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Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein
- Source :
- PLoS Computational Biology, Vol 16, Iss 11, p e1008293 (2020), PLoS Computational Biology
- Publication Year :
- 2020
- Publisher :
- Public Library of Science (PLoS), 2020.
-
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.<br />Author summary Förster (fluorescence) resonance energy transfer (FRET) has been used extensively by biophysicists as a molecular-scale ruler that yields fundamental structural and kinetic insights into transient processes including complex formation and conformational rearrangements required for biological function. FRET techniques require the identification of informative fluorophore labeling sites, spaced at defined distances to inform on a reaction coordinate of interest and consideration of noise sources that have the potential to obscure quantitative interpretations. Here, we describe an approach to leverage advancements in computationally efficient all-atom structure-based molecular dynamics simulations in which structural dynamics observed via FRET can be interpreted in full atomistic detail on commensurate time scales. We demonstrate the potential of this approach using a model FRET system, the amino acid binding protein LIV-BPSS conjugated to self-healing organic fluorophores. LIV-BPSS exhibits large scale, sub-millisecond clamshell-like conformational changes between open and closed conformations associated with ligand unbinding and binding, respectively. Our findings inform on the molecular basis of the dynamics observed by smFRET and on strategies to optimize fluorophore labeling sites, the manner of fluorophore attachment, and fluorophore composition.
- Subjects :
- 0301 basic medicine
Protein Conformation
Biosensing Techniques
Molecular Dynamics
Biochemistry
Systems Science
01 natural sciences
Resonance (particle physics)
Fluorophotometry
chemistry.chemical_compound
Molecular dynamics
Spectrum Analysis Techniques
Computational Chemistry
Fluorescence Resonance Energy Transfer
Biochemical Simulations
Biology (General)
Free Energy
Physics
Ecology
Simulation and Modeling
Resolution (electron density)
Single-molecule FRET
Chemistry
Computational Theory and Mathematics
Spectrophotometry
Time and Motion Studies
Modeling and Simulation
Physical Sciences
Thermodynamics
Biological system
Research Article
Biophysical Simulations
Computer and Information Sciences
Fluorophore
QH301-705.5
Biophysics
Molecular Dynamics Simulation
Research and Analysis Methods
Dipole Moments
010402 general chemistry
Reaction coordinate
03 medical and health sciences
Cellular and Molecular Neuroscience
Electromagnetism
Genetics
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Proteins
Biology and Life Sciences
Computational Biology
0104 chemical sciences
030104 developmental biology
Förster resonance energy transfer
chemistry
Amino acid binding
Mathematics
Dwell Time
Subjects
Details
- ISSN :
- 15537358
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- PLOS Computational Biology
- Accession number :
- edsair.doi.dedup.....195270deee4598032c5a167c6dad3a57