X-ray Crystallographic Studies and Refinement

Molecular modeling represents a theoretical approach to the refinement of enzyme reaction mechanisms (Kollman, 1985 Briinger and Karplus, 1991). The method can be divided into two classes [Pg.361]

Model building, in which molecular structure is represented by experimental data as input and this structure is manipulated with use of stereochemical rules. This includes computer graphics and distance geometry refinement. [Pg.361]

Energy functions include ab initio, semiempirical quantum and molecular mechanical calculations to effect energy minimization and molecular dynamic simulations. The application of molecular mechanical calculation has been discussed in Chapter 9. [Pg.361]

A large number of enzyme mechanisms, including the enzyme structures, kinetic behavior and the overall chemical pathways of the reactions are known (Sinnott, 1998). Herewith, examples from each enzyme classes are given [Pg.361]

1 Oxidoreductase dehydrogenase and flavoenzymes. Nicotinamide adenine dinucleotide (NAD+)/nicotinamide adenine dinucleotide phosphate (NADF) and flavin mononucleotide (FMN)/flavin adenine dinucleotide (FAD) are the two major types of redox coenzymes. [Pg.361]