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Ab initio models for receptor‐ligand interactions in proteins. 4. Model assembly study of the catalytic mechanism of triosephosphate isomerase
Author(s) -
Peräkylä Mikael,
Pakkanen Tapani A.
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199606)25:2<225::aid-prot8>3.0.co;2-g
Subject(s) - triosephosphate isomerase , active site , dihydroxyacetone phosphate , dhap , chemistry , substrate (aquarium) , ab initio , ligand (biochemistry) , isomerase , qm/mm , reaction mechanism , glyceraldehyde , computational chemistry , stereochemistry , catalysis , molecular dynamics , enzyme , dehydrogenase , organic chemistry , biochemistry , oceanography , receptor , geology
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 Glu167 was calculated at the MP2/3‐21G (*) //3‐21G (*) 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. © 1996 Wiley‐Liss, Inc.