Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

Hongxing Lei, Chun Wu, Haiguang Liu, Yong Duan

Research output: Contribution to journalArticlepeer-review

190 Scopus citations

Abstract

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C α-rmsd from the x-ray structure was 0.46 Å, and the Cα-rmsd of the center of the most populated cluster was 1.78 Å at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature Tm = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived Tm = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

Original languageEnglish (US)
Pages (from-to)4925-4930
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume104
Issue number12
DOIs
StatePublished - Mar 20 2007
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General

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