ArticlePLoS computational biology2020
Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- Multimodal dynamics control activity of a glial glutamate transporter.bioRxiv : the preprint server for biology · 2026Article
- Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.Current opinion in structural biology · 2026Review
- Integrating Molecular Dynamics Simulations and Single-molecule FRET Spectroscopy: From Computational FRET Estimation to Experimental Data Interpretation.The journal of physical chemistry. B · 2026Review
- Accuracy of distance distributions and dynamics from single-molecule FRET.Biophysical journal · 2025Article
- Advancing Single-Molecule Biophysics: Next-Generation Organic Fluorophores with Tailored Labeling Strategies.Chemical & biomedical imaging · 2025Review
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation.Nature methods · 2024Article
- Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function.Annual review of biophysics · 2024Review
- Dissecting the mechanism of atlastin-mediated homotypic membrane fusion at the single-molecule level.Nature communications · 2024Article
- FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries.Communications biology · 2024Article
- Forces and energetics of the canonical tetrameric cation channel gating.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies.Journal of the American Chemical Society · 2023Article
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.Nucleic acids research · 2022Article
- Article
- Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches.The journal of physical chemistry. B · 2021Article
- Exploring safe and potent bioactives for the treatment of non-small cell lung cancer.3 Biotech · 2021Article
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.