The solution structure of adenosylcobalamin and adenosylcobinamide determined by nOe-restrained molecular dynamics simulations

The solution structure of coenzyme B₁₂ (5′-deoxyadenosylcobalamin, AdoCbl) and the corresponding cobinamide, AdoCbi⁺, in which the axial nucleotide has been chemically removed, have been investigated using NMR-restrained molecular dynamics (MD) and simulated annealing (SA) calculations. The nOe cross peaks in the ROESY spectrum of both AdoCbl and AdoCbi⁺ are consistent with the presence of at least two principal conformations for each compound in solution. In the first, termed the southern conformation, the adenosyl (Ado) ligand is over the C ring of the molecule, the structure observed in the solid state. In the second, the Ado ligand has undergone an anticlockwise rotation and is over C10 in the eastern quadrant of the molecule. A two-state MD/SA simulation was used omitting nOes that arise only from the eastern conformation and that arise only from the southern conformation, respectively. Consensus structures were obtained by averaging the coordinates of 25 annealed structures of the southern and eastern conformations, respectively, of AdoCbl and AdoCbi⁺, followed by energy minimization. The consensus structure of the southern conformation of AdoCbl agrees well with the solid-state structure and has a very similar corrin fold angle. Several observations show that AdoCbl is considerably more rigid than AdoCbi⁺, and indeed is one of the most rigid cobalt corrinoids studied by these methods to date: the variability in the conformations of the corrin ring between the family of 25 annealed structure and the consensus structure is much smaller for AdoCbl than for AdoCbi⁺; during MD simulations, the previously demonstrated flexibility of the corrin ring as gauged by the corrin ruf angle (C5–Co–C15) is preserved for AdoCbi⁺ but is considerably diminished in AdoCbl because of a decrease in the maximum fold angle and an increase in the minimum fold angle achieved in the latter; the range of values of the Co–C bond length experienced in AdoCbi⁺ is substantially larger than in AdoCbl; the Ado ligand visits many more orientations relative to the corrin ring in AdoCbi⁺ than in AdoCbl; the pyrrole rings in AdoCbl undergo smaller deformations than in AdoCbi⁺; and the “breathing motion” of the corrin ring in which C5, C10 and C15 oscillate from above to below the mean corrin plane is much less pronounced in AdoCbl than in AdoCbi⁺. This rigidity is attributed to the presence of two bulky ligands in AdoCbl, the Ado ligand in the upper (β) axial position and the 5,6-dimethylbenzimidazole (bzm) ligand in the lower () axial ligand position, in contrast to the other structures which have only one or other of these two bulky ligands. The corrin fold angle in AdoCbl is significantly larger than that in AdoCbi⁺, a finding that is in agreement with a previous observation that CH₃Cbl has a larger fold angle than CH₃Cbi⁺; this implies that base-on corrins are under steric strain.