View Communities & Collections

2025

Vitalis, Andreas; Parker, David; Radler, Fabian; Vargas-Rosales, Pablo Andrés; Zhang, Yang; Marchand, Jean-Rémy; Caflisch, Amedeo (2025). Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening. Journal of Computational Chemistry, 46(7):e70074.

Vitalis, Andreas; Winkler, Steffen; Zhang, Yang; Widmer, Julian; Caflisch, Amedeo (2025). A FAIR-Compliant Management Solution for Molecular Simulation Trajectories. Journal of Chemical Information and Modeling, 65(5):2443-2455.

Tröster, Vera; Wong, Ronald P; Börgel, Arne; Cakilkaya, Baris; Renz, Christian; Möckel, Martin M; Eifler-Olivi, Karolin; Marinho, Joana; Reinberg, Thomas; Furler, Sven; Schaefer, Jonas V; Plückthun, Andreas; Wolf, Eva; Ulrich, Helle D (2025). Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast. Cell Reports, 44(3):115353.

Muhar, Matthias F; Farnung, Jakob; Cernakova, Martina; Hofmann, Raphael; Henneberg, Lukas T; Pfleiderer, Moritz M; Denoth-Lippuner, Annina; Kalčic, Filip; Nievergelt, Ajse S; Peters Al-Bayati, Marwa; Sidiropoulos, Nikolaos D; Beier, Viola; Mann, Matthias; Jessberger, Sebastian; Jinek, Martin; Schulman, Brenda A; Bode, Jeffrey W; Corn, Jacob E (2025). C-terminal amides mark proteins for degradation via SCF-FBXO31. Nature, 638(8050):519-527.

Stipp, Robin Torben. Dynamic Structural Insights into the β2-Adrenergic Receptor: Time-Resolved Analysis of a Photoswitchable Ligand. 2025, University of Zurich, Faculty of Science.

Thavarasah, Sujani. Investigating the Enigmatic Phenomenon of Drug Efflux \\by Deep Mutational Scanning. 2025, University of Zurich, Faculty of Science.

Vargas Rosales, Pablo Andres. Simulation Studies of Allostery, Amyloid Degradation, and Epitranscriptomic Proteins. 2025, University of Zurich, Faculty of Science.

Loeff, Luuk; Walter, Alexander; Rosalen, Gian Tizio; Jinek, Martin (2025). DNA end sensing and cleavage by the Shedu anti-phage defense system. Cell, 188(3):721-733.e17.

Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2025). The physics-AI dialogue in drug design. RSC Medicinal Chemistry:Epub ahead of print.

Liziczai, Márton; Fuchs, Ariane; Manatschal, Cristina; Dutzler, Raimund (2025). Structural basis for metal ion transport by the human SLC11 proteins DMT1 and NRAMP1. Nature Communications, 16(1):761.

Jungfer, Kenny; Moravčík, Štefan; Garcia-Doval, Carmela; Knörlein, Anna; Hall, Jonathan; Jinek, Martin (2025). Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes. Nucleic Acids Research, 53(2):gkae1277.

Münick, Philipp; Strubel, Alexander; Balourdas, Dimitrios-Ilias; Funk, Julianne S; Mernberger, Marco; Osterburg, Christian; Dreier, Birgit; Schaefer, Jonas V; Tuppi, Marcel; Yüksel, Büşra; Schäfer, Birgit; Knapp, Stefan; Plückthun, Andreas; Stiewe, Thorsten; Joerger, Andreas C; Dötsch, Volker (2025). DARPin-induced reactivation of p53 in HPV-positive cells. Nature Structural & Molecular Biology:Epub ahead of print.

Wang, Baihui; Luo, Qiang; Medalia, Ohad (2025). Lamins and chromatin join forces. Advances in Biological Regulation, 95:101059.

2024

Tippett, David. The Study of SLC26 Transport Diversity and CFTR-SLC26 Interactions. 2024, University of Zurich, Faculty of Science.

Newcombe, Estella A; Due, Amanda D; Sottini, Andrea; Elkjær, Steffie; Theisen, Frederik Friis; Fernandes, Catarina B; Staby, Lasse; Delaforge, Elise; Bartling, Christian R O; Brakti, Inna; Bugge, Katrine; Schuler, Benjamin; Skriver, Karen; Olsen, Johan G; Kragelund, Birthe B (2024). Stereochemistry in the disorder-order continuum of protein interactions. Nature, 636(8043):762-768.

Münick, Philipp; Zielinski, Jasmin; Strubel, Alexander; Gutfreund, Niklas; Dreier, Birgit; Schaefer, Jonas V; Schäfer, Birgit; Gebel, Jakob; Osterburg, Christian; Chaikuad, Apirat; Knapp, Stefan; Plückthun, Andreas; Dötsch, Volker (2024). DARPins as a novel tool to detect and degrade p73. Cell Death and Disease, 15(12):909.

Vargsa Rosales, Pablo Andrés. Simulation Studies of Allostery and Epitranscriptomic Proteins. 2024, University of Zurich, Faculty of Science.

Quinodoz, Mathieu; Rutz, Sonja; Peter, Virginie; Garavelli, Livia; Innes, A Micheil; Lehmann, Elena F; Kellenberger, Stephan; Peng, Zhong; Barone, Angelica; Campos-Xavier, Belinda; Unger, Sheila; Rivolta, Carlo; Dutzler, Raimund; Superti-Furga, Andrea (2024). De novo variants in LRRC8C resulting in constitutive channel activation cause a human multisystem disorder. The EMBO Journal, 44(2):413-436.

Janke, Carsten; Medalia, Ohad (2024). Editorial: Modern approaches in cytoskeleton-related topics. Current Opinion in Cell Biology, 91:102423.

Widmer, Julian; Vitalis, Andreas; Caflisch, Amedeo (2024). On the specificity of the recognition of m6A-RNA by YTH reader domains. Journal of Biological Chemistry, 300(12):107998.

Notbohm, Judith; Perica, Tina (2024). Biochemistry and genetics are coming together to improve our understanding of genotype to phenotype relationships. Current Opinion in Structural Biology, 89:102952.

Kono, Yohei; Pack, Chan-Gi; Ichikawa, Takehiko; Komatsubara, Arata; Adam, Stephen A; Miyazawa, Keisuke; Rolas, Loïc; Nourshargh, Sussan; Medalia, Ohad; Goldman, Robert D; Fukuma, Takeshi; Kimura, Hiroshi; Shimi, Takeshi (2024). Roles of the lamin A-specific tail region in the localization to sites of nuclear envelope rupture. PNAS Nexus, 3(12):pgae527.

Tarullo, Marco; Fernandez Rodriguez, Guillermo; Iaiza, Alessia; Venezia, Sara; Macone, Alberto; Incocciati, Alessio; Masciarelli, Silvia; Marchioni, Marcella; Giorgis, Marta; Lolli, Marco Lucio; Fornaseri, Federico; Proietti, Ludovica; Grebien, Florian; Rosignoli, Serena; Paiardini, Alessandro; Rotili, Dante; Mai, Antonello; Bochenkova, Elena; Caflisch, Amedeo; Fazi, Francesco; Fatica, Alessandro (2024). Off-Target Inhibition of Human Dihydroorotate Dehydrogenase (hDHODH) Highlights Challenges in the Development of Fat Mass and Obesity-Associated Protein (FTO) Inhibitors. ACS Pharmacology & Translational Science, 7(12):4096-4111.

Henkin, Gil; Brito, Cláudia; Plückthun, Andreas; Surrey, Thomas (2024). Preparation of Polarity-Marked Microtubules Using a Plus-End Capping DARPin. Bio-protocol, 14(22):e5109.

Holla, Andrea; Martin, Erik W; Dannenhoffer-Lafage, Thomas; Ruff, Kiersten M; König, Sebastian L B; Nüesch, Mark F; Chowdhury, Aritra; Louis, John M; Soranno, Andrea; Nettels, Daniel; Pappu, Rohit V; Best, Robert B; Mittag, Tanja; Schuler, Benjamin (2024). Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations. JACS Au, 4(12):4729-4743.

Zhang, Yang. Combining Molecular Dynamics and Machine Learning for Drug Design. 2024, University of Zurich, Faculty of Science.

Kurz, Lisa Katharina. Defining Identity and Differentiation Trajectories of Fibroblastic Reticular Cells in Murine and Human Lymph Nodes. 2024, University of Zurich, Faculty of Science.

Nai, Francesco. Development of Chemical Probes for Epitranscriptomic Proteins. 2024, University of Zurich, Faculty of Science.

Weiss, Fabian. Engineered Modular Adapters for Targeted Adenoviral Gene Delivery to Dendritic Cells with Implications for Tumor Vaccination. 2024, University of Zurich, Faculty of Science.

Antunes Westmann, Cauã. Navigating Spaces of the Possible: In Vivo Genotype-Phenotype Maps of Gene Regulation. 2024, University of Zurich, Faculty of Science.

Vukovic, David; Winkelvoss, Dorothea; Kapp, Jonas N; Hänny, Anna-Carina; Bürgisser, Héloïse; Riermeier, Luca; Udovcic, Anto; Tiefenboeck, Peter; Plückthun, Andreas (2024). Protein degradation kinetics measured by microinjection and live-cell fluorescence microscopy. Scientific Reports, 14(1):27153.

Cazzanelli, Giulia; Dalle Vedove, Andrea; Sbardellati, Nicolo; Valer, Luca; Caflisch, Amedeo; Lolli, Graziano (2024). Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors. Protein Science, 33(11):e5191.

Mahran, Randa; Kapp, Jonas N; Valtonen, Salla; Champagne, Allison; Ning, Jinying; Gillette, William; Stephen, Andrew G; Hao, Feng; Plückthun, Andreas; Härmä, Harri; Pantsar, Tatu; Kopra, Kari (2024). Beyond KRAS(G12C): Biochemical and Computational Characterization of Sotorasib and Adagrasib Binding Specificity and the Critical Role of H95 and Y96. ACS Chemical Biology, 19(10):2152-2164.

Hwang, Wonmuk; Austin, Steven L; Blondel, Arnaud; Boittier, Eric D; Boresch, Stefan; Buck, Matthias; Buckner, Joshua; Caflisch, Amedeo; Chang, Hao-Ting; Cheng, Xi; Choi, Yeol Kyo; Chu, Jhih-Wei; Crowley, Michael F; Cui, Qiang; Damjanovic, Ana; Deng, Yuqing; Devereux, Mike; Ding, Xinqiang; Feig, Michael F; Gao, Jiali; Glowacki, David R; Gonzales, James E; Hamaneh, Mehdi Bagerhi; Harder, Edward D; Hayes, Ryan L; Huang, Jing; Huang, Yandong; Hudson, Phillip S; Im, Wonpil; Islam, Shahidul M; et al (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. Journal of Physical Chemistry B, 128(41):9976-10042.

Winkelvoss, Dorothea. Elucidating Design Principles for Efficient bioPROTACs for Induced Degradation of Intracellular Proteins. 2024, University of Zurich, Faculty of Science.

Zhakparov, Damir. Identification of Relevant Features in Complex Biomedical Datasets Using Artificial Intelligence. 2024, University of Zurich, Faculty of Science.

Kapp, Jonas. Mechanisms of Ras Oncogene Inhibition. 2024, University of Zurich, Faculty of Science.

Ivașcu, Anastasia. Mechanistic Investigations of Reverse Transcriptase-Associated CRISPR Integrase Complexes. 2024, University of Zurich, Faculty of Science.

Vukovic, David. Rational Design of Degradation-Inducing Molecules. 2024, University of Zurich, Faculty of Science.

Raimondi, Federica; Siow, Kah Mun; Wrona, Dominik; Fuster-García, Carla; Pastukhov, Oleksandr; Schmitz, Michael; Bargsten, Katja; Kissling, Lucas; Swarts, Daan C; Andrieux, Geoffroy; Cathomen, Toni; Modlich, Ute; Jinek, Martin; Siler, Ulrich; Reichenbach, Janine (2024). Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements. Communications Biology, 7(1):1291.

Zhou, Zhiwei; Nguyen, Tra Ly; Li, Xingxiao; Poujol, Christel; Berlinska, Ewa; Michelina, Sandra Vietti; Kapp, Jonas N; Plückthun, Andreas; Winslow, Monte M; Ambrogio, Chiara; Shan, Yibing; Santamaría, David; Westover, Kenneth D (2024). Experimental variables determine the outcome of RAS-RAS interactions. Journal of Biological Chemistry, 300(11):107859.

Cheng-Sánchez, Iván; Gosselé, Katherine; Palaferri, Leonardo; Laul, Eleen; Riccabella, Gionata; Bedi, Rajiv K; Li, Yaozong; Müller, Anna; Corbeski, Ivan; Caflisch, Amedeo; Nevado, Cristina (2024). Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity. JACS Au, 4(9):3466-3474.

Freitag, Patrick C; Kolibius, Jonas; Wieboldt, Ronja; Weber, Remi; Hartmann, K Patricia; van Gogh, Merel; Brücher, Dominik; Läubli, Heinz; Plückthun, Andreas (2024). DARPin-fused T cell engager for adenovirus-mediated cancer therapy. Molecular therapy. Oncology, 32(3):200821.

Siow, Kah Mun; Güngör, Merve; Wrona, Dominik; Raimondi, Federica; Pastukhov, Oleksandr; Tsapogas, Panagiotis; Menzi, Timon; Schmitz, Michael; Kulcsár, Péter István; Schwank, Gerald; Schulz, Ansgar; Jinek, Martin; Modlich, Ute; Siler, Ulrich; Reichenbach, Janine (2024). Targeted knock-in of NCF1 cDNA into the NCF2 locus leads to myeloid phenotypic correction of p47 $^{phox}$ -deficient chronic granulomatous disease. Molecular Therapy : Nucleic Acids, 35(3):102229.

Widmer, Julian Paul. Making Sense of Molecular Dynamics Simulations. 2024, University of Zurich, Faculty of Science.

Jungfer, Kenny. Molecular Mechanisms of Cyclic Oligoadenylate Signaling During Type III CRISPR-Cas Interference. 2024, University of Zurich, Faculty of Science.

Thom, Cristian. Structure Determination of Class A Peptide-Binding G Protein-Coupled Receptors by Cryogenic Electron Microscopy. 2024, University of Zurich, Faculty of Science.

Zhou, Jiangtao; Assenza, Salvatore; Tatli, Meltem; Tian, Jiawen; Ilie, Ioana M; Starostin, Eugene L; Caflisch, Amedeo; Knowles, Tuomas P J; Dietler, Giovanni; Ruggeri, Francesco S; Stahlberg, Henning; Sekatskii, Sergey K; Mezzenga, Raffaele (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs. Advanced Science, 11(32):e2402740.

Weibel, Nathalie; Curcio, Martina; Schreiber, Atilla; Arriaga, Gabriel; Mausy, Marine; Mehdy, Jana; Brüllmann, Lea; Meyer, Andreas; Roth, Len; Flury, Tamara; Pecina, Valerie; Starlinger, Kim; Dernič, Jan; Jungfer, Kenny; Ackle, Fabian; Earp, Jennifer; Hausmann, Martin; Jinek, Martin; Rogler, Gerhard; Antunes Westmann, Cauã (2024). Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases. ACS Synthetic Biology, 13(8):2376-2390.

Coelho-Rato, Leila S; Parvanian, Sepideh; Andrs Salajkova, Sarka; Medalia, Ohad; Eriksson, John E (2024). Intermediate filaments at a glance. Journal of Cell Science, 137(16):jcs261386.

Kechagia, Zanetta; Eibauer, Matthias; Medalia, Ohad (2024). Structural determinants of intermediate filament mechanics. Current Opinion in Cell Biology, 89:102375.

Earp, Jennifer. Structural and Functional Characterization of the Mycobacterial Siderophore Exporter MmpL4. 2024, University of Zurich, Faculty of Science.

Auger, Shelby A; Venkatachalapathy, Sneha; Suazo, Kiall Francis G; Wang, Yiao; Sarkis, Alexander W; Bernhagen, Kaitlyn; Justyna, Katarzyna; Schaefer, Jonas V; Wollack, James W; Plückthun, Andreas; Li, Ling; Distefano, Mark D (2024). Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene-Tetrazine Click Chemistry. Bioconjugate Chemistry, 35(7):922-933.

Nüesch, Mark F; Pietrek, Lisa; Holmstrom, Erik D; Nettels, Daniel; von Roten, Valentin; Kronenberg-Tenga, Rafael; Medalia, Ohad; Hummer, Gerhard; Schuler, Benjamin (2024). Nanosecond chain dynamics of single-stranded nucleic acids. Nature Communications, 15(1):6010.

Loeff, Luuk; Adams, David W; Chanez, Christelle; Stutzmann, Sandrine; Righi, Laurie; Blokesch, Melanie; Jinek, Martin (2024). Molecular mechanism of plasmid elimination by the DdmDE defense system. Science, 385(6705):188-194.

Thom, Cristian. Structure Determination of Peptide-Binding G Protein-Coupled Receptors by Cryogenic Electron Microscopy. 2024, University of Zurich, Faculty of Science.

Reginato, Giordano; Dello Stritto, Maria Rosaria; Wang, Yanbo; Hao, Jingzhou; Pavani, Raphael; Schmitz, Michael; Halder, Swagata; Morin, Vincent; Cannavo, Elda; Ceppi, Ilaria; Braunshier, Stefan; Acharya, Ananya; Ropars, Virginie; Charbonnier, Jean-Baptiste; Jinek, Martin; Nussenzweig, Andrè; Ha, Taekjip; Cejka, Petr (2024). HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nature Communications, 15(1):5789.

Stark, Yvonne; Menard, Faye; Jeliazkov, Jeliazko R; Ernst, Patrick; Chembath, Anupama; Ashraf, Mohammed; Hine, Anna V; Plückthun, Andreas (2024). Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules. Proceedings of the National Academy of Sciences of the United States of America, 121(27):e2318198121.

Houvast, Ruben D; Badr, Nada; March, Taryn; de Muynck, Lysanne D A N; Sier, Vincent Q; Schomann, Timo; Bhairosingh, Shadhvi; Baart, Victor M; Peeters, Judith A H M; van Westen, Gerard J P; Plückthun, Andreas; Burggraaf, Jacobus; Kuppen, Peter J K; Vahrmeijer, Alexander L; Sier, Cornelis F M (2024). Preclinical evaluation of EpCAM-binding designed ankyrin repeat proteins (DARPins) as targeting moieties for bimodal near-infrared fluorescence and photoacoustic imaging of cancer. European Journal of Nuclear Medicine and Molecular Imaging, 51(8):2179-2192.

Dederer, Verena; Sanz Murillo, Marta; Karasmanis, Eva P; Hatch, Kathryn S; Chatterjee, Deep; Preuss, Franziska; Abdul Azeez, Kamal R; Nguyen, Landon Vu; Galicia, Christian; Dreier, Birgit; Plückthun, Andreas; Versees, Wim; Mathea, Sebastian; Leschziner, Andres E; Reck-Peterson, Samara L; Knapp, Stefan (2024). A designed ankyrin-repeat protein that targets Parkinson's disease-associated LRRK2. Journal of Biological Chemistry, 300(7):107469.

Bastiaanssen, Carolien; Bobadilla Ugarte, Pilar; Kim, Kijun; Finocchio, Giada; Feng, Yanlei; Anzelon, Todd A; Köstlbacher, Stephan; Tamarit, Daniel; Ettema, Thijs J G; Jinek, Martin; MacRae, Ian J; Joo, Chirlmin; Swarts, Daan C; Wu, Fabai (2024). RNA-guided RNA silencing by an Asgard archaeal Argonaute. Nature Communications, 15(1):5499.

Cui, Zhenling; Ayva, Cagla Ergun; Liew, Yi Jin; Guo, Zhong; Mutschler, Roxane; Dreier, Birgit; Fiorito, Maria M; Walden, Patricia; Howard, Christopher B; Ely, Fernanda; Plückthun, Andreas; Pretorius, Carel; Ungerer, Jacobus Pj; Buckle, Ashley M; Alexandrov, Kirill (2024). mRNA Display Pipeline for Protein Biosensor Construction. ACS Sensors, 9(6):2846-2857.

Drożdżyk, Katarzyna; Peter, Martina; Dutzler, Raimund (2024). Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs. eLife, 13:RP96138.

Nüesch, Mark. Conformational Dynamics and Molecular Ensembles of Biopolymers Investigated with Single-Molecule Spectroscopy. 2024, University of Zurich, Faculty of Science.

Zálešák, František; Nai, Francesco; Herok, Marcin; Bochenkova, Elena; Bedi, Rajiv K; Li, Yaozong; Errani, Francesco; Caflisch, Amedeo (2024). Structure-Based Design of a Potent and Selective YTHDC1 Ligand. Journal of Medicinal Chemistry, 67(11):9516-9535.

Eibauer, Matthias; Weber, Miriam S; Kronenberg-Tenga, Rafael; Beales, Charlie T; Boujemaa-Paterski, Rajaa; Turgay, Yagmur; Sivagurunathan, Suganya; Kraxner, Julia; Köster, Sarah; Goldman, Robert D; Medalia, Ohad (2024). Vimentin filaments integrate low-complexity domains in a complex helical structure. Nature Structural & Molecular Biology, 31(6):939-949.

Kronenberg-Tenga, Rafael Carl Emanuel. $\textit{In Cellulo}$ Analysis of the Nuclear Envelope by Cryo-Electron Tomography. 2024, University of Zurich, Faculty of Science.

Nai, Francesco; Flores Espinoza, Maria Paula; Invernizzi, Annalisa; Vargas-Rosales, Pablo Andrés; Bobileva, Olga; Herok, Marcin; Caflisch, Amedeo (2024). Small-Molecule Inhibitors of the m7G-RNA Writer METTL1. ACS Bio & Med Chem Au, 4(2):100-110.

Ivanova, Julia R; Benk, Amelie S; Schaefer, Jonas V; Dreier, Birgit; Hermann, Leon O; Plückthun, Andreas; Missirlis, Dimitris; Spatz, Joachim P (2024). Designed Ankyrin Repeat Proteins as Actin Labels of Distinct Cytoskeletal Structures in Living Cells. ACS Nano, 18(12):8919-8933.

Hartmann, Karen Patricia. Paracrine Adenoviral Delivery of Therapeutic Payloads for Cancer Therapy. 2024, University of Zurich, Faculty of Science.

Rutz, Sonja. Insights into the Activation and Heteromerization of LRRC8A/C Volume-Regulated Anion Channels. 2024, University of Zurich, Faculty of Science.

Drozdzyk, Katarzyna. Structural and Functional Studies of Large-Pore Channels of the CALHM Family. 2024, University of Zurich, Faculty of Science.

Glover, Hannah. Studying Binding Pocket Dynamics in the Human A$_{2A}$ Receptor Using Synthetic Photoswitches and Serial Crystallography. 2024, University of Zurich, Faculty of Science.

Corbeski, Ivan; Vargas-Rosales, Pablo Andrés; Bedi, Rajiv Kumar; Deng, Jiahua; Coelho, Dylan; Braud, Emmanuelle; Iannazzo, Laura; Li, Yaozong; Huang, Danzhi; Ethève-Quelquejeu, Mélanie; Cui, Qiang; Caflisch, Amedeo (2024). The catalytic mechanism of the RNA methyltransferase METTL3. eLife, 12:RP92537.

Weber, Yanik; Böck, Desirée; Ivașcu, Anastasia; Mathis, Nicolas; Rothgangl, Tanja; Ioannidi, Eleonora I; Blaudt, Alex C; Tidecks, Lisa; Vadovics, Máté; Muramatsu, Hiromi; Reichmuth, Andreas; Marquart, Kim F; Kissling, Lucas; Pardi, Norbert; Jinek, Martin; Schwank, Gerald (2024). Enhancing prime editor activity by directed protein evolution in yeast. Nature Communications, 15(1):2092.

Schmidheini, Lukas; Mathis, Nicolas; Marquart, Kim Fabiano; Rothgangl, Tanja; Kissling, Lucas; Böck, Desirée; Chanez, Christelle; Wang, Jingrui Priscilla; Jinek, Martin; Schwank, Gerald (2024). Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility. Nature Chemical Biology, 20(3):333-343.

Thalmann, Lars; Martín-González, Natalia; Brücher, Dominik; Plückthun, Andreas; de Pablo, Pedro J; Suomalainen, Maarit; Greber, Urs (2024). Gutless helper-dependent and first generation HAdV5 vectors have similar mechanical properties and common transduction mechanisms. Human Gene Therapy, 35(5-6):163-176.

Klinnert, Sarah; Schenkel, Corinne D; Freitag, Patrick C; Günthard, Huldrych F; Plückthun, Andreas; Metzner, Karin J (2024). Targeted shock-and-kill HIV-1 gene therapy approach combining CRISPR activation, suicide gene tBid and retargeted adenovirus delivery. Gene Therapy, 31(3-4):74-84.

Pacesa, Martin; Pelea, Oana; Jinek, Martin (2024). Past, present, and future of CRISPR genome editing technologies. Cell, 187(5):1076-1100.

Finocchio, Giada; Koopal, Balwina; Potocnik, Ana; Heijstek, Clint; Westphal, Adrie H; Jinek, Martin; Swarts, Daan C (2024). Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Research, 52(4):2012-2029.

Errani, Francesco; Invernizzi, Annalisa; Herok, Marcin; Bochenkova, Elena; Stamm, Fiona; Corbeski, Ivan; Romanucci, Valeria; Di Fabio, Giovanni; Zálešák, František; Caflisch, Amedeo (2024). Proteolysis Targeting Chimera Degraders of the METTL3-14 m$^{6}$A-RNA Methyltransferase. JACS Au, 4(2):713-729.

Saha, Aakash; Ahsan, Mohd; Arantes, Pablo R; Schmitz, Michael; Chanez, Christelle; Jinek, Martin; Palermo, Giulia (2024). An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nature Communications, 15(1):1473.

Abdul-Ridha, Alaa; de Zhang, Lazarus A; Betrie, Ashenafi Haileyesus; Deluigi, Mattia; Vaid, Tasneem M; Whitehead, Alice; Zhang, Yifan; Davis, Ben; Harris, Richard; Simmonite, Heather; Hubbard, Roderick E; Gooley, Paul R; Plückthun, Andreas; Bathgate, Ross A D; Chalmers, David K; Scott, Daniel J (2024). Identification of a Novel Subtype-Selective α$_{1B}$-Adrenoceptor Antagonist. ACS Chemical Neuroscience, 15(3):671-684.

Grabenhorst, Lennart; Sturzenegger, Flurin; Hasler, Moa; Schuler, Benjamin; Tinnefeld, Philip (2024). Single-Molecule FRET at 10 MHz Count Rates. Journal of the American Chemical Society, 146(5):3539-3544.

Tinzl, Matthias; Diedrich, Johannes V; Mittl, Peer R E; Clémancey, Martin; Reiher, Markus; Proppe, Jonny; Latour, Jean-Marc; Hilvert, Donald (2024). Myoglobin-Catalyzed Azide Reduction Proceeds via an Anionic Metal Amide Intermediate. Journal of the American Chemical Society, 146(3):1957-1966.

Jungfer, Kenny; Sigg, Annina; Jinek, Martin (2024). Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2. Nucleic Acids Research, 52(1):462-473.

2023

Leka, Oneda; Wu, Yufan; Zanetti, Giulia; Furler, Sven; Reinberg, Thomas; Marinho, Joana; Schaefer, Jonas V; Plückthun, Andreas; Li, Xiaodan; Pirazzini, Marco; Kammerer, Richard A (2023). A DARPin promotes faster onset of botulinum neurotoxin A1 action. Nature Communications, 14(1):8317.

Lam, Andy Km; Dutzler, Raimund (2023). Mechanistic basis of ligand efficacy in the calcium-activated chloride channel TMEM16A. The EMBO Journal, 42(24):e115030.

Cucuzza, Stefano; Sitnik, Malgorzata; Jurt, Simon; Michel, Erich; Dai, Wenzhao; Müntener, Thomas; Ernst, Patrick; Häussinger, Daniel; Plückthun, Andreas; Zerbe, Oliver (2023). Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nature Communications, 14(1):7823.

Baumann, Christian; Chiang, Wan‐Chin; Valsecchi, Renato; Jurt, Simon; Deluigi, Mattia; Schuster, Matthias; Rosengren, Karl Johan; Plückthun, Andreas; Zerbe, Oliver (2023). Side‐chain dynamics of the α$_{1B}$ ‐adrenergic receptor determined by NMR via methyl relaxation. Protein Science, 32(11):e4801.

Buxboim, Amnon; Kronenberg-Tenga, Rafael; Salajkova, Sarka; Avidan, Nili; Shahak, Hen; Thurston, Alice; Medalia, Ohad (2023). Scaffold, mechanics and functions of nuclear lamins. FEBS letters, 597(22):2791-2805.

Pacesa, Martin; Loeff, Luuk; Querques, Irma; Muckenfuss, Lena M; Sawicka, Marta; Jinek, Martin (2023). Publisher Correction: R-loop formation and conformational activation mechanisms of Cas9. Nature, 623(7987):E10.

Strubel, Alexander; Münick, Philipp; Hartmann, Oliver; Chaikuad, Apirat; Dreier, Birgit; Schaefer, Jonas V; Gebel, Jakob; Osterburg, Christian; Tuppi, Marcel; Schäfer, Birgit; Buck, Viktoria; Rosenfeldt, Mathias; Knapp, Stefan; Plückthun, Andreas; Diefenbacher, Markus E; Dötsch, Volker (2023). DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma. Cell Death and Disease, 14(10):674.

Bobrovs, Raitis; Drunka, Laura; Kanepe, Iveta; Jirgensons, Aigars; Caflisch, Amedeo; Salvalaglio, Matteo; Jaudzems, Kristaps (2023). Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. Journal of Chemical Information and Modeling, 63(21):6890-6899.

Chowdhury, Aritra; Borgia, Alessandro; Ghosh, Souradeep; Sottini, Andrea; Mitra, Soumik; Eapen, Rohan S; Borgia, Madeleine B; Yang, Tianjin; Galvanetto, Nicola; Ivanović, Miloš T; Łukijańczuk, Paweł; Zhu, Ruijing; Nettels, Daniel; Kundagrami, Arindam; Schuler, Benjamin (2023). Driving forces of the complex formation between highly charged disordered proteins. Proceedings of the National Academy of Sciences of the United States of America, 120(41):e2304036120.

Hartmann, K Patricia; van Gogh, Merel; Freitag, Patrick C; Kast, Florian; Nagy-Davidescu, Gabriela; Borsig, Lubor; Plückthun, Andreas (2023). FAP-retargeted Ad5 enables in vivo gene delivery to stromal cells in the tumor microenvironment. Molecular Therapy, 31(10):2914-2928.

Zhao, Lin; Koseki, Sabrina R T; Silverstein, Rachel A; Amrani, Nadia; Peng, Christina; Kramme, Christian; Savic, Natasha; Pacesa, Martin; Rodríguez, Tomás C; Stan, Teodora; Tysinger, Emma; Hong, Lauren; Yudistyra, Vivian; Ponnapati, Manvitha R; Jacobson, Joseph M; Church, George M; Jakimo, Noah; Truant, Ray; Jinek, Martin; Kleinstiver, Benjamin P; Sontheimer, Erik J; Chatterjee, Pranam (2023). PAM-flexible genome editing with an engineered chimeric Cas9. Nature Communications, 14(1):6175.

Yang, Tianjin; Buholzer, Karin J; Sottini, Andrea; Cao, Xiaobao; deMello, Andrew; Nettels, Daniel; Schuler, Benjamin (2023). Rapid droplet-based mixing for single-molecule spectroscopy. Nature Methods, 20(10):1479-1482.

Maliqi, Liridona; Friedrich, Nikolas; Glögl, Matthias; Schmutz, Stefan; Schmidt, Daniel; Rusert, Peter; Schanz, Merle; Zaheri, Maryam; Pasin, Chloé; Niklaus, Cyrille; Foulkes, Caio; Reinberg, Thomas; Dreier, Birgit; Abela, Irene; Peterhoff, David; Hauser, Alexandra; Kouyos, Roger D; Günthard, Huldrych F; van Gils, Marit J; Sanders, Rogier W; Wagner, Ralf; Plückthun, Andreas; Trkola, Alexandra (2023). Assessing immunogenicity barriers of the HIV-1 envelope trimer. npj vaccines, 8(1):148.

Sottini, Andrea; Borgia, Alessandro; Borgia, Madeleine B; Bugge, Katrine; Nettels, Daniel; Chowdhury, Aritra; Heidarsson, Pétur O; Zosel, Franziska; Best, Robert B; Kragelund, Birthe B; Schuler, Benjamin (2023). Author Correction: Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nature Communications, 14(1):5864.

Li, Wenhong; Chung, Wen-Lu; Kozlov, Michael M; Medalia, Ohad; Geiger, Benjamin; Bershadsky, Alexander D (2023). Chiral growth of adherent filopodia. Biophysical Journal, 122(18):3704-3721.

Lone, Museer A; Zeng, Sen; Bourquin, Florence; Wang, Mengli; Huang, Shunxiang; Lin, Zhiqiang; Tang, Beisha; Zhang, Ruxu; Hornemann, Thorsten (2023). SPTLC1 p.Leu38Arg, a novel mutation associated with childhood ALS. Biochimica and Biophysica Acta. Molecular and Cell Biology of Lipids, 1868(9):159359.

Eichenberger, Michael; Schwander, Thomas; Hüppi, Sean; Kreuzer, Jan; Mittl, Peer R E; Peccati, Francesca; Jiménez-Osés, Gonzalo; Naesby, Michael; Buller, Rebecca M (2023). The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis. Nature Catalysis, 6(10):927-938.

Stach, Oliver. Functional Dynamics and Structural Disorder of RNA-Binding Proteins Studied with Single-Molecule Spectroscopy. 2023, University of Zurich, Faculty of Science.

Glögl, Matthias; Friedrich, Nikolas; Cerutti, Gabriele; Lemmin, Thomas; Kwon, Young D; Gorman, Jason; Maliqi, Liridona; Mittl, Peer R E; Hesselman, Maria C; Schmidt, Daniel; Weber, Jacqueline; Foulkes, Caio; Dingens, Adam S; Bylund, Tatsiana; Olia, Adam S; Verardi, Raffaello; Reinberg, Thomas; Baumann, Nicolas S; Rusert, Peter; Dreier, Birgit; Shapiro, Lawrence; Kwong, Peter D; Plückthun, Andreas; Trkola, Alexandra (2023). Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nature Structural & Molecular Biology, 30(9):1323-1336.

Cazzanelli, Giulia; Dalle Vedove, Andrea; Parolin, Eleonora; D'Agostino, Vito Giuseppe; Unzue, Andrea; Nevado, Cristina; Caflisch, Amedeo; Lolli, Graziano (2023). Reevaluation of bromodomain ligands targeting BAZ2A. Protein Science, 32(9):e4752.

Chung, Weng-Lu. Structural Insights into the Molecular Architecture of Lamellipodia and Focal Adhesions. 2023, University of Zurich, Faculty of Science.

Galvanetto, Nicola; Ivanović, Miloš T; Chowdhury, Aritra; Sottini, Andrea; Nüesch, Mark F; Nettels, Daniel; Best, Robert B; Schuler, Benjamin (2023). Extreme dynamics in a biomolecular condensate. Nature, 619(7971):876-883.

Franz, Florian; Tapia-Rojo, Rafael; Winograd-Katz, Sabina; Boujemaa-Paterski, Rajaa; Li, Wenhong; Unger, Tamar; Albeck, Shira; Aponte-Santamaria, Camilo; Garcia-Manyes, Sergi; Medalia, Ohad; Geiger, Benjamin; Gräter, Frauke (2023). Allosteric activation of vinculin by talin. Nature Communications, 14(1):4311.

Vargas-Rosales, Pablo Andrés; D'Addio, Alessio; Zhang, Yang; Caflisch, Amedeo (2023). Disrupting Dimeric β-Amyloid by Electric Fields. ACS Physical Chemistry Au, 3(5):456-466.

Widmer, Julian; Langini, Cassiano; Vitalis, Andreas; Caflisch, Amedeo (2023). Optimized reaction coordinates for analysis of enhanced sampling. Journal of Chemical Physics, 159(1):015101.

Shi, Jie; Hauschulte, Kristine; Mikicic, Ivan; Maharjan, Srijana; Arz, Valerie; Strauch, Tina; Heidelberger, Jan B; Schaefer, Jonas V; Dreier, Birgit; Plückthun, Andreas; Beli, Petra; Ulrich, Helle D; Wollscheid, Hans-Peter (2023). Nuclear myosin VI maintains replication fork stability. Nature Communications, 14(1):3787.

Becker, Jan; Peters, Jack S; Crooks, Ivor; Helmi, Seham; Synakewicz, Marie; Schuler, Benjamin; Kukura, Philipp (2023). A Quantitative Description for Optical Mass Measurement of Single Biomolecules. ACS photonics, 10(8):2699-2710.

Tippett, David N; Breen, Colum; Butler, Stephen J; Sawicka, Marta; Dutzler, Raimund (2023). Structural and functional properties of the transporter SLC26A6 reveal mechanism of coupled anion exchange. eLife, 12:RP87178.

Bedi, Rajiv Kumar; Huang, Danzhi; Li, Yaozong; Caflisch, Amedeo (2023). Structure-Based Design of Inhibitors of the m$^{6}$A-RNA Writer Enzyme METTL3. ACS Bio & Med Chem Au, 3(4):359-370.

Ilie, Ioana M; Ehrhardt, Claus; Caflisch, Amedeo; Weitz-Schmidt, Gabriele (2023). Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 63(12):3878-3891.

Freitag, Patrick C; Kaulfuss, Meike; Flühler, Lea; Mietz, Juliane; Weiss, Fabian; Brücher, Dominik; Kolibius, Jonas; Hartmann, K Patricia; Smith, Sheena N; Münz, Christian; Chijioke, Obinna; Plückthun, Andreas (2023). Targeted adenovirus-mediated transduction of human T cells in vitro and in vivo. Molecular Therapy - Methods & Clinical Development, 29:120-132.

Leuppi, Jörg D; Bridevaux, Pierre-Olivier; Charbonnier, Florian; Clarenbach, Christian F; Duchna, Hans-Werner; Fellrath, Jean-Marc; Gianella, Pietro; Jochmann, Anja; Kern, Lukas; Pavlov, Nikolay; Rothe, Thomas; Steurer-Stey, Claudia; von Garnier, Christophe (2023). COPD – eine unterschätzte Erkrankung. Praxis, 112(7-8):403-412.

Becker, Lukas; Plückthun, Andreas (2023). DARPins bind their cytosolic targets after having been translocated through the protective antigen pore of anthrax toxin. Scientific Reports, 13(1):8048.

Gut, Melanie; Dreier, Birgit; Furler, Sven; Sobek, Jens; Plückthun, Andreas; Holland, Jason P (2023). Designed ankyrin repeat proteins for detecting prostate-specific antigen expression in vivo. RSC Chemical Biology, 4(7):494-505.

Blanc, Marine; Lettl, Clara; Guérin, Jérémy; Vieille, Anaïs; Furler, Sven; Briand-Schumacher, Sylvie; Dreier, Birgit; Bergé, Célia; Plückthun, Andreas; Vadon-Le Goff, Sandrine; Fronzes, Rémi; Rousselle, Patricia; Fischer, Wolfgang; Terradot, Laurent (2023). Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathogens, 19(5):e1011368.

Chowdhury, Aritra; Nettels, Daniel; Schuler, Benjamin (2023). Interaction Dynamics of Intrinsically Disordered Proteins from Single-Molecule Spectroscopy. Annual Review of Biophysics, 52(1):433-462.

Straub, Monique. Structural and Functional Characterization of the Apoptotic Lipid Scramblase rXKR9. 2023, University of Zurich, Faculty of Science.

Ramanadane, Karthik; Liziczai, Márton; Markovic, Dragana; Straub, Monique S; Rosalen, Gian T; Udovcic, Anto; Dutzler, Raimund; Manatschal, Cristina (2023). Structural and functional properties of a plant NRAMP-related aluminum transporter. eLife, 12:e85641.

Schubert, Rajib; Bae, Taegeun; Simic, Branko; Smith, Sheena N; Park, Seong-Ho; Nagy-Davidescu, Gabriela; Gradinaru, Viviana; Plückthun, Andreas; Hur, Junho K (2023). CRISPR-clear imaging of melanin-rich B16-derived solid tumors. Communications Biology, 6(1):370.

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 (2023). Author Correction: The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nature Cell Biology, 25(4):626.

Klenk, Christoph; Scrivens, Maria; Niederer, Anina; Shi, Shuying; Mueller, Loretta; Gersz, Elaine; Zauderer, Maurice; Smith, Ernest S; Strohner, Ralf; Plückthun, Andreas (2023). A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Nature Communications, 14(1):1770.

Wimmer, Benedikt H; Moraïs, Sarah; Zalk, Ran; Mizrahi, Itzhak; Medalia, Ohad (2023). Phylogenetic diversity of core rumen microbiota as described by cryo-ET. microLife, 4:uqad010.

Lehmann, Elena Farah; Liziczai, Márton; Drożdżyk, Katarzyna; Altermatt, Patrick; Langini, Cassiano; Manolova, Vania; Sundstrom, Hanna; Dürrenberger, Franz; Dutzler, Raimund; Manatschal, Cristina (2023). Structures of ferroportin in complex with its specific inhibitor vamifeport. eLife, 12:e83053.

Schmitz, Michael. Structural and Mechanistic Studies of Type V CRISPR-Associated Transposons. 2023, University of Zurich, Faculty of Science.

Mathy, Christopher J P; Mishra, Parul; Flynn, Julia M; Perica, Tina; Mavor, David; Bolon, Daniel N A; Kortemme, Tanja (2023). A complete allosteric map of a GTPase switch in its native cellular network. Cell Systems, 14(3):237-246.e7.

Reimann, Regina R; Puzio, Martina; Rosati, Antonella; Emmenegger, Marc; Schneider, Bernard L; Valdés, Pamela; Huang, Danzhi; Caflisch, Amedeo; Aguzzi, Adriano (2023). Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathology, 33(2):e13130.

Schellhorn, Sebastian; Brücher, Dominik; Wolff, Natascha A; Schröer, Katrin; Sallard, Erwan; Mese, Kemal; Zhang, Wenli; Ehrke-Schulz, Eric; Thévenod, Frank; Plückthun, Andreas; Ehrhardt, Anja (2023). Targeting Oncolytic Adenoviruses to Cancer Cells Using a Designed Ankyrin Repeat Protein Lipocalin-2 Fusion Protein. Human Gene Therapy, 34(5-6):203-216.

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 (2023). NLRP3 tyrosine phosphorylation is controlled by protein tyrosine phosphatase PTPN22. Journal of Clinical Investigation, 133(4):e169304.

Geiger, Benjamin; Boujemaa-Paterski, Rajaa; Winograd-Katz, Sabina E; Balan Venghateri, Jubina; Chung, Wen-Lu; Medalia, Ohad (2023). The Actin Network Interfacing Diverse Integrin-Mediated Adhesions. Biomolecules, 13(2):294.

Xiang, Yusen; Zhai, Guanglei; Li, Yaozong; Wang, Mengge; Chen, Xixiang; Wang, Ruyu; Xie, Hang; Zhang, Weidong; Ge, Guangbo; Zhang, Qian; Xu, Yechun; Caflisch, Amedeo; Xu, Jianrong; Chen, Hongzhuan; Chen, Lili (2023). Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. International Journal of Biological Macromolecules, 226:780-792.

Michel, Erich; Cucuzza, Stefano; Mittl, Peer R E; Zerbe, Oliver; Plückthun, Andreas (2023). Improved Repeat Protein Stability by Combined Consensus and Computational Protein Design. Biochemistry, 62(2):318-329.

Wojtinek, Matthias. In Cellulo Architecture and Assembly of the Nuclear Pore Complex. 2023, University of Zurich, Faculty of Science.

Freitag, Patrick C. Adapter Development for Targeted Adenoviral-Mediated Engineering of Human T Cells in Vitro and In Vivo. 2023, University of Zurich, Faculty of Science.

Wang, Chunyang; Wojtynek, Matthias; Medalia, Ohad (2023). Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography. Advances in Biological Regulation, 87:100923.

Rutz, Sonja; Deneka, Dawid; Dittmann, Antje; Sawicka, Marta; Dutzler, Raimund (2023). Structure of a volume-regulated heteromeric LRRC8A/C channel. Nature Structural & Molecular Biology, 30(1):52-61.

Tapia-Rojo, Rafael; Mora, Marc; Board, Stephanie; Walker, Jane; Boujemaa-Paterski, Rajaa; Medalia, Ohad; Garcia-Manyes, Sergi (2023). Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape. Nature Physics, 19(1):52-60.

2022

Strubel, Alexander; Münick, Philipp; Chaikuad, Apirat; Dreier, Birgit; Schaefer, Jonas; Gebel, Jakob; Osterburg, Christian; Tuppi, Marcel; Schäfer, Birgit; Knapp, Stefan; Plückthun, Andreas; Dötsch, Volker (2022). Designed Ankyrin Repeat Proteins as a tool box for analyzing p63. Cell Death and Differentiation, 29(12):2445-2458.

Schmitz, Michael; Querques, Irma; Oberli, Seraina; Chanez, Christelle; Jinek, Martin (2022). Structural basis for the assembly of the type V CRISPR-associated transposon complex. Cell, 185(26):4999-5010.e17.

Buholzer, Karin J; McIvor, Jordan; Zosel, Franziska; Teppich, Christian; Nettels, Daniel; Mercadante, Davide; Schuler, Benjamin (2022). Multilayered allosteric modulation of coupled folding and binding by phosphorylation, peptidyl-prolyl cis/trans isomerization, and diversity of interaction partners. Journal of Chemical Physics, 157(23):235102.

Sturzenegger, Flurin. Probing Transition Path Times of Biomolecular Reactions Using Single-Molecule Techniques. 2022, University of Zurich, Faculty of Science.

Chung, Wen-Lu; Eibauer, Matthias; Li, Wenhong; Boujemaa-Paterski, Rajaa; Geiger, Benjamin; Medalia, Ohad (2022). A network of mixed actin polarity in the leading edge of spreading cells. Communications Biology, 5(1):1338.

Sottini, Andrea. Study of the Functional Disorder and Dynamics of Biological Polyelectrolyte Complexes. 2022, University of Zurich, Faculty of Science.

Kono, Yohei; Adam, Stephen A; Sato, Yuko; Reddy, Karen L; Zheng, Yixian; Medalia, Ohad; Goldman, Robert D; Kimura, Hiroshi; Shimi, Takeshi (2022). Nucleoplasmic lamin C rapidly accumulates at sites of nuclear envelope rupture with BAF and cGAS. Journal of Cell Biology, 221(12):e202201024.

Philippi, Michael; Richter, Christian P; Kappen, Marie; Watrinet, Isabelle; Miao, Yi; Runge, Mercedes; Jorde, Lara; Korneev, Sergej; Holtmannspötter, Michael; Kurre, Rainer; Holthuis, Joost C M; Garcia, K Christopher; Plückthun, Andreas; Steinhart, Martin; Piehler, Jacob; You, Changjiang (2022). Biofunctional Nanodot Arrays in Living Cells Uncover Synergistic Co-Condensation of Wnt Signalodroplets. Small, 18(50):2203723.

Kiss, Cedric; Gall, Flavio M; Dreier, Birgit; Adams, Michael; Riedl, Rainer; Plückthun, Andreas; Mittl, Peer R E (2022). Structure of a hydrophobic leucinostatin derivative determined by host lattice display. Acta Crystallographica. Section D: Structural Biology, 78(Pt 12):1439-1450.

de Leeuw, Rebecca; Kronenberg-Tenga, Rafael; Eibauer, Matthias; Medalia, Ohad (2022). Filament assembly of the C. elegans lamin in the absence of helix 1A. Nucleus, 13(1):49-57.

Arndt, Melanie; Alvadia, Carolina; Straub, Monique S; Clerico Mosina, Vanessa; Paulino, Cristina; Dutzler, Raimund (2022). Structural basis for the activation of the lipid scramblase TMEM16F. Nature Communications, 13(1):6692.

Ilie, Ioana M; Caflisch, Amedeo (2022). Antibody binding increases the flexibility of the prion protein. BBA - Proteins and Proteomics, 1870(11-12):140827.

Kipnis, Yakov; Chaib, Anissa Ouald; Vorobieva, Anastassia A; Cai, Guangyang; Reggiano, Gabriella; Basanta, Benjamin; Kumar, Eshan; Mittl, Peer R E; Hilvert, Donald; Baker, David (2022). Design and optimization of enzymatic activity in a de novo β-barrel scaffold. Protein Science, 31(11):e4405.

Campbell, Benjamin F N; Dittmann, Antje; Dreier, Birgit; Plückthun, Andreas; Tyagarajan, Shiva K (2022). A DARPin-based molecular toolset to probe gephyrin and inhibitory synapse biology. eLife, 11:e80895.

Pacesa, Martin; Lin, Chun-Han; Cléry, Antoine; Saha, Aakash; Arantes, Pablo R; Bargsten, Katja; Irby, Matthew J; Allain, Frédéric H-T; Palermo, Giulia; Cameron, Peter; Donohoue, Paul D; Jinek, Martin (2022). Structural basis for Cas9 off-target activity. Cell, 185(22):4067-4081.e21.

Vacca, Santiago. Structural Characterization of Human Epidermal Growth Factor Receptor 2 Using Cryo-EM. 2022, University of Zurich, Faculty of Science.

Weber, Miriam S. Structural Analysis of Keratin Filaments by Cryo-Electron Microscopy and Tomography. 2022, University of Zurich, Faculty of Science.

Dehabadi, Maryam Haji; Caflisch, Amedeo; Ilie, Ioana M; Firouzi, Rohoullah (2022). Interactions of Curcumin's Degradation Products with the Aβ$_{42}$ Dimer: A Computational Study. Journal of Physical Chemistry B, 126(39):7627-7637.

Fay, Rachael; Törő, Imre; Schinke, Anna-Lena; Simic, Branko; Schaefer, Jonas V; Dreier, Birgit; Plückthun, Andreas; Holland, Jason P (2022). Sortase-Mediated Site-Specific Conjugation and 89Zr-Radiolabeling of Designed Ankyrin Repeat Proteins for PET. Molecular Pharmaceutics, 19(10):3576-3585.

Nierzwicki, Łukasz; East, Kyle W; Binz, Jonas M; Hsu, Rohaine V; Ahsan, Mohd; Arantes, Pablo R; Skeens, Erin; Pacesa, Martin; Jinek, Martin; Lisi, George P; Palermo, Giulia (2022). Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR-Cas9. Nature Catalysis, 5(10):912-922.

Strittmatter, Tobias; Wang, Yidan; Bertschi, Adrian; Scheller, Leo; Freitag, Patrick C; Ray, Preetam Guha; Stuecheli, Pascal; Schaefer, Jonas V; Reinberg, Thomas; Tsakiris, Dimitrios; Plückthun, Andreas; Ye, Haifeng; Fussenegger, Martin (2022). Programmable DARPin-based receptors for the detection of thrombotic markers. Nature Chemical Biology, 18(10):1125-1134.

Zhang, Yi; Wang, Yiao; Uslu, Safak; Venkatachalapathy, Sneha; Rashidian, Mohammad; Schaefer, Jonas V; Plückthun, Andreas; Distefano, Mark D (2022). Enzymatic Construction of DARPin-Based Targeted Delivery Systems Using Protein Farnesyltransferase and a Capture and Release Strategy. International Journal of Molecular Sciences, 23(19):11537.

Camus, Anna; Truong, Gisèle; Mittl, Peer R E; Markert, Greta; Hilvert, Donald (2022). Reprogramming Nonribosomal Peptide Synthetases for Site-Specific Insertion of α-Hydroxy Acids. Journal of the American Chemical Society, 144(38):17567-17575.

Anand, Uttpal; Shteinfer-Kuzmine, Anna; Sela, Gal; Santhanam, Manikandan; Gottschalk, Benjamin; Boujemaa-Paterski, Rajaa; Medalia, Ohad; Graier, Wolfgang F; Shoshan-Barmatz, Varda (2022). The Multicellular Effects of VDAC1 N-Terminal-Derived Peptide. Biomolecules, 12(10):1387.

Freitag, Patrick C; Brandl, Fabian; Brücher, Dominik; Weiss, Fabian; Dreier, Birgit; Plückthun, Andreas (2022). Modular Adapters Utilizing Binders of Different Molecular Types Expand Cell-Targeting Options for Adenovirus Gene Delivery. Bioconjugate Chemistry, 33(9):1595-1601.

Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2022). Domino Effect in Allosteric Signaling of Peptide Binding. Journal of Molecular Biology, 434(17):167661.

Muckenfuss, Lena Maria; Migenda Herranz, Anabel Carmen; Boneberg, Franziska Maria; Clerici, Marcello; Jinek, Martin (2022). Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis. eLife, 11:e80332.

Nai, Francesco; Nachawati, Raed; Zálešák, František; Wang, Xiang; Li, Yaozong; Caflisch, Amedeo (2022). Fragment Ligands of the m$^{6}$A-RNA Reader YTHDF2. ACS Medicinal Chemistry Letters, 13(9):1500-1509.

Dalle Vedove, Andrea; Cazzanelli, Giulia; Batiste, Laurent; Marchand, Jean-Rémy; Spiliotopoulos, Dimitrios; Corsi, Jessica; D'Agostino, Vito Giuseppe; Caflisch, Amedeo; Lolli, Graziano (2022). Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. ACS Medicinal Chemistry Letters, 13(9):1434-1443.

Bedi, Rajiv K. Design and Development of Chemical Probes for the Proteins Involved in the Methylation of Human RNAs. 2022, University of Zurich, Faculty of Science.

Beales, Charlie T; Medalia, Ohad (2022). Gold nanomaterials and their potential use as cryo-electron tomography labels. Journal of Structural Biology, 214(3):107880.

Pacesa, Martin; Loeff, Luuk; Querques, Irma; Muckenfuss, Lena M; Sawicka, Marta; Jinek, Martin (2022). R-loop formation and conformational activation mechanisms of Cas9. Nature, 609(7925):191-196.

Kralt, Annemarie; Wojtynek, Matthias; Fischer, Jonas S; Agote-Aran, Arantxa; Mancini, Roberta; Dultz, Elisa; Noor, Elad; Uliana, Federico; Tatarek-Nossol, Marianna; Antonin, Wolfram; Onischenko, Evgeny; Medalia, Ohad; Weis, Karsten (2022). An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae. eLife, 11:e78385.

Ilie, Ioana M; Bacci, Marco; Vitalis, Andreas; Caflisch, Amedeo (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal, 121(14):2813-2825.

Waltenspühl, Yann; Ehrenmann, Janosch; Vacca, Santiago; Thom, Cristian; Medalia, Ohad; Plückthun, Andreas (2022). Structural basis for the activation and ligand recognition of the human oxytocin receptor. Nature Communications, 13:4153.

Becker, Lukas. Cytosolic delivery of DARPins by retargeted anthrax lethal toxin. 2022, University of Zurich, Faculty of Science.

Kirchhammer, Nicole; Trefny, Marcel P; Natoli, Marina; Brücher, Dominik; Smith, Sheena N; Werner, Franziska; Koch, Victoria; Schreiner, David; Bartoszek, Ewelina; Buchi, Mélanie; Schmid, Markus; Breu, Daniel; Hartmann, K Patricia; Zaytseva, Polina; Thommen, Daniela S; Läubli, Heinz; Böttcher, Jan P; Stanczak, Michal A; Kashyap, Abhishek S; Plückthun, Andreas; Zippelius, Alfred (2022). NK cells with tissue-resident traits shape response to immunotherapy by inducing adaptive antitumor immunity. Science Translational Medicine, 14(653):eabm9043.

Muckenfuss, Lena M. Molecular Mechanisms of Human Pre-mRNA 3’ End Processing. 2022, University of Zurich, Faculty of Science.

Kopra, Kari; Valtonen, Salla; Mahran, Randa; Kapp, Jonas N; Hassan, Nazia; Gillette, William; Dennis, Bryce; Li, Lianbo; Westover, Kenneth D; Plückthun, Andreas; Härmä, Harri (2022). Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. International Journal of Molecular Sciences, 23(13):7095.

Sawicka, Marta; Dutzler, Raimund (2022). Regulators of cell volume: The structural and functional properties of anion channels of the LRRC8 family. Current Opinion in Structural Biology, 74:102382.

Tatli, Meltem; Moraïs, Sarah; Tovar-Herrera, Omar E; Bomble, Yannick J; Bayer, Edward A; Medalia, Ohad; Mizrahi, Itzhak (2022). Nanoscale resolution of microbial fiber degradation in action. eLife, 11:e76523.

Lam, Andy K M; Rutz, Sonja; Dutzler, Raimund (2022). Inhibition mechanism of the chloride channel TMEM16A by the pore blocker 1PBC. Nature Communications, 13:2798.

Guimaraes Koch, Sofia S; Thorpe, Robin; Kawasaki, Nana; Lefranc, Marie-Paule; Malan, Sarel; Martin, Andrew C R; Mignot, Gilles; Plückthun, Andreas; Rizzi, Menico; Shubat, Stephanie; Weisser, Karin; Balocco, Raffaella (2022). International nonproprietary names for monoclonal antibodies: an evolving nomenclature system. mAbs, 14(1):2075078.

García-Viñuales, Sara; Ilie, Ioana M; Santoro, Anna Maria; Romanucci, Valeria; Zarrelli, Armando; Di Fabio, Giovanni; Caflisch, Amedeo; Milardi, Danilo (2022). Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. BBA - Proteins and Proteomics, 1870(5):140772.

Salutari, Ilaria. Computational studies of protein-ligand interactions in TCR/pMHC and CREB-Binding Protein. 2022, University of Zurich, Faculty of Science.

Wang, Longlong; Moreira, Etori Aguiar; Kempf, Georg; Miyake, Yasuyuki; Oliveira Esteves, Blandina I; Fahmi, Amal; Schaefer, Jonas V; Dreier, Birgit; Yamauchi, Yohei; Alves, Marco P; Plückthun, Andreas; Matthias, Patrick (2022). Disrupting the HDAC6-ubiquitin interaction impairs infection by influenza and Zika virus and cellular stress pathways. Cell Reports, 39(4):110736.

Gisdon, Florian J; Kynast, Josef P; Ayyildiz, Merve; Hine, Anna V; Plückthun, Andreas; Höcker, Birte (2022). Modular peptide binders - development of a predictive technology as alternative for reagent antibodies. Biological Chemistry, 403(5-6):535-543.

Dultz, Elisa; Wojtynek, Matthias; Medalia, Ohad; Onischenko, Evgeny (2022). The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells, 11(9):1456.

Cocina, Francesco. Unsupervised Identification of States in Protein Dynamics and Neural Recordings. 2022, University of Zurich, Faculty of Science.

Martinsen, Jacob H; Saar, Daniel; Fernandes, Catarina B; Schuler, Benjamin; Bugge, Katrine; Kragelund, Birthe B (2022). Structure, dynamics, and stability of the globular domain of human linker histone H1.0 and the role of positive charges. Protein Science, 31(4):918-932.

Stelzl, Lukas S; Pietrek, Lisa M; Holla, Andrea; Oroz, Javier; Sikora, Mateusz; Köfinger, Jürgen; Schuler, Benjamin; Zweckstetter, Markus; Hummer, Gerhard (2022). Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au, 2(3):673-686.

Wu, Huayin; Shen, Yinan; Sivagurunathan, Suganya; Weber, Miriam Sarah; Adam, Stephen A; Shin, Jennifer H; Fredberg, Jeffrey J; Medalia, Ohad; Goldman, Robert; Weitz, David A (2022). Vimentin intermediate filaments and filamentous actin form unexpected interpenetrating networks that redefine the cell cortex. Proceedings of the National Academy of Sciences of the United States of America, 119(10):e2115217119.

Nass, Karol J; Ilie, Ioana M; Saller, Manfred J; Driessen, Arnold J M; Caflisch, Amedeo; Kammerer, Richard A; Li, Xiaodan (2022). The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Biochimica et biophysica acta. Biomembranes, 1864(3):183825.

Vahabikashi, Amir; Adam, Stephen A; Medalia, Ohad; Goldman, Robert D (2022). Nuclear lamins: Structure and function in mechanobiology. APL bioengineering, 6(1):011503.

Schöppe, Jendrik; Ehrenmann, Janosch; Waltenspühl, Yann; Plückthun, Andreas (2022). Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP. Nature Protocols, 17(3):698-726.

Salutari, Ilaria; Caflisch, Amedeo (2022). Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. Journal of Chemical Information and Modeling, 62(4):1014-1024.

Qi, Chao; Lavriha, Pia; Mehta, Ved; Khanppnavar, Basavraj; Mohammed, Inayathulla; Li, Yong; Lazaratos, Michalis; Schaefer, Jonas V; Dreier, Birgit; Plückthun, Andreas; Bondar, Ana-Nicoleta; Dessauer, Carmen W; Korkhov, Volodymyr M (2022). Structural basis of adenylyl cyclase 9 activation. Nature Communications, 13:1045.

Heidarsson, Pétur O; Mercadante, Davide; Sottini, Andrea; Nettels, Daniel; Borgia, Madeleine B; Borgia, Alessandro; Kilic, Sinan; Fierz, Beat; Best, Robert B; Schuler, Benjamin (2022). Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein. Nature Chemistry, 14(2):224-231.

Deluigi, Mattia. Structural, Functional, and Pharmacological Studies on the Mechanisms of Receptor Activation and Ligand Selectivity in G Protein-Coupled Receptors. 2022, University of Zurich, Faculty of Science.

Deluigi, Mattia; Morstein, Lena; Schuster, Matthias; Klenk, Christoph; Merklinger, Lisa; Cridge, Riley R; de Zhang, Lazarus A; Klipp, Alexander; Vacca, Santiago; Vaid, Tasneem M; Mittl, Peer R E; Egloff, Pascal; Eberle, Stefanie A; Zerbe, Oliver; Chalmers, David K; Scott, Daniel J; Plückthun, Andreas (2022). Crystal structure of the α$_{1B}$-adrenergic receptor reveals molecular determinants of selective ligand recognition. Nature Communications, 13(1):382.

Matsuda, Shinya; Schaefer, Jonas V; Mii, Yusuke; Hori, Yutaro; Bieli, Dimitri; Taira, Masanori; Plückthun, Andreas; Affolter, Markus (2022). Author Correction: Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nature Communications, 13(1):389.

Nüesch, Mark F; Ivanović, Miloš T; Claude, Jean-Benoît; Nettels, Daniel; Best, Robert B; Wenger, Jérôme; Schuler, Benjamin (2022). Single-molecule Detection of Ultrafast Biomolecular Dynamics with Nanophotonics. Journal of the American Chemical Society, 144(1):52-56.

Ramanadane, Karthik; Straub, Monique S; Dutzler, Raimund; Manatschal, Cristina (2022). Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family. eLife, 11:e74589.

Schilling, Johannes; Jost, Christian; Ilie, Ioana Mariuca; Schnabl, Joachim; Buechi, Oralea; Eapen, Rohan S; Truffer, Rafaela; Caflisch, Amedeo; Forrer, Patrik (2022). Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Journal of Biological Chemistry, 298(1):101403.

Zosel, Franziska; Holla, Andrea; Schuler, Benjamin (2022). Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy. In: Munoz, Victor. Protein Folding Methods and Protocols. New York: Springer, 207-233.

Giordano, Deborah; Langini, Cassiano; Caflisch, Amedeo; Marabotti, Anna; Facchiano, Angelo (2022). Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis. Computational and Structural Biotechnology Journal, 20:3924-3934.

Lone, Museer A; Bourquin, Florence; Hornemann, Thorsten (2022). Serine Palmitoyltransferase Subunit 3 and Metabolic Diseases. In: Jiang, Xian-Cheng. Sphingolipid Metabolism and Metabolic Disease. Singapore: Springer, 47-56.

Cocina, Francesco; Vitalis, Andreas; Caflisch, Amedeo (2022). Spiking burstiness and working memory in the human medial temporal lobe. Cerebral Cortex Communications, 3(4):tgac039.

2021

Dalle Vedove, Andrea; Cazzanelli, Giulia; Corsi, Jessica; Sedykh, Maria; D’Agostino, Vito Giuseppe; Caflisch, Amedeo; Lolli, Graziano (2021). Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining. ACS Bio & Med Chem Au, 1(1):5-10.

Bieri, Manuela; Hendrickx, Rodinde; Bauer, Michael; Yu, Bin; Jetzer, Tania; Dreier, Birgit; Mittl, Peer R E; Sobek, Jens; Plückthun, Andreas; Greber, Urs F; Hemmi, Silvio (2021). The RGD-binding integrins αvβ6 and αvβ8 are receptors for mouse adenovirus-1 and -3 infection. PLoS Pathogens, 17(12):e1010083.

Tatli, Meltem. Structural Characterization of Macromolecular Complexes Using CryoElectron Microscopy and Tomography. 2021, University of Zurich, Faculty of Science.

Thom, Cristian; Ehrenmann, Janosch; Vacca, Santiago; Waltenspühl, Yann; Schöppe, Jendrik; Medalia, Ohad; Plückthun, Andreas (2021). Structures of neurokinin 1 receptor in complex with Gq and Gs proteins reveal substance P binding mode and unique activation features. Science Advances, 7(50):eabk2872.

Bradbury, Andrew R M; Dübel, Stefan; Knappik, Achim; Plückthun, Andreas (2021). Animal- versus in vitro-derived antibodies: avoiding the extremes. mAbs, 13:1950265.

Kroupova, Alena; Ackle, Fabian; Asanović, Igor; Weitzer, Stefan; Boneberg, Franziska M; Faini, Marco; Leitner, Alexander; Chui, Alessia; Aebersold, Ruedi; Martinez, Javier; Jinek, Martin (2021). Molecular architecture of the human tRNA ligase complex. eLife, 10:e71656.

Cucuzza, Stefano; Güntert, Peter; Plückthun, Andreas; Zerbe, Oliver (2021). Correction to: An automated iterative approach for protein structure refinement using pseudocontact shifts. Journal of Biomolecular NMR, 75(10-12):429-430.

Friedrich, Nikolas; Stiegeler, Emanuel; Glögl, Matthias; Lemmin, Thomas; Hansen, Simon; Kadelka, Claus; Wu, Yufan; Ernst, Patrick; Maliqi, Liridona; Foulkes, Caio; Morin, Mylène; Eroglu, Mustafa; Liechti, Thomas; Ivan, Branislav; Reinberg, Thomas; Schaefer, Jonas V; Karakus, Umut; Ursprung, Stephan; Mann, Axel; Rusert, Peter; Kouyos, Roger D; Robinson, John A; Günthard, Huldrych F; Plückthun, Andreas; Trkola, Alexandra (2021). Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization. Nature Communications, 12:6705.

Langini, Cassiano. Computational Studies of Bromodomains and Their Interactions with Natural and Synthetic Ligands. 2021, University of Zurich, Faculty of Science.

Matsuda, Shinya; Schaefer, Jonas V; Mii, Yusuke; Hori, Yutaro; Bieli, Dimitri; Taira, Masanori; Plückthun, Andreas; Affolter, Markus (2021). Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nature Communications, 12:6435.

Cocina, Francesco; Vitalis, Andreas; Caflisch, Amedeo (2021). Unsupervised Methods for Detection of Neural States: Case Study of Hippocampal-Amygdala Interactions. eNeuro, 8(6):0484-20.

Klose, Daniel; Holla, Andrea; Gmeiner, Christoph; Nettels, Daniel; Ritsch, Irina; Bross, Nadja; Yulikov, Maxim; Allain, Frédéric H-T; Schuler, Benjamin; Jeschke, Gunnar (2021). Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries. Biophysical Journal, 120(21):4842-4858.

Perica, Tina; Mathy, Christopher J P; Xu, Jiewei; Jang, Gwendolyn Μ; Zhang, Yang; Kaake, Robyn; Ollikainen, Noah; Braberg, Hannes; Swaney, Danielle L; Lambright, David G; Kelly, Mark J S; Krogan, Nevan J; Kortemme, Tanja (2021). Systems-level effects of allosteric perturbations to a model molecular switch. Nature, 599(7883):152-157.

Querques, Irma; Schmitz, Michael; Oberli, Seraina; Chanez, Christelle; Jinek, Martin (2021). Target site selection and remodelling by type V CRISPR-transposon systems. Nature, 599(7885):497-502.

Makasheva, Kristina; Bryan, Louise C; Anders, Carolin; Panikulam, Sherin; Jinek, Martin; Fierz, Beat (2021). Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor. Journal of the American Chemical Society, 143(40):16313-16319.

Moroz-Omori, Elena V; Huang, Danzhi; Kumar Bedi, Rajiv; Cheriyamkunnel, Sherry J; Bochenkova, Elena; Dolbois, Aymeric; Rzeczkowski, Maciej D; Li, Yaozong; Wiedmer, Lars; Caflisch, Amedeo (2021). METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes. ChemMedChem, 16(19):3035-3043.

Mysore, Venkatesh P; Zhou, Zhi-Wei; Ambrogio, Chiara; Li, Lianbo; Kapp, Jonas N; Lu, Chunya; Wang, Qi; Tucker, Maxwell R; Okoro, Jeffrey J; Nagy-Davidescu, Gabriela; Bai, Xiaochen; Plückthun, Andreas; Jänne, Pasi A; Westover, Kenneth D; Shan, Yibing; Shaw, David E (2021). A structural model of a Ras-Raf signalosome. Nature Structural & Molecular Biology, 28(10):847-857.

Merten, Hannes; Brandl, Fabian; Zimmermann, Martina; Schaefer, Jonas V; Irpinio, Linda; Sand, Kine M K; Nilsen, Jeannette; Andersen, Jan Terje; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2021). Half-life extension of efficiently produced DARPin serum albumin fusions as a function of FcRn affinity and recycling. European Journal of Pharmaceutics and Biopharmaceutics, 167:104-113.

Schuller, Anthony P; Wojtynek, Matthias; Mankus, David; Tatli, Meltem; Kronenberg-Tenga, Rafael; Regmi, Saroj G; Dip, Phat V; Lytton-Jean, Abigail K R; Brignole, Edward J; Dasso, Mary; Weis, Karsten; Medalia, Ohad; Schwartz, Thomas U (2021). The cellular environment shapes the nuclear pore complex architecture. Nature, 598(7882):667-671.

Nemergut, Michal; Škrabana, Rostislav; Berta, Martin; Plückthun, Andreas; Sedlák, Erik (2021). Purification of MBP fusion proteins using engineered DARPin affinity matrix. International Journal of Biological Macromolecules, 187:105-112.

Stephens, Erin A; Ludwicki, Morgan B; Meksiriporn, Bunyarit; Li, Mingji; Ye, Tianzheng; Monticello, Connor; Forsythe, Katherine J; Kummer, Lutz; Zhou, Pengbo; Plückthun, Andreas; DeLisa, Matthew P (2021). Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase. ACS Synthetic Biology, 10(9):2396-2408.

de Leeuw, Rebecca. "Assembly of C. elegans lamin filaments revealed by cryo-electron microscopy. 2021, University of Zurich, Faculty of Science.

Deneka, Dawid; Rutz, Sonja; Hutter, Cedric A J; Seeger, Markus A; Sawicka, Marta; Dutzler, Raimund (2021). Allosteric modulation of LRRC8 channels by targeting their cytoplasmic domains. Nature Communications, 12:5435.

Sorrentino, Simona; Conesa, Jose Javier; Cuervo, Ana; Melero, Roberto; Martins, Bruno; Fernandez-Gimenez, Estrella; de Isidro-Gomez, Federico P; de la Morena, Jimenez; Studt, Jan-Dirk; Sorzano, Carlos Oscar S; Eibauer, Matthias; Carazo, Jose Maria; Medalia, Ohad (2021). Structural analysis of receptors and actin polarity in platelet protrusions. Proceedings of the National Academy of Sciences of the United States of America, 118(37):e2105004118.

Dolbois, Aymeric; Bedi, Rajiv K; Bochenkova, Elena; Müller, Anna; Moroz-Omori, Elena V; Huang, Danzhi; Caflisch, Amedeo (2021). 1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors. Journal of Medicinal Chemistry, 64(17):12738-12760.

Pacesa, Martin. "Molecular Mechanism of Target DNA Specificity of the CRISPR-Associated Genome Editor Nuclease Cas9. 2021, University of Zurich, Faculty of Science.

Donohoue, Paul D; Pacesa, Martin; Lau, Elaine; Vidal, Bastien; Irby, Matthew J; Nyer, David B; Rotstein, Tomer; Banh, Lynda; Toh, Mckenzi S; Gibson, Jason; Kohrs, Bryan; Baek, Kevin; Owen, Arthur L G; Slorach, Euan M; van Overbeek, Megan; Fuller, Christopher K; May, Andrew P; Jinek, Martin; Cameron, Peter (2021). Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Molecular Cell, 81(17):3637-3649.e5.

Cucuzza, Stefano; Güntert, Peter; Plückthun, Andreas; Zerbe, Oliver (2021). An automated iterative approach for protein structure refinement using pseudocontact shifts. Journal of Biomolecular NMR, 75(8-9):319-334.

Kosareva, Alexandra; Punjabi, Mukesh; Ochoa-Espinosa, Amanda; Xu, Lifen; Schaefer, Jonas V; Dreier, Birgit; Plückthun, Andreas; Kaufmann, Beat A (2021). Designed Ankyrin Repeat Proteins as Novel Binders for Ultrasound Molecular Imaging. Ultrasound in Medicine & Biology, 47(9):2664-2675.

Garolini, Davide. Unsupervised Identification of Behavioral States in Functional Networks of Spiking Neurons. 2021, University of Zurich, Faculty of Science.

Dingfelder, Fabian; Macocco, Iuri; Benke, Stephan; Nettels, Daniel; Faccioli, Pietro; Schuler, Benjamin (2021). Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. JACS Au, 1(8):1217-1230.

Lee, Joo-Hyung; Wang, Ruoyu; Xiong, Feng; Krakowiak, Joanna; Liao, Zian; Nguyen, Phuoc T; Moroz-Omori, Elena V; Shao, Jiaofang; Zhu, Xiaoyu; Bolt, Michael J; Wu, Haoyi; Singh, Pankaj K; Bi, Mingjun; Shi, Caleb J; Jamal, Naadir; Li, Guojie; Mistry, Ragini; Jung, Sung Yun; Tsai, Kuang-Lei; Ferreon, Josephine C; Stossi, Fabio; Caflisch, Amedeo; Liu, Zhijie; Mancini, Michael A; Li, Wenbo (2021). Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Molecular Cell, 81(16):3368-3385.e9.

Becker, Lukas; Singh Badwal, Jasleen; Brandl, Fabian; Verdurmen, Wouter P R; Plückthun, Andreas (2021). Thermodynamic Stability Is a Strong Predictor for the Delivery of DARPins to the Cytosol via Anthrax Toxin. Pharmaceutics, 13(8):1285.

Sukalskaia, Anastasiia; Straub, Monique S; Deneka, Dawid; Sawicka, Marta; Dutzler, Raimund (2021). Cryo-EM structures of the TTYH family reveal a novel architecture for lipid interactions. Nature Communications, 12:4893.

Sapra, K Tanuj; Medalia, Ohad (2021). Bend, Push, Stretch: Remarkable Structure and Mechanics of Single Intermediate Filaments and Meshworks. Cells, 10(8):1960.

Rothgangl, Tanja; Dennis, Melissa K; Lin, Paulo J C; Oka, Rurika; Witzigmann, Dominik; Villiger, Lukas; Qi, Weihong; Hruzova, Martina; Kissling, Lucas; Lenggenhager, Daniela; Borrelli, Costanza; Egli, Sabina; Frey, Nina; Bakker, Noëlle; Walker, John A; Kadina, Anastasia P; Victorov, Denis V; Pacesa, Martin; Kreutzer, Susanne; Kontarakis, Zacharias; Moor, Andreas; Jinek, Martin; Weissman, Drew; Stoffel, Markus; van Boxtel, Ruben; Holden, Kevin; Pardi, Norbert; Thöny, Beat; Häberle, Johannes; Tam, Ying K; Semple, Sean C; Schwank, Gerald (2021). In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nature Biotechnology, 39(8):949-957.

Weber, Miriam S; Eibauer, Matthias; Sivagurunathan, Suganya; Magin, Thomas M; Goldman, Robert D; Medalia, Ohad (2021). Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy. eLife, 10:e70307.

Straub, Monique S; Alvadia, Carolina; Sawicka, Marta; Dutzler, Raimund (2021). Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. eLife, 10:e69800.

Ramanadane, Karthik. Determinants of Selectivity in the SLC11/NRAMP Family. 2021, University of Zurich, Faculty of Science.

Radom, Filip; Vonrhein, Clemens; Mittl, Peer R E; Plückthun, Andreas (2021). Crystal structures of HER3 extracellular domain 4 in complex with the designed ankyrin-repeat protein D5. Acta Crystallographica. Section F: Structural Biology and Crystallization Communications, 77(Pt 7):192-201.

Pohl, Marie O; Busnadiego, Idoia; Marrafino, Francesco; Wiedmer, Lars; Hunziker, Annika; Fernbach, Sonja; Glas, Irina; Moroz-Omori, Elena V; Hale, Benjamin G; Caflisch, Amedeo; Stertz, Silke (2021). Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. Journal of General Virology, 102(7):001625.

Pott, Moritz; Tinzl, Matthias; Hayashi, Takahiro; Ota, Yusuke; Dunkelmann, Daniel; Mittl, Peer R E; Hilvert, Donald (2021). Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme. Angewandte Chemie Internationale Edition, 60(27):15063-15068.

Benke, Stephan; Holla, Andrea; Wunderlich, Bengt; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin (2021). Combining Rapid Microfluidic Mixing and Three-Color Single-Molecule FRET for Probing the Kinetics of Protein Conformational Changes. Journal of Physical Chemistry B, 125(24):6617-6628.

Stüber, Jakob C; Richter, Christian P; Bellón, Junel Sotolongo; Schwill, Martin; König, Iwo; Schuler, Benjamin; Piehler, Jacob; Plückthun, Andreas (2021). Apoptosis-inducing anti-HER2 agents operate through oligomerization-induced receptor immobilization. Communications Biology, 4:762.

Kast, Florian; Schwill, Martin; Stüber, Jakob C; Pfundstein, Svende; Nagy-Davidescu, Gabriela; Rodríguez, Josep M Monné; Seehusen, Frauke; Richter, Christian P; Honegger, Annemarie; Hartmann, Karen Patricia; Weber, Thomas G; Kroener, Felix; Ernst, Patrick; Piehler, Jacob; Plückthun, Andreas (2021). Engineering an anti-HER2 biparatopic antibody with a multimodal mechanism of action. Nature Communications, 12:3790.

Bawankar, Praveen; Lence, Tina; Paolantoni, Chiara; Haussmann, Irmgard U; Kazlauskiene, Migle; Jacob, Dominik; Heidelberger, Jan B; Richter, Florian M; Nallasivan, Mohanakarthik P; Morin, Violeta; Kreim, Nastasja; Beli, Petra; Helm, Mark; Jinek, Martin; Soller, Matthias; Roignant, Jean-Yves (2021). Hakai is required for stabilization of core components of the m6A mRNA methylation machinery. Nature Communications, 12:3778.

Asanović, Igor; Strandback, Emilia; Kroupova, Alena; et al; Jinek, Martin (2021). The oxidoreductase PYROXD1 uses NAD(P) + as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Molecular Cell, 81(12):2520-2532.e16.

Hartmann, Jessica; Münch, Robert C; Freiling, Ruth-Therese; Schneider, Irene C; Dreier, Birgit; Samukang, Washington; Koch, Joachim; Seeger, Markus A; Plückthun, Andreas; Buchholz, Christian J (2021). Erratum: A Library-Based Screening Strategy for the Identification of DARPins as Ligands for Receptor-Targeted AAV and Lentiviral Vectors. Molecular Therapy - Methods & Clinical Development, 21:728.

Deneka, Dawid. Structural and Functional Characterization of Volume-Regulated Anion Channels of the LRRC8 Family. 2021, University of Zurich, Faculty of Science.

Vulovic, Ivan; Yao, Qing; Park, Young-Jun; Courbet, Alexis; Norris, Andrew; Busch, Florian; Sahasrabuddhe, Aniruddha; Merten, Hannes; Sahtoe, Danny D; Ueda, George; Fallas, Jorge A; Weaver, Sara J; Hsia, Yang; Langan, Robert A; Plückthun, Andreas; Wysocki, Vicki H; Veesler, David; Jensen, Grant J; Baker, David (2021). Generation of ordered protein assemblies using rigid three-body fusion. Proceedings of the National Academy of Sciences of the United States of America, 118(23):e2015037118.

Pinto, Maria Filipa; Baici, Antonio; Pereira, Pedro José Barbosa; Macedo-Ribeiro, Sandra; Pastore, Annalisa; Rocha, Fernando; Martins, Pedro M (2021). interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis. Journal of Molecular Biology, 433(11):166613.

Smith, Sheena N; Schubert, Rajib; Simic, Branko; Brücher, Dominik; Schmid, Markus; Kirk, Niels; Freitag, Patrick C; Gradinaru, Viviana; Plückthun, Andreas (2021). The SHREAD gene therapy platform for paracrine delivery improves tumor localization and intratumoral effects of a clinical antibody. Proceedings of the National Academy of Sciences of the United States of America, 118(21):e2017925118.

Kroupova, Alena. Structural Studies of Eukaryotic RNA Processing Enzymes. 2021, University of Zurich, Faculty of Science.

Martins, Bruno; Sorrentino, Simona; Chung, Wen-Lu; Tatli, Meltem; Medalia, Ohad; Eibauer, Matthias (2021). Unveiling the polarity of actin filaments by cryo-electron tomography. Structure, 29(5):488-498.e4.

Alvadia, Carolina. Structural and functional characterization of the lipid scramblase TMEM16F. 2021, University of Zurich, Faculty of Science.

König, Iwo; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin (2021). Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angewandte Chemie Internationale Edition, 60(19):10724-10729.

Incaviglia, Ilaria; Frutiger, Andreas; Blickenstorfer, Yves; Treindl, Fridolin; Ammirati, Giulia; Lüchtefeld, Ines; Dreier, Birgit; Plückthun, Andreas; Vörös, Janos; Reichmuth, Andreas M (2021). An Approach for the Real-Time Quantification of Cytosolic Protein-Protein Interactions in Living Cells. ACS Sensors, 6(4):1572-1582.

Waltenspühl, Yann; Jeliazkov, Jeliazko R; Kummer, Lutz; Plückthun, Andreas (2021). Directed evolution for high functional production and stability of a challenging G protein-coupled receptor. Scientific Reports, 11:8630.

Li, Wenhong; Sancho, Ana; Chung, Wen-Lu; Vinik, Yaron; Groll, Jürgen; Zick, Yehiel; Medalia, Ohad; Bershadsky, Alexander D; Geiger, Benjamin (2021). Differential cellular responses to adhesive interactions with galectin-8- and fibronectin-coated substrates. Journal of Cell Science, 134(8):jcs252221.

Kittisopikul, Mark; Shimi, Takeshi; Tatli, Meltem; Tran, Joseph Riley; Zheng, Yixian; Medalia, Ohad; Jaqaman, Khuloud; Adam, Stephen A; Goldman, Robert D (2021). Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. Journal of Cell Biology, 220(4):e202007082.

Lerner, Eitan; Barth, Anders; Hendrix, Jelle; et al; Nettels, Daniel; Schuler, Benjamin (2021). FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife, 10:e60416.

Kronenberg-Tenga, Rafael; Tatli, Meltem; Eibauer, Matthias; Wu, Wei; Shin, Ji-Yeon; Bonne, Gisèle; Worman, Howard J; Medalia, Ohad (2021). A lamin A/C variant causing striated muscle disease provides insights into filament organization. Journal of Cell Science, 134(6):jcs256156.

Waltenspühl, Yann; Ehrenmann, Janosch; Klenk, Christoph; Plückthun, Andreas (2021). Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules, 26(5):1465.

Brücher, Dominik; Kirchhammer, Nicole; Smith, Sheena N; Schumacher, Jatina; Schumacher, Nina; Kolibius, Jonas; Freitag, Patrick C; Schmid, Markus; Weiss, Fabian; Keller, Corina; Grove, Melanie; Greber, Urs F; Zippelius, Alfred; Plückthun, Andreas (2021). iMATCH: an integrated modular assembly system for therapeutic combination high-capacity adenovirus gene therapy. Molecular Therapy - Methods & Clinical Development, 20:572-586.

Zhang, Meng; Gui, Miao; Wang, Zi-Fu; Gorgulla, Christoph; Yu, James J; Wu, Hao; Sun, Zhen-Yu J; Klenk, Christoph; Merklinger, Lisa; Morstein, Lena; Hagn, Franz; Plückthun, Andreas; Brown, Alan; Nasr, Mahmoud L; Wagner, Gerhard (2021). Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs. Nature Structural & Molecular Biology, 28(3):258-267.

Brücher, Dominik. A Modular Assembly and Production System for High-Capacity Adenoviral Combination Vectors. 2021, University of Zurich, Faculty of Science.

Waltenspühl, Yann. Protein Engineering and Structure Determination of G Protein-Coupled Receptors. 2021, University of Zurich, Faculty of Science.

Milardi, Danilo; Gazit, Ehud; Radford, Sheena E; Xu, Yong; Gallardo, Rodrigo U; Caflisch, Amedeo; Westermark, Gunilla T; Westermark, Per; Rosa, Carmelo La; Ramamoorthy, Ayyalusamy (2021). Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chemical Reviews, 121(3):1845-1893.

Li, Yaozong; Bedi, Rajiv Kumar; Wiedmer, Lars; Sun, Xianqiang; Huang, Danzhi; Caflisch, Amedeo (2021). Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation, 17(2):1240-1249.

Lam, Andy K M; Rheinberger, Jan; Paulino, Cristina; Dutzler, Raimund (2021). Gating the pore of the calcium-activated chloride channel TMEM16A. Nature Communications, 12:785.

Lam, Andy K M; Dutzler, Raimund (2021). Mechanism of pore opening in the calcium-activated chloride channel TMEM16A. Nature Communications, 12:786.

Cappelletti, Valentina; Hauser, Thomas; Piazza, Ilaria; Pepelnjak, Monika; Malinovska, Liliana; Fuhrer, Tobias; Li, Yaozong; Dörig, Christian; Boersema, Paul; Gillet, Ludovic; Grossbach, Jan; Dugourd, Aurelien; Saez-Rodriguez, Julio; Beyer, Andreas; Zamboni, Nicola; Caflisch, Amedeo; de Souza, Natalie; Picotti, Paola (2021). Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell, 184(2):545-559.e22.

Mallona, Izaskun; Ilie, Ioana Mariuca; Karemaker, Ino Dominiek; Butz, Stefan; Manzo, Massimiliano; Caflisch, Amedeo; Baubec, Tuncay (2021). Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49(1):145-157.

Goba, Inguna; Goricanec, David; Schum, Dominik; Hillenbrand, Matthias; Plückthun, Andreas; Hagn, Franz (2021). Probing the Conformation States of Neurotensin Receptor 1 Variants by NMR Site-Directed Methyl Labeling. Chembiochem, 22(1):139-146.

Teale, William D; Pasternak, Taras; Dal Bosco, Cristina; Dovzhenko, Alexander; Kratzat, Krystyna; Bildl, Wolfgang; Schwörer, Manuel; Falk, Thorsten; Ruperti, Benadetto; Schaefer, Jonas V; Shahriari, Mojgan; Pilgermayer, Lena; Li, Xugang; Lübben, Florian; Plückthun, Andreas; Schulte, Uwe; Palme, Klaus (2021). Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport. The EMBO Journal, 40:e104416.

Deluigi, Mattia; Klipp, Alexander; Klenk, Christoph; Merklinger, Lisa; Eberle, Stefanie A; Morstein, Lena; Heine, Philipp; Mittl, Peer R E; Ernst, Patrick; Kamenecka, Theodore M; He, Yuanjun; Vacca, Santiago; Egloff, Pascal; Honegger, Annemarie; Plückthun, Andreas (2021). Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism. Science Advances, 7(5):eabe5504.

2020

Saha, Aakash; Arantes, Pablo R; Hsu, Rohaine V; Narkhede, Yogesh B; Jinek, Martin; Palermo, Giulia (2020). Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. Journal of Chemical Information and Modeling, 60(12):6427-6437.

Li, Yaozong; Bedi, Rajiv K; Moroz-Omori, Elena V; Caflisch, Amedeo (2020). Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. Journal of Chemical Information and Modeling, 60(12):5932-5935.

Karakus, Ufuk; Sahin, Dilara; Mittl, Peer R E; Mooij, Petra; Koopman, Gerrit; Boyman, Onur (2020). Receptor-gated IL-2 delivery by an anti-human IL-2 antibody activates regulatory T cells in three different species. Science Translational Medicine, 12(574):eabb9283.

Sapra, K Tanuj; Qin, Zhao; Dubrovsky-Gaupp, Anna; Aebi, Ueli; Müller, Daniel J; Buehler, Markus J; Medalia, Ohad (2020). Nonlinear mechanics of lamin filaments and the meshwork topology build an emergent nuclear lamina. Nature Communications, 11:6205.

Casalino, Lorenzo; Nierzwicki, Łukasz; Jinek, Martin; Palermo, Giulia (2020). Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics. ACS Catalysis, 10(22):13596-13605.

Khayat, Maayan; Deri, Shani; Wolf, David; Trigano, Tom; Medalia, Ohad; Ben-Harush, Kfir (2020). Biomimetic nuclear lamin fibers with remarkable toughness and stiffness. International Journal of Biological Macromolecules, 163:2060-2067.

Boujemaa-Paterski, Rajaa; Martins, Bruno; Eibauer, Matthias; Beales, Charlie T; Geiger, Benjamin; Medalia, Ohad (2020). Talin-activated vinculin interacts with branched actin networks to initiate bundles. eLife, 9:e53990.

Sottini, Andrea; Borgia, Alessandro; Borgia, Madeleine B; Bugge, Katrine; Nettels, Daniel; Chowdhury, Aritra; Heidarsson, Pétur O; Zosel, Franziska; Best, Robert B; Kragelund, Birthe B; Schuler, Benjamin (2020). Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nature Communications, 11(1):5736.

Brandl, Fabian; Busslinger, Sarah; Zangemeister-Wittke, Uwe; Plückthun, Andreas (2020). Optimizing the anti-tumor efficacy of protein-drug conjugates by engineering the molecular size and half-life. Journal of Controlled Release, 327:186-197.

Gray, Alison; Bradbury, Andrew R M; Knappik, Achim; Plückthun, Andreas; Borrebaeck, Carl A K; Dübel, Stefan (2020). Animal-free alternatives and the antibody iceberg. Nature Biotechnology, 38(11):1234-1239.

Marchand, Jean-Rémy; Knehans, Tim; Caflisch, Amedeo; Vitalis, Andreas (2020). An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. Journal of Chemical Information and Modeling, 60(10):5188-5202.

Goossens, Kenneth; Wroblowski, Berthold; Langini, Cassiano; van Vlijmen, Herman; Caflisch, Amedeo; De Winter, Hans (2020). Assessment of the fragment docking program SEED. Journal of Chemical Information and Modeling, 60(10):4881-4893.

Nowak, Kathrin; Rosenthal, Florian; Karlberg, Tobias; Bütepage, Mareike; Thorsell, Ann-Gerd; Dreier, Birgit; Grossmann, Jonas; Sobek, Jens; Imhof, Ralph; Lüscher, Bernhard; Schüler, Herwig; Plückthun, Andreas; Leslie Pedrioli, Deena M; Hottiger, Michael O (2020). Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins. Nature Communications, 11:5199.

Cocina, Francesco; Vitalis, Andreas; Caflisch, Amedeo (2020). Sapphire-based clustering. Journal of Chemical Theory and Computation, 16(10):6383-6396.

Zijlstra, Niels; Nettels, Daniel; Satija, Rohit; Makarov, Dmitrii E; Schuler, Benjamin (2020). Transition Path Dynamics of a Dielectric Particle in a Bistable Optical Trap. Physical Review Letters, 125(14):146001.

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.

Tenga, Rafael; Medalia, Ohad (2020). Structure and unique mechanical aspects of nuclear lamin filaments. Current Opinion in Structural Biology, 64:152-159.

Starck, Yvonne. Side-Chain-Specific Selection of Designed Armadillo Repeat Proteins for Modular Peptide Recognition. 2020, University of Zurich, Faculty of Science.

Brandl, Fabian. Engineering and Preclinical Evaluation of Half-Life Extended DARPin- Auristatin Drug Conjugates for Enhanced In Vivo Anti-Tumor Efficacy. 2020, University of Zurich, Faculty of Science.

Dolbois, Aymeric; Batiste, Laurent; Wiedmer, Lars; Dong, Jing; Brütsch, Manuela; Huang, Danzhi; Deerain, Nicholas M; Spiliotopoulos, Dimitrios; Cheng-Sánchez, Iván; Laul, Eleen; Nevado, Cristina; Śledź, Paweł; Caflisch, Amedeo (2020). Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. ACS Medicinal Chemistry Letters, 11(8):1573-1580.

Becker, Lukas; Verdurmen, Wouter P R; Plückthun, Andreas (2020). Reengineering anthrax toxin protective antigen for improved receptor-specific protein delivery. BMC Biology, 18(1):100.

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.

Kassube, Susanne A; Thomä, Nicolas H (2020). Structural insights into Fe-S protein biogenesis by the CIA targeting complex. Nature Structural & Molecular Biology, 27(8):735-742.

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.

Gordon, David E; Jang, Gwendolyn M; Bouhaddou, Mehdi; Xu, Jiewei; Obernier, Kirsten; White, Kris M; O'Meara, Matthew J; Rezelj, Veronica V; Guo, Jeffrey Z; Swaney, Danielle L; Tummino, Tia A; Hüttenhain, Ruth; Kaake, Robyn M; Richards, Alicia L; Tutuncuoglu, Beril; Foussard, Helene; Batra, Jyoti; Haas, Kelsey; Modak, Maya; Kim, Minkyu; Haas, Paige; Polacco, Benjamin J; Braberg, Hannes; Fabius, Jacqueline M; Eckhardt, Manon; Soucheray, Margaret; Bennett, Melanie J; Cakir, Merve; McGregor, Michael J; Li, Qiongyu; et al (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816):459-468.

Waltenspühl, Yann; Schöppe, Jendrik; Ehrenmann, Janosch; Kummer, Lutz; Plückthun, Andreas (2020). Crystal structure of the human oxytocin receptor. Science Advances, 6(29):eabb5419.

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.

Stivala, Simona; Sorrentino, Simona; Gobbato, Sara; Bonetti, Nicole R; Camici, Giovanni G; Lüscher, Thomas F; Medalia, Ohad; Beer, Jürg H (2020). Glycoprotein Ib clustering in platelets can be inhibited by alpha-linolenic acid as revealed by cryo-electron tomography. Haematologica, 105(6):1660-1666.

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.

Ehrenmann, Janosch. Protein Engineering and Structure Determination of G Protein-Coupled Receptors. 2020, University of Zurich, Faculty of Science.

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.

Schuler, Benjamin; Borgia, Alessandro; Borgia, Madeleine B; Heidarsson, Pétur O; Holmstrom, Erik D; Nettels, Daniel; Sottini, Andrea (2020). Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Current Opinion in Structural Biology, 60:66-76.

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.

Unzue, Andrea; Jessen-Trefzer, Claudia; Spiliotopoulos, Dimitrios; Gaudio, Eugenio; Tarantelli, Chiara; Dong, Jing; Zhao, Hongtao; Pachmayr, Johanna; Zahler, Stefan; Bernasconi, Elena; Sartori, Giulio; Cascione, Luciano; Bertoni, Francesco; Śledź, Paweł; Caflisch, Amedeo; Nevado, Cristina (2020). Understanding the mechanism of action of pyrrolo[3,2-b]quinoxaline-derivatives as kinase inhibitors. RSC Medicinal Chemistry, 11(6):665-675.

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.

Voskuil, Jan L A; Bandrowski, Anita; Begley, C Glenn; Bradbury, Andrew R M; Chalmers, Andrew D; Gomes, Aldrin V; Hardcastle, Travis; Lund-Johansen, Fridtjof; Plückthun, Andreas; Roncador, Giovanna; Solache, Alejandra; Taussig, Michael J; Trimmer, James S; Williams, Cecilia; Goodman, Simon L (2020). The Antibody Society's antibody validation webinar series. mAbs, 12(1):e1794421.

2019

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.

2018

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 C A S; 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. The EMBO Journal, 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. The EMBO Journal, 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.

2017

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.

Palermo, Giulia; Ricci, Clarisse G; Fernando, Amendra; Basak, Rajshekhar; Jinek, Martin; Rivalta, Ivan; Batista, Victor S; McCammon, J Andrew (2017). Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9. Journal of the American Chemical Society, 139(45):16028-16031.

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.

Harapin, Jan. Structural characterization of macromolecular complexes within thick specimens using cryo-focused-ion-beam scanning electron microscopy (cryo-FIB-SEM) and cryo-electron-tomography (cryo-ET). 2017, University of Zurich, Faculty of Science.

2016

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. The EMBO Journal, 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.

Xu, Min. Molecular dynamics simulations of protein-ligand complex systems and applications to drug design. 2016, University of Zurich, Faculty of Science.

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.

2015

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.

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.

Poms, Martin. Solution NMR studies on fragments of the yeast GPCR Ste2p. 2015, University of Zurich, Faculty of Science.

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.

2014

Perica, Tina; Kondo, Yasushi; Tiwari, Sandhya P; McLaughlin, Stephen H; Kemplen, Katherine R; Zhang, Xiuwei; Steward, Annette; Reuter, Nathalie; Clarke, Jane; Teichmann, Sarah A (2014). Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science, 346(6216):1254346.

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.

2013

Zhang, Xiuwei; Perica, Tina; Teichmann, Sarah A (2013). Evolution of protein structures and interactions from the perspective of residue contact networks. Current Opinion in Structural Biology, 23(6):954-963.

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

Kassube, Susanne A; Fang, Jie; Grob, Patricia; Yakovchuk, Petro; Goodrich, James A; Nogales, Eva (2013). Structural insights into transcriptional repression by noncoding RNAs that bind to human Pol II. Journal of Molecular Biology, 425(19):3639-3648.

Roller, Masa; Lucić, Vedran; Nagy, István; Perica, Tina; Vlahovicek, Kristian (2013). Environmental shaping of codon usage and functional adaptation across microbial communities. Nucleic Acids Research, 41(19):8842-8852.

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.

Marsh, Joseph A; Hernández, Helena; Hall, Zoe; Ahnert, Sebastian E; Perica, Tina; Robinson, Carol V; Teichmann, Sarah A (2013). Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell, 153(2):461-470.

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.

2012

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.

Kassube, Susanne A; Stuwe, Tobias; Lin, Daniel H; Antonuk, C Danielle; Napetschnig, Johanna; Blobel, Günter; Hoelz, André (2012). Crystal structure of the N-terminal domain of Nup358/RanBP2. Journal of Molecular Biology, 423(5):752-765.

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.

Perica, Tina; Marsh, Joseph A; Sousa, Filipa L; Natan, Eviatar; Colwell, Lucy J; Ahnert, Sebastian E; Teichmann, Sarah A (2012). The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochemical Society Transactions, 40(3):475-491.

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; et al (2012). The interface of protein structure, protein biophysics, and molecular evolution. Protein Science, 21(6):769-85.

Perica, Tina; Chothia, Cyrus; Teichmann, Sarah A (2012). Evolution of oligomeric state through geometric coupling of protein interfaces. Proceedings of the National Academy of Sciences of the United States of America, 109(21):8127-8132.

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.