Molecular Dynamics Analysis of Structural Factors Influencing Back Door P i Release in Myosin

Abstract

The back door has been proposed to be an exit pathway from the myosin active site for phosphate (P i) generated by adenosine 5′-triphosphate hydrolysis. We used molecular dynamics simulations to investigate the interaction of P i with the back door and the plausibility of P i release via this route. Molecular dynamics simulations were performed on the Dictyostelium motor domain with bound Mg·adenosine 5′-diphosphate (ADP) and P i, modeled upon the Mg·ADP·BeF x and Mg·ADP·V i structures. Simulations revealed that the relaxation of ADP and free P i from their initial positions reduced the diameter of the back door via motions of switch 1 and switch 2 located in the upper and lower 50-kDa subdomains, respectively. In neither simulation could P i freely diffuse out the back door. Water molecules, however, could flux through the back door in the Mg·ADP·BeF x-based simulation but not in the Mg·ADP·V i-based simulation. In neither structure was water observed fluxing through the main (front door) entrance. These observations suggest that the ability of P i to leave via the back door is linked tightly to conformational changes between the upper and lower 50-kDa subdomains. The simulations offer structural explanations for 18O-exchange with P i at the active site, and P i release being the rate-limiting step in the myosin adenosine 5′-triphosphatase.