ArticleProceedings of the National Academy of Sciences of the United States of America2019
Atomic-level characterization of protein-protein association.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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Who cites it
96 citing papers in PubMed.
- Article
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- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
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- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations.The journal of physical chemistry. B · 2025Article
- Exploring Placental Protein-Target Protein Interactions:Current protein & peptide science · 2025Article
- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies.Nature communications · 2024Article
- Dynamic formation of the protein-lipid prefusion complex.Biophysical journal · 2024Article
- Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD.Communications biology · 2024Article
- Dynamic Formation of the Protein-Lipid Pre-fusion Complex.bioRxiv : the preprint server for biology · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants.Journal of chemical information and modeling · 2024Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the biological importance of protein-protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein-protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)-based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein-protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.
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