BIOPHYSICAL THEORY AND MODELING |
A Molecular Dynamics study and free energy analysis of
complexes between the Mlc1p protein and two IQ motif
peptides
Assaf Ganoth 1, Ran Friedman 1, Esther Nachliel 1 and Menachem Gutman 1*
1 Tel Aviv University
* To whom correspondence should be addressed. E-mail: me{at}hemi.tau.ac.il.
Submitted on March 20, 2006
Revised on April 14, 2006
Accepted on 3 July 2006
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Abstract |
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The Mlc1p protein from the budding yeast Saccharomyces cerevisiae is a Calmodulin-like protein, which interacts with IQ-motif peptides located at the yeast's myosin neck. In the present study, we report a molecular dynamics study of the Mlc1p-IQ2 protein-peptide complex, starting with its crystal structure, and investigate its dynamics in an aqueous solution. The results are compared with those obtained by a previous study, where we followed the solution structure of the Mlc1p-IQ4 protein-peptide complex by molecular dynamics simulations (Ganoth, A., E. Nachliel, R. Friedman, and M. Gutman, 2006, Proteins 64:133-146). Following the simulations, we performed an interaction free energy analysis using the MM-PBSA approach. Based on the dynamics of the Mlc1p-IQ protein-peptide complexes, the structure of the Light Chain-Binding Domain (LCBD) of myosin V from the yeast Saccharomyces cerevisiae is discussed.
Key Words:
Calmodulin, Molecular Dynamics, Myosin V, Protein-Protein interactions
