Abstract:
We describe the divide-and-conquer technique for linear-scaling semiempirical quantum mechanical calculations. This method has been successfully applied to study cytidine deaminase. Large-scale simulations were performed for optimizing geometries surrounding the active site of the enzyme and obtaining related energetics. The results of the minimizations provide a significant complement to experimental efforts and aid in the understanding of the enzymatic profile of cytidine deaminase. More specifically, we present our predictions about the structure of the active species and the structure of the active site for low pH. Finally, we present our results for the structure of the zinc ion coordination for different substrates which represent points along the reaction profile. In particular, we find that our results for the Zn-Sγ132 and the Zn-Sγ129 bondlengths yield similar trends compared to x-ray crystallography data as the enzyme structure changes from the ground-state to the transition-state analog and from the transition-state analog to the product. © 1999 Academic Press.
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