ArticleThe journal of physical chemistry letters2019
Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data.
Article in The journal of physical chemistry letters, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- ProGuide: a flexible framework for modeling global conformational rearrangements in proteins using DEER-derived distance restraints.bioRxiv : the preprint server for biology · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Review
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.PLoS computational biology · 2022Article
- Modeling biomolecular kinetics with large-scale simulation.Current opinion in structural biology · 2022Review
- Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.PLoS computational biology · 2021Article
- Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements.The journal of physical chemistry letters · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Multistructured biomolecular systems play crucial roles in a wide variety of cellular processes but have resisted traditional methods of structure determination, which often resolve only a few low-energy states. High-resolution structure determination using experimental methods that yield distributional data remains extremely difficult, especially when the underlying conformational ensembles are quite heterogeneous. We have therefore developed a method to integrate sparse, multimultimodal spectroscopic data to obtain high-resolution estimates of conformational ensembles. We have tested our method by incorporating double electron-electron resonance data on the soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein syntaxin-1a into biased molecular dynamics simulations. We find that our method substantially outperforms existing state-of-the-art methods in capturing syntaxin's open-closed conformational equilibrium and further yields new conformational states that are consistent with experimental data and may help in understanding syntaxin's function. Our improved methods for refining heterogeneous conformational ensembles from spectroscopic data will greatly accelerate the structural understanding of such systems.
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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.