NMR-restrained molecular modeling of cobalt corrinoids: cyanocobalamin (vitamin B 12) and methylcobalt corrinoids

Abstract

NMR-restrained molecular dynamics (MD) and simulated annealing (SA) calculations have been performed on cyanocobalamin (CNCbl, vitamin B 12), and three methylcobalt corrinoids, the coenzymatically active methylcobalamin (CH 3Cbl), and two analogs of its base-off species, methylcobinamide (CH 3Cbi +), which lacks an axial nucleotide, and methyl-3,5,6-trimethyl-benzimidazolylcobamide (CH 3Me 3BzmCba +), in which the coordinating nitrogen of the pendent nucleotide is blocked by a methyl group. Consensus structures, obtained by averaging the coordinates of 25 structures generated by nOe-restrained SA calculations followed by energy minimization for each compound, agree well with the known crystal structures of the two complete cobalamins, CNCbl and CH 3Cbl, and, importantly, duplicate the corrin ring fold angles of the crystal structures closely. For the base-off analogs of CH 3Cbl, which have never been crystallized, the corrin ring fold angles of the calculated structures are significantly smaller than that of CH 3Cbl itself, implying that the base-on Cbl is under steric strain. NMR-restrained MD simulations permit, for the first time, a detailed analysis of the internal motions of these cobalt corrinoids. The corrin ring is found to be highly flexible, with its fold angle varying by 40–45° as a function of time, an observation which supports the feasibility of mechanisms for the enzymatic activation of the B 12 coenzyme (5′-deoxyadenosylcobalamin) for carbon–cobalt bond cleavage via steric labilization engendered by upward folding of the corrin ring. These simulations also find significant flexibility in the four corrin ring pyrroles and a pronounced `breathing motion' of the corrin ring as a whole. The side chains have considerable flexibility, but not all of the previously identified locally minimum side chain conformations are adopted, and the side chain motional freedom at 300 K is lower than might have been expected. In the base-off analog, CH 3Me 3BzmCba +, the nucleotide loop has considerable freedom of motion, but the pendent nucleotide remains in the vicinity of the lower ( α) face of the corrin, at least in part due to a `sentinel-like' effect of the three downwardly projecting propionamide side chains.