Molecular Dynamics Simulations of NAD+-induced Domain Closure in Horse Liver Alcohol Dehydrogenase
Steven Hayward 1* and Akio Kitao 2
1 University of East Anglia
2 University of Tokyo
* To whom correspondence should be addressed. E-mail: sjh{at}cmp.uea.ac.uk.
Submitted on March 27, 2006
Revised on April 20, 2006
Accepted on 4 May 2006
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Abstract |
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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 nanoseconds of molecular dynamics simulations, the mechanism of NAD+-induced domain closure was investigated. When the well-known loop at the domain interface was modelled 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 so 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, as in the absence of NAD+ it would prevent the occurrence of an unliganded closed subunit when the other subunit closes upon NAD+. Simulations that started with one subunit open and one closed supported this.
Key Words:
Allosteric, Cooperativity, Domain movements, DynDom, Hinge Bending, Principal Component Analysis
