title: Transition state stabilization and alpha-amino carbon acidity in alanine racemase.
abstract: Combined QM/MM simulations have been carried out to investigate the origin of the carbon acidity enhancement in the alanine racemization reaction catalyzed by alanine racemase (AlaR). The present studies show that enhancement of carbon acidity of alpha-amino acids by cofactor pyridoxal 5'-phosphate, PLP, with an unusual, unprotonated pyridine is due to solvation effects, in contrast to the intrinsic electron-withdrawing stabilization by the pyridinium ion to form a quinonoid intermediate. Alanine racemase further lowers the alpha-proton acidity and provides an overall 14-17 kcal/mol transition state stabilization. Our computational results are consistent with the hypothesis that the use of the unusual form of PLP cofactor in AlaR is to raise the free energy of the intermediate, thereby increasing the reprotonation rate and enhancing the enzyme selectivity for racemization.
authors.affiliation: Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA. major@chem.umn.edu
authors.forename: Dan T
authors.initials: DT
authors.lastname: Major
authors.forename: Kwangho
authors.initials: K
authors.lastname: Nam
authors.forename: Jiali
authors.initials: J
authors.lastname: Gao
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000411:Alanine Racemase / Q000737:chemistry*; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D015394:Molecular Structure; D011522:Protons; D011732:Pyridoxal Phosphate / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013237:Stereoisomerism
chemical_list: D011522:Protons; D012997:Solvents; D011732:Pyridoxal Phosphate; D000411:Alanine Racemase; D000409:Alanine