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  • Title: Effects of CMAP and electrostatic cutoffs on the dynamics of an integral membrane protein: the phospholamban study.
    Author: Houndonougbo Y, Kuczera K, Jas GS.
    Journal: J Biomol Struct Dyn; 2008 Aug; 26(1):17-34. PubMed ID: 18533723.
    Abstract:
    In our effort to understand the microscopic structure and dynamics of phospholamban (PLB), a small integral membrane protein, we have performed a series of 5-20 ns molecular dynamics simulations to explore the influence of environment (solution and lipid bi-layer) and force field (CMAP correction and Ewald summation) on the protein behavior. Under all simulation conditions, we have observed the same major features: existence of two well-defined helical domains at the N- and C-termini, and large-amplitude rigid-body motions of these domains. The average inter-helix angle of PLB was sensitive to the environment. In the methanol and water solution trajectories, the two helical domains tended to adopt a closed orientation, with the inter-helix angle below 90 degrees, while in the lipid bi-layer the domains tend to be in an open conformation, with the inter-helix angle above 90 degrees. Within each studied environment, simulations employing different force field models provided qualitatively similar description of PLB structure and dynamics. The only significant discrepancy was the presence of pi-helical hydrogen bonds in trajectories generated with the standard CHARMM22 force field. Simulations with the CMAP correction, with both cutoff and Ewald electrostatics, exhibited predominantly alpha-helical and some 3(10)-helical hydrogen bonding interactions, and no pi-helical hydrogen bonding, in accord with NMR data. Thus, our results indicate that models including CMAP, with both cutoff and Ewald electrostatics, provide the most realistic description of PLB structure and dynamics. Results obtained from these simulations are in a good agreement with the experimental observables. These include helical secondary structure of PLB, the range explored by the inter-helix angle in methanol, as well as the inter-helix distance and C-terminal helix orientation in the DPPC bi-layer. The observed effect of opening up of the PLB inter-helix angle in the lipid environment relative to solution is also qualitatively reproduced in the simulations, as is the more rigid and compact structure of the C-terminal domain in the membrane relative to solution. The populations of conformations with relatively open inter-domain angles, as well as large fluctuations of this coordinate in DPPC bi-layers allow the N-terminal helix to come into contact with the PLB binding site on the calcium ATPase. Additionally, the presence of a twisting motion around the helical axis enables the helix to orient the correct face to the binding site. Another interesting observation is that the phosphorylation sites Ser(16) and Thr(17) are essentially always accessible to solvent, and presumably also to phosphorylation.
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