TCBG Seminar

Combined QM/MM simulations: From Opsin Shifts to Enzymatic Reactions

Professor Jiali Gao
Department of Chemistry
University of Minnesota
Minneapolis, Minnesota

Monday, December 3, 2001
3:00 pm (CT)
3269 Beckman Institute


We employ a combined quantum mechanical and molecular mechanical (QM/ MM) simulation method to investigate the origin of the opsin shift in bacteriorhodopsin (bR) in the membrane matrix. We found that both solvation and interactions with the protein significantly shifts the absorption maximum of the retinal protonated Schiff base, but the effects are much more pronounced in polar solvents than in the protein environment. Structural analysis of the PSB binding site in the lipid membrane revealed the specific interactions that make contributions to the observed opsin shift. In addition, the effects of amino acid mutations on the absorption energy in the visual pigment rhodopsin have been analyzed. In this talk, I will also discuss recent studies of enzymatic reactions, including the reaction mechanism of orotidine 5'- monophosphate (OMP) decarboxylase. OMP decarboxylase is the most proficient enzyme known today, which catalyzes the last decarboxylation step in pyrimidine nucleotide biosynthesis. Our computational study reveals that ground state destabilization effects provide the dominant contribution to the enzymatic rate acceleration, whereas transition state stabilization only plays a minor role.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.

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