ArticleProceedings of the National Academy of Sciences of the United States of America2008
Universality and diversity of folding mechanics for three-helix bundle proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A.bioRxiv : the preprint server for biology · 2025Article
- AbMelt: Learning antibody thermostability from molecular dynamics.Biophysical journal · 2024Article
- Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations.Biophysical journal · 2020Article
- An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin.The Journal of biological chemistry · 2016Article
- Thermostability of Enzymes from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2016Article
- Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences.PLoS computational biology · 2015Article
- Equilibrium kinetic network of the villin headpiece in implicit solvent.Biophysical journal · 2015Article
- Accounting for a mirror-image conformation as a subtle effect in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Electronic polarization stabilizes tertiary structure prediction of HP-36.Journal of molecular modeling · 2014Article
- High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.Journal of chemical theory and computation · 2013Article
- Native state conformational heterogeneity of HP35 revealed by time-resolved FRET.The journal of physical chemistry. B · 2012Article
- Is there an en route folding intermediate for Cold shock proteins?Protein science : a publication of the Protein Society · 2012Article
- The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential.Proteins · 2011Article
- Contribution of hydrophobic interactions to protein stability.Journal of molecular biology · 2011Article
- Challenges in protein folding simulations: Timescale, representation, and analysis.Nature physics · 2010Article
- Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations.Biophysical journal · 2010Article
- What can solid state NMR contribute to our understanding of protein folding?Biophysical chemistry · 2010Review
- Engineering a two-helix bundle protein for folding studies.Protein engineering, design & selection : PEDS · 2010Article
- Coordinate-dependent diffusion in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance.Journal of the American Chemical Society · 2010Article
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3 authors.
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Abstract
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.
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