Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.

Autor: Girodat D; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America., Pati AK; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America., Terry DS; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America., Blanchard SC; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America., Sanbonmatsu KY; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.; New Mexico Consortium, Los Alamos, New Mexico, United States of America.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2020 Nov 05; Vol. 16 (11), pp. e1008293. Date of Electronic Publication: 2020 Nov 05 (Print Publication: 2020).
DOI: 10.1371/journal.pcbi.1008293
Abstrakt: Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BPSS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BPSS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BPSS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BPSS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R0) and fluorophore orientation factor (κ2) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.
Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: SCB holds an equity interest in Lumidyne Technologies.
Databáze: MEDLINE
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