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. 2005 May 10;102(19):6807-12.
doi: 10.1073/pnas.0408343102. Epub 2005 Apr 5.

Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase

Kim F Wong  1 , Tzvia Selzer, Stephen J Benkovic, Sharon Hammes-Schiffer
Affiliations

Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase

Kim F Wong et al. Proc Natl Acad Sci U S A. .

Abstract

A comprehensive analysis of the network of coupled motions correlated to hydride transfer in dihydrofolate reductase is presented. Hybrid quantum/classical molecular dynamics simulations are combined with a rank correlation analysis method to extract thermally averaged properties that vary along the collective reaction coordinate according to a prescribed target model. Coupled motions correlated to hydride transfer are identified throughout the enzyme. Calculations for wild-type dihydrofolate reductase and a triple mutant, along with the associated single and double mutants, indicate that each enzyme system samples a unique distribution of coupled motions correlated to hydride transfer. These coupled motions provide an explanation for the experimentally measured nonadditivity effects in the hydride transfer rates for these mutants. This analysis illustrates that mutations distal to the active site can introduce nonlocal structural perturbations and significantly impact the catalytic rate by altering the conformational motions of the entire enzyme and the probability of sampling conformations conducive to the catalyzed reaction.

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Figures

Fig. 1.
Fig. 1.
The 3D structure of WT DHFR. The important loop regions are labeled. The substrate and cofactor are depicted in red, and the residues involved in the mutants studied are identified with yellow spheres.
Fig. 2.
Fig. 2.
Target models for the variation of the thermally averaged property as a function of the reaction coordinate. (A) SYMM. (B) MONO.
Fig. 3.
Fig. 3.
Correlation maps for WT DHFR using the target models SYMM (A) and MONO (B). Each map depicts the correlation of thermally averaged interatomic distances in the enzyme with the target model along the collective reaction coordinate. The correlations are calculated with Kendall's tau method. Red denotes correlated regions (τ = 1), and blue denotes anticorrelated regions (τ =–1). The two axes are identical and represent the atoms of the enzyme in sequential order. The three sites of mutation are identified on the vertical axis, and three key loop regions are identified on the horizontal axis.
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