ArticleNature chemistry2017
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling.
Article in Nature chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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Who cites it
140 citing papers in PubMed.
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- Learning data-efficient coarse-grained molecular dynamics from forces and noise.Nature communications · 2026Article
- Building multiscale Markov state models by systematic mapping of temporal communities.Bioinformatics (Oxford, England) · 2026Article
- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
- Dissociation kinetics of G proteins from G protein-coupled receptors and effects of allosteric modulation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Accommodating Statistical and Physics-Based Computational Protocols for Molecular Glue Model and Evaluation.Journal of chemical information and modeling · 2025Article
- Deciphering the folding code of collagens.Nature communications · 2025Article
- Ionic liquids as stabilisers of therapeutic protein formulations: a review of insulin and monoclonal antibodies.Biophysical reviews · 2025Review
- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics.Journal of chemical theory and computation · 2024Article
- Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD.Communications biology · 2024Article
- Structure prediction of alternative protein conformations.Nature communications · 2024Article
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
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- Structural biology in the age of X-ray free-electron lasers and exascale computing.Current opinion in structural biology · 2024Review
- Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants.Protein science : a publication of the Protein Society · 2024Review
- Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
80 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.
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28937668What OpenQuestion holds
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.