Catalysis superoxide dismutase models

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... 

Mn catalase cycles between the Mn /Mfo and the Mn /Mn oxidation states during catalysis and is thus, in some sense, the two-electron analog of Mn superoxide dismutase. One possible mechanistic model, based on the known coordination chemistry of Mn dimers and the crystal structures of Mn catalase, is shown in Scheme 3. In this scheme, the bridging solvent molecules play a critical role in... 

Nid has square planar coordination involving two bridging cysteine thiolates and two main chain N atoms (Fig. 4A). A similar structure has been described recently for the active site of nickel superoxide dismutase (NiSOD) [117,118] (Fig. 4B). In NiSOD, Ni(II) reacts with superoxide and is oxidized to Ni(III)-peroxide. On the other hand, ACS functions in reducing environments and Nij is thought to remain as Ni(II) throughout catalysis. Model chemistry supports this proposal indicating that Nip is much more... 

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