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Molecular dynamics study of a calmodulin‐like protein with an IQ peptide: Spontaneous refolding of the protein around the peptide
Author(s) -
Ganoth Assaf,
Nachliel Esther,
Friedman Ran,
Gutman Menachem
Publication year - 2006
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.20956
Subject(s) - calmodulin , peptide , dynamics (music) , biophysics , molecular dynamics , chemistry , biochemistry , biology , physics , computational chemistry , enzyme , acoustics
The Calmodulin (CaM) is a small (16.7 kDa), highly acidic protein that is crucial to all eukaryotes by serving as a prototypical calcium sensor. In the present study, we investigated, through molecular dynamics simulations, the dynamics of a complex between the Mlc1p protein, which is a CaM‐like protein, and the IQ4 peptide. This protein‐peptide interaction is of high importance because IQ motifs are widely distributed among different kinds of CaM‐binding proteins. The Mlc1p‐IQ4 complex, which had been resolved by crystallography to 2.1 Å, confers to a Ca +2 ‐independent stable structure. During the simulations, the complex undergoes a complicated modulation process, which involves bending of the angles between the α‐helices of the protein, breaking of the α‐helical structure of the IQ4 peptide into two sections, and formation of new contact points between the protein and the peptide. The dynamics of the process consist of fast sub picosecond events and much slower ones that take a few nanoseconds to completion. Our study expands the information embedded in the crystal structure of the Mlc1p‐IQ4 complex by describing its dynamic behavior as it evolves from the crystal structure to a form stable in solution. The article shows that careful application of molecular dynamics simulations can be used for extending the structural information presented by the crystal structure, thereby revealing the dynamic configuration of the protein in its physiological environment. Proteins 2006. © 2006 Wiley‐Liss, Inc.