Protein Dynamics in Enzymatic Catalysis

DESCRIPTION (provided by applicant): The goal of this Program Project, entitled Protein Dynamics in Enzymatic Catalysis, is to understand how atomic motion affects enzymatic catalysis. We propose to study the evolution of structure of protein-ligand complexes as the system moves along the reaction coordinate between enzyme-substrate and enzyme-product. In this study, concepts of how the dynamical nature of proteins affects enzymic function are explored. We bring together a research group consisting of researchers specializing in the theory of dynamics, computational chemistry, spectroscopy with broad time-resolution, enzymatic chemical mechanisms, protein chemistry and labeling, synthetic organic chemists, and transition state formation and structure. There are four projects and three cores. Project 1: Protein Dynamics in Catalysis by LDH and DHFR (Callender, PI) will examine the motions and time scales of how substrates and cofactors are brought together with important protein residues to bring about hydride and proton transfer in NAD(P)-linked enzymes using lactate dehydrogenase and dihydrofolate reductase as model enzymes. Project 2: Coordination of Protein Dynamics and Chemistry in PNP (Schramm) studies purine nucleoside phosphorylase in a program aimed at characterizing the dynamics of the substrate-enzyme system as it develops along the reaction pathway from Michaelis complex to transition state. Project 3: Proton Transfer Dynamics in Heme-Copper Oxidases (Dyer) is an investigation of the protein structures and evolution of these structures as the heme-copper oxidases bring about redox driven proton pumping. Project 4: Promoting Vibrations in LDH and PNP (Schwartz) examines whether or not protein dynamics has a direct role in the catalysis of bond formation and cleavage by studying how and to what extent the rapid motion of promoting vibrations couple to reaction dynamics in the enzyme-catalyzed reactions of LDH and PNP. The findings will be subjected to experimental investigation. The Chemistry Core (Core A) is designed to supply the proteins, mutants, and site specific isotopic labeled proteins and small molecules needed by the experimental studies. The Equipment Core (Core B) supports the temperature jump relaxation and difference spectrometers required of most of the experimental studies to characterize protein-ligand complex motion at the atomic level.