ArticleProceedings of the National Academy of Sciences of the United States of America2013
Native contacts determine protein folding mechanisms in atomistic simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 282 papers.
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282 citing papers in PubMed.
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- Coupled Binding and Folding of NS2B/NS3 Protease and Linker Effects Revealed by Topology-Based Modeling.The journal of physical chemistry. B · 2026Article
- MAHLER: Integrating Metadynamics and Inverse Folding to Predict Antibody-Antigen Kinetics.bioRxiv : the preprint server for biology · 2026Article
- Structures of protein folding intermediates on the ribosome.Nature structural & molecular biology · 2026Article
- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
- Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme.ACS synthetic biology · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Coupled Binding and Folding of NS2B/NS3 Protease and Linker Effects Revealed by Topology-based Modeling.bioRxiv : the preprint server for biology · 2026Article
- The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP.bioRxiv : the preprint server for biology · 2026Article
- Lost in Projection? Gaussian Filtering Recovers Hidden Conformational States.The journal of physical chemistry letters · 2026Article
- Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates.Nature communications · 2026Article
222 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q, captures remarkably well the transition states for all the proteins with a folding free energy barrier. Going beyond this global picture, we devise two different measures to quantify the importance of individual interresidue contacts in the folding mechanism: (i) the log-ratio of lifetimes of contacts during folding transition paths and in the unfolded state and (ii) a Bayesian measure of how predictive the formation of each contact is for being on a transition path. Both of these measures indicate that native, or near-native, contacts are important for determining mechanism, as might be expected. More remarkably, however, we found that for almost all the proteins, with the designed protein α3D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms.
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