title: Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations.
abstract: A novel enzyme mechanism has been predicted by computer simulations for formation of the thiohemiacetal intermediate in the rat ALDH3A1 enzyme. We used molecular mechanics simulations to study the atomic details of substrate binding and quantum mechanical/molecular mechanical methods to study the Cys-243 thiolate attack on benzaldehyde (BA) substrate. BA was found to produce more reactive conformers when aligned for formation of the tetrahedral thiohemiacetal in the R-configuration. In addition, the sulfhydryl proton was seen to be important for initial binding of the substrate. Finally, the free energy differences between forming a thiohemiacetal oxyanion intermediate versus forming a neutral thiohemiacetal intermediate where a proton is donated to the intermediate from the surroundings strongly favor the latter. Our results suggest that the proton donor is the amide proton from the Cys-243 backbone supported by interactions with Lys-235.
authors.affiliation: Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA. wymore@psc.edu
authors.forename: Troy
authors.initials: T
authors.lastname: Wymore
authors.forename: David W
authors.initials: DW
authors.lastname: Deerfield
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Field
authors.forename: John
authors.initials: J
authors.lastname: Hempel
authors.forename: Hugh B
authors.initials: HB
authors.lastname: Nicholas
mesh_terms: D000444:Aldehyde Dehydrogenase / Q000737:chemistry / Q000378:metabolism*; D000818:Animals; D002384:Catalysis; D008958:Models, Molecular; D051381:Rats
chemical_list: C030863:corneal protein 54, bovine; D000444:Aldehyde Dehydrogenase