ArticleBiophysical journal2015
Quantitative interpretation of FRET experiments via molecular simulation: force field and validation.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
- Article
- 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
- Labelizer: systematic selection of protein residues for covalent fluorophore labeling.Nature communications · 2025Article
- FRET-guided modeling of nucleic acids.Nucleic acids research · 2024Article
- FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries.Communications biology · 2024Article
- Deducing the conformational space for an octa-proline helix.Chemical science · 2024Article
- Single-molecule Detection of Ultrafast Biomolecular Dynamics with Nanophotonics.Journal of the American Chemical Society · 2022Article
- Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting.Biophysical journal · 2021Article
- FRETraj: integrating single-molecule spectroscopy with molecular dynamics.Bioinformatics (Oxford, England) · 2021Article
- Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries.Biophysical journal · 2021Article
- Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins.Methods (San Diego, Calif.) · 2021Article
- Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins.Essays in biochemistry · 2021Review
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- Time-Resolved Fluorescence Anisotropy and Molecular Dynamics Analysis of a Novel GFP Homo-FRET Dimer.Biophysical journal · 2021Article
- Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations.Chemical science · 2021Article
- Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems.Current topics in medicinal chemistry · 2021Review
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Authors and funding
4 authors.
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Abstract
Molecular simulation is a valuable and complementary tool that may assist with the interpretation of single-molecule Förster resonance energy transfer (FRET) experiments, if the energy function is of sufficiently high quality. Here we present force-field parameters for one of the most common pairs of chromophores used in experiments, AlexaFluor 488 and 594. From microsecond molecular-dynamics simulations, we are able to recover both experimentally determined equilibrium constants and association/dissociation rates of the chromophores with free tryptophan, as well as the decay of fluorescence anisotropy of a labeled protein. We find that it is particularly important to obtain a correct balance of solute-water interactions in the simulations in order to faithfully capture the experimental anisotropy decays, which provide a sensitive benchmark for fluorophore mobility. Lastly, by a combination of experiment and simulation, we address a potential complication in the interpretation of experiments on polyproline, used as a molecular ruler for FRET experiments, namely the potential association of one of the chromophores with the polyproline helix. Under conditions where simulations accurately capture the fluorescence anisotropy decay, we find at most a modest, transient population of conformations in which the chromophores associate with the polyproline. Explicit calculation of FRET transfer efficiencies for short polyprolines yields results in good agreement with experiment. These results illustrate the potential power of a combination of molecular simulation and experiment in quantifying biomolecular dynamics.
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