Slow Conformational Motions That Favor Sub-picosecond Motions Important for Catalysis

Abstract

It has been accepted for many years that functionally important motions are crucial to binding properties of ligands in such molecules as hemoglobin and myoglobin. In enzymatic reactions, theory and now experiment, are beginning to confirm the importance of motions on a fast (ps) timescale in the chemical step of the catalytic process. What is missing is a clear physical picture of how slow conformational fluctuations are related to the fast motions that have been identified as crucial. This paper presents a theoretical analysis of this issue for human heart lactate dehydrogenase. We will examine how slow conformational motions bring the system to conformations that are distinguished as catalytically competent because they favor specific fast motions.

Triple Isotope Effects Support Concerted Hydride and Proton Transfer and Promoting Vibrations in Human Heart Lactate Dehydrogenase

“…56–59 QM/MM simulations suggested slow motions guides the enzyme toward chemically competent conformations by favoring specific fast dynamics. 29 For example, closure of the Thr95-Leu107 loop (Figure 1A) on the ms time scale isolates the active site from bulk solvent, which is assisted by protein and water rearrangements on the ns time scale. 60 Closure of this loop also brings Arg106 into hydrogen bond contact with the ligands, 61 where Arg106 participates in the promoting vibrations on the fs-ps time scale to promote the hydride–proton transfer chemistry (Figure 1).…”

Free Energy Surface of the Michaelis Complex of Lactate Dehydrogenase: A Network Analysis of Microsecond Simulations

“…This supports our previous calculations that showed the reactive conformation to be a minority population. 24 …”

Protein Dynamics and the Enzymatic Reaction Coordinate

“…Thus, if one wishes to locate the functionally important conformations, they must all have the donor acceptor distance within a range that allows reaction 24 . The specific computational tool we choose was to restrain this distance to that found in the crystal structure, and allow the rest of the protein to explore conformational space via Langevin dynamics and minimization 25 . Once a set of candidate conformations were obtained in this fashion, they were further minimized with gradual release of the donor acceptor constraints.…”

“…Finally, using a simplified reaction coordinate, we can employ QM/MM sampling to obtain the chemical barrier along the conformational coordinate. These methods have been described in detail 25 .…”