The essential dynamics of thermolysin: Confirmation of the hinge‐bending motion and comparison of simulations in vacuum and water

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Abstract
Comparisons of the crystal structures of thermolysin and the thermolysin‐like protease produced by B. cereus have recently led to the hypothesis that neutral proteases undergo a hinge‐bending motion. We have investigated this hypothesis by analyzing molecular dynamics simulations of thermolysin in vacuum and water, using the essential dynamics method. This method is able to extract large concerted atomic motions of biological importance from a molecular dynamics trajectory. The analysis of the thermolysin trajectories indeed revealed a large rigid body hinge‐bending motion of the Nterminal and C‐terminal domains, similar to the motion hypothesized from the crystal structure comparisons. In addition, it appeared that the essential dynamics properties derived from the vacuum simulation were similar to those derived from the solvent simulation.