Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes.

摘要: A dynamical model of interdomain "hinge bending" T4 lysozyme in aqueous solution has been developed on the basis molecular dynamics (MD) simulation. The MD study provides a description conformational reorganization expected to occur for protein as compared crystalline environment. Three different 500 ps simulations were calculated, each using distinctly crystal conformation starting points simulations. Crystal structures wild-type and "open" "closed" forms M61 variant analyzed this study. Large-scale, molecular-conformational rearrangements observed all three simulations, largest structural change was found open form allomorph. All simulated proteins had closed relative structure, closure "jaws" active site cleft occurred gradually over time course trajectories. average structures, calculated final 50 trajectory, adapted conformations more similar other than their incipient forms. Using protocol cytochrome P450BM-3 [M. D. Paulsen R. L. Ornstein (1995) Proteins: Structure Function Genetics, Vol. 27, pp. 237-243] we have that opposite type motion is, opened greater degree structure form. Therefore do not believe either result is merely simulation artifact, but rather are due relaxation absence packing forces environments.