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FRETraj: integrating single-molecule spectroscopy with molecular dynamics


Steffen, Fabio D; Sigel, Roland K O; Börner, Richard (2021). FRETraj: integrating single-molecule spectroscopy with molecular dynamics. Bioinformatics, 37(21):3953-3955.

Abstract

Quantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact volumes (ACV) and simulated photon statistics. FRETraj helps to identify optimal fluorophore positions on a biomolecule of interest by rapidly evaluating donor-acceptor distances. FRETraj is scalable and fully integrated into PyMOL and the Jupyter ecosystem. Here, we describe the conformational dynamics of a DNA hairpin by computing multiple ACVs along a molecular dynamics trajectory and compare the predicted FRET distribution with single-molecule experiments. FRET-assisted modeling will accelerate the analysis of structural ensembles in particular dynamic, non-coding RNAs and transient protein-nucleic acid complexes.

Abstract

Quantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact volumes (ACV) and simulated photon statistics. FRETraj helps to identify optimal fluorophore positions on a biomolecule of interest by rapidly evaluating donor-acceptor distances. FRETraj is scalable and fully integrated into PyMOL and the Jupyter ecosystem. Here, we describe the conformational dynamics of a DNA hairpin by computing multiple ACVs along a molecular dynamics trajectory and compare the predicted FRET distribution with single-molecule experiments. FRET-assisted modeling will accelerate the analysis of structural ensembles in particular dynamic, non-coding RNAs and transient protein-nucleic acid complexes.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Uncontrolled Keywords:Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability
Language:English
Date:5 November 2021
Deposited On:08 Feb 2022 15:17
Last Modified:27 May 2024 01:52
Publisher:Oxford University Press
ISSN:1367-4803
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bioinformatics/btab615
Project Information:
  • : FunderSNSF
  • : Grant ID200020_165868
  • : Project TitleMetal Ions in Structure and Function of Regulatory RNAs
  • : FunderSNSF
  • : Grant ID200020_192153
  • : Project TitlePrinciples of Metal-Ion-Assisted Folding and Structure of Functional RNAs
  • : FunderUZH Forschungskredit
  • : Grant IDFK-17-098
  • : Project Title
  • Content: Published Version
  • Licence: Creative Commons: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)