Mechanistic Implications of Reductive Co-C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase

Vitamin B12-dependent enzymes catalyze several difficult radical reactions. However, there are fundamental open questions that need to be addressed to fully understand the formation of highly reactive radical species, its dynamics, and interaction with substrate and enzyme. In this work, Car-Parrinello molecular dynamics (CPMD) was performed within a QM/MM framework on a reduced AdoCbl cofactor, which was taken as a post-PCET initial step in the activation of the AdoCbl-dependent methylmalonyl CoA mutase (MCM) enzyme. The calculated free energy profile reveals two possible pathways with similar energies, stepwise (I) and concerted (II) for the reductive Co-C cleavage and subsequent H-abstraction. The computed activation barrier from metadynamics (MTD) for both the pathways is comparable (78.5 and 76.2 kJ/mol, respectively), however, the concerted pathway may be preferred kinetically, because it avoids the formation of a high-energy radical intermediate with possibly a larger recrossing rate. Our results a...