Electron tunneling and ab initio calculations related to the one-electron oxidation of NAD(P)H bound to catalase.
Models for NAD(P)H le- oxidation in bovine catalase were studied using Hartree-Fock ab initio calculations, along with information taken from the published X-ray structure of the enzyme. Geometries and energies of ground states and transition states were calculated at the 6-31G* level for N-methyl-1,4-dihydropyridine and N-methyl-1,4-dihydronicotinamide undergoing the pathway (i) le- oxidation to yield the radical cation, (ii) general-base-catalyzed (hydroxide and/or imidazole) deprotonation of the radical cation to yield the neutral radical, and (iii) le- oxidation of the neutral radical to the N-methylpyridinium or N-methylnicotinamide cation. Barrier heights for deprotonation of the radical cation intermediates were calculated to be 7-11 kcal/mol. Kinetic isotope effects were calculated for general-base-catalyzed deprotonation of the N-methyl-1,4-dihydropyridine radical cation and the 4,4-dideuterio species and found to be kH/kD2 = 5.38 (hydroxide) or 3.64 (imidazole), in qualitative agreement with published experimental isotope effects for the analogous deprotonation of N-methyl-1,10-dihydroacridan or the N-methyl-1,10-dideuterioacridan radical cation. In the calculated transition state for imidazole deprotonation of the N-methyl-1,4-dihydronicotinamide radical cation, an unusual short contact was calculated and interpreted as a hydrogen bond (2.35 A) between the amide oxygen and the hydrogen attached to C2 of imidazole. Similar hydrogen bonds were also observed and calculated at the 3-21G and 6-31G* levels between His234 of catalase and the amide oxygen of bound NAD(P)H and complexes of N,N'-dimethyl-1,4-dihydronicotinamide or cis-N-methylformamide with N-methylimidazole. Comparison of these results to the X-ray structure of bovine catalase allows for further interpretation of the possible roles of the imidazole bases His234 and His304 and the hydrogen-bonded contacts in the NAD(P)H binding site. Electron tunneling pathways between NAD(P)H and the iron protoporphyrin IX (PP-IX) axial tyrosinate ligand Tyr357 in molecular dynamics and X-ray crystal structures of bovine catalase were calculated using PATHWAYS II (version 2.01). The pathways which were calculated included those involving the amino acid residue Tyr214, which is near the NAD(P)H binding site. Coupling involving Tyr357 was not particularly efficient; however, strong coupling between Tyr214 and iron-protoporphyrin IX was observed. These pathways may be important if electron transfer is stepwise; i.e., Tyr214 oxidized first, followed by NAD(P)H.
Olson
L P
LP
Department of Chemistry, University of California at Santa Barbara 93106, USA.
Bruice
T C
TC
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002374:Catalase / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure; D002417:Cattle; D003196:Computer Graphics; D018360:Crystallography, X-Ray / Q000379:methods; D007700:Kinetics; D016252:Microscopy, Scanning Tunneling / Q000379:methods; D008958:Models, Molecular; D008968:Molecular Conformation; D009243:NAD / Q000737:chemistry / Q000378:metabolism*; D009249:NADP / Q000737:chemistry / Q000378:metabolism*; D010084:Oxidation-Reduction; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D009243:NAD; D009249:NADP; D002374:Catalase