ArticleProceedings of the National Academy of Sciences of the United States of America2014
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- Recent Advances in Protein Folding Pathway Prediction through Computational Methods.Current medicinal chemistry · 2024Review
- Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.Journal of chemical theory and computation · 2023Article
- Early Stages of RNA-Mediated Conversion of Human Prions.The journal of physical chemistry. B · 2022Article
- Mechanistic Kinetic Model Reveals How Amyloidogenic Hydrophobic Patches Facilitate the Amyloid-β Fibril Elongation.ACS chemical neuroscience · 2022Article
- Wild-TypeFrontiers in molecular biosciences · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Missense Mutations Modify the Conformational Ensemble of theFrontiers in molecular biosciences · 2021Article
- Sequence-Based Prediction of Metamorphic Behavior in Proteins.Biophysical journal · 2020Article
- New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain.The journal of physical chemistry. B · 2020Article
- Article
- LinkingeLife · 2018Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
- High-Resolution Mapping of the Folding Transition State of a WW Domain.Journal of molecular biology · 2016Article
- Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach.The Journal of chemical physics · 2015Article
- Preventing fibril formation of a protein by selective mutation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Accelerated molecular dynamics simulations of protein folding.Journal of computational chemistry · 2015Article
- Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.Journal of chemical theory and computation · 2015Article
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9 authors.
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Abstract
To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.
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