New Insights into the Nature of Observable Reaction Intermediates in Cytochrome P450 NO Reductase by Using a Combination of Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculations

被引:21
作者
Riplinger, Christoph [1 ]
Bill, Eckhard [1 ]
Daiber, Andreas [2 ]
Ullrich, Volker [3 ]
Shoun, Hirofumi [4 ]
Neese, Frank [1 ]
机构
[1] Max Planck Inst Chem Energy Convers, D-45470 Mulheim, Germany
[2] Univ Med Ctr Mainz, D-55101 Mainz, Germany
[3] Univ Konstanz, Dept Biol, D-78457 Constance, Germany
[4] Univ Tokyo, Dept Biotechnol, Tokyo 1138657, Japan
关键词
enzymes; metalloenzymes; qm/mm calculations; spectroscopy; theoretical spectroscopy; NITRIC-OXIDE REDUCTASE; DENSITY-FUNCTIONAL THEORY; ZETA VALENCE QUALITY; GAUSSIAN-BASIS SETS; ELECTRONIC-STRUCTURE; FUSARIUM-OXYSPORUM; CORRELATION-ENERGY; HARTREE-FOCK; HYBRID DFT; AB-INITIO;
D O I
10.1002/chem.201302443
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Cytochrome P450 NO reductase is an unusual member of the cytochrome P450 superfamily. It catalyzes the reduction of nitric oxide to nitrous oxide. The reaction intermediates were studied in detail by a combination of experimental and computational methods. They have been characterized experimentally by UV/Vis, EPR, Mossbauer, and MCD spectroscopy. In conjunction with quantum mechanics/molecular mechanics (QM/MM) calculations, we sought to characterize the resting state and the two detectable intermediates in detail and to elucidate the nature of the key intermediate I of the reaction. Six possible candidates were taken into account for the unknown key intermediate in the computational study, differing in protonation state and electronic structure. Two out of the six candidates could be identified as putative intermediates I with the help of the spectroscopic data: singlet diradicals Fe-III-NHO center dot- and Fe-III-NHOH center dot. In a companion publication (C. Riplinger, F. Neese, ChemPhysChem 2011, 12, 3192) we have used QM/MM models based on these structures and performed a kinetic simulation. The combination of these two studies shows the nature of the key intermediate to be the singlet diradical, Fe-III-NHOH center dot.
引用
收藏
页码:1602 / 1614
页数:13
相关论文
共 81 条
[1]   Electronic structure of bispidine Iron(IV) oxo complexes [J].
Anastasi, Anna E. ;
Comba, Peter ;
McGrady, John ;
Lienke, Achim ;
Rohwer, Heidi .
INORGANIC CHEMISTRY, 2007, 46 (16) :6420-6426
[2]   Hybrid models for combined quantum mechanical and molecular mechanical approaches [J].
Bakowies, D ;
Thiel, W .
JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (25) :10580-10594
[3]   Electronic structure of bis(imino)pyridine iron dichloride, monochloride, and neutral ligand complexes: A combined structural, spectroscopic, and computational study [J].
Bart, Suzanne C. ;
Chlopek, Krzysztof ;
Bill, Eckhard ;
Bouwkamp, Marco W. ;
Lobkovsky, Emil ;
Neese, Frank ;
Wieghardt, Karl ;
Chirik, Paul J. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (42) :13901-13912
[4]   Very fast prediction and rationalization of pKa values for protein-ligand complexes [J].
Bas, Delphine C. ;
Rogers, David M. ;
Jensen, Jan H. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2008, 73 (03) :765-783
[5]   DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652
[6]   DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT ASYMPTOTIC-BEHAVIOR [J].
BECKE, AD .
PHYSICAL REVIEW A, 1988, 38 (06) :3098-3100
[7]   DETERMINING ATOM-CENTERED MONOPOLES FROM MOLECULAR ELECTROSTATIC POTENTIALS - THE NEED FOR HIGH SAMPLING DENSITY IN FORMAMIDE CONFORMATIONAL-ANALYSIS [J].
BRENEMAN, CM ;
WIBERG, KB .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1990, 11 (03) :361-373
[8]   Low-temperature MCD studies of low-spin ferric complexes of tetramesitylporphyrinate: Evidence for the novel (d(xz),d(yz))(4)(d(xy))(1) ground state which models the spectroscopic properties of heme d [J].
Cheesman, MR ;
Walker, FA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (31) :7373-7380
[9]   Isotope effects and intermediates in the reduction of NO by P450NOR [J].
Daiber, A ;
Nauser, T ;
Takaya, N ;
Kudo, T ;
Weber, P ;
Hultschig, C ;
Shoun, H ;
Ullrich, V .
JOURNAL OF INORGANIC BIOCHEMISTRY, 2002, 88 (3-4) :343-352
[10]   Nitric oxide reductase (P450nor) from Fusarium oxysporum [J].
Dalber, A ;
Shoun, H ;
Ullrich, V .
JOURNAL OF INORGANIC BIOCHEMISTRY, 2005, 99 (01) :185-193