ArticleProteins2011
The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin.The Journal of biological chemistry · 2016Article
- Preventing fibril formation of a protein by selective mutation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences.PLoS computational biology · 2015Article
- Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- PRIMO: A Transferable Coarse-grained Force Field for Proteins.Journal of chemical theory and computation · 2013Article
- A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations.PLoS computational biology · 2012Article
- Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.Journal of the American Chemical Society · 2011Article
- The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel.The Journal of chemical physics · 2011Article
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3 authors.
Funding
Abstract
In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo simulations starting from random coils find native-like (Cα RMSD of 2.68 Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β-hairpins, the folding mechanism of each individual β-hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous P(fold) analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation.
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