Computational modelling of chemical reactions catalyzed by cobalamin (B12)-dependent enzymes : mechanistic insights.
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thesis / dissertation description
The biologically active derivatives of vitamin B12 (cobalamin) possess the only examples containing organometallic Co-C bonds in living systems where the cleavage of Co-C bond initiates the catalytic cycle of the enzymatic reactions. In this dissertation, the electronic structure of various intermediates and the mechanistic details of the methyl transfer reactions involved in the catalytic cycle of the methionine synthase (MetH) have been computationally investigated using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, density functional theory (DFT), and complete active space self-consistent field with second order perturbation theory (CASSCF/QDPT2) computational methodologies. QM/MM calculations in particular reveal that the cob(I)alamin intermediate is not axially coordinated inside the enzyme which is consistent with free cob(I)alamin in solution, thus indicating an unprecedented role of enzyme-bound cob(I)alamin. In addition, DFT and high-level ab initio CASSCF/QDPT2 calculations further elucidate that the ground state of the cob(I)alamin is multiconfigurational where the diradical Co(II)-corrin· radical configuration contributes to the electronic structure of the cob(I)alamin intermediate, indicating a noninnocent behavior of the corrin ring. Furthermore, our QM/MM study reveals the traditionally assumed SN2 mechanism for the formation CH3-cob(III)alamin and the activation energy barrier for SN2 reaction is found to be comparable with respect to the experimental rate constant. However, the possibility of an alternative ET-based radical mechanism consistent with the close-lying diradical states has also been suggested, where an electron transfer (ET) from His-on cob(I)alamin to pterin ring of the protonated CH3-H4Folate takes place, indicating CoII(d7)-pterin radical (?*)I state, followed by a methyl radical transfer. The similar mechanistic details of SN2 and ET-based radical pathway have also been investigated in the second-half catalytic cycle of MetH as indicated by ionic and diradical states of the MeCbl:Homocysteine reaction complex. The mechanistic details of the MetH could also help in understanding some of the critical aspects related to the enzymatic methyl transfer reactions in other methyltransferases. In addition, the role of tyrosine active site in AdoCbl-dependent enzyme methylmalonyl CoA mutase (MCM) has been studied using density functional reactivity theory in which the charge separation propensity of electron transfer site is often distant from the proton-acceptor site, indicating that one electron reduced form AdoCb may be involved in the initial step of AdoCbl-dependent catalysis. As a result, the QM/MM optimized intermediates and transition states along with their calculated energetic profiles indicate that the reaction consisting of Co-C bond cleavage and subsequent hydrogen abstraction occurs in a concerted fashion when the reduced form of AdoCbl cofactor is involved in the reaction, whereas it takes place in a stepwise manner in a neutral form. The concerted pathway was further supported by the free energy metadynamics simulations.