ArticleProceedings of the National Academy of Sciences of the United States of America2012
Protein folding kinetics and thermodynamics from atomistic simulation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
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Who cites it
133 citing papers in PubMed.
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- A Practical Guide to Transition State Analysis in Biomolecular Simulations with TS-DAR.The journal of physical chemistry. B · 2025Article
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- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Simulation of the trimeric globular head of C1q reveals temperature-sensitive network: implications for inflammation.Journal of molecular modeling · 2025Article
- Combining simulations and experiments - a perspective on maximum entropy methods.Physical chemistry chemical physics : PCCP · 2025Review
- Improved Data-Driven Collective Variables for Biased Sampling through Iteration on Biased Data.The journal of physical chemistry. B · 2025Article
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73 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Advances in simulation techniques and computing hardware have created a substantial overlap between the timescales accessible to atomic-level simulations and those on which the fastest-folding proteins fold. Here we demonstrate, using simulations of four variants of the human villin headpiece, how simulations of spontaneous folding and unfolding can provide direct access to thermodynamic and kinetic quantities such as folding rates, free energies, folding enthalpies, heat capacities, Φ-values, and temperature-jump relaxation profiles. The quantitative comparison of simulation results with various forms of experimental data probing different aspects of the folding process can facilitate robust assessment of the accuracy of the calculations while providing a detailed structural interpretation for the experimental observations. In the example studied here, the analysis of folding rates, Φ-values, and folding pathways provides support for the notion that a norleucine double mutant of villin folds five times faster than the wild-type sequence, but following a slightly different pathway. This work showcases how computer simulation has now developed into a mature tool for the quantitative computational study of protein folding and dynamics that can provide a valuable complement to experimental techniques.
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