SIMULATION OF THE BIMOLECULAR REACTION BETWEEN SUPEROXIDE AND SUPEROXIDE-DISMUTASE - SYNTHESIS OF THE ENCOUNTER AND REACTION STEPS

Brownian dynamics simulations of the diffusional encounter of reactant s can be combined with more detailed molecular dynamics simulations of subsequent events by use of Markov chain models. These methods are us ed here to show that fluctuations in the encounter complex of the enzy me superoxide dismutase and its substrate reduce the overall bimolecul ar reaction rate by 50% compared to simulations based on a rigid enzym e. The possible utility of these methods for other systems is also dis cussed.