Catalysis and Specificity in Enzymes: A Study of Triosephosphate Isomerase and Comparison with Methyl Glyoxal Synthase

Abstract

This chapter uses a specific example for a detailed study of the ways an enzyme works and illustrates how present-day computational methodologies can be applied, successfully in this case, to provide an understanding of the catalytic function of an enzyme. This study of triosephosphate isomerase (TIM) examines the essential aspects of the function of this enzyme, starting with the preparation of the active site, an important step in many enzymes. It accelerates the rate of dihydroxyacetone phosphate (DHAP) to GAP (glyceraldehyde 3-phosphate) conversion by a factor of 10 9 relative to the solution reaction. The chapter describes the theoretical results for the energetics along different possible pathways of the TIM catalyzed reactions and shows that only certain of these are likely to make a significant contribution to the overall reaction. The chapter also determines the primary contributions to the rate increase in the enzyme by comparing the results with models for the same sets of reactions in the gas phase and solution. By use of a perturbation analysis the (electrostatic) contributions of specific amino acids to the rate enhancement have been identified. The chapter compares TIM with an enzyme mutant methylglyoxal synthase (MGS) that has a very similar active site, but catalyzes the conversion of DHAP to methylglyoxal, a side reaction that is avoided in TIM. The origin of the difference is described in the chapter.