THE ESSENTIAL DYNAMICS OF THERMOLYSIN - CONFIRMATION OF THE HINGE-BENDING MOTION AND COMPARISON OF SIMULATIONS IN VACUUM AND WATER

Comparisons of the crystal structures of thermolysin and the thermolys in-like protease produced by B. cereus have recently led to the hypoth esis that neutral proteases undergo a hinge-bending motion. We have in vestigated this hypothesis by analyzing molecular dynamics simulations of thermolysin in vacuum and water, using the essential dynamics meth od. This method is able to extract large concerted atomic motions of b iological importance from a molecular dynamics trajectory. The analysi s of the thermolysin trajectories indeed revealed a large rigid body h inge-bending motion of the N-terminal and C-terminal domains, similar to the motion hypothesized from the crystal structure comparisons. In addition, it appeared that the essential dynamics properties derived f rom the vacuum simulation were similar to those derived from the solve nt simulation. (C) 1995 Wiley-Liss, Inc.