The elusive 5'-deoxyadenosyl radical in coenzyme-B12-mediated reactions.
Vitamin B(12) and its biologically active counterparts possess the only examples of carbon-cobalt bonds in living systems. The role of such motifs as radical reservoirs has potential application in future catalytic and electronic nanodevices. To fully understand radical generation in coenzyme B(12) (dAdoCbl)-dependent enzymes, however, major obstacles still need to be overcome. In this work, we have used Car-Parrinello molecular dynamics (CPMD) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate the initial stages of the methylmalonyl-CoA-mutase-catalyzed reaction. We demonstrate that the 5'-deoxyadenosyl radical (dAdo(•)) exists as a distinct entity in this reaction, consistent with the results of extensive experimental and some previous theoretical studies. We report free energy calculations and first-principles trajectories that help understand how B(12) enzymes catalyze coenzyme activation and control highly reactive radical intermediates.
School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia. bucher.denis@gmail.com
Denis
D
Bucher
Gregory M
GM
Sandala
Bo
B
Durbeej
Leo
L
Radom
David M
DM
Smith
D003038:Cobamides / Q000737:chemistry / Q000378:metabolism; D004789:Enzyme Activation; D005609:Free Radicals / Q000737:chemistry / Q000378:metabolism; D008765:Methylmalonyl-CoA Mutase / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011424:Propionibacterium / Q000737:chemistry / Q000201:enzymology*; D013816:Thermodynamics; D014805:Vitamin B 12 / Q000737:chemistry / Q000378:metabolism*
D003038:Cobamides; D005609:Free Radicals; D008765:Methylmalonyl-CoA Mutase; C000913:cobamamide; D014805:Vitamin B 12