Date on Master's Thesis/Doctoral Dissertation
Cobalamin; Mutases; Coenzyme B12; Co2+/Co1+; Methyltransferase; Cob(I)alamin
Enzymes--Metabolism; Vitamin B12
The role of the active site tyrosine residue in the Co-C5' bond activation in the context of adenosylcobalamin-dependent mutases has been computationally investigated. The density functional, complete active space self-consistent field and quantum mechanics/molecular mechanics calculations have predicted that the deprotonated tyrosine can serve as a redox center potentially causing the one-electron reduction of B12 cofactor. As a result, the reduced form of adenosylcobalamin has been suggested to participate in B12 catalysis and an alternate mechanism for explaining the origin of catalysis in adenosylcobalamin-dependent mutases has been proposed. The implications of the involvement of the reduced B12 cofactor in the initial step of B12 catalysis that involve Co-C5' cleavage and subsequent hydrogen atom abstraction from the substrate has been computationally studied by means of density functional calculations. The energetic demands of the reaction have been found to be significantly lowered when the reaction is mediated by the one-electron reduced form of the cofactor. During the second part of this dissertation, an unprecedented Co 1+ ion induced H-bonding interaction (Co1+--H) has been computationally validated. The H-bond forming capacity of Co1+ ion that is a dominant d8 configuration has been suggested to be rooted in the availability of appropriately oriented filled d-orbitals which can serve as H-bond acceptors to interact with the acidic ends of the axial ligands. Because of a Co1+--H interaction, cob(l)alamin, a Co1+ ion-based ubiquitous B12 intermediate, has been suggested to be a pentacoordinated square pyramidal or hexacoordinated octahedral complex in addition to its commonly accepted tetracoordinated square planar geometry. In specific, the QM/MM calculations on methionine synthase-bound cob(l)alamin (PDB-code: 3IVA @ 2.2 A resolution; 1BMT @ 3.0 A resolution) has provided the convincing evidence of an enzyme-induced Co 1+ --H interaction. The Co 1+ --H interaction exerts an anodic shift upon the reduction potential of the Co2+/Co 1+ process which is a common chemical event in a large family of methyltransferases and ATP:corrinoid adenosyltransferases. Building upon these insights, an alternate mechanistic pathway for the enzyme-induced Co2+/Co1+ redox process has been suggested that is mediated by the square pyramidal cob(l)alamin rather than its square planar form.
Kumar, Manoj, "Computational modelling of cobalamin-dependent enzymatic reactions : activation of Co-C bond in adenosylcobalamin-dependent mutases and cob(II)alamin/cob(I)alamin redox process in methyltransferases." (2012). Electronic Theses and Dissertations. Paper 779.