ArticleScientific reports2017
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
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18 citing papers in PubMed.
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- Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicA.Biophysical journal · 2025Article
- CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules.JACS Au · 2024Article
- The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition.Communications biology · 2024Article
- Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters.bioRxiv : the preprint server for biology · 2024Article
- Functional regulation of aquaporin dynamics by lipid bilayer composition.Nature communications · 2024Article
- Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition.bioRxiv : the preprint server for biology · 2023Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE.PLoS computational biology · 2021Article
- UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study.The journal of physical chemistry. B · 2021Article
- Adaptive Markov state model estimation using short reseeding trajectories.The Journal of chemical physics · 2020Article
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- SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes.Scientific reports · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the major challenges in atomistic simulations of proteins is efficient sampling of pathways associated with rare conformational transitions. Recent developments in statistical methods for computation of direct evolutionary couplings between amino acids within and across polypeptide chains have allowed for inference of native residue contacts, informing accurate prediction of protein folds and multimeric structures. In this study, we assess the use of distances between evolutionarily coupled residues as natural choices for reaction coordinates which can be incorporated into Markov state model-based adaptive sampling schemes and potentially used to predict not only functional conformations but also pathways of conformational change, protein folding, and protein-protein association. We demonstrate the utility of evolutionary couplings in sampling and predicting activation pathways of the β
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