Internal degrees of freedom, structural motifs, and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study.
The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order Møller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.
Khoroshun
Dmitry V
DV
Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
Warncke
Kurt
K
Ke
Shyue-Chu
SC
Musaev
Djamaladdin G
DG
Morokuma
Keiji
K
D000225:Adenine / Q000737:chemistry; D003038:Cobamides / Q000737:chemistry* / Q000378:metabolism; D003838:Deoxyadenine Nucleotides / Q000737:chemistry* / Q000378:metabolism; D004798:Enzymes / Q000737:chemistry; D005609:Free Radicals / Q000737:chemistry / Q000378:metabolism; D005740:Gases; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D012266:Ribose / Q000737:chemistry; D013816:Thermodynamics
D003038:Cobamides; D003838:Deoxyadenine Nucleotides; D004798:Enzymes; D005609:Free Radicals; D005740:Gases; C012873:2'-deoxy-5'-adenosine monophosphate; D012266:Ribose; C000913:cobamamide; D000225:Adenine