ArticleThe Journal of chemical physics2017
Modeling the mechanism of CLN025 beta-hairpin formation.
Article in The Journal of chemical physics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance.Nature communications · 2025Article
- Markov State Models: To Optimize or Not to Optimize.Journal of chemical theory and computation · 2024Article
- Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations.Journal of chemical theory and computation · 2023Article
- Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding.The journal of physical chemistry. B · 2023Article
- Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering.Biomacromolecules · 2023Article
- Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.The Journal of chemical physics · 2023Article
- DADApy: Distance-based analysis of data-manifolds in Python.Patterns (New York, N.Y.) · 2022Article
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
- Effects of Externally Applied Electric Fields on the Manipulation of Solvated-Chignolin Folding: Static- versus Alternating-Field Dichotomy at Play.The journal of physical chemistry. B · 2022Article
- Deep learning the slow modes for rare events sampling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles.Bioinformatics (Oxford, England) · 2021Article
- TorchMD: A Deep Learning Framework for Molecular Simulations.Journal of chemical theory and computation · 2021Article
- Coarse graining molecular dynamics with graph neural networks.The Journal of chemical physics · 2020Article
- Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.Journal of chemical theory and computation · 2019Article
- Heterogeneity in the Folding of Villin Headpiece Subdomain HP36.The journal of physical chemistry. B · 2018Article
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Authors and funding
3 authors.
Funding
Abstract
Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.
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