A Brownian dynamics simulation method has been implemented to study the superoxide-superoxide dismutase association reaction. Electrostatic potential and forces are calculated solving the linearized finite difference Poisson-Boltzmann equation. The accuracy of the algorithm has been tested carrying out simulations at different ionic strengths values on bovine Cu,Zn superoxide dismutase (SOD), whose three-dimensional structure is known at 2 Å resolution, and comparing the calculated association rates with the experimentally determined catalytic rates. Application of the algorithm to six Cu,Zn SOD variants shows that simulations well reproduce the experimental catalytic rate and demonstrate that the diffusion of the superoxide anyon to the active site copper is the rate-limiting step in the catalytic process of Cu,Zn superoxide dismutase.
Simulation of Superoxide-Superoxide Dismutase Association Rate for Six Natural Variants. Comparison with the Experimental Catalytic Rate
SERGI, ALESSANDRO;FERRARIO, Mauro;DESIDERI, Alessandro
1994-01-01
Abstract
A Brownian dynamics simulation method has been implemented to study the superoxide-superoxide dismutase association reaction. Electrostatic potential and forces are calculated solving the linearized finite difference Poisson-Boltzmann equation. The accuracy of the algorithm has been tested carrying out simulations at different ionic strengths values on bovine Cu,Zn superoxide dismutase (SOD), whose three-dimensional structure is known at 2 Å resolution, and comparing the calculated association rates with the experimentally determined catalytic rates. Application of the algorithm to six Cu,Zn SOD variants shows that simulations well reproduce the experimental catalytic rate and demonstrate that the diffusion of the superoxide anyon to the active site copper is the rate-limiting step in the catalytic process of Cu,Zn superoxide dismutase.Pubblicazioni consigliate
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