ArticleJournal of molecular biology2007
Two-stage folding of HP-35 from ab initio simulations.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.Journal of chemical theory and computation · 2018Article
- Article
- Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.Protein science : a publication of the Protein Society · 2016Article
- Computational evidence that fast translation speed can increase the probability of cotranslational protein folding.Scientific reports · 2015Article
- Elucidation of the Aggregation Pathways of Helix-Turn-Helix Peptides: Stabilization at the Turn Region Is Critical for Fibril Formation.Biochemistry · 2015Article
- A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain.Biophysical journal · 2015Article
- Equilibrium kinetic network of the villin headpiece in implicit solvent.Biophysical journal · 2015Article
- REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain.Journal of molecular modeling · 2014Article
- Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- 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
- Trends in template/fragment-free protein structure prediction.Theoretical chemistry accounts · 2011Article
- Folding network of villin headpiece subdomain.Biophysical journal · 2010Article
- Challenges in protein folding simulations: Timescale, representation, and analysis.Nature physics · 2010Article
- The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.Biophysical journal · 2010Article
- Folding simulations of a de novo designed protein with a betaalphabeta fold.Biophysical journal · 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
- Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations.The Journal of chemical physics · 2009Article
- Common structural transitions in explicit-solvent simulations of villin headpiece folding.Biophysical journal · 2009Article
- Quantitative determination of site-specific conformational distributions in an unfolded protein by solid-state nuclear magnetic resonance.Journal of molecular biology · 2009Article
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2 authors.
Funding
Abstract
Accurate ab initio simulation of protein folding is a critical step toward elucidation of protein-folding mechanisms. Here, we demonstrate highly accurate folding of the 35 residue villin headpiece subdomain (HP35) by all-atom molecular dynamics simulations using AMBER FF03 and the generalized-Born solvation model. In a set of 20 micros long simulations, the protein folded to the native state in multiple trajectories, with the lowest C(alpha) RMSD being 0.39 A for residues 2-34 (excluding residues 1 and 35). The native state had the highest population among all sampled conformations, and the center of most populated cluster had a C(alpha) RMSD of 1.63 A. Folding of this protein can be described as a two-stage process that followed a well-defined pathway. In the first stage, formation of helices II and III as a folding intermediate constituted the rate-limiting step and was initiated at a folding nucleus around residues Phe17 and Pro21. The folding intermediate further acted as a template that facilitated the folding and docking of helix I in the second stage. Detailed descriptions of the folding kinetics and the roles of key residues are presented.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.