Transition state structure invariance to model system size and calculationlevels: a QM/MM study of the carboxylation step catalyzed by Rubisco

The present study elucidates structural features related to the molecular m echanism in the carboxylation step of the reaction catalyzed by Rubisco. St arting from the initial X-ray Protein Data Brink structure of a Rubisco mon omer, the reactive subsystem in vacuo is subjected to quantum chemical semi empirical and ab initio studies, while the effects of the protein environme nts are included by means of a hybrid quantum mechanical/molecular mechanic al (QM/MM) approach. The QM/MM is used to characterize the transition struc ture for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme. Comparisons between the in vacuo and in situ t ransition structures show remarkable invariance with respect to geometric p arameters, index and transition vector amplitudes. The transition state cou ples the carbon dioxide attack to the C2 center of the substrate in its die nol form with a simultaneous intramolecular hydrogen transfer from the C2 a tom to the hydroxyl group linked to the C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 ce nter in the enzyme.