The Role of Protein Side Chains in Enzyme-Activating Conformational Changes: Lessons from Studies on Variant Enzymes

The active sites at the unliganded forms of many of Nature’s most proficient catalysts of metabolic reactions do not show a good fit for the enzymatic transition state; this fit is created by utilization of substrate binding energy to drive protein conformational changes that move side chains to positions that provide optimal transition-state stabilization. Static protein X-ray crystal structures of enzyme Michaelis complexes provide a critical starting point for determination of the roles of these side chains in stabilizing the enzymatic transition state but provide little insight into the catalytic role of the substrate-driven protein conformational change. Important elements of the mechanism of action of nature’s most proficient enzyme catalysts are therefore only revealed after examination of the structure for unliganded enzyme active sites and their substrate-driven transformations to structured forms that are complementary to reaction transition states. There have been few studies to determine the effect on enzyme activity of site-directed substitution of protein side chains that participate in substrate-driven enzyme conformational changes. The fascinating effects of these substitutions were probed by site-directed substitution of amino acid side chains that take part in conformational changes during catalysis by triosephosphate isomerase, glycerol phosphate dehydrogenase, and orotidine 5′-monophosphate decarboxylase.