Position-dependent rate molecular dynamics simulation

Another illustration of the power of molecular dynamics simulation can be drawn from the sphere of enzyme catalysis. Many enzyme-catalyzed reactions proceed at a rate that depends on the diffusion-limited association of the substrate with the active site. Sharp et al. [28] have carried out Brownian dynamics simulations of the association of superoxide anions with superoxide dismutase (SOD). The active center in SOD is a positively charged copper atom. The distribution of charge over the enzyme is not uniform, and so an electric field is produced. Using their model, Sharp et al. [28] have shown that the electric field enhances the association of the substrate with the enzyme by a factor of 30 or more. Their calculations also predict correctly the response of the association rate to changes in ionic strength and amino... 

Where cp is a factor correcting for the population of the inodes. The rate of collisions, for exanple in CClhas been calculated by a molecular dynamics simulation (18), and thus we are in the position to calculate the probability factor and to compare it to the theoretical predictions. It has been found that the commonly used calculations based upon the breathing sphere model of the internal degrees of freedom are too rough and cannot reproduce the observed temperature dependence of x If we use instead a mode... 

A similar conclusion has been reached by Ciccotti et al. s-iao jj, their studies of the model ion association reaction. Their system consisted of two equally massive ions, modeled as Lennard-Jones spheres with a positive or negative charge, in a solvent of dipolar molecules. Each solvent molecule was modeled as a Lennard-Jones sphere with a dipole moment of either 2.4 or 3.0 D and with a mass equal to that of the ionic mass. As with the simulations of Karim and McCammon, Ciccotti et al. started the dynamics at the transition state, as determined from the free energy calculations, and ran 104-144 trajectories to determine the transmission coefficient. The values of the transmission coefficient they found were 0.18 in the 2.4 D solvent and 0.16 in the 3.0 D solvent (which are surprisingly, and perhaps coincidentally, close to the results of Karim and McCammon e). Ciccotti et al. also calculated the frequency-dependent friction that the solvent exerted on the reaction coordinate in order to compare the simulation results with Grote-Hynes theory for the rates. The comparison with Grote-Hynes theory was quite close, although within the outer reaches of the calculated uncertainties in the molecular dynamics transmission coefficients. 

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