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Molecular dynamics simulations from putative transition states of α‐spectrin SH3 domain
Author(s) -
Periole Xavier,
Vendruscolo Michele,
Mark Alan E.
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21491
Subject(s) - spectrin , transition (genetics) , molecular dynamics , domain (mathematical analysis) , sh3 domain , dynamics (music) , physics , statistical physics , computational biology , biophysics , biology , genetics , cytoskeleton , gene , quantum mechanics , mathematics , kinase , cell , proto oncogene tyrosine protein kinase src , mathematical analysis , acoustics
A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of α‐spectrin, which were generated by Lindorff‐Larsen et al. (Nat Struct Mol Biol 2004;11:443–449) using molecular dynamics simulations in which experimental Φ ‐ 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 ns. Complete folding was observed in one case, while in the other simulations partial folding or unfolding events 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. Proteins 2007. © 2007 Wiley‐Liss, Inc.