Dynamic Model for Enzyme Action

Qinyi      Zhao

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