Integrating Molecular Dynamics Simulations and Single-molecule FRET Spectroscopy: From Computational FRET Estimation to Experimental Data Interpretation
Stephanie Sauve, Ehsaneh Khodadadi, Ahmed Shubbar, Ehsan Khodadadi, Mahmoud Moradi
TL;DR
This paper reviews how combining molecular dynamics simulations with single-molecule FRET spectroscopy helps study biomolecular structures and dynamics at an atomic level.
Contribution
The paper provides a comprehensive review of recent advancements in integrating MD simulations and smFRET for studying biomolecular dynamics.
Findings
Combining MD simulations and smFRET improves understanding of conformational dynamics and structural changes in biomolecules.
MD simulations help estimate FRET efficiencies and interpret experimental data from smFRET.
The integration has revealed insights into binding mechanisms, allosteric effects, and structural dynamics.
Abstract
Molecular dynamics (MD) simulations can characterize biomolecular processes at an exceptional spatiotemporal resolution not able to be accessed experimentally. As the limitations associated with MD simulations lessen and the method advances toward greater capabilities, the simulations are being applied to a wide array of new applications. For example, the integration of MD simulations and single-molecule Förster resonance energy transfer (smFRET) spectroscopy is a newly developing and growing application combining experimental and computational approaches. The integration of these techniques provides valuable insight into the conformational dynamics of biomolecules on an atomic-level, thereby enhancing the understanding of complex biological processes. This review compiles information on simulating FRET dyes and estimating FRET efficiencies from MD simulations and using MD simulations…
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Taxonomy
TopicsAdvanced Fluorescence Microscopy Techniques · Spectroscopy and Quantum Chemical Studies · DNA and Nucleic Acid Chemistry