Three 1-ns molecular dynamics (MD) simulations have been used to study the active-site structure of catechol O-methyltransferase when containing catechol, catecholate, or the transition state. It was found that the physical properties of the enzyme active sites are very similar when containing either catecholate or the transition state. The calculated root-mean-squared deviation and positional fluctuations of the active-site residues within 10 Å of the methyl group of S-adenosyl-L-methionine (AdoMet) for the catecholate and transition-state-simulations are similar, and the average solvent accessible surface areas for these residues are almost identical. It was found in the ground-state simulation with catecholate that interactions between AdoMet and the enzyme are critical in positioning AdoMet into near attack conformers (NACs) which resemble the transition-state geometry. The CB of Tyr68 influences the distance between the methyl carbon of AdoMet and the ionized oxygen of catecholate. Interactions between the backbone amide carbonyls of Met40 and Asp141 control the angular positioning of the AdoMet relative to catecholate. When the interactions dissipated, the angle formed by the sulfur and methyl carbon of AdoMet and ionized oxygen of catecholate decreased and no longer fulfilled the NAC criteria. Comparisons of these 3 MD simulations in combination with results from previous quantum mechanical calculations from this lab suggest that the catalytic power of this enzyme in going from E·S to E·TS is not due to transition-state stabilization but from the ability of the active site of catechol O-methyltransferase to arrange the reactants into conformers that closely resemble the transition state. Overall, in E·S going to E·TS one would also consider as a driving force catecholate and AdoMet desolvation.
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