A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides.
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 this 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. After the simulations, we performed an interaction free-energy analysis using the molecular mechanics Poisson-Boltzmann surface area approach. Based on the dynamics of the Mlc1p-IQ protein-peptide complexes, the structure of the light-chain-binding domain of myosin V from the yeast S. cerevisiae is discussed.
Ganoth
Assaf
A
Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Friedman
Ran
R
Nachliel
Esther
E
Gutman
Menachem
M
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D018994:Myosin Light Chains / Q000737:chemistry*; D009218:Myosins / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D012996:Solutions; D055672:Static Electricity
C113979:MLC1 protein, S cerevisiae; D018994:Myosin Light Chains; D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions; D009218:Myosins