, 21(9):1298-1314.

Henderson, Richard; Sali, Andrej; Baker, Matthew L; Carragher, Bridget; Devkota, Batsal; Downing, Kenneth H; Egelman, Edward H; Feng, Zukang; Frank, Joachim; Grigorieff, Nikolaus; Jiang, Wen; Ludtke, Steven J; Medalia, Ohad; Penczek, Pawel A; Rosenthal, Peter B; Rossmann, Michael G; Schmid, Michael F; Schröder, Gunnar F; Steven, Alasdair C; Stokes, David L; Westbrook, John D; Wriggers, Willy; Yang, Huanwang; Young, Jasmine; Berman, Helen M; Chiu, Wah; Kleywegt, Gerard J; Lawson, Catherine L (2012). Outcome of the first electron microscopy validation task force meeting. Structure, 20(2):205-214.

Steiner, Sandra; Caflisch, Amedeo (2012). Peptide binding to the PDZ3 domain by conformational selection. Proteins, 80(11):2562-2572.

Adler-Abramovich, Lihi; Vaks, Lilach; Carny, Ohad; Trudler, Dorit; Magno, Andrea; Caflisch, Amedeo; Frenkel, Dan; Gazit, Ehud (2012). Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nature Chemical Biology, 8(8):701-706.

Waldauer, Steven A; Hassan, Shabir; Paoli, Beatrice; Donaldson, Paul M; Pfister, Rolf; Hamm, Peter; Caflisch, Amedeo; Pellarin, Riccardo (2012). Photocontrol of reversible amyloid formation with a minimal-design peptide. Journal of Physical Chemistry B, 116(30):8961-8973.

Hofmann, Hagen; Soranno, Andrea; Borgia, Alessandro; Gast, Klaus; Nettels, Daniel; Schuler, Benjamin (2012). Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 109(40):16155-16160.

Kebbel, Fabian; Kurz, Mareike; Grütter, Markus G; Stahlberg, Henning (2012). Projection structure of the secondary citrate/sodium symporter CitS at 6 Å resolution by electron crystallography. Journal of Molecular Biology, 418(1-2):117-126.

Crespo, Maria D; Puorger, Chasper; Schärer, Martin A; Eidam, Oliv; Grütter, Markus G; Capitani, Guido; Glockshuber, Rudi (2012). Quality control of disulfide bond formation in pilus subunits by the chaperone FimC. Nature Chemical Biology, 8(8):707-713.

Pedersen, Jeppe T; Hureau, Christelle; Hemmingsen, Lars; Heegaard, Niels H H; Østergaard, Jesper; Vašák, Milan; Faller, Peter (2012). Rapid exchange of metal between Zn(7)-metallothionein-3 and amyloid-β peptide promotes amyloid-related structural changes. Biochemistry, 51(8):1697-1706.

Dreier, Birgit; Plückthun, Andreas (2012). Rapid selection of high-affinity binders using ribosome display. Methods in Molecular Biology, 805:261-286.

Bokstad, Melanie; Sabanay, Helena; Dahan, Idit; Geiger, Benjamin; Medalia, Ohad (2012). Reconstructing adhesion structures in tissues by cryo-electron tomography of vitrified frozen sections. Journal of Structural Biology, 178(2):76-83.

Plückthun, Andreas (2012). Ribosome Display: A Perspective. Methods in Molecular Biology, 805:3-28.

Medalia, Ohad; Frangakis, Achilleas (2012). Special issue on electron tomography. Journal of Structural Biology, 178(2):75.

Kummer, L; Parizek, P; Rube, P; Millgramm, B; Prinz, A; Mittl, P R E; Kaufholz, M; Zimmermann, B; Herberg, F W; Pluckthun, A (2012). Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 109(34):E2248-E2257.

Bank, Erin M; Ben-Harush, Kfir; Feinstein, Naomi; Medalia, Ohad; Gruenbaum, Yosef (2012). Structural and physiological phenotypes of disease-linked lamin mutations in C. elegans. Journal of Structural Biology, 177(1):106-112.

Fernandez, F J; de Vries, D; Peña-Soler, E; Coll, M; Christen, P; Gehring, H; Vega, M C (2012). Structure and mechanism of a cysteine sulfinate desulfinase engineered on the aspartate aminotransferase scaffold. Biochimica et Biophysica Acta, 1824(2):339-349.

Madhurantakam, Chaithanya; Varadamsetty, Gautham; Grütter, Markus G; Plückthun, Andreas; Mittl, Peer R E (2012). Structure-based optimization of designed Armadillo-repeat proteins. Protein Science, 21(7):1015-1028.

Zhou, Qi; Schneider, Irene C; Edes, Inan; Honegger, Annemarie; Bach, Patricia; Schönfeld, Kurt; Schambach, Axel; Wels, Winfried S; Kneissl, Sabrina; Uckert, Wolfgang; Buchholz, Christian J (2012). T-cell receptor gene transfer exclusively to human CD8+ cells enhances tumor cell killing. Blood, 120(22):4334-4342.

Grütter, Markus G; Luban, Jeremy (2012). TRIM5 structure, HIV-1 capsid recognition, and innate immune signaling. Current Opinion in Virology, 2(2):142-150.

Meloni, Gabriele; Crameri, Andrea; Fritz, Günter; Davies, Paul; Brown, David R; Kroneck, Peter M H; Vašák, Milan (2012). The catalytic redox activity of prion protein-Cu(II) is controlled by metal exchange with the Zn(II) -thiolate clusters of Zn(7) metallothionein-3. ChemBioChem, 13(9):1261-1265.

Maimon, Tal; Elad, Nadav; Dahan, Idit; Medalia, Ohad (2012). The human nuclear pore complex as revealed by cryo-electron tomography. Structure, 20(6):998-1006.

Marino, J; Geertsma, E R; Zerbe, O (2012). Topogenesis of heterologously expressed fragments of the human Y4 GPCR. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1818(12):3055-3063.

Schaefer, J V; Pluckthun, A (2012). Transfer of engineered biophysical properties between different antibody formats and expression systems. Protein Engineering Design and Selection : PEDS, 25(10):485-506.

Eicher, Thomas; Cha, Hi-jea; Seeger, Markus A; Brandstätter, Lorenz; El-Delik, Jasmin; Bohnert, Jürgen A; Kern, Winfried V; Verrey, François; Grütter, Markus G; Diederichs, Kay; Pos, Klaas M (2012). Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 109(15):5687-5692.

Seeger, Markus A; Mittal, Anshumali; Velamakanni, Saroj; Hohl, Michael; Schauer, Stefan; Salaa, Ihsene; Grütter, Markus G; van Veen, Hendrik W (2012). Tuning the drug efflux activity of an ABC transporter in vivo by in vitro selected DARPin binders. PLoS ONE, 7(6):e37845.

Scalco, Riccardo; Caflisch, Amedeo (2012). Ultrametricity in Protein Folding Dynamics. Journal of Chemical Theory and Computation, 8(5):1580-1588.

Zwerger, Monika; Medalia, Ohad (2012). Unravelling the lamina network. Nature Reviews. Molecular Cell Biology, 13(3):140.


Batyuk, A. Protein engineering approaches in developing new crystallization chaperones and their application to membrane protein crystallography. 2011, University of Zurich, Faculty of Science.

Schätzle, Philipp. Functional analysis of the N-terminal segment of Agrin and characterization of the response of dendritic spines to cholinergic stimulation. 2011, University of Zurich, Faculty of Science.

Sokolowska, E. Physiological and behavioral consequences of activity-dependent Agrin cleavage by Neurotrypsin. 2011, University of Zurich, Faculty of Science.

Züger, S. Receptors in innate immunity: towards structure determination of NLRP3, TRIM5alpha and Fas. 2011, University of Zurich, Faculty of Science.

Varadamsetty, G. Reengineering and selections of designed Armadillo repeat proteins: a novel technology for modular peptide recognition. 2011, University of Zurich, Faculty of Science.

Cooksley-Decasper, S L. Antibody phage display assisted discovery of potential biomarkers for atheroscelosis. 2011, University of Zurich, Faculty of Science.

Wagner, A (2011). On the energy and material cost of gene duplication. In: Dittmar, K; Liberles, D. Evolution after gene duplication. Hoboken, NJ: Wiley-Blackwell, 207-214.

Bank, E M; Ben-Harush, K; Wiesel-Motiuk, N; Barkan, R; Feinstein, N; Lotan, O; Medalia, O; Gruenbaum, Y (2011). A laminopathic mutation disrupting lamin filament assembly causes disease-like phenotypes in Caenorhabditis elegans. Molecular Biology of the Cell, 22(15):2716-2728.

Wu, F; Christen, P; Gehring, H (2011). A novel approach to inhibit intracellular vitamin B6-dependent enzymes: proof of principle with human and plasmodium ornithine decarboxylase and human histidine decarboxylase. FASEB Journal, 25(7):2109-2122.

Martin-Killias, P; Stefan, N; Rothschild, S; Plückthun, A; Zangemeister-Wittke, U (2011). A novel fusion toxin derived from an EpCAM-specific designed ankyrin repeat protein has potent antitumor activity. Clinical Cancer Research, 17(1):100-110.

Huwiler, A; Bourquin, F; Kotelevets, N; Pastukhov, O; Capitani, G; Grütter, M G; Zangemeister-Wittke, U (2011). A prokaryotic S1P lyase degrades extracellular S1P in vitro and in vivo: Implication for treating hyperproliferative disorders. PLoS ONE, 6(8):e22436.

Geertsma, E R; Dutzler, R (2011). A versatile and efficient high-throughput cloning tool for structural biology. Biochemistry, 50(15):3272-3278.

Oufir, M; Bisset, L R; Hoffmann, S R K; Xue, G; Klauser, S; Bergamaschi, B; Gervaix, A; Böni, J; Schüpbach, J; Gutte, B (2011). Artificial 64-residue HIV-1 enhancer-binding peptide is a potent inhibitor of viral replication in HIV-1-infected cells. Advances in Virology, 2011:165871.

Tamir, A; Elad, N; Medalia, O (2011). Assembly and breakdown of microtubules within the midbody. Communicative & Integrative Biology, 4(5):552-553.

Boersma, Y L; Chao, G; Steiner, D; Wittrup, K D; Plückthun, A (2011). Bispecific designed ankyrin repeat proteins (DARPins) targeting epidermal growth factor receptor inhibit A431 cell proliferation and receptor recycling. Journal of Biological Chemistry, 286(48):41273-41285.

Vašák, M; Meloni, G (2011). Chemistry and biology of mammalian metallothioneins. Journal of Biological Inorganic Chemistry, 16(7):1067-1078.

Yahav, T; Maimon, T; Grossman, E; Dahan, I; Medalia, O (2011). Cryo-electron tomography: gaining insight into cellular processes by structural approaches. Current Opinion in Structural Biology, 21(5):670-677.

Boersma, Y L; Plückthun, A (2011). DARPins and other repeat protein scaffolds: advances in engineering and applications. Current Opinion in Biotechnology, 22(6):849-857.

Stefan, N; Martin-Killias, P; Wyss-Stoeckle, S; Honegger, A; Zangemeister-Wittke, U; Plückthun, A (2011). DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency. Journal of Molecular Biology, 413(4):826-43.

Münch, R C; Mühlebach, M D; Schaser, T; Kneissl, S; Jost, C; Plückthun, A; Cichutek, K; Buchholz, C J (2011). DARPins: an efficient targeting domain for lentiviral vectors. Molecular Therapy, 19(4):686-693.

Zheng, W; Qi, B; Rohrdanz, M A; Caflisch, A; Dinner, A R; Clementi, C (2011). Delineation of folding pathways of a β-sheet miniprotein. Journal of Physical Chemistry. B, 115(44):13065-13074.

Monroe, N; Sennhauser, G; Seeger, M A; Briand, C; Grütter, M G (2011). Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface. Journal of Structural Biology, 174(2):269-281.

Convertino, M; Vitalis, A; Caflisch, A (2011). Disordered binding of small molecules to aβ(12-28). Journal of Biological Chemistry, 286(48):41578-41588.

Mishra, S; Caflisch, A (2011). Dynamics in the active site of β-Secretase: a network analysis of atomistic simulations. Biochemistry, 50(43):9328-9339.

Scalco, R; Caflisch, A (2011). Equilibrium distribution from distributed computing (simulations of protein folding). Journal of Physical Chemistry. B, 115(19):6358-6365.

Dodevski, I; Plückthun, A (2011). Evolution of three human GPCRs for higher expression and stability. Journal of Molecular Biology, 408(4):599-615.

Flütsch, A; Schroeder, T; Grütter, M G; Patzke, Greta R (2011). HIV-1 protease inhibition potential of functionalized polyoxometalates. Bioorganic & Medicinal Chemistry Letters, 21(4):1162-1166.

Dreier, B; Mikheeva, G; Belousova, N; Parizek, P; Boczek, E; Jelesarov, I; Forrer, P; Plückthun, A; Krasnykh, V (2011). Her2-specific multivalent adapters confer designed tropism to adenovirus for gene targeting. Journal of Molecular Biology, 405(2):410-426.

Zhao, H; Huang, D (2011). Hydrogen bonding penalty upon ligand binding. PLoS ONE, 6(6):e19923.

Ganesan, R; Jelakovic, S; Mittl, P R E; Caflisch, A; Grütter, M G (2011). In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications, 67(Pt 8):842-850.

Boenzli, E; Robert-Tissot, C; Sabatino, G; Cattori, V; Meli, Marina L; Gutte, B; Rovero, P; Flynn, N; Hofmann-Lehmann, R; Lutz, H (2011). In vitro inhibition of feline leukaemia virus infection by synthetic peptides derived from the transmembrane domain. Antiviral Therapy, 16(6):905-913.

Stevens, G B; Krüger, M; Latychevskaia, T; Lindner, P; Plückthun, A; Fink, H-W (2011). Individual filamentous phage imaged by electron holography. European Biophysics Journal, 40(10):1197-1201.

Zimmermann, I; Dutzler, R (2011). Ligand activation of the prokaryotic pentameric ligand-gated ion channel ELIC. PLoS Biology, 9(6):e1001101.

Manso, Y; Adlard, P A; Carrasco, J; Vašák, M; Hidalgo, J (2011). Metallothionein and brain inflammation. Journal of Biological Inorganic Chemistry, 16(7):1103-1113.

Vašák, M (2011). Metallothioneins: chemical and biological challenges. Journal of Biological Inorganic Chemistry, 16(7):975-976.

Elad, N; Abramovitch, S; Sabanay, H; Medalia, O (2011). Microtubule organization in the final stages of cytokinesis as revealed by cryo-electron tomography. Journal of Cell Science, 124(Pt 2):207-215.

Devi, V S; Mittl, P R E (2011). Monitoring the disulfide bond formation of a cysteine-rich repeat protein from Helicobacter pylori in the periplasm of Escherichia coli. Current Microbiology, 62(3):903-907.

Sharma, S K; Goloubinoff, P; Christen, P (2011). Non-native proteins as newly-identified targets of heavy metals and metalloids. In: Banfalvi, G. Cellular Effects of Heavy Metals. Heidelberg: Springer, 263-274.

Bourquin, F; Capitani, G; Grütter, M G (2011). PLP-dependent enzymes as entry and exit gates of sphingolipid metabolism. Protein Science, 20(9):1492-1508.

Hoffmann, A; Nettels, D; Clark, J; Borgia, A; Radford, S E; Clarke, J; Schuler, B (2011). Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP). Physical Chemistry Chemical Physics (PCCP), 13(5):1857-1871.

Schätzle, P; Ster, J; Verbich, D; McKinney, R A; Gerber, U; Sonderegger, P; María Mateos, J (2011). Rapid and reversible formation of spine head filopodia in response to muscarinic receptor activation in CA1 pyramidal cells. Journal of Physiology, 589(17):4353-4364.

Roschitzki, B; Schauer, S; Mittl, P R E (2011). Recognition of host proteins by Helicobacter cysteine-rich protein C. Current Microbiology, 63(3):239-249.

Meloni, G; Vasák, M (2011). Redox activity of α-synuclein-Cu is silenced by Zn(7)-metallothionein-3. Free Radical Biology and Medicine, 50(11):1471-1479.

Dreier, B; Plückthun, A (2011). Ribosome display: a technology for selecting and evolving proteins from large libraries. Methods in Molecular Biology, 687:283-306.

Borgia, M B; Borgia, A; Best, R B; Steward, A; Nettels, D; Wunderlich, B; Schuler, B; Clarke, J (2011). Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins. Nature, 474(7353):662-665.

Huang, D; Caflisch, A (2011). Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations. ChemMedChem, 6(9):1578-1580.

Frydman-Marom, A; Convertino, M; Pellarin, R; Lampel, A; Shaltiel-Karyo, R; Segal, D; Caflisch, A; Shalev, D E; Gazit, E (2011). Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. ACS Chemical Biology, 6(11):1265-1276.

Schärer, M A; Eliot, A C; Grütter, M G; Capitani, G (2011). Structural basis for reduced activity of 1-aminocyclopropane-1-carboxylate synthase affected by a mutation linked to andromonoecy. FEBS Letters, 585(1):111-114.

Hoefling, M; Lima, N; Haenni, D; Seidel, C A M; Schuler, B; Grubmüller, H (2011). Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS ONE, 6(5):e19791.

Friedman, R; Caflisch, A (2011). Surfactant effects on amyloid aggregation kinetics. Journal of Molecular Biology, 414(2):303-312.

Pertel, T; Hausmann, S; Morger, D; Züger, S; Guerra, J; Lascano, J; Reinhard, C; Santoni, F A; Uchil, P D; Chatel, L; Bisiaux, A; Albert, M L; Strambio-De-Castillia, C; Mothes, W; Pizzato, M; Grütter, M G; Luban, J (2011). TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Nature, 472(7343):361-365.

Yuan, H; Xia, T; Schuler, B; Orrit, M (2011). Temperature-cycle single-molecule FRET microscopy on polyprolines. Physical Chemistry Chemical Physics (PCCP), 13(5):1762-1769.

Huang, D; Caflisch, A (2011). The free energy landscape of small molecule unbinding. PLoS Computational Biology, 7(2):e1002002.

Leemann-Zakaryan, R P; Pahlich, S; Grossenbacher, D; Gehring, H (2011). Tyrosine phosphorylation in the C-terminal nuclear localization and retention signal (C-NLS) of the EWS protein. Sarcoma, 2011:ID 218483.

Seeber, M; Felline, A; Raimondi, F; Muff, S; Friedman, R; Rao, F; Caflisch, A; Fanelli, F (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry, 32(6):1183-1194.


Bichsel, M; Barbour, A D; Wagner, A (2010). The early phase of a bacterial insertion sequence infection. Theoretical Population Biology, 78(4):278-288.

Prunotto, A. Systematic study and enhancement of an implicit solvent model. 2010, University of Zurich, Faculty of Science.

Monroe, N. Structural and functionalstudies of eukaryotic and prokaryotic multidrug transporters. 2010, University of Zurich, Faculty of Science.

Klingler, D. Biomarker for the Proteolytic Activity of Neurotrypsin in vivo. 2010, University of Zurich, Faculty of Science.

Müller-Späth, S. Single-molecule fluorescence spectroscopy of protein folding: probing denatured state interactions and folding transitions. 2010, University of Zurich, Faculty of Science.

Messner, S; Altmeyer, M; Zhao, H; Pozivil, A; Roschitzki, B; Gehrig, P; Rutishauser, D; Huang, D; Caflisch, A; Hottiger, M O (2010). PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Research, 38(19):6350-6362.

Manso, Y; Serra, M; Comes, G; Giralt, M; Carrasco, J; Cols, N; Vasák, M; González-Duarte, P; Hidalgo, J (2010). The comparison of mouse full metallothionein-1 versus alpha and beta domains and metallothionein-1-to-3 mutation following traumatic brain injury reveals different biological motifs. Journal of Neuroscience Research, 88(8):1708-1718.

Serra-Batiste, M; Cols, N; Alcaraz, L A; Donaire, A; González-Duarte, P; Vasák, M (2010). The metal-binding properties of the blue crab copper specific CuMT-2: a crustacean metallothionein with two cysteine triplets. Journal of Biological Inorganic Chemistry, 15(5):759-776.

Casutt, M. Functional and Structural Investigations of a Multisubunit Redox Pump, the Na+-translocating NADH: Quinone Oxidoreductase from Vibrio cholerae. 2010, University of Zurich, Faculty of Science.

Keller, N; Grütter, M G; Zerbe, O (2010). Studies of the molecular mechanism of caspase-8 activation by solution NMR. Cell Dath and Differentiation, 17(4):710-718.

Hofstetter, M. From plaques to pretzels to fragments: Maturation and aging of the neuromuscular junction. 2010, University of Zurich, Faculty of Medicine.

Melkko, S; Mannocci, L; Dumelin, C E; Villa, A; Sommavilla, R; Zhang, Y; Grütter, M; Keller, N; Jermutus, L; Jackson, R H; Scheuermann, J; Neri, D (2010). Isolation of a small-molecule inhibitor of the antiapoptotic protein Bcl-xL from a DNA-encoded chemical library. ChemMedChem, 5(4):584-590.

Kaiser-Bunbury, C N; Muff, S; Memmott, J; Müller, C B; Caflisch, A (2010). The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecology Letters, 13(4):442-452.

Romero-Isart, N; Oliva, B; Vašák, M (2010). Influence of NH-S gamma bonding interactions on the structure and dynamics of metallothioneins. Journal of Molecular Modeling, 16(3):387-394.

Huang, D; Caflisch, A (2010). Library screening by fragment-based docking. Journal of Molecular Recognition, 23(2):183-193.

de Groot, C O; Jelesarov, I; Damberger, F F; Bjelić, S; Schärer, M A; Bhavesh, N S; Grigoriev, I; Buey, R M; Wüthrich, K; Capitani, G; Akhmanova, A; Steinmetz, M O (2010). Molecular insights into mammalian end-binding protein heterodimerization. Journal of Biological Chemistry, 285(8):5802-5814.

Sonda, S; Morf, L; Bottova, I; Baetschmann, H; Rehrauer, H; Caflisch, A; Hakimi, M-A; Hehl, A B (2010). Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Molecular Microbiology, 76(1):48-67.

Merz, T M. BapA – an unusual bacterial aminopeptidase. 2010, University of Zurich, Faculty of Science.

Shalaby, T; et al; Nagasawa, K; Jelesarov, I (2010). Disabling c-Myc in Childhood Medulloblastoma and Atypical Teratoid/Rhabdoid Tumor Cells by the Potent G-Quadruplex Interactive Agent S2T1-6OTD. Molecular Cancer Therapeutics, 9(1):167-169.

Exner, V; Alexandre, C; Rosenfeldt, G; Alfarano, P; Nater, M; Caflisch, A; Gruissem, W; Batschauer, A; Hennig, L (2010). A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering. Plant Physiology, 154(4):1633-1645.

Bányai, L; Sonderegger, P; Patthy, L (2010). Agrin binds BMP2, BMP4 and TGFbeta1. PLoS ONE, 5(5):e10758.

Pellarin, R; Schuetz, P; Guarnera, E; Caflisch, A (2010). Amyloid fibril polymorphism is under kinetic control. Journal of the American Chemical Society, 132(42):14960-14970.

Schiffmann, Florian. An atomistic picture of the active interface in dye sensitized solar cells. 2010, University of Zurich, Faculty of Science.

Schärer, M A; Grütter, M G; Capitani, G (2010). CRK: an evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts. Proteins, 78(12):2707-2713.

Müller-Späth, S; Soranno, A; Hirschfeld, V; Hofmann, H; Rüegger, S; Reymond, L; Nettels, D; Schuler, B (2010). Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(33):14609-14614.

Zhou, T; Lafleur, K; Caflisch, A (2010). Complementing ultrafast shape recognition with an optical isomerism descriptor. Journal of Molecular Graphics and Modelling, 29(3):443-449.

Scherzer-Attali, R; Pellarin, R; Convertino, M; Frydman-Marom, A; Egoz-Matia, N; Peled, S; Levy-Sakin, M; Shalev, D E; Caflisch, A; Gazit, E; Segal, D (2010). Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor. PLoS ONE, 5(6):e11101.

Zahnd, C; Sarkar, C A; Plückthun, A (2010). Computational analysis of off-rate selection experiments to optimize affinity maturation by directed evolution. Protein Engineering Design and Selection : PEDS, 23(4):175-184.

Novinec, M; Kovacic, L; Lenarcic, B; Baici, A (2010). Conformational flexibility and allosteric regulation of cathepsin K. Biochemical Journal, 429(2):379-389.

Schaefer, J V; Honegger, A; Plückthun, A (2010). Construction of scFv fragments from hybridoma or spleen cells by PCR assembly. In: Kontermann, R; Dübel, S. Antibody Engineering. Berlin Heidelberg: Springern-Verlag, 21-44.

Magno, A; Caflisch, A; Pellarin, R (2010). Crowding effects on amyloid aggregation kinetics. Journal of Physical Chemistry Letters, (1):3027-3032.

Casutt, M S; Wendelspiess, S; Steuber, J; Fritz, G (2010). Crystallization of the Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications, 66(Pt 12):1677-1679.

Martin Killias, Patricia. Designed ankyrin repeat proteins for targeted cancer therapy. 2010, University of Zurich, Faculty of Science.

Theurillat, J P; Dreier, B; Nagy-Davidescu, G; Seifert, Burkhardt; Behnke, S; Zürrer-Härdi, U; Ingold, F; Plückthun, A; Moch, H (2010). Designed ankyrin repeat proteins: a novel tool for testing epidermal growth factor receptor 2 expression in breast cancer. Modern Pathology, 23(9):1289-1297.

Vincent, Myriam. Designed degradation of a specific protein in the cell. 2010, University of Zurich, Faculty of Science.

Bütikofer, Lukas. Destabilization of the NMJ by neurotrypsin-mediated agrin cleavage results in precocious sarcopenia. 2010, University of Zurich, Faculty of Science.

Dodevski, Igor. Directed evolution of G-protein-coupled receptors for expression and stability. 2010, University of Zurich, Faculty of Science.

Zahnd, C; Kawe, M; Stumpp, M T; de Pasquale, C; Tamaskovic, R; Nagy-Davidescu, G; Dreier, B; Schibli, R; Binz, H K; Waibel, R; Plückthun, A (2010). Efficient tumor targeting with high-affinity designed ankyrin repeat proteins: effects of affinity and molecular size. Cancer Research, 70(4):1595-1605.

Qi, B; Muff, S; Caflisch, A; Dinner, A R (2010). Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. Journal of Physical Chemistry. B, 114(20):6979-6989.

Schuetz, P; Wuttke, R; Schuler, B; Caflisch, A (2010). Free energy surfaces from single-distance information. Journal of Physical Chemistry. B, 114(46):15227-15235.

Pham, Q T; Bouchard, A; Grütter, M G; Berthoux, L (2010). Generation of human TRIM5alpha mutants with high HIV-1 restriction activity. Gene Therapy, 17(7):859-871.

Humphreys, Aelys M. Generic delimitation and macroevolutionary studies in Danthonioideae (Poaceae), with emphasis on the wallaby grasses, Rytidosperma Steud. s.l. 2010, University of Zurich, Faculty of Science.

Samal, A; Matias Rodrigues, J F; Jost, J; Martin, O C; Wagner, A (2010). Genotype networks in metabolic reaction spaces. BMC Systems Biology, 4:30.

Plückthun, A (2010). HIV: Antibodies with a split personality. Nature, 467(7315):537-538.

Burkart, V; Siegenthaler, R K; Blasius, E; Vandenbroeck, K; Alloza, I; Fingberg, W; Schloot, N C; Christen, P; Kolb, H (2010). High affinity binding of hydrophobic and autoantigenic regions of proinsulin to the 70 kDa chaperone DnaK. BMC Biochemistry, 11:44.

Zhou, T; Caflisch, A (2010). High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. ChemMedChem, 5(7):1007-1014.

Schaefer, J V; Plückthun, A (2010). Improving expression of scFv fragments by co-expression of periplasmic chaperones. In: Kontermann, R; Dübel, S. Antibody Engineering. Berlin Heidelberg: Springern-Verlag, 345-361.

Huang, D; Zhou, T; Lafleur, K; Nevado, C; Caflisch, A (2010). Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics, 26(2):198-204.

Brient-Litzler, E; Plückthun, A; Bedouelle, H (2010). Knowledge-based design of reagentless fluorescent biosensors from a designed ankyrin repeat protein. Protein Engineering Design and Selection : PEDS, 23(4):229-241.

Casutt, M S; Huber, T; Brunisholz, R; Tao, M; Fritz, G; Steuber, J (2010). Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH: quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. The Journal of Biological Chemistry, 285(35):27088-27099.

Morf, Laura. Machineries for change: differentiation in the minimized eukaryote Giardia lamblia. 2010, University of Zurich, Faculty of Science.

Vitalis, A; Caflisch, A (2010). Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. Journal of Molecular Biology, 403(1):148-165.

Schaefer, J V; Lindner, P; Plückthun, A (2010). Miniantibodies. In: Kontermann, R; Dübel, S. Antibody Engineering. Berlin Heidelberg, Germany: Springern-Verlag, 85-99.

Rankin, D J; Bichsel, M; Wagner, A (2010). Mobile DNA can drive lineage extinction in prokaryotic populations. Journal of Evolutionary Biology, 23(11):2422-2431.

Steuble, M; Gerrits, B; Ludwig, A; Mateos, J M; Diep, T M; Tagaya, M; Stephan, A; Schätzle, P; Kunz, B; Streit, P; Sonderegger, P (2010). Molecular characterization of a trafficking organelle: dissecting the axonal paths of calsyntenin-1 transport vesicles. Proteomics, 10(21):3775-3788.

Friedman, R; Caflisch, A (2010). On the orientation of the catalytic dyad in aspartic proteases. Proteins, 78(6):1575-1582.

Steffen, W; Gemperli, A C; Cvetesic, N; Steuber, J (2010). Organelle-specific expression of subunit ND5 of human complex I (NADH dehydrogenase) alters cation homeostasis in Saccharomyces cerevisiae. FEMS Yeast Research, 10(6):648-659.

Schenker, P; Baici, A (2010). Paradoxical interactions between modifiers and elastase-2. FEBS Journal, 277(11):2486-2495.

Sulc, P; Wagner, A; Martin, O C (2010). Quantifying slow evolutionary dynamics in RNA fitness landscapes. Journal of Bioinformatics and Computational Biology, 8(6):1027-1040.

Zhou, T; Huang, D; Caflisch, A (2010). Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry, 10(1):33-45.

Zhou, Ting. Quantum mechanical methods for structure-based drug design. 2010, University of Zurich, Faculty of Science.

Wetzel, S K; Ewald, C; Settanni, G; Jurt, S; Plückthun, A; Zerbe, O (2010). Residue-resolved stability of full-consensus ankyrin repeat proteins probed by NMR. Journal of Molecular Biology, 402(1):241-258.

Kindermann, M; Roschitzki-Voser, H; Caglic, D; Repnik, U; Miniejew, C; Mittl, P R E; Kosec, G; Grütter, M G; Turk, B; Wendt, K U (2010). Selective and sensitive monitoring of caspase-1 activity by a novel bioluminescent activity-based probe. Chemistry & Biology, 17(9):999-1007.

Hofmann, H; Hillger, F; Pfeil, S H; Hoffmann, A; Streich, D; Haenni, D; Nettels, D; Lipman, E A; Schuler, B (2010). Single-molecule spectroscopy of protein folding in a chaperonin cage. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(26):11793-11798.

Paoli, B; Pellarin, R; Caflisch, A (2010). Slow folding of cross-linked alpha-helical peptides due to steric hindrance. Journal of Physical Chemistry. B, 114(5):2023-2027.

Friedman, R; Pellarin, R; Caflisch, A (2010). Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles. Journal of Physical Chemistry Letters:471-474.

Espinosa-Soto, C; Wagner, A (2010). Specialization can drive the evolution of modularity. PLoS Computational Biology, 6(3):e1000719.

Bolliger, M F; Zurlinden, A; Lüscher, D; Bütikofer, L; Shakhova, O; Francolini, M; Kozlov, S V; Cinelli, P; Stephan, A; Kistler, A D; Rülicke, T; Pelczar, P; Ledermann, B; Fumagalli, G; Gloor, S M; Kunz, B; Sonderegger, P (2010). Specific proteolytic cleavage of agrin regulates maturation of the neuromuscular junction. Journal of Cell Science, 123(Pt 22):3944-3955.

Kramer, Michaela Andrea. Structural analysis of DARPin mutants and biochemical characterization of ABC transporters and SGT1. 2010, University of Zurich, Faculty of Science.

Hilf, R J C; Bertozzi, C; Zimmermann, I; Reiter, A; Trauner, D; Dutzler, R (2010). Structural basis of open channel block in a prokaryotic pentameric ligand-gated ion channel. Nature Structural and Molecular Biology, 17(11):1330-1336.

Kramer, M A; Wetzel, S K; Plückthun, A; Mittl, P R E; Grütter, M G (2010). Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned C-capping module. Journal of Molecular Biology, 404(3):381-391.

Hoffmann, Armin. Structure and dynamics of unfolded proteins probed with advanced spectroscopic techniques and microfluidic mixing. 2010, University of Zurich, Faculty of Science.

Bourquin, F; Riezman, H; Capitani, G; Grütter, M G (2010). Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism. Structure, 18(8):1054-1065.

Alfarano, Pietro. Structure-based methods for virtual screening, protein design, and protein function studies. 2010, University of Zurich, Faculty of Science.

Schoep, T D; Fulurija, A; Good, F; Lu, W; Himbeck, R P; Schwan, C; Choi, S S; Berg, D E; Mittl, P R E; Benghezal, M; Marshall, B J (2010). Surface properties of Helicobacter pylori urease complex are essential for persistence. PLoS ONE, 5(11):e15042.

Falconer, R J; Penkova, A; Jelesarov, I; Collins, B M (2010). Survey of the year 2008: applications of isothermal titration calorimetry. Journal of Molecular Recognition, 23(5):395-413.

Dityatev, A; Schachner, M; Sonderegger, P (2010). The dual role of the extracellular matrix in synaptic plasticity and homeostasis. Nature Reviews. Neuroscience, 11(11):735-746.

Bragg, J G; Wagner, A (2010). The evolution of protein material costs. In: Caetano-Anolles, G. Evolutionary genomics and systems biology. New York: Wiley-Blackwell, 203-211.

Sharma, S K; De los Rios, P; Christen, P; Lustig, A; Goloubinoff, P (2010). The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase. Nature chemical biology, 6(12):914-920.

Nikolaev, Y; Deillon, C; Hoffmann, S R K; Bigler, L; Friess, S; Zenobi, R; Pervushin, K; Hunziker, P; Gutte, B (2010). The leucine zipper domains of the transcription factors GCN4 and c-Jun have ribonuclease activity. PLoS ONE, 5(5):e10765.

Bottova, Iveta. The role of P-glycoprotein in host-pathogen interactions. 2010, University of Zurich, Faculty of Science.

Marković, Sandra. The structural basis for the regulation of ClC chloride channels and transporters by cytoplasmic domains. 2010, University of Zurich, Faculty of Science.


Friedman, R; Pellarin, R; Caflisch, A (2009). Amyloid aggregation on lipid bilayers and its impact on membrane permeability. Journal of Molecular Biology, 387(2):407-415.

Rankin, D J; Dos Santos, M; Wedekind, C (2009). The evolutionary significance of costly punishment is still to be demonstrated. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 106(50):E135.

Bourquin, F. Structural and functional studies of sphingosine-1-phosphate lyase. 2009, University of Zurich, Faculty of Science.

Nogueira, T; Rankin, D J; Touchon, M; Taddei, F; Brown, S P; Rocha, E P C (2009). Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Current Biology, 19(20):1683-1691.

Jelesarov, I; Karshikoff, A (2009). Defining the role of salt bridges in protein stability. In: Shriver, J W. Protein structures, stability and interactions. Totowa, NJ: Humana Press (Springer books), Chapter 10.

Pahlich, S; Quero, L; Roschitzki, B; Leemann-Zakaryan, R P; Gehring, H (2009). Analysis of Ewing Sarcoma (EWS)-Binding Proteins: Interaction with hnRNP M, U, and RNA-Helicases p68/72 within Protein-RNA Complexes. Journal of Proteome Research, 8(10):4455-4465.

Gut, H; Dominici, P; Pilati, S; Astegno, A; Petoukhov, M V; Svergun, D I; Grütter, M G; Capitani, G (2009). A common structural basis for pH- and calmodulin-mediated regulation in plant glutamate decarboxylase. Journal of Molecular Biology, 392(2):334-351.

Binter, A; Staunig, N; Jelesarov, I; Lohner, K; Palfey, B A; Deller, S; Gruber, K; Macheroux, P (2009). A single intersubunit salt bridge affects oligomerization and catalytic activity in a bacterial quinone reductase. FEBS Journal, 276(18):5263-5274.

Gopich, I V; Nettels, D; Schuler, B; Szabo, A (2009). Protein dynamics from single-molecule fluorescence intensity correlation functions. Journal of Chemical Physics, 131(9):095102.

Karotki, A V; Vasák, M (2009). Reaction of human metallothionein-3 with cisplatin and transplatin. Journal of Biological Inorganic Chemistry, 14(7):1129-1138.

Hafner, M; Koeppl, H; Wagner, A (2009). Evolution of feedback loops in oscillatory systems. In: Proceedings of the Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009), Denver, CO, USA, 9 August 2009 - 12 August 2009, 157-160.

Hilf, R J; Dutzler, R (2009). A prokaryotic perspective on pentameric ligand-gated ion channel structure. Current Opinion in Structural Biology, 19(4):418-424.

Honnappa, S; Gouveia, S M; Weisbrich, A; Damberger, F F; Bhavesh, N S; Jawhari, H; Grigoriev, I; van Rijssel, F J A; Buey, R M; Lawera, A; Jelesarov, I; Winkler, F K; Wüthrich, K; Akhmanova, A; Steinmetz, M O (2009). An EB1-binding motif acts as a microtubule tip localization signal. Cell, 138(2):366-376.

Roschitzki-Voser, H. Specificities of human caspases: Biochemical and structural investigations. 2009, University of Zurich, Faculty of Science.

Derfuss, T; Parikh, K; Velhin, S; Braun, M; Mathey, E; Krumbholz, M; Kümpfel, T; Moldenhauer, A; Rader, C; Sonderegger, P; Pöllmann, W; Tiefenthaller, C; Bauer, J; Lassmann, H; Wekerle, H; Karagogeos, D; Hohlfeld, R; Linington, C; Meinl, E (2009). Contactin-2/TAG-1-directed autoimmunity is identified in multiple sclerosis patients and mediates gray matter pathology in animals. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 106(20):8302-8307.

Interlandi, G (2009). Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics simulations. Proteins, 75(3):659-670.

Ludwig, A; Blume, J; Diep, T M; Yuan, J; Mateos, J M; Leuthäuser, K; Steuble, M; Streit, P; Sonderegger, P (2009). Calsyntenins mediate TGN exit of APP in a Kinesin-1-dependent manner. Traffic, 10(5):572-589.

Karotki, A. The role of metallothioneins in cancer treatment with platinum-based drugs. 2009, University of Zurich, Faculty of Science.

Dumrese, C; Slomianka, L; Ziegler, U; Choi, S S; Kalia, A; Fulurija, A; Lu, W; Berg, D E; Benghezal, M; Marshall, B; Mittl, P R E (2009). The secreted Helicobacter cysteine-rich protein A causes adherence of human monocytes and differentiation into a macrophage-like phenotype. FEBS Letters, 583(10):1637-1643.

Paoli, B; Seeber, M; Backus, E H; Ihalainen, J A; Hamm, P; Caflisch, A (2009). Bulky Side Chains and Non-native Salt Bridges Slow down the Folding of a Cross-Linked Helical Peptide: A Combined Molecular Dynamics and Time-Resolved Infrared Spectroscopy Study. Journal of Physical Chemistry. B, 113(13):4435-4442.

Sebastian, S; Grütter, C; de Castillia, C S; Pertel, T; Olivari, S; Grütter, M G; Luban, J (2009). An invariant surface patch on the TRIM5alpha PRYSPRY domain is required for retroviral restriction but dispensable for capsid binding. Journal of Virology, 83(7):3365-3373.

Ekonomiuk, Dariusz. Flaviviral protease flexibility analyzed by molecular dynamics and exploited to identify non-peptidic inhibitors by high-throughput docking. 2009, University of Zurich, Faculty of Science.

Muff, S; Caflisch, A (2009). Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics, 130(12):125104.

Matsumoto-Miyai, K; Sokolowska, E; Zurlinden, A; Gee, C E; Lüscher, D; Hettwer, S; Wölfel, J; Ladner, A P; Ster, J; Gerber, U; Rülicke, T; Kunz, B; Sonderegger, P (2009). Coincident pre- and postsynaptic activation induces dendritic filopodia via neurotrypsin-dependent agrin cleavage. Cell, 136(6):1161-1171.

Kochhar, S; Mouratou, B; Christen, P (2009). Amino acid analysis by precolumn derivatization with 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide (Marfey agent). In: Walker, J M. The Protein Protocols Handbook. Totowa, NJ: Humana Press, 567-572.

Baici, A; Schenker, P; Wächter, M; Rüedi, P (2009). 3-Fluoro-2,4-dioxa-3-phosphadecalins as inhibitors of acetylcholinesterase: a reappraisal of kinetic mechanisms and diagnostic methods. Chemistry & Biodiversity, 6(3):261-282.

Muff, S; Caflisch, A (2009). ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations. Journal of Physical Chemistry. B, 113(10):3218-3226.

Keller, M; Mares, J; Zerbe, O; Grütter, M G (2009). Structural and biochemical studies on procaspase-8: New insights on initiator caspase activation. Structure, 17(3):438-448.

Leemann-Zakaryan, R P; Pahlich, S; Sedda, M; Quero, L; Grossenbacher, D; Gehring, H (2009). Dynamic subcellular localization of the EWS proto-oncoprotein and its association with and stabilization of microtubules. Journal of Molecular Biology, 386(1):1-13.

Tao, M. Na+-translocating NADH: quinone oxidoreductase from vibrio cholerae : Structural and functional aspects. 2009, University of Zurich, Faculty of Science.

Kawe, M; Horn, U; Plückthun, A (2009). Facile promoter deletion in Escherichia coli in response to leaky expression of very robust and benign proteins from common expression vectors. Microbial Cell Factories, 8:8.

Ekonomiuk, D; Su, X-C; Ozawa, K; Bodenreider, C; Lim, S P; Yin, Z; Keller, T H; Beer, D; Patel, V; Otting, G; Caflisch, A; Huang, D (2009). Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Neglected Tropical Diseases, 3(1):e356.

Bragg, J G; Wagner, A (2009). Protein material costs: single atoms can make an evolutionary difference. Trends in Genetics, 25(1):5-8.

Hilf, R; Dutzler, R (2009). Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel. Nature, 457(7225):115-118.

Hafner, M; Koeppl, H; Hasler, M; Wagner, A (2009). 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biology, 5(10):e1000534.

Convertino, M; Pellarin, R; Catto, M; Carotti, A; Caflisch, A (2009). 9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Science, 18(4):792-800.

Bodenreider, C; Beer, D; Keller, T H; Sonntag, S; Wen, D; Yap, L; Yau, Y H; Shochat, S G; Huang, D; Zhou, T; Caflisch, A; Su, X C; Ozawa, K; Otting, G; Vasudevan, S G; Lescar, J; Lim, S P (2009). A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease. Analytical Biochemistry, 395(2):195-204.

Hilf, Ricarda J C. A prokaryotic perspective on pentameric ligand-gated ion channels. 2009, University of Zurich, Faculty of Science.

Ekonomiuk, D; Caflisch, A (2009). Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Science, 18(5):1003-1011.

Plückthun, A (2009). Alternative scaffolds: Expanding the options of antibodies. In: Little, M. Recombinant antibodies for immunotherapy. New York: Cambridge University Press, 243-271.

Wagner, A (2009). Andreas Wagner. In: Oftedal, G; Olsen, J K B; Rossell, P; Norup, M S. Evolutionary theory: 5 questions. [S.l.]: Automatic Press/VIP, ?-?.

Warmuth, Stefan. Biochemical and structural characterization of cation chloride cotransporters. 2009, University of Zurich, Faculty of Science.

Brooks, B R; Brooks, C L; Mackerell, A D; Nilsson, L; Petrella, R J; Roux, B; Won, Y; Archontis, G; Bartels, C; Boresch, S; Caflisch, A; Caves, L; Cui, Q; Dinner, A R; Feig, M; Fischer, S; Gao, J; Hodoscek, M; Im, W; Kuczera, K; Lazaridis, T; Ma, J; Ovchinnikov, V; Paci, E; Pastor, R W; Post, C B; Pu, J Z; Schaefer, M; Tidor, B; Venable, R M; Woodcock, H L; Wu, X; Yang, W; York, D M; Karplus, M (2009). CHARMM: the biomolecular simulation program. Journal of Computational Chemistry, 30(10):1545-1614.

Kovacic, Lidija; Novinec, Marko; Petan, Toni; Baici, Antonio; Krizaj, Igor (2009). Calmodulin is a nonessential activator of secretory phospholipase A(2). Biochemistry, 48(47):11319-11328.

Veesler, D; Dreier, B; Blangy, S; Lichière, J; Tremblay, D; Moineau, S; Spinelli, S; Tegoni, M; Plückthun, A; Campanacci, V; Cambillau, C (2009). Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode. Journal of Biological Chemistry, 284(44):30718-30726.

Sennhauser, G; Bukowska, M A; Briand, C; Grütter, M G (2009). Crystal structure of the multidrug exporter MexB from Pseudomonas aeruginosa. Journal of Molecular Biology, 389(1):134-145.

Zhou, T; Caflisch, A (2009). Data management system for distributed virtual screening. Journal of Chemical Information and Modeling, 49(1):145-152.

Schütz, Philipp. Development of network-analysis tools and applications in biochemistry. 2009, University of Zurich, Faculty of Science.

Sharma, S K; Christen, P; Goloubinoff, P (2009). Disaggregating chaperones: an unfolding story. Current Protein and Peptide Science, 10(5):432-446.

Friedman, R; Caflisch, A (2009). Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem, 4(8):1317-1326.

Meloni, G; Polanski, T; Braun, O; Vasák, M (2009). Effects of Zn(2+), Ca(2+), and Mg(2+) on the structure of Zn(7)metallothionein-3: evidence for an additional zinc binding site. Biochemistry, 48(24):5700-5707.

Martin, O C; Wagner, A (2009). Effects of recombination on complex regulatory circuits. Genetics, 183(2):673-684.

Winkler, J; Martin-Killias, P; Plückthun, A; Zangemeister-Wittke, U (2009). EpCAM-targeted delivery of nanocomplexed siRNA to tumor cells with designed ankyrin repeat proteins. Molecular Cancer Therapeutics, 8(9):2674-2683.

Wagner, A (2009). Evolutionary constraints permeate large metabolic networks. BMC Evolutionary Biology, 9:231.

de la Chaux, N; Wagner, A (2009). Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. BMC Evolutionary Biology, 9:205.

Matias Rodrigues, J F; Wagner, A (2009). Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Computational Biology, 5(12):e1000613.

Ekonomiuk, D; Su, X C; Ozawa, K; Bodenreider, C; Lim, S P; Otting, G; Huang, D; Caflisch, A (2009). Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. Journal of Medicinal Chemistry, 52(15):4860-4868.

Vorburger, T; Stein, A; Ziegler, U; Kaim, G; Steuber, J (2009). Functional role of a conserved aspartic acid residue in the motor of the Na(+)-driven flagellum from Vibrio cholerae. Biochimica et Biophysica Acta, 1787(10):1198-1204.

Guarnera, E; Pellarin, R; Caflisch, A (2009). How does a simplified-sequence protein fold? Biophysical Journal, 97(6):1737-1746.

Vasak, Milan; Meloni, Gabriele (2009). Metallothionein-3, Zinc, and Copper in the Central Nervous System. In: Sigel, Astrid; Sigel, Helmut; Sigel, Roland K O. Metallothioneins and Related Chelators. Cambridge: The Royal Society of Chemistry, 319-352.

Paoli, Beatrice. Molecular dynamics studies of the folding of α-helical cross-linked peptides. 2009, University of Zurich, Faculty of Science.

Su, X C; Ozawa, K; Yagi, H; Lim, S P; Wen, D; Ekonomiuk, D; Huang, D; Keller, T H; Sonntag, S; Caflisch, A; Vasudevan, S G; Otting, G (2009). NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS Journal, 276(15):4244-4255.

Wagner, A (2009). Networks in molecular evolution. In: Meyers, R A. Encyclopedia of complexity and systems science ; Part 13. New York, NY, US: Springer, 5655-5667.

Schulz, B L; Stirnimann, C U; Grimshaw, J P A; Brozzo, M S; Fritsch, F; Mohorko, E; Capitani, G; Glockshuber, R; Grütter, M G; Aebi, M (2009). Oxidoreductase activity of oligosaccharyltransferase subunits Ost3p and Ost6p defines site-specific glycosylation efficiency. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 106(27):11061-11066.

Müller, I B; Wu, F; Bergmann, B; Knöckel, J; Walter, R D; Gehring, H; Wrenger, C (2009). Poisoning pyridoxal 5-phosphate-dependent enzymes: a new strategy to target the malaria parasite Plasmodium falciparum. PLoS ONE, 4(2):e4406.

Neagu, M R; Ziegler, P; Pertel, T; Strambio-De-Castillia, C; Grütter, C; Martinetti, G; Mazzucchelli, L; Grütter, M; Manz, M G; Luban, J (2009). Potent inhibition of HIV-1 by TRIM5-cyclophilin fusion proteins engineered from human components. Journal of Clinical Investigation, 119(10):3035-3047.

Benedix, A; Becker, C M; de Groot, B L; Caflisch, A; Böckmann, R A (2009). Predicting free energy changes using structural ensembles. Nature Methods, 6(1):3-4.

Schenker, Patricia. Quest for peptidase activity modifiers: benefits of kinetic strategies. 2009, University of Zurich, Faculty of Science.

Milovnik, P; Ferrari, D; Sarkar, C A; Plückthun, A (2009). Selection and characterization of DARPins specific for the neurotensin receptor 1. Protein Engineering Design and Selection : PEDS, 22(6):357-366.

Schenker, Patricia; Baici, Antonio (2009). Simultaneous interaction of enzymes with two modifiers: reappraisal of kinetic models and new paradigms. Journal of Theoretical Biology, 261(2):318-329.

Kügler, M; Stein, C; Schwenkert, M; Saul, D; Vockentanz, L; Huber, T; Wetzel, S K; Scholz, O; Plückthun, A; Honegger, A; Fey, G H (2009). Stabilization and humanization of a single-chain Fv antibody fragment specific for human lymphocyte antigen CD19 by designed point mutations and CDR-grafting onto a human framework. Protein Engineering Design and Selection : PEDS, 22(3):135-147.

Wu, F; Gehring, H (2009). Structural requirements for novel coenzyme-substrate derivatives to inhibit intracellular ornithine decarboxylase and cell proliferation. FASEB Journal, 23(2):565-574.

Hidalgo, J; Chung, R; Penkowa, M; Vasak, Milan (2009). Structure and Function of Vertebrate Metallothioneins. In: Sigel, Astrid; Sigel, Helmut; Sigel, Roland K O. Metallothioneins and Related Chelators. Cambridge: The Royal Society of Chemistry, 279-318.

Lafleur, K; Huang, D; Zhou, T; Caflisch, A; Nevado, C (2009). Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). Journal of Medicinal Chemistry, 52(20):6433-6446.

Exner, V; Aichinger, E; Shu, H; Wildhaber, T; Alfarano, P; Caflisch, A; Gruissem, W; Köhler, C; Hennig, L (2009). The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS ONE, 4(4):e5335.

Baumgartner, R; Meder, G; Briand, C; Decock, A; D'arcy, A; Hassiepen, U; Morse, R; Renatus, M (2009). The crystal structure of caspase-6, a selective effector of axonal degeneration. Biochemical Journal, 423(3):429-439.

Weinert, C; Grütter, C; Roschitzki-Voser, H; Mittl, P R E; Grütter, M G (2009). The crystal structure of human pyrin b30.2 domain: implications for mutations associated with familial Mediterranean fever. Journal of Molecular Biology, 394(2):226-236.

Honegger, A; Malebranche, A D; Röthlisberger, D; Plückthun, A (2009). The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains. Protein Engineering Design and Selection : PEDS, 22(3):121-134.

Scocchi, M; Lüthy, C; Decarli, P; Mignogna, G; Christen, P; Gennaro, R (2009). The proline-rich antibacterial peptide Bac7 binds to and inhibits in vitro the molecular chaperone DnaK. International Journal of Peptide Research and Therapeutics, 15(2):147-155.

Wagner, A (2009). Transposable elements as genomic diseases. Molecular BioSystems, 5(1):32-35.

Warmuth, S; Zimmermann, I; Dutzler, R (2009). X-ray structure of the C-terminal domain of a prokaryotic cation-chloride cotransporter. Structure, 17(4):538-546.


Grütter, C; Wilkinson, T; Turner, R; Podichetty, S; Finch, D; McCourt, M; Loning, S; Jermutus, L; Grütter, M G (2008). A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(51):20251-20256.

Kane, A S; Hoffmann, A; Baumgärtel, P; Seckler, R; Reichardt, G; Horsley, D A; Schuler, B; Bakajin, O (2008). Microfluidic mixers for the investigation of rapid protein folding kinetics using synchrotron radiation circular dichroism spectroscopy. Analytical Chemistry, 80(24):9534-9541.

Wahl, M; Rahn, H J; Röhlicke, T; Kell, G; Nettels, D; Hillger, F; Schuler, B; Erdmann, R (2008). Scalable time-correlated photon counting system with multiple independent input channels. Review of Scientific Instruments, 79:123113.

Lüscher, D. Characterisation of the interaction of neurotrypsin and agrin. 2008, University of Zurich, Faculty of Medicine.

Jorg, T; Martin, O C; Wagner, A (2008). Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinformatics, 9:464.

Steiner, D; Forrer, P; Plückthun, A (2008). Efficient selection of DARPins with sub-nanomolar affinities using SRP phage display. Journal of Molecular Biology, 382(5):1211-1227.

Cui, T; Gao, Y; Ang, C X; Puah, C M; Gutte, B; Lam, Y (2008). Hydrogen peroxide enhances enterokinase-catalysed proteolytic cleavage of fusion protein. Recent Patents on Biotechnology, 2(3):189-190.

Narzi, D; Siu, S W I; Stirnimann, C U; Grimshaw, J P A; Glockshuber, R; Capitani, G; Böckmann, R A (2008). Evidence for proton shuffling in a thioredoxin-like protein during catalysis. Journal of Molecular Biology, 382(4):978-986.

Sennhauser, G; Grütter, M G (2008). Chaperone-assisted crystallography with DARPins. Structure, 16(10):1443-1453.

Vamvaca, K; Jelesarov, J; Hilvert, D (2008). Kinetics and thermodynamics of ligand binding to a molten globular enzyme and its native counterpart. Journal of Molecular Biology, 382(4):971-977.

Vasak, M; Meloni, G (2008). Metallothionein structure and reactivity. In: Zatta, P. Metallothioneins in Biochemistry and Patholgy. Singapore: World Scientific Publishing, 1-24.

Lin, P C; Puhar, A; Steuber, J (2008). NADH oxidation drives respiratory Na(+) transport in mitochondria from Yarrowia lipolytica. Archives of Microbiology, 190(4):471-480.

Sarkar, C A; Dodevski, I; Kenig, M; Dudli, S; Mohr, A; Hermans, E; Plückthun, A (2008). Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(39):14808-14813.

Parmeggiani, F. Design of armadillo repeat protein scaffolds. 2008, University of Zurich, Faculty of Medicine.

Karotki, A; Vasak, M (2008). Interaction of Metallothionein-2 with Platinum-Modified 5′-Guanosine Monophosphate and DNA. Biochemistry, 47(41):10961-10969.

Lebeurrier, N; Launay, S; Macrez, R; Maubert, E; Legros, H; Leclerc, A; Jamin, S P; Picard, J Y; Marret, S; Laudenbach, V; Berger, P; Sonderegger, P; Ali, C; di Clemente, N; Vivien, D (2008). Anti-Mullerian-hormone-dependent regulation of the brain serine-protease inhibitor neuroserpin. Journal of Cell Science, 121(20):3357-3365.

Reif, R; Sales, S; Dreier, B; Lüscher, D; Wölfel, J; Gisler, C; Baici, A; Kunz, B; Sonderegger, P (2008). Purification and enzymological characterization of murine neurotrypsin. Protein Expression and Purification, 61(1):13-21.

Bjelic, S; Jelesarov, I (2008). A survey of the year 2007 literature on applications of isothermal titration calorimetry. Journal of Molecular Recognition, 21:289-311.

Wölfel, J. In vitro investigations on the fine-tuned interaction between neurotrypsin and agrin. 2008, University of Zurich, Faculty of Medicine.

Hillger, F; Hänni, D; Nettels, D; Geister, S; Grandin, M; Textor, M; Schuler, B (2008). Probing protein-chaperone interactions with single-molecule fluorescence spectroscopy. Angewandte Chemie Internationale Edition, 47(33):6184-6188.

Ludwig, A. The function of calsyntenins in intracellular trafficking. 2008, University of Zurich, Faculty of Medicine.

Mukhopadhyay, D; Howell, K S; Riezman, H; Capitani, G (2008). Identifying key residues of sphinganine-1-phosphate lyase for function in vivo and in vitro. Journal of Biological Chemistry, 283(29):20159-20169.

Ihalainen, J A; Paoli, B; Muff, S; Backus, E H G; Bredenbeck, J; Woolley, G A; Caflisch, A; Hamm, P (2008). Alpha-Helix folding in the presence of structural constraints. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(28):9588-9593.

Coutelier, M; Andries, S; Ghariani, S; Dan, B; Duyckaerts, C; van Rijckevorsel, K; Raftopoulos, C; Deconinck, N; Sonderegger, P; Scaravilli, F; Vikkula, M; Godfraind, C (2008). Neuroserpin mutation causes electrical status epilepticus of slow-wave sleep. Neurology, 71(1):64-66.

Krivov, S V; Muff, S; Caflisch, A; Karplus, M (2008). One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. Journal of Physical Chemistry. B, 112(29):8701-8714.

Wright, J; Wagner, A (2008). Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Systems Biology, 2:61.

Sharma, S K; Goloubinoff, P; Christen, P (2008). Heavy metal ions are potent inhibitors of protein folding. Biochemical and Biophysical Research Communications (BBRC), 372(2):341-345.

Tao, M; Casutt, M S; Fritz, G; Steuber, J (2008). Oxidant-induced formation of a neutral flavosemiquinone in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. Biochim. Biophys. Acta: Bioenergetics, 1777(7-8):696-702.

Ferrada, E; Wagner, A (2008). Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proceedings of the Royal Society B: Biological Sciences, 275(1643):1595-1602.

Vacca, R A; Giannattasio, S; Capitani, G; Marra, E; Christen, P (2008). Molecular evolution of B6 enzymes: binding of pyridoxal-5'-phosphate and Lys41Arg substitution turn ribonuclease A into a model B6 protoenzyme. BMC Biochemistry, 9:17.

Stephan, A; Mateos, J M; Kozlov, S V; Cinelli, P; Kistler, A D; Hettwer, S; Rülicke, T; Streit, P; Kunz, B; Sonderegger, P (2008). Neurotrypsin cleaves agrin locally at the synapse. FASEB Journal, 22(6):1861-73.

Frey, D; Huber, T; Plückthun, A; Grütter, M G (2008). Structure of the recombinant antibody Fab fragment f3p4. Acta Crystallographica. Section D, Biological Crystallography, 64(Pt 6):636-643.

Wright, J; Wagner, A (2008). The Systems Biology Research Tool: evolvable open-source software. BMC Systems Biology, 2:55.

Orihuela, R; Domènech, J; Bofill, R; You, C; Mackay, E A; Kägi, J H R; Capdevila, M; Atrian, S (2008). The metal-binding features of the recombinant mussel Mytilus edulis MT-10-IV metallothionein. Journal of Biological Inorganic Chemistry, 13(5):801-12.

Stallmach, R; Gloor, S M (2008). Neurobin/TMPRSS11c, a novel type II transmembrane serine protease that cleaves fibroblast growth factor-2 in vitro. Biochemical Journal, 412(1):81-91.

Meloni, G; Sonois, V; Delaine, T; Guilloreau, L; Gillet, A; Teissie, J; Faller, P; Vasak, M (2008). Metal swap between Zn7metallothionein–3 and amyloid–β–Cu protects against amyloid–β toxicity. Nature Chemical Biology, 4(6):366-372.

Ishihara, H; Kubota, H; Lindberg, R L P; Leppert, D; Gloor, S M; Errede, M; Virgintino, D; Fontana, A; Yonekawa, Y; Frei, K (2008). Endothelial cell barrier impairment induced by glioblastomas and transforming growth factor beta2 involves matrix metalloproteinases and tight junction proteins. Journal of Neuropathology and Experimental Neurology, 67(5):435-448.

Steuble, M. Proteomic analysis of calsyntenin-1 organelles and their functional and structural characterization. 2008, University of Zurich, Faculty of Medicine.

Schuetz, P; Caflisch, A (2008). Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement. Physical Review E, 77(046112):046112-1-046112-7.

Stephan, A. Analysis of the functional interaction of neurotrypsin and agrin in the murine central nervous system. 2008, University of Zurich, Faculty of Medicine.

Kolb, P; Kipouros, C B; Huang, D; Caflisch, A (2008). Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors. Proteins, 73(1):11-8.

Rindler, M J; Xu, C-F; Gumper, I; Cen, C; Sonderegger, P; Neubert, T A (2008). Calsyntenins are secretory granule proteins in anterior pituitary gland and pancreatic islet alpha cells. Journal of Histochemistry and Cytochemistry, 56(4):381-388.

Puorger, C; Eidam, O; Capitani, G; Erilov, D; Grütter, M G; Glockshuber, R (2008). Infinite kinetic stability against dissociation of supramolecular protein complexes through donor strand complementation. Structure, 16(4):631-642.

Martin, O C; Wagner, A (2008). Multifunctionality and robustness trade-offs in model genetic circuits. Biophysical Journal, 94(8):2927-2937.

Gutte, B (2008). Solid-phase synthesis for a lifetime. Biopolymers, 90(3):214.

Wu, F; Yu, J; Gehring, H (2008). Inhibitory and structural studies of novel coenzyme-substrate analogs of human histidine decarboxylase. FASEB Journal, 22(3):890-897.

Hartmann, C; Chami, M; Zachariae, U; de Groot, B L; Engel, A; Grütter, M G (2008). Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. Journal of Molecular Biology, 377(2):352-363.

Stallmach, R. Neurobin/TMPRSS11c, a novel type II transmembrane serine protease of the nervous system which cleaves fibroblast growth factor-2 in vitro. 2008, University of Zurich, Faculty of Medicine.

Curioni-Fontecedro, A; Knights, A J; Tinguely, M; Nuber, N; Schneider, C; Thomson, C W; von Boehmer, I; Bossart, W; Pahlich, S; Gehring, H; Moch, H; Renner, C; Knuth, A; Zippelius, A (2008). MAGE-C1/CT7 is the dominant cancer-testis antigen targeted by humoral immune responses in patients with multiple myeloma. Leukemia, 22(8):1646-1648.

Eidam, O; Dworkowski, F S N; Glockshuber, R; Grütter, M G; Capitani, G (2008). Crystal structure of the ternary FimC-FimF(t)-FimD(N) complex indicates conserved pilus chaperone-subunit complex recognition by the usher FimD. FEBS Letters, 582(5):651-655.

Eidam, O. Structural and functional insights into the assemblyof type 1 pili from uropathogenic E.coli. 2008, University of Zurich, Department of Biochemistry, Faculty of Medicine.

Wagner, A (2008). Gene duplications, robustness and evolutionary innovations. BioEssays, 30(4):367-373.

Rothe, C; Urlinger, S; Löhning, C; Prassler, J; Stark, Y; Jäger, U; Hubner, B; Bardroff, M; Pradel, I; Boss, M; Bittlingmaier, R; Bataa, T; Frisch, C; Brocks, B; Honegger, A; Urban, M (2008). The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. Journal of Molecular Biology, 376(4):1182-1200.

Frischknecht, R; Fejtova, A; Viesti, M; Stephan, A; Sonderegger, P (2008). Activity-induced synaptic capture and exocytosis of the neuronal serine protease neurotrypsin. Journal of Neuroscience, 28(7):1568-1579.

Wetzel, S K; Settanni, G; Kenig, M; Binz, H K; Plückthun, A (2008). Folding and unfolding mechanism of highly stable full-consensus ankyrin repeat proteins. Journal of Molecular Biology, 376(1):241-257.

Merz, T; Wetzel, S K; Firbank, S; Plückthun, A; Grütter, M G; Mittl, P R E (2008). Stabilizing ionic interactions in a full-consensus ankyrin repeat protein. Journal of Molecular Biology, 376(1):232-240.

Nettels, D; Hoffmann, A; Schuler, B (2008). Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. Journal of Physical Chemistry. B, 112(19):6137-6146.

Bjelic, S; Wieninger, S; Jelesarov, I; Karshikoff, A (2008). Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study. Proteins, 70(3):810-822.

Schuler, B; Eaton, W A (2008). Protein folding studied by single-molecule FRET. Current Opinion in Structural Biology, 18(1):16-26.

Karshikoff, A; Jelesarov, I (2008). Salt bridges and conformational flexibility: effect on protein stability. Biotechnology and Biotechnological Equipment, 22(1):606-611.

Wetzel, S K. Folding and unfolding mechanism of designed ankyrin repeat proteins. 2008, University of Zurich, Faculty of Medicine.

Tao, M; Fritz, G; Steuber, J (2008). The Na+ -translocating NADH:quinone oxidoreductase (Na+ -NQR) from Vibrio cholerae enhances insertion of FeS in overproduced NqrF subunit. J. Inorg. Biochem., 102(5-6):1366-1372.

Interlandi, G; Wetzel, S K; Settanni, G; Plückthun, A; Caflisch, A (2008). Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. Journal of Molecular Biology, 375(3):837-854.

Okhrimenko, O; Jelesarov, I (2008). A survey of the year 2006 literature on applications of isothermal titration calorimetry. Journal of Molecular Recognition, 21(1):1-19.

Jelesarov, I; Karshikoff, A (2008). Meet to fold: the peculiar folding of oligomeric proteins. Biotechnology and Biotechnological Equipment, 22(1):598-605.

Wagner, A (2008). Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B: Biological Sciences, 275(1630):91-100.

Schenker, P; Alfarano, P; Kolb, P; Caflisch, A; Baici, A (2008). A double-headed cathepsin B inhibitor devoid of warhead. Protein Science : a Publication of the Protein Society, 17(12):2145-2155.

Parmeggiani, F; Pellarin, R; Larsen, A P; Varadamsetty, G; Stumpp, M T; Zerbe, O; Caflisch, A; Plückthun, A (2008). Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. Journal of Molecular Biology, 376(5):1282-1304.

Kolb, P; Huang, D; Dey, F; Caflisch, A (2008). Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. Journal of Medicinal Chemistry, 51(5):1179-1188.

Wagner, A; de la Chaux, N (2008). Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Molecular Genetics and Genomics, 280(5):397-408.

Grimshaw, J P A; Stirnimann, C U; Brozzo, M S; Malojcic, G; Grütter, M G; Capitani, G; Glockshuber, R (2008). DsbL and DsbI form a specific dithiol oxidase system for periplasmic arylsulfate sulfotransferase in uropathogenic Escherichia coli. Journal of Molecular Biology, 380(4):667-680.

Honegger, A (2008). Engineering antibodies for stability and efficient folding. In: Chernajovsky, Y; Nissim, A. Therapeutic Antibodies. Berlin, Heidelberg: Springer, 47-68.

Haberthür, U; Caflisch, A (2008). FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry, 29(5):701-715.

Dey, F; Caflisch, A (2008). Fragment-based de novo ligand design by multiobjective evolutionary optimization. Journal of Chemical Information and Modeling, 48(3):679-690.

Pahlich, S; Zakaryan, R; Gehring, H (2008). Identification of proteins interacting with protein arginine methyltransferase 8: The Ewing sarcoma (EWS) protein binds independent of its methylation state. Proteins, 72(4):1125-1137.

Zhou, T; Huang, D; Caflisch, A (2008). Is quantum mechanics necessary for predicting binding free energy? Journal of medicinal chemistry, 51(14):4280-4288.

Muff, S; Caflisch, A (2008). Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins, 70(4):1185-1195.

Schuetz, P; Caflisch, A (2008). Multistep greedy algorithm identifies community structure in real-world and computer-generated networks. Physical Review E, 78(026112):026112-1.

Wagner, A (2008). Neutralism and selectionism: a network-based reconciliation. Nature Reviews. Genetics, 9(12):965-974.

Muff, S. New computational methods for the investigation of thermodynamics and kinetics of protein folding. 2008, University of Zurich, Faculty of Medicine.

Friedman, R; Caflisch, A (2008). Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins, 73(4):814-827.

Félix, M A; Wagner, A (2008). Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity, 100(2):132-140.

Schuler, B (2008). Single molecule spectroscopy in protein folding: From ensembles to single molecules. In: Muñoz, V. Protein Folding, Misfolding and Aggregation. Cambridge UK: The Royal Society of Chemistry, 139-160.

Sennhauser, Gaby. Structural studies of bacterial RND-transporters. 2008, University of Zurich, Faculty of Science.

Guarnera, E. Theoretical and computational strategies for the study of protein folding mechanisms. 2008, University of Zurich, Faculty of Medicine.

Fuller, M; Wagner, A; Enquist, J (2008). Using network analysis to characterize forest structure. Natural Resources Modeling, 21(2):225-247.

Hilf, R; Dutzler, R (2008). X-ray structure of a prokaryotic pentameric ligand-gated ion channel. Nature, 452(20):375-379.


Cui, T; Gao, Y; Liew, O W; Puah, C M; Gutte, B (2007). Efficient preparation of an acyclic permutant of kalata B1 from a recombinant fusion protein with thioredoxin. Journal of Biotechnology, 130(4):378-384.

Gemperli, A C; Schaffitzel, C; Jakob, C; Steuber, J (2007). Transport of Na+ and K+ by an antiporter-related subunit from the Escherichia coli NADH dehydrogenase I produced in Saccharomyces cerevisiae. Archives of Microbiology, 188(5):509-521.

Sonderegger, P; Patthy, L (2007). Comment on "Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila". Science, 316(5832):1698.

Galliciotti, G; Glatzel, M; Kinter, J; Kozlov, S V; Cinelli, P; Rülicke, T; Sonderegger, P (2007). Accumulation of mutant neuroserpin precedes development of clinical symptoms in familial encephalopathy with neuroserpin inclusion bodies. American Journal of Pathology, 170(4):1305-1313.

Sennhauser, G; Amstutz, P; Briand, C; Storchenegger, O; Grütter, M G (2007). Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors. PLoS Biology, 5(1):e7.

Dutzler, R (2007). A structural perspective on ClC channel and transporter function. FEBS letters, 581(15):2839-44.

Wagner, A (2007). From bit to it: How a complex metabolic network transforms information into living matter. BMC Systems Biology, 1:33.

Wu, F; Grossenbacher, D; Gehring, H (2007). New transition state-based inhibitor for human ornithine decarboxylase inhibits growth of tumor cells. Molecular Cancer Therapeutics, 6(6):1831-1839.

Meyer, S; Savaresi, S; Forster, I C; Dutzler, R (2007). Nucleotide recognition by the cytoplasmic domain of the human chloride transporter ClC-5. Nature Structural and Molecular Biology, 14(1):60-7.

Hust, M; Jostock, T; Menzel, C; Voedisch, B; Mohr, A; Brenneis, M; Kirsch, M I; Meier, D; Dübel, S (2007). Single chain Fab (scFab) fragment. BMC Biotechnology, 7:14.

Alioth, S; Meyer, S; Dutzler, R; Pervushin, K (2007). The cytoplasmic domain of the chloride channel ClC-0: structural and dynamic characterization of flexible regions. Journal of Molecular Biology, 369(5):1163-1169.

Markovic, S; Dutzler, R (2007). The structure of the cytoplasmic domain of the chloride channel ClC-Ka reveals a conserved interaction interface. Structure, 15(6):715-25.


Zakaryan, R P; Gehring, H (2006). Identification and characterization of the nuclear localization/retention signal in the EWS proto-oncoprotein. Journal of Molecular Biology, 363(1):27-38.

Simonin, Y; Charron, Y; Sonderegger, P; Vassalli, J D; Kato, A C (2006). An inhibitor of serine proteases, neuroserpin, acts as a neuroprotective agent in a mouse model of neurodegenerative disease. Journal of Neuroscience, 26(41):10614-10619.

Pahlich, S; Zakaryan, R P; Gehring, H (2006). Protein arginine methylation: Cellular functions and methods of analysis. Biochimica et Biophysica Acta, 1764(12):1890-1903.

Konecna, A; Frischknecht, R; Kinter, J; Ludwig, A; Steuble, M; Meskenaite, V; Indermühle, M; Engel, M; Cen, Chuan; Mateos, J M; Streit, P; Sonderegger, P (2006). Calsyntenin-1 docks vesicular cargo to kinesin-1. Molecular Biology of the Cell, 17(8):3651-3663.

Galliciotti, G; Sonderegger, P (2006). Neuroserpin. Frontiers in Bioscience, 11:33-45.

Meyer, S; Dutzler, R (2006). Crystal structure of the cytoplasmic domain of the chloride channel ClC-0. Structure, 14(2):299-307.

Accardi, A; Lobet, S; Williams, C; Miller, C J; Dutzler, R (2006). Synergism between halide binding and proton transport in a CLC-type exchanger. Journal of Molecular Biology, 362(4):691-699.

Dutzler, R (2006). The ClC family of chloride channels and transporters. Current Opinion in Structural Biology, 16(4):439-46.


Lebeurrier, N; Liot, G; Lopez-Atalaya, J P; Orset, C; Fernandez-Monreal, M; Sonderegger, P; Ali, C; Vivien, D (2005). The brain-specific tissue-type plasminogen activator inhibitor, neuroserpin, protects neurons against excitotoxicity both in vitro and in vivo. Molecular and Cellular Neuroscience, 30(4):552-558.

Pahlich, S; Bschir, K; Chiavi, C; Belyanskaya, L L; Gehring, H (2005). Different methylation characteristics of protein arginine methyltransferase 1 and 3 toward the Ewing Sarcoma protein and a peptide. Proteins, 61(1):164-175.

Schrimpf, S P; Meskenaite, V; Brunner, E; Rutishauser, D; Walther, P; Eng, J K; Aebersold, R; Sonderegger, P (2005). Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics, 5(10):2531-2541.

Röthlisberger, D; Honegger, A; Plückthun, A (2005). Domain interactions in the Fab fragment: a comparative evaluation of the single-chain Fv and Fab format engineered with variable domains of different stability. Journal of Molecular Biology, 347(4):773-789.

Ott, D; Neldner, Y; Cèbe, R; Dodevski, I; Plückthun, A (2005). Engineering and functional immobilization of opioid receptors. Protein Engineering Design and Selection : PEDS, 18(3):153-160.

Schild, Andreas. Protein phosphatase 2A in Alzheimer's disease pathogenesis, memory and development. 2005, University of Zurich, Faculty of Science.


Fernandez, F J; Vega, M C; Lehmann, F; Sandmeier, E; Gehring, H; Christen, P; Wilmanns, M (2004). Structural studies of the catalytic reaction pathway of a hyperthermophilic histidinol-phosphate aminotransferase. Journal of Biological Chemistry, 279(20):21478-21488.

Navarro-Yubero, C; Cuadrado, A; Sonderegger, P; Muñoz, A (2004). Neuroserpin is post-transcriptionally regulated by thyroid hormone. Molecular Brain Research, 123(1-2):56-65.

Röthlisberger, D; Pos, K M; Plückthun, A (2004). An antibody library for stabilizing and crystallizing membrane proteins - selecting binders to the citrate carrier CitS. FEBS Letters, 564(3):340-348.

Ott, D; Frischknecht, R; Plückthun, A (2004). Construction and characterization of a kappa opioid receptor devoid of all free cysteines. Protein Engineering Design and Selection : PEDS, 17(1):37-48.

Dutzler, R (2004). Structural basis for ion conduction and gating in ClC chloride channels. FEBS Letters, 564(3):229-33.

Dutzler, R (2004). The structural basis of ClC chloride channel function. Trends in Neurosciences, 27(6):315-20.


Gygi, D J; Zumstein, P; Grossenbacher, D; Altwegg, L; Lüscher, T F; Gehring, H (2003). Human connective tissue growth factor expressed in Escherichia coli is a non-mitogenic inhibitor of apoptosis. Biochemical and Biophysical Research Communications (BBRC), 311(3):685-690.

Molinari, F; Meskanaite, Virginia; Munnich, A; Sonderegger, P; Colleaux, L (2003). Extracellular proteases and their inhibitors in genetic diseases of the central nervous system. Human Molecular Genetics, 12(S2):R195-R200.

Madani, Rime; Kozlov, S V; Akhmedov, A; Cinelli, P; Kinter, J; Lipp, H P; Sonderegger, P; Wolfer, D P (2003). Impaired explorative behavior and neophobia in genetically modified mice lacking or overexpressing the extracellular serine protease inhibitor neuroserpin. Molecular and Cellular Neuroscience, 23(3):473-494.

Wannier-Morino, P; Rager, G; Sonderegger, P; Grabs, D (2003). Expression of neuroserpin in the visual cortex of the mouse during the developmental critical period. European Journal of Neuroscience, 17(9):1853-1860.

Belyanskaya, L L; Delattre, O; Gehring, H (2003). Expression and subcellular localization of Ewing sarcoma (EWS) protein is affected by the methylation process. Experimental Cell Research, 288(2):374-381.

Dutzler, R; Campbell, E B; MacKinnon, R (2003). Gating the selectivity filter in ClC chloride channels. Science, 300(5616):108-12.


Molinari, F; Rio, M; Meskenaite, V; Encha-Razavi, F; Augé, J; Bacq, D; Briault, S; Vekemans, M; Munnich, A; Attié-Bitach, T; Sonderegger, P; Colleaux, L (2002). Truncating neurotrypsin mutation in autosomal recessive nonsyndromic mental retardation. Science, 298(5599):1779-1781.

Hintsch, G; Zurlinden, A; Meskenaite, V; Steuble, M; Fink-Widmer, K; Kinter, J; Sonderegger, P (2002). The calsyntenins--a family of postsynaptic membrane proteins with distinct neuronal expression patterns. Molecular and Cellular Neuroscience, 21(3):393-409.

Minder, D; Böni, J; Schüpbach, J; Gehring, H (2002). Immunophilins and HIV-1 infection. Archives of Virology, 147(8):1531-1542.

Cuadrado, A; Navarro-Yubero, C; Furneaux, H; Kinter, J; Sonderegger, P; Muñoz, A (2002). HuD binds to three AU-rich sequences in the 3'-UTR of neuroserpin mRNA and promotes the accumulation of neuroserpin mRNA and protein. Nucleic Acids Research, 30(10):2202-2211.

Kunz, B; Lierheimer, R; Rader, C; Spirig, M; Ziegler, U; Sonderegger, P (2002). Axonin-1/TAG-1 mediates cell-cell adhesion by a cis-assisted trans-interaction. Journal of Biological Chemistry, 277(6):4551-4557.

Dutzler, R; Schirmer, T; Karplus, M; Fischer, S (2002). Translocation mechanism of long sugar chains across the maltoporin membrane channel. Structure, 10(9):1273-84.

Dutzler, R; Campbell, E B; Cadene, M; Chait, B T; MacKinnon, R (2002). X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity. Nature, 415(6869):287-94.


Cinelli, P; Madani, R; Tsuzuki, N; Vallet, P; Arras, M; Zhao, C N; Osterwalder, T; Rülicke, T; Sonderegger, P (2001). Neuroserpin, a neuroprotective factor in focal ischemic stroke. Molecular and Cellular Neuroscience, 18(5):443-457.

Wolfer, D P; Lang, R; Cinelli, P; Madani, R; Sonderegger, P (2001). Multiple roles of neurotrypsin in tissue morphogenesis and nervous system development suggested by the mRNA expression pattern. Molecular and Cellular Neuroscience, 18(4):407-433.

Alvarez-Dolado, M; Figueroa, A; Kozlov, S V; Sonderegger, P; Furley, A J; Muñoz, A (2001). Thyroid hormone regulates TAG-1 expression in the developing rat brain. European Journal of Neuroscience, 14(8):1209-1218.

Briand, C; Kozlov, S V; Sonderegger, P; Grütter, M G (2001). Crystal structure of neuroserpin: a neuronal serpin involved in a conformational disease. FEBS Letters, 505(1):18-22.

Bernard, A; Fitzli, D; Sonderegger, P; Delamarche, E; Michel, B; Bosshard, H R; Biebuyck, H (2001). Affinity capture of proteins from solution and their dissociation by contact printing. Nature Biotechnology, 19(9):866-869.

Plagge, A; Sendtner-Voelderndorff, L; Sirim, P; Freigang, J; Rader, C; Sonderegger, P; Brümmendorf, T (2001). The contactin-related protein FAR-2 defines purkinje cell clusters and labels subpopulations of climbing fibers in the developing cerebellum. Molecular and Cellular Neuroscience, 18(1):91-107.

Silverman, M A; Kaech, S; Jareb, M; Burack, M A; Vogt, L; Sonderegger, P; Banker, G (2001). Sorting and directed transport of membrane proteins during development of hippocampal neurons in culture. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 98(13):7051-7057.

Belyanskaya, L L; Gehrig, P M; Gehring, H (2001). Exposure on cell surface and extensive arginine methylation of ewing sarcoma (EWS) protein. Journal of Biological Chemistry, 276(22):18681-18687.

Sorribas, H; Braun, D; Leder, L; Sonderegger, P; Tiefenauer, L (2001). Adhesion proteins for a tight neuron-electrode contact. Journal of Neuroscience Methods, 104(2):133-141.

Vogt, L; Schrimpf, S P; Meskenaite, V; Frischknecht, R; Kinter, J; Leone, D P; Ziegler, U; Sonderegger, P (2001). Calsyntenin-1, a proteolytically processed postsynaptic membrane protein with a cytoplasmic calcium-binding domain. Molecular and Cellular Neuroscience, 17(1):151-166.

Sonderegger, P; Kunz, S; Rader, C; Suter, D M; Stoeckli, E T (2001). Analysis of Cell-Cell Contact Mediated by Ig Superfamily Cell Adhesion Molecules. Current Protocols in Cell Biology:9.5.1-9.5.52.

Van Gelder, P; Dutzler, R; Dumas, F; Koebnik, R; Schirmer, T (2001). Sucrose transport through maltoporin mutants of Escherichia coli. Protein engineering, 14(11):943-8.


Alvarez-Dolado, M; Cuadrado, A; Navarro-Yubero, C; Sonderegger, P; Furley, A J; Bernal, J; Muñoz, A (2000). Regulation of the L1 cell adhesion molecule by thyroid hormone in the developing brain. Molecular and Cellular Neuroscience, 16(4):499-514.

Kasper, P; Christen, P; Gehring, H (2000). Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK. Proteins, 40(2):185-192.

Fitzli, D; Stoeckli, E T; Kunz, S; Siribour, K; Rader, C; Kunz, B; Kozlov, S V; Buchstaller, A; Lane, R P; Suter, D M; Dreyer, W J; Sonderegger, P (2000). A direct interaction of axonin-1 with NgCAM-related cell adhesion molecule (NrCAM) results in guidance, but not growth of commissural axons. Journal of Cell Biology, 149(4):951-968.

Freigang, J; Proba, K; Leder, L; Diederichs, K; Sonderegger, P; Welte, W (2000). The crystal structure of the ligand binding module of axonin-1/TAG-1 suggests a zipper mechanism for neural cell adhesion. Cell, 101(4):425-433.

Görlach, A; Camenisch, G; Kvietikova, I; Vogt, L; Wenger, R H; Gassmann, M (2000). Efficient translation of mouse hypoxia-inducible factor-1alpha under normoxic and hypoxic conditions. Biochimica et Biophysica Acta, 1493(1-2):125-134.

Finckh, U; Müller-Thomsen, T; Mann, U; Eggers, C; Marksteiner, J; Meins, W; Binetti, G; Alberici, A; Sonderegger, P; Hock, C; Nitsch, R M; Gal, A (2000). High frequency of mutations in four different disease genes in early-onset dementia. Annals of the New York Academy of Sciences, 920:100-106.

Camuzat, A; Verpillat, P; Dubois, B; Penet, C; Agid, Y; Brice, A; Moreaud, O; Puel, M; Clerget-Darpoux, F; Kinter, J; Kozlov, S; Berger, P; Sonderegger, P; Raux, G; Campion, C; Hannequin, D; Febourg, T (2000). Mutations in the neuroserpin gene are rare in familial dementia. Annals of Neurology, 47(5):688.


Sorribas, H; Padeste, C; Mezzacasa, T; Tiefenauer, L; Leder, L; Fitzli, D; Sonderegger, P (1999). Neurite outgrowth on microstructured surfaces functionalized by a neural adhesion protein. Journal of Materials Science: Materials in Medicine, 10(12):787-791.

Berger, P; Kozlov, S V; Cinelli, P; Krüger, S R; Vogt, L; Sonderegger, P (1999). Neuronal depolarization enhances the transcription of the neuronal serine protease inhibitor neuroserpin. Molecular and Cellular Neuroscience, 14(6):455-467.

Graber, R; Kasper, P; Malashkevich, V N; Strop, P; Gehring, H; Jansonius, J N; Christen, P (1999). Conversion of aspartate aminotransferase into an L-aspartate beta-decarboxylase by a triple active-site mutation. Journal of Biological Chemistry, 274(44):31203-1325.

Davis, R L; Shrimpton, A E; Holohan, P D; Bradshaw, C; Feiglin, D; Collins, G H; Sonderegger, P; Kinter, J; Becker, L M; Lacbawan, F; Krasnewich, D; Muenke, M; Lawrence, D A; Yerby, M S; Shaw, C M; Gooptu, B; Elliott, P R; Finch, J T; Carrell, R W; Lomas, D A (1999). Familial dementia caused by polymerization of mutant neuroserpin. Nature, 401(6751):376-379.

Endrich, M M; Gehrig, P; Gehring, H (1999). Maturation-induced conformational changes of HIV-1 capsid protein and identification of two high affinity sites for cyclophilins in the C-terminal domain. Journal of Biological Chemistry, 274(9):5326-5332.

Mouratou, B; Kasper, P; Gehring, H; Christen, P (1999). Conversion of tyrosine phenol-lyase to dicarboxylic amino acid beta-lyase, an enzyme not found in nature. Journal of Biological Chemistry, 274(3):1320-1325.

Kozlov, S V; Riegel, M; Kinter, J; Hintsch, G; Cinelli, P; Schinzel, A; Sonderegger, P (1999). Assignment of the gene encoding the neuronal multidomain serine protease neurotrypsin (PRSS12) to human chromosome band 4q25-->q26 by in situ hybridization. Cytogenetic and Genome Research, 84(1-2):107-108.

Dutzler, R; Rummel, G; Albertí, S; Hernández-Allés, S; Phale, P; Rosenbusch, J; Benedí, V; Schirmer, T (1999). Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae. Structure, 7(4):425-34.

Ringhofer, S; Kallen, J; Dutzler, R; Billich, A; Visser, A J; Scholz, D; Steinhauser, O; Schreiber, H; Auer, M; Kungl, A J (1999). X-ray structure and conformational dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: agreement of time-resolved spectroscopy and molecular dynamics simulations. Journal of Molecular Biology, 286(4):1147-59.


Kunz, S; Spirig, M; Ginsburg, C; Buchstaller, A; Berger, P; Lanz, R; Rader, C; Vogt, L; Kunz, B; Sonderegger, P (1998). Neurite fasciculation mediated by complexes of axonin-1 and Ng cell adhesion molecule. Journal of Cell Biology, 143(6):1673-1690.

Berger, P; Kozlov, S V; Krueger, S R; Sonderegger, P (1998). Structure of the mouse gene for the serine protease inhibitor neuroserpin (PI12). Gene, 214(1-2):25-33.

Endrich, M M; Gehring, H (1998). The V3 loop of human immunodeficiency virus type-1 envelope protein is a high-affinity ligand for immunophilins present in human blood. FEBS Journal, 252(3):441-446.

Proba, K; Gschwend, T P; Sonderegger, P (1998). Cloning and sequencing of the cDNA encoding human neurotrypsin. Biochimica et Biophysica Acta, 1396(2):143-147.

Wolfer, D P; Giger, R J; Stagliar, M; Sonderegger, P; Lipp, H P (1998). Expression of the axon growth-related neural adhesion molecule TAG-1/axonin-1 in the adult mouse brain. Anatomy and Embryology, 197(3):177-185.

Osterwalder, T; Cinelli, P; Baici, A; Pennella, A; Krueger, S R; Schrimpf, S P; Meins, M; Sonderegger, P (1998). The axonally secreted serine proteinase inhibitor, neuroserpin, inhibits plasminogen activators and plasmin but not thrombin. Journal of Biological Chemistry, 273(4):2312-2321.

Sonderegger, P; Kunz, S; Rader, C; Buchstaller, A; Berger, P; Vogt, L; Kozlov, S V; Ziegler, U; Kunz, B; Fitzli, D; Stoeckli, E T (1998). Discrete clusters of axonin-1 and NgCAM at neuronal contact sites: facts and speculations on the regulation of axonal fasciculation. Progress in Brain Research, 117:93-104.


Krueger, S R; Ghisu, G P; Cinelli, P; Gschwend, T P; Osterwalder, T; Wolfer, D P; Sonderegger, P (1997). Expression of neuroserpin, an inhibitor of tissue plasminogen activator, in the developing and adult nervous system of the mouse. Journal of Neuroscience, 17(23):8984-8996.

Sonderegger, P (1997). Axonin-1 and NgCAM as "recognition" components of the pathway sensor apparatus of growth cones: a synopsis. Cell and Tissue Research, 290(2):429-439.

Schrimpf, S P; Bleiker, A J; Brecevic, L; Kozlov, S V; Berger, P; Osterwalder, T; Krueger, S R; Schinzel, A; Sonderegger, P (1997). Human neuroserpin (PI12): cDNA cloning and chromosomal localization to 3q26. Genomics, 40(1):55-62.

Stoeckli, E T; Sonderegger, P; Pollerberg, G E; Landmesser, L T (1997). Interference with axonin-1 and NrCAM interactions unmasks a floor-plate activity inhibitory for commissural axons. Neuron, 18(2):209-221.

Lierheimer, R; Kunz, B; Vogt, L; Savoca, R; Brodbeck, U; Sonderegger, P (1997). The neuronal cell-adhesion molecule axonin-1 is specifically released by an endogenous glycosylphosphatidylinositol-specific phospholipase. FEBS Journal, 243(1-2):502-510.

Giger, R J; Ziegler, U; Hermens, W T J M C; Kunz, B; Kunz, S; Sonderegger, P (1997). Adenovirus-mediated gene transfer in neurons: construction and characterization of a vector for heterologous expression of the axonal cell adhesion molecule axonin-1. Journal of Neuroscience Methods, 71(1):99-111.

Wang, Y F; Dutzler, R; Rizkallah, P J; Rosenbusch, J P; Schirmer, T (1997). Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin. Journal of Molecular Biology, 272(1):56-63.

Denzinger, T; Przybylski, M; Savoca, R; Sonderegger, P (1997). Mass spectrometric characterisation of primary structure, sequence heterogeneity, and intramolecular disulfide loops of the cell adhesion protein axonin-1 from chicken. European Journal of Mass Spectrometry, 3(5):379-389.

Gschwend, T P; Krueger, S R; Kozlov, S V; Wolfer, D P; Sonderegger, P (1997). Neurotrypsin, a novel multidomain serine protease expressed in the nervous system. Molecular and Cellular Neuroscience, 9(3):207-219.


Buchstaller, A; Kunz, S; Berger, P; Kunz, B; Ziegler, U; Rader, C; Sonderegger, P (1996). Cell adhesion molecules NgCAM and axonin-1 form heterodimers in the neuronal membrane and cooperate in neurite outgrowth promotion. Journal of Cell Biology, 135(6 Pt 1):1593-1607.

Kunz, S; Ziegler, U; Kunz, B; Sonderegger, P (1996). Intracellular signaling is changed after clustering of the neural cell adhesion molecules axonin-1 and NgCAM during neurite fasciculation. Journal of Cell Biology, 135(1):253-267.

Kasper, P; Sterk, M; Christen, P; Gehring, H (1996). Molecular-dynamics simulation of domain movements in aspartate aminotransferase. FEBS Journal, 240(3):751-755.

Vogt, L; Giger, R J; Ziegler, U; Kunz, B; Buchstaller, A; Hermens, W T J M C; Kaplitt, M G; Rosenfeld, M R; Pfaff, D W; Verhaagen, J; Sonderegger, P (1996). Continuous renewal of the axonal pathway sensor apparatus by insertion of new sensor molecules into the growth cone membrane. Current Biology, 6(9):1153-1158.

Stoeckli, E T; Ziegler, U; Bleiker, A J; Groscurth, P; Sonderegger, P (1996). Clustering and functional cooperation of Ng-CAM and axonin-1 in the substratum-contact area of growth cones. Developmental Biology, 177(1):15-29.

Christen, P; Kasper, P; Gehring, H; Sterk, M (1996). Stereochemical constraint in the evolution of pyridoxal-5'-phosphate-dependent enzymes. A hypothesis. FEBS Letters, 389(1):12-14.

Osterwalder, T; Contartese, J; Stoeckli, E T; Kuhn, T B; Sonderegger, P (1996). Neuroserpin, an axonally secreted serine protease inhibitor. The EMBO Journal, 15(12):2944-2953.

Rader, C; Kunz, B; Lierheimer, R; Giger, R J; Berger, P; Tittmann, P; Gross, H; Sonderegger, P (1996). Implications for the domain arrangement of axonin-1 derived from the mapping of its NgCAM binding site. The EMBO Journal, 15(9):2056-2068.

Morino, P; Buchstaller, A; Giger, R J; Sonderegger, P; Rager, G (1996). Differential expression of the mRNAs of the axonal glycoproteins axonin-1 and NgCAM in the developing chick retina. Developmental Brain Research, 91(2):252-259.

Rager, G; Morino, P; Schnitzer, J; Sonderegger, P (1996). Expression of the axonal cell adhesion molecules axonin-1 and Ng-CAM during the development of the chick retinotectal system. Journal of Comparative Neurology, 365(4):594-609.

Endrich, M M; Grossenbacher, D; Geistlich, A; Gehring, H (1996). Apoptosis-induced concomitant release of cytosolic proteins and factors which prevent cell death. Biology of the Cell, 88(1-2):15-22.

Dutzler, R; Wang, Y F; Rizkallah, P; Rosenbusch, J P; Schirmer, T (1996). Crystal structures of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway. Structure, 4(2):127-34.


Kozlov, S V; Giger, R J; Hasler, T; Korvatska, E; Schorderet, D F; Sonderegger, P (1995). The human TAX1 gene encoding the axon-associated cell adhesion molecule TAG-1/axonin-1: genomic structure and basic promoter. Genomics, 30(2):141-148.

Suter, D M; Pollerberg, G E; Buchstaller, A; Giger, R J; Dreyer, W J; Sonderegger, P (1995). Binding between the neural cell adhesion molecules axonin-1 and Nr-CAM/Bravo is involved in neuron-glia interaction. Journal of Cell Biology, 131(4):1067-1081.

Graber, R; Kasper, P; Malashkevich, V N; Sandmeier, E; Berger, P; Gehring, H; Jansonius, J N; Christen, P (1995). Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme. FEBS Journal, 232(2):686-690.

Giger, R J; Vogt, L; Zuellig, R A; Rader, C; Henehan-Beatty, A; Wolfer, D P; Sonderegger, P (1995). The gene of chicken axonin-1. Complete structure and analysis of the promoter. FEBS Journal, 227(3):617-628.

Malashkevich, V N; Jäger, J; Ziak, M; Sauder, U; Gehring, H; Christen, P; Jansonius, J N (1995). Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue. Biochemistry, 34(2):405-414.

Savoca, R; Ziegler, U; Sonderegger, P (1995). Effects of L-serine on neurons in vitro. Journal of Neuroscience Methods, 61(1-2):159-167.


Bonaïti-Pellié, C; Poisson, N; Bechtel, Y; Bechtel, P (1992). Sensitivity of transmission probabilities to paternity exclusion in segregation analysis. Genetic Epidemiology, 9(1):67-71.


Schweizer, Matthias; Peter, Martina A; Filipovic, Djordje; Tinner, Rahel; Bosshard, Hans Rudolf; Oertle, Maja (1991). Mechanism of monoclonal antibody inhibition/ stimulation of reactions catalyzed by cytochrome P450IIB1. Archives of Biochemistry and Biophysics, 288(1):64-70.

This list was generated on Wed Aug 12 22:46:43 2020 CEST.