Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

Periole, X, Vendruscolo, M and Mark, AE (2007) Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain. Proteins-structure Function And Bioinformatics, 69 3: 536-550. doi:10.1002/prot.21491


Author Periole, X
Vendruscolo, M
Mark, AE
Title Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain
Journal name Proteins-structure Function And Bioinformatics   Check publisher's open access policy
ISSN 0887-3585
Publication date 2007-03-07
Sub-type Article (original research)
DOI 10.1002/prot.21491
Volume 69
Issue 3
Start page 536
End page 550
Total pages 15
Place of publication Hoboken
Publisher Wiley-liss
Collection year 2008
Language eng
Subject C1
780103 Chemical sciences
780105 Biological sciences
Abstract A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which experimental (Phi-values were incorporated as restraints. Two of the nine models were simulated 10 times for 200 ns and the remaining models simulated two times for 200 us. Complete folding was observed in one case, while in the other simulations partial folding or unfolding even ts were observed, which were characterized by a regularization of elements of secondary structure. These results are consistent with recent experimental evidence that the folding of SH3 domains involves low populated intermediate states. (C) 2007 Wiley-Liss, Inc.
Keyword Biochemistry & Molecular Biology
Biophysics
molecular dynamics
transition state
protein folding
phi-value
Pfold
Phi-value Analysis
Chymotrypsin Inhibitor-2
Atomic-resolution
Denatured State
Protein
Ensemble
Intermediate
Pathways
Kinetics
Peptide
Q-Index Code C1
Q-Index Status Confirmed Code

 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 10 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 12 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Tue, 19 Feb 2008, 01:27:32 EST