Molecular relaxation and metalloenzyme active site modeling


  • James W. Whittaker

    1. Department of Biochemistry and Molecular Biology, OGI School of Science and Engineering at OHSU, 20000 N.W. Walker Road, Beaverton, OR 97006
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Metalloenzymes represent a broad class of important biomolecules containing an essential metal ion cofactor in their catalytic active sites, forming biologic metal complexes that perform a wide range of important functions: activation of small molecules (O2, N2, H2, CO), atom transfer chemistry, and the control of oxidation equivalents. The structures of many metalloenzyme active sites have been defined by X-ray crystallography, revealing transition metal ions in unique low-symmetry environments. These bioinorganic complexes present significant challenges for computational studies aimed at going beyond crystal structures to develop a detailed understanding of the catalytic mechanisms. Considerable progress has been made in the theoretical characterization of these sites in recent years, supported by the availability of efficient computational tools, in particular density functional methods. However, the ultimate success of a theoretical model depends on a number of factors independent of the specific computational method used, including the quality of the initial structural data, the identification of important environmental perturbations and constraints, and experimental validation of theoretical predictions. We explore these issues in detail and illustrate the effects of molecular relaxation in calculations of two metalloenzymes, manganese superoxide dismutase and galactose oxidase. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002