title: Ab initio models for receptor-ligand interactions in proteins. 4. Model assembly study of the catalytic mechanism of triosephosphate isomerase.
abstract: The catalytic mechanism of triosephosphate isomerase (TIM) was investigated with ab initio quantum mechanical calculations. Electrostatic interactions between the quantum mechanical active site and the protein and solvent environment were modeled using the finite difference Poission-Boltzman method. The complexes of TIM with the substrate dihydroxyacetone phosphate (DHAP), five possible intermediates and the product glyceraldehyde-3-phosphate (GAP) were optimized in the active-site model at the 3-21G(*) level and energy profile for the proton abstraction from DHAP by the active-site Glu 167 was calculated at the MP2/3-21G(*)13-21G(*) level. Calculated energetics of the enzyme reaction were found to be in reasonable agreement with the experimental findings. Calculations revealed that an enediol of the substrate is a probable intermediate in the enzyme reaction. It was suggested that the proton abstracted from the substrate by the active-site glutamate goes to the carbonyl oxygen of the substrate producing enediol intermediate either directly or after it is exchanged with solvent.
authors.affiliation: Department of Chemistry, University of Joensuu, Finland.
authors.forename: M
authors.initials: M
authors.lastname: Peräkylä
authors.forename: T A
authors.initials: TA
authors.lastname: Pakkanen
mesh_terms: D001665:Binding Sites; D002384:Catalysis; D004099:Dihydroxyacetone Phosphate / Q000737:chemistry* / Q000378:metabolism; D004563:Electrochemistry; D004735:Energy Transfer; D005986:Glyceraldehyde 3-Phosphate / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D011522:Protons; D014305:Triose-Phosphate Isomerase / Q000737:chemistry* / Q000378:metabolism
chemical_list: D008024:Ligands; D011522:Protons; D005986:Glyceraldehyde 3-Phosphate; D004099:Dihydroxyacetone Phosphate; D014305:Triose-Phosphate Isomerase