TIME-DEPENDENT RATE COEFFICIENTS FROM BROWNIAN DYNAMICS SIMULATIONS

The kinetics of a diffusion-influenced reaction is described by a time -dependent rate coefficient k(t). In this paper, we implement an algor ithm for calculating k(t), introduced by one of us, in the UHBD softwa re package. In the implementation, the electrostatic force exerted on a diffusing substrate by an enzyme is obtained from a finite-differenc e solution of the Poisson equation. The rate coefficient is obtained b y starting the substrate in the active site and monitoring its surviva l probability using Brownian dynamics simulations. The technique is ap plied to the binding of superoxide to Cu/Zn superoxide dismutase. The long-time limit of k(t) is found to be in agreement with both the expe rimental value and that calculated using an algorithm designed specifi cally for finding k(infinity).