ArticleProceedings of the National Academy of Sciences of the United States of America2024
On the role of native contact cooperativity in protein folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Signatures of protein fold switching in the unfolded state.Biophysical journal · 2026Article
- Article
- Cooperative Native Contact Formation Facilitates Free Energy Barrier Crossing in Protein Folding.Physical review letters · 2026Article
- Article
- Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT.Journal of chemical information and modeling · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Pathway regulation mechanism by cotranslational protein folding.Communications chemistry · 2025Article
- Transient Poly(ADP-Ribose) Triggers FUS Condensation Hysteresis via a Prion-Like Mechanism.bioRxiv : the preprint server for biology · 2025Article
- Article
- On the role of native contact cooperativity in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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3 authors.
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Abstract
The consistency of energy landscape theory predictions with available experimental data, as well as direct evidence from molecular simulations, have shown that protein folding mechanisms are largely determined by the contacts present in the native structure. As expected, native contacts are generally energetically favorable. However, there are usually at least as many energetically favorable nonnative pairs owing to the greater number of possible nonnative interactions. This apparent frustration must therefore be reduced by the greater cooperativity of native interactions. In this work, we analyze the statistics of contacts in the unbiased all-atom folding trajectories obtained by Shaw and coworkers, focusing on the unfolded state. By computing mutual cooperativities between contacts formed in the unfolded state, we show that native contacts form the most cooperative pairs, while cooperativities among nonnative or between native and nonnative contacts are typically much less favorable or even anticooperative. Furthermore, we show that the largest network of cooperative interactions observed in the unfolded state consists mainly of native contacts, suggesting that this set of mutually reinforcing interactions has evolved to stabilize the native state.
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