Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase.
Horse liver alcohol dehydrogenase is a homodimer, the protomer having a coenzyme-binding domain and a catalytic domain. Using all available x-ray structures and 50 ns of molecular dynamics simulations, we investigated the mechanism of NAD+-induced domain closure. When the well-known loop at the domain interface was modeled to its conformation in the closed structure, the NAD+-induced domain closure from the open structure could be simulated with remarkable accuracy. Native interactions in the closed structure between Arg369, Arg47, His51, Ala317, Phe319, and NAD+ were seen to form at different stages during domain closure. Removal of the Arg369 side-chain charge resulted in the loss of the tendency to close, verifying that specific interactions do help drive the domains closed. Further simulations and a careful analysis of x-ray structures suggest that the loop prevents domain closure in the absence of NAD+, and a cooperative mechanism operates between the subunits for domain closure. This cooperative mechanism explains the role of the loop as a block to closure because in the absence of NAD+ it would prevent the occurrence of an unliganded closed subunit when the other subunit closes on NAD+. Simulations that started with one subunit open and one closed supported this.
Hayward
Steven
S
School of Computing Sciences and School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom. sjh@cmp.uea.ac.uk
Kitao
Akio
A
D000426:Alcohol Dehydrogenase / Q000737:chemistry* / Q000648:ultrastructure*; D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D004789:Enzyme Activation; D006736:Horses; D008099:Liver / Q000201:enzymology*; D008956:Models, Chemical; D008958:Models, Molecular; D009243:NAD / Q000737:chemistry*; D010084:Oxidation-Reduction; D016062:Porosity; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
D009243:NAD; D000426:Alcohol Dehydrogenase