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Simulation of FRET dyes allows quantitative comparison against experimental data

Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

Fully understanding biomolecular function requires detailed insight into the systems’ structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

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Verlagsausgabe §
DOI: 10.5445/IR/1000078618
Veröffentlicht am 10.01.2018
DOI: 10.1063/1.5010434
Zitationen: 11
Web of Science
Zitationen: 11
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Angewandte Physik (APH)
Steinbuch Centre for Computing (SCC)
Institut für Toxikologie und Genetik (ITG)
Institut für Nanotechnologie (INT)
Publikationstyp Zeitschriftenaufsatz
Publikationsdatum 28.03.2018
Sprache Englisch
Identifikator ISSN: 0021-9606, 1089-7690
KITopen-ID: 1000078618
HGF-Programm 46.11.01 (POF III, LK 01)
Computational Science and Mathematical Methods
Erschienen in The journal of chemical physics
Band 148
Heft 12
Seiten 123321
Nachgewiesen in Web of Science
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