The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
The Elusive Oxidant Species of Cytochrome P450 Enzymes: Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations
Abstract
The primary oxidant of cytochrome P450 enzymes, Compound I, is hard to detect experimentally; in the case of cytochrome P450(cam), this intermediate does not accumulate in solution during the catalytic cycle even at temperatures as low as 200 K (ref 4). Theory can play an important role in characterizing such elusive species. We present here combined quantum mechanical/molecular mechanical (QM/MM) calculations of Compound I of cytochrome P450(cam) in the full enzyme environment as well as density functional studies of the isolated QM region. The calculations assign the ground state of the species, quantify the effect of polarization and hydrogen bonding on its properties, and show that the protein environment and its specific hydrogen bonding to the cysteinate ligand are crucial for sustaining the Fe-S bond and for preventing the full oxidation of the sulfur.
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Cites
Density-functional thermochemistry. III. The role of exact exchange
Becke, A. D. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464913 · Cited by 103,767
Lee, C., Yang, W., & Parr, R. G. (1988) · Physical Review B · doi:10.1103/physrevb.37.785 · Cited by 100,874
Density-functional exchange-energy approximation with correct asymptotic behavior
Becke, A. D. (1988) · Physical Review A · doi:10.1103/physreva.38.3098 · Cited by 53,711
Hehre, W. J., Ditchfield, R., & Pople, J. A. (1972) · The Journal of Chemical Physics · doi:10.1063/1.1677527 · Cited by 15,855
The influence of polarization functions on molecular orbital hydrogenation energies
Hariharan, P. C., & Pople, J. A. (1973) · Theoretica Chimica Acta · doi:10.1007/bf00533485 · Cited by 15,816
Hay, P. J., & Wadt, W. R. (1985) · The Journal of Chemical Physics · doi:10.1063/1.448975 · Cited by 15,577
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 14,944
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,311
Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971) · The Journal of Chemical Physics · doi:10.1063/1.1674902 · Cited by 10,612
Electronic structure calculations on workstation computers: The program system turbomole
Ahlrichs, R., Bär, M., Häser, M., Horn, H., & Kölmel, C. (1989) · Chemical Physics Letters · doi:10.1016/0009-2614(89)85118-8 · Cited by 8,433
Clark, T., Chandrasekhar, J., Spitznagel, G. W., & Schleyer, P. V. R. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040303 · Cited by 7,224
Sono, M., Roach, M. P., Coulter, E. D., & Dawson, J. H. (1996) · Chemical Reviews · doi:10.1021/cr9500500 · Cited by 2,441
DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package
Smith, W., & Forester, T. R. (1996) · Journal of Molecular Graphics · doi:10.1016/s0263-7855(96)00043-4 · Cited by 2,229
The Catalytic Pathway of Cytochrome P450cam at Atomic Resolution
Schlichting, I., Berendzen, J., Chu, K., Stock, A. M., Maves, S. A., Benson, D. E., Sweet, R. M., Ringe, D., Petsko, G. A., & Sligar, S. G. (2000) · Science · doi:10.1126/science.287.5458.1615 · Cited by 1,331
Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches
Bakowies, D., & Thiel, W. (1996) · The Journal of Physical Chemistry · doi:10.1021/jp9536514 · Cited by 1,261
Self-citationCytochrome P450: Structure, Mechanism, and Biochemistry
(1995) · Springer eBooks · doi:10.1007/978-1-4757-2391-5 · Cited by 594
Billeter, S. R., Turner, A. J., & Thiel, W. (2000) · Physical Chemistry Chemical Physics · doi:10.1039/a909486e · Cited by 468
Self-citationDavydov, R., Makris, T. M., Kofman, V., Werst, D. E., Sligar, S. G., & Hoffman, B. M. (2001) · Journal of the American Chemical Society · doi:10.1021/ja003583l · Cited by 443
Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials
Gao, J. (1996) · Reviews in Computational Chemistry · doi:10.1002/9780470125847.ch3 · Cited by 424
Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations
de Vries, A. H., Sherwood, P., Collins, S. J., Rigby, A. M., Rigutto, M., & Kramer, G. J. (1999) · The Journal of Physical Chemistry B · doi:10.1021/jp9913012 · Cited by 391
Groves, J. T., & Watanabe, Y. (1988) · Journal of the American Chemical Society · doi:10.1021/ja00233a021 · Cited by 313
Ogliaro, F., de Visser, S. P., Cohen, S., Sharma, P. K., & Shaik, S. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0171963 · Cited by 303
Self-citationLoew, G. H., & Harris, D. L. (2000) · Chemical Reviews · doi:10.1021/cr980389x · Cited by 257
Schulz, C. E., Rutter, R., Sage, J. T., Debrunner, P. G., & Hager, L. P. (1984) · Biochemistry · doi:10.1021/bi00315a033 · Cited by 255
The role of the proximal ligand in heme enzymes
Poulos, T. L. (1996) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s007750050064 · Cited by 247
Chloroperoxidase compound I: electron paramagnetic resonance and Moessbauer studies
Rutter, R., Hager, L. P., Dhonau, H., Hendrich, M. P., Valentine, M., & Debrunner, P. G. (1984) · Biochemistry · doi:10.1021/bi00321a082 · Cited by 236
Kinetic Characterization of Compound I Formation in the Thermostable Cytochrome P450 CYP119
Kellner, D. G., Hung, S.-C., Weiss, K. E., & Sligar, S. G. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.c100745200 · Cited by 222
Evidence for Sulfur-Based Radicals in Thiolate Compound I Intermediates
Green, M. T. (1999) · Journal of the American Chemical Society · doi:10.1021/ja991541v · Cited by 206
Evidence for Compound I Formation in the Reaction of Cytochrome-P450cam with m-Chloroperbenzoic Acid
Egawa, T., Shimada, H., & Ishimura, Y. (1994) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1994.1868 · Cited by 187
Ogliaro, F., Cohen, S., de Visser, S. P., & Shaik, S. (2000) · Journal of the American Chemical Society · doi:10.1021/ja005619f · Cited by 169
Self-citationYoshioka, S., Takahashi, S., Ishimori, K., & Morishima, I. (2000) · Journal of Inorganic Biochemistry · doi:10.1016/s0162-0134(00)00097-0 · Cited by 123
Meunier, B., & Bernadou, J. (2007) · Springer eBooks · doi:10.1007/3-540-46592-8_1 · Cited by 80
Antony, J., Grodzicki, M., & TRAUTWEIN, A. X. (1997) · The Journal of Physical Chemistry A · doi:10.1021/jp9632955 · Cited by 64
On the Treatment of Link Atoms in Hybrid Methods
Antes, I., & Thiel, W. (1998) · ACS symposium series · doi:10.1021/bk-1998-0712.ch004 · Cited by 62
Self-citationSigman, J. A., Pond, A. E., Dawson, J. H., & Lu, Y. (1999) · Biochemistry · doi:10.1021/bi990815o · Cited by 61
Cytochrome P450: Significance, reaction mechanisms and active site analogues
Woggon, W. (1996) · Topics in current chemistry · doi:10.1007/3-540-61388-9_62 · Cited by 54
Kinetic Isotope Effects in a C−H Bond Dissociation by the Iron-Oxo Species of Cytochrome P450
Yoshizawa, K., Kagawa, Y., & Shiota, Y. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp001950+ · Cited by 46
Cited by
Heme Enzyme Structure and Function
Poulos, T. L. (2014) · Chemical Reviews · doi:10.1021/cr400415k · Cited by 1,443
P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations
Shaik, S., Cohen, S., Wang, Y., Chen, H., Kumar, D., & Thiel, W. (2010) · Chemical Reviews · doi:10.1021/cr900121s · Cited by 1,083
Self-citationSchöneboom, J. C., Neese, F., & Thiel, W. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0424732 · Cited by 260
Self-citation
Metadata
- Authors
- Schöneboom, J. C., Lin, H., Reuter, N., Thiel, W., Cohen, S., Ogliaro, F., & Shaik, S.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-06-14
- Volume
- 124
- Issue
- 27
- Pages
- 8142-8151
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2091087315
- Cited by
- 309
- References
- 37
- FWCI
- 15.90
- Type
- journal article
- Language
- en
- Open access
- closed
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