Journal Article

FZJ-2018-00908

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Simulation of FRET dyes allows quantitative comparison against experimental data

Reinartz, I. ; Sinner, C. ; Nettels, D. ; Stucki-Buchli, B. ; Stockmar, F. ; Panek, P. T. ; Jacob, C. R. ; Nienhaus, G. U. ; Schuler, B. ; Schug, A. (Corresponding author)FZJ*

2018
American Institute of Physics Melville, NY

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Please use a persistent id in citations: http://hdl.handle.net/2128/16885  doi:10.1063/1.5010434

Abstract: 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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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. John von Neumann - Institut für Computing (NIC)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)

Appears in the scientific report 2018

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Database coverage:
; ; Current Contents - Physical, Chemical and Earth Sciences ; Ebsco Academic Search ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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