Anticorrelated motions as a driving force in enzyme catalysis: The dehydrogenase reaction

Abstract

A present issue concerns the occurrence of rate-promoting vibrations, which assist in lowering barrier height in enzyme catalysis (1-5). A related issue addressed here is the question of whether certain thermal Brownian motions of an enzymesubstrate complex (E⅐S) participate in lowering the energy barrier of activation (6) by creating the most reactive groundstate conformations [near-attack conformers (NACs) (7)]. One such possibility is that ground-state conformations, which lead directly to the lowest energy-transition state (NACs), are formed with assistance of anticorrelated motions of residues proximal to the active site.From Eq. 1, the free energy of activation is equal to the sum of the standard free energies for formation of reactive E⅐NAC conformers (⌬GЊ NAC ) plus the activation energy (⌬G TS ‡ ) for conversion of E⅐NAC to E⅐TS as shown in Eq. 2.We report here the findings of a study of correlated and anticorrelated motions of an E⅐S complex, the role of certain anticorrelated motions in the formation of E⅐NAC, as well as the demonstration that reactions that pass through E⅐NAC follow a kinetically favored trajectory. The reaction of interest is the oxidation of a primary alcohol by horse liver alcohol dehydrogenase (HLADH⅐NAD ϩ ). The computational tools used have been molecular dynamics (MD) simulations, crosscorrelation analysis, and quantum mechanics (QM)͞molecular mechanics (MM).HLADH (EC 1.1.1.1) (8) consists of two subunits of identical composition in which a 12-stranded ␤-sheet makes up the central core (9). Each subunit binds a molecule of NAD ϩ and a Zn 2ϩ at the active site and an additional Zn 2ϩ , which is structural. Alcohol oxidation by NAD ϩ involves first the proton dissociation of RCH 2 OH followed by transfer of a hydride equivalent from RCH 2 O Ϫ to NAD ϩ (Eq. 3).In an earlier study we carried out MD simulations (10) for 1-2 ns the structures of HLADH⅐NAD ϩ ⅐PhCH 2 OH, HLADH⅐NAD ϩ ⅐PhCH 2 O Ϫ , and HLADH⅐NADH⅐PhCHO using one subunit covered by a 32-Å-radius pool of transferable intermolecular potential three-point water molecules. By doing so we were able to derive an ensemble of dynamic conformations for the reactive HLADH⅐NAD ϩ ⅐PhCH 2 O Ϫ species, define the paths of H ϩ transfer to water, and established the presence of a water channel, which facilitates proton shuttling (10). We reported that the Michaels complex assumed the conformation of a reactive conformer [NAC (7)] 60% of the time. We defined the NAC as a conformer in which the distances between the transferring of an H Ϫ equivalent from C7 of PhCH 2 O Ϫ and acceptor C4 of NAD ϩ are Յ3.0 Å (3.9 Å for the heavy atoms C7 and C4) and the angles of C7-H-NC4 range from 132°to 180°. Concurrently, an investigation from Karplus and coworkers (11) appeared in which the kinetic features, the adiabatic potential barrier heights, the rate constants (including quantum mechanical effects such as tunneling), and potential of mean force of the HLADH⅐NAD ϩ ⅐PhCH 2 O Ϫ species were described by use of self-consistent charge density functio...

Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD+ and Fluoroalcohols Define Strained Michaelis Complexes

“…Molecular dynamics and normal mode analyses suggest that motions of domains (related to the global conformational change) could “push” the substrates together. 13,86 Equilibrium, vibrational motions might also be sufficient, however, as temperature factors of 10 Å 2 (observed in these structures, albeit at 100 K) could correspond to motions of 0.35 Å, leading to a decrease in the donor-acceptor distance from 3.4 to 2.7 Å. However, a recent, empirically-parameterized model suggests that the “tunneling ready state” could have a donor acceptor distance of 3.2 Å.…”

Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants

“…Such motion allows substrate diffusion to the active site of the enzyme. Previous studies of enzyme MD by Bruice and coworkers (24) have also identified anticorrelated motions of the active sites as signatures of enzymatic activity. Thus, correlated motions between monomers arise on the nanosecond time scale and are, remarkably, disrupted in the mutant dimers.…”

Update 1 of: Tunneling and Dynamics in Enzymatic Hydride Transfer

“…95 In subsequent molecular dynamics calculations, residues were ranked as either correlated (moving together) or anticorrelated (moving in opposite directions), with the anticorrelated motions within the cofactor and substrate binding domains proposed to contribute to the reactive conformations leading to catalysis. 96 Schwartz and co-workers have developed a very interesting algorithm for identifying promoting modes in proteins. 97 Using computer modeling with HLADH, they “scale” various active site residues with regard to the likelihood that their motions will be linked to the hydrogen transfer step.…”