Evolutionarily Conserved Linkage Between Enzyme Fold, Flexibility, and Catalysis

Abstract

Proteins are not static but rather are intrinsically flexible molecules. The role of internal protein motions in designated function, such as enzyme catalysis, is widely debated. The role of protein structure in enzyme catalysis is well established; and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not just inconsequential random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including the catalytic efficiency of enzymes. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Results from three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase and nuclease) catalyzing diverse chemical reactions will be presented. The identification and characterization of the internal proteins in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction show motions inducing remarkably similar changes in the enzyme-substrate interactions during catalysis. Examination of conformational sub-states along the reaction pathways also provides vital insights into role of enzyme flexibility in enabling the attainment of transition states. The results indicate that the reaction-coupled flexibility (along with structural features) is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme-substrate interactions, thereby impacting the mechanism of catalyzed chemistry.