QM/MM Metadynamics Study of the Direct Decarboxylation Mechanism for Orotidine-5'-monophosphate Decarboxylase Using Two Different QM Regions:Acceleration Too Small To Explain Rate of Enzyme Catalysis

摘要

Despite decades of study,the mechanism by which orotidine-5'-monophosphate decarboxylase(ODCase)catalyzes the decarboxylation of orotidine monophosphate remains unresolved.A computational investigation of the direct decarboxylation mechanism has been performed using mixed quantum mechanical/molecular mechanical(QM/MM)dynamics simulations.The study was performed with the program CP2K that integrates classical dynamics and ab initio dynamics based on the Born-Oppenheimer approach.Two different QM regions were explored.The free energy barriers for direct decarboxylation of orotidine-5'-monophosphate(OMP)in solution and in the enzyme(using the larger QM region)were determined with the metadynamics method to be 40 and 33 kcal/mol,respectively.The calculated change in activation free energy(DELTA DELTA G)on going from solution to the enzyme is therefore-7 kcal/mol,far less than the experimental change of-23 kcal/mol(for k_(cat)./k_(uncat):Radzicka,A.;Wolfenden,R.,Science 1995,267,90-92).These results do not support the direct decarboxylation mechanism that has been proposed for the enzyme.However,in the context of QM/MM calculations,it was found that the size of the QM region has a dramatic effect on the calculated reaction barrier.