Abstract

Protein thermodynamic structure theory is an integrated approach to the study of protein dynamics and the mechanisms of enzyme catalysis. In this paper, a hypothesis arising from this theory is examined. The timescale of an enzymatic reaction (TER) gives a key to characterizing enzyme conformational changes. The aspects of timescale important in our approach are: (i) it is logically related to internal motions of the main chain of a protein; (ii) it sets the upper limit on the size or scope of protein conformational changes. Feature (i) is linked to the dynamic properties of enzyme-reactant complexes. Feature (ii) is linked to the dynamic sites of the main chain (promoting motion) involved in enzyme activity. Our analysis shows that a comprehensive understanding of enzymology can be established on the basis of protein thermodynamic structure theory.

Keywords: Motion, enzyme, flexibility, mechanism, conformation, dynamics, Protein thermodynamic structure theory, timescale of an enzymatic reaction (TER), protein conformational changes, enzyme-reactant complexes, induced-fit, energetic pre-organization of active sites, enzyme-catalyzed reaction, ligand-protein binding, ENZYMATIC REACTION, free Gibbs energy, entropy, multiple kinetic steps, subtle conformational changes, allodynamic regulation, Kcat of enzymes, Kcat value, T4 lysozyme, Loop 52-72, ENZYMATIC REACTIONS, enzyme-substrate binding, rate-limiting steps, Gibbs free energy, enzyme-catalyzed process, enzyme-catalyzed reactionsMotion, enzyme, flexibility, mechanism, conformation, dynamics, Protein thermodynamic structure theory, timescale of an enzymatic reaction (TER), protein conformational changes, enzyme-reactant complexes, induced-fit, energetic pre-organization of active sites, enzyme-catalyzed reaction, ligand-protein binding, ENZYMATIC REACTION, free Gibbs energy, entropy, multiple kinetic steps, subtle conformational changes, allodynamic regulation, Kcat of enzymes, Kcat value, T4 lysozyme, Loop 52-72, ENZYMATIC REACTIONS, enzyme-substrate binding, rate-limiting steps, Gibbs free energy, enzyme-catalyzed process, enzyme-catalyzed reactions