Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations

Biopolymers

Volumn 101, Issue 3, 2014, Pages 197-209

  Verma, Rajni ^a,b   Schwaneberg, Ulrich ^b   Roccatano, Danilo ^a  

^a JACOBS UNIVERSITY BREMEN   (Germany)

^b RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

cytochrome P450 monooxygenase; HEME FMN complex; interdomain electron transfer

Indexed keywords

ELECTRON TRANSFER; HEME/FMN COMPLEX; MOLECULAR DYNAMICS SIMULATIONS; MONOOXYGENASES; OPTIMAL ARRANGEMENT; PHYSIOLOGICAL CONDITION; PROTEIN COMPLEXES; REDOX PARTNER INTERACTIONS;

ACTIVATION ANALYSIS; AMINO ACIDS; BINDING ENERGY; ELECTRON TRANSITIONS; MOLECULAR DYNAMICS; PORPHYRINS;

IRON COMPOUNDS;

AMINO ACID; CYTOCHROME P450 BM3; FLAVINE MONONUCLEOTIDE; HEME; MULTIPROTEIN COMPLEX; BACTERIAL PROTEIN; CYTOCHROME P450; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE FERRIHEMOPROTEIN REDUCTASE;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ELECTRON TRANSPORT; MOLECULAR DYNAMICS; OXIDATION REDUCTION STATE; PATHWAYS PATH METHOD; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; THEORETICAL STUDY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; OXIDATION REDUCTION REACTION;

BACTERIAL PROTEINS; BINDING SITES; CYTOCHROME P-450 ENZYME SYSTEM; FLAVIN MONONUCLEOTIDE; HEME; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NADPH-FERRIHEMOPROTEIN REDUCTASE; OXIDATION-REDUCTION;

EID: 84890604929     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.22301     Document Type: Article

References (53)

1. Chefson, A.,;, Auclair, K., Mol Biosyst 2006, 2, 462-469.
2. Wong, L. L., Curr Opin Chem Biol 1998, 2, 263-268.
3. Guengerich, F. P., Chem Res Toxicol 2001, 14, 611-650.
4. Narhi, L. O.,;, Fulco, A., J. J Biol Chem 1986, 261, 7160-7169.
5. Narhi, L. O.,;, Fulco, A., J. J Biol Chem 1987, 262, 6683-6690.
6. Whitehouse, C. J.,;, Bell, S. G.,;, Wong, L. L., Chem Soc Rev 2012, 41, 1218-1260.
7. Di Nardo, G.,;, Gilardi, G., Int J Mol Sci 2012, 13, 15901-15924.
8. Munro, A. W.,;, Girvan, H. M.,;, McLean, K., J. Biochim Biophys Acta 2007, 1770, 345-359.
9. Munro, A. W.,;, Lindsay, J. G.,;, Coggins, J. R.,;, Kelly, S. M.,;, Price, N. C., FEBS Lett 1994, 343, 70-74.
10. Warman, A. J.,;, Roitel, O.,;, Neeli, R.,;, Girvan, H. M.,;, Seward, H. E.,;, Murray, S. A.,;, McLean, K. J.,;, Joyce, M. G.,;, Toogood, H.,;, Holt, R. A.,;, Leys, D.,;, Scrutton, N. S.,;, Munro, A. W., Biochem Soc Trans 2005, 33, 747-753.
11. Munro, A. W.,;, Leys, D. G.,;, McLean, K. J.,;, Marshall, K. R.,;, Ost, T. W.,;, Daff, S.,;, Miles, C. S.,;, Chapman, S. K.,;, Lysek, D. A.,;, Moser, C. C.,;, Page, C. C.,;, Dutton, P. L., Trends Biochem Sci 2002, 27, 250-257.
12. Girvan, H. M.,;, Waltham, T. N.,;, Neeli, R.,;, Collins, H. F.,;, McLean, K. J.,;, Scrutton, N. S.,;, Leys, D.,;, Munro, A. W., Biochem Soc Trans 2006, 34, 1173-1177.
13. Peterson, J. A.,;, Sevrioukova, I.,;, Truan, G.,;, GrahamLorence, S. E., Steroids 1997, 62, 117-123.
14. Munro, A. W.,;, Daff, S.,;, Coggins, J. R.,;, Lindsay, J. G.,;, Chapman, S. K., Eur J Biochem 1996, 239, 403-409.
15. Sevrioukova, I. F.,;, Li, H. Y.,;, Zhang, H.,;, Peterson, J. A.,;, Poulos, T. L., Proc Natl Acad Sci USA 1999, 96, 1863-1868.
16. Joyce, M. G.,;, Ekanem, I. S.,;, Roitel, O.,;, Dunford, A. J.,;, Neeli, R.,;, Girvan, H. M.,;, Baker, G. J.,;, Curtis, R. A.,;, Munro, A. W.,;, Leys, D., FEBS J 2012, 279, 1694-1706.
17. Page, C. C.,;, Moser, C. C.,;, Chen, X.,;, Dutton, P. L., Nature 1999, 402, 47-52.
18. Hazzard, J. T.,;, Govindaraj, S.,;, Poulos, T. L.,;, Tollin, G., J Biol Chem 1997, 272, 7922-7926.
19. Roccatano, D.,;, Wong, T. S.,;, Schwaneberg, U.,;, Zacharias, M., Biopolymers 2006, 83, 467-476.
20. Roccatano, D.,;, Wong, T. S.,;, Schwaneberg, U.,;, Zacharias, M., Biopolymers 2005, 78, 259-267.
21. Verma, R.,;, Schwaneberg, U.,;, Roccatano, D., J Chem Theory Comput 2013, 9, 96-105.
22. Beratan, D. N.,;, Betts, J. N.,;, Onuchic, J. N., Science 1991, 252, 1285-1288.
23. van Gunsteren, W. F.,;, Billeter, S. R.,;, Eising, A. A.,;, Hunenberger, P. H.,;, Kruger, P.,;, Mark, A. E.,;, Scott, W. R. P.,;, Tironi, I. G., Biomolecular Simulation: The GROMOS96 Manual and User Guide; 1996.
24. Helms, V.,;, Deprez, E.,;, Gill, E.,;, Barret, C.,;, Hui Bon Hoa, G.,;, Wade, R. C., Biochemistry 1996, 35, 1485-1499.
25. Zheng, Y.-J.,;, Ornstein, R. L., J Am Chem Soc 1996, 118, 9402-9408.
26. Berendsen, H. J. C.,;, Postma, J. P. M.,;, van Gunsteren, W. F.,;, Hermans, J. Intermolecular Forces 1981, 331-342.
27. Hess, B.,;, Bekker, H.,;, Berendsen, H. J. C.,;, Fraaije, J. G. E. M., J Comput Chem 1997, 18, 1463-1472.
28. Miyamoto, S.,;, Kollman, P. A., J Comput Chem 1992, 13, 952-962.
29. Darden, T.,;, York, D.,;, Pedersen, L., J Chem Phys 1993, 98, 10089-10092.
30. Berendsen, H. J. C.,;, Postma, J. P. M.,;, Vangunsteren, W. F.,;, Dinola, A.,;, Haak, J. R., J Chem Phys 1984, 81, 3684-3690.
31. Hess, B.,;, Kutzner, C.,;, van der Spoel, D.,;, Lindahl, E., J Chem Theory Comput 2008, 4, 435-447.
32. Kabsch, W.,;, Sander, C., Biopolymers 1983, 22, 2577-2637.
33. Daura, X.,;, Gademann, K.,;, Jaun, B.,;, Seebach, D.,;, van Gunsteren, W. F.,;, Mark, A. E., Angew Chem Int Ed 1999, 38, 236-240.
34. Balabin, I. A.,;, Hu, X.,;, Beratan, D. N., J Comput Chem 2012, 33, 906-910.
35. Humphrey, W.,;, Dalke, A.,;, Schulten, K., J Mol Graph 1996, 14, 33.
36. Marcus, R. A.,;, Sutin, N., Biochim Biophys Acta 1985, 811, 265-322.
37. Moser, C. C.,;, Keske, J. M.,;, Warncke, K.,;, Farid, R. S.,;, Dutton, P. L., Nature 1992, 355, 796-802.
38. Amadei, A.,;, Linssen, A. B.,;, Berendsen, H., J. Proteins 1993, 17, 412-425.
39. Amadei, A.,;, Linssen, A. B.,;, de Groot, B. L.,;, van Aalten, D. M.,;, Berendsen, H., J. J Biomol Struct Dyn 1996, 13, 615-625.
40. Pettersen, E. F.,;, Goddard, T. D.,;, Huang, C. C.,;, Couch, G. S.,;, Greenblatt, D. M.,;, Meng, E. C.,;, Ferrin, T. E., J Comput Chem 2004, 25, 1605-1612.
41. Amadei, A.,;, Ceruso, M. A.,;, Di Nola, A., Proteins 1999, 36, 419-424.
42. Chang, Y. T.,;, Loew, G. H., J Biomol Struct Dyn 1999, 16, 1189-1203.
43. Sevrioukova, I.,;, Shaffer, C.,;, Ballou, D. P.,;, Peterson, J. A., Biochemistry 1996, 35, 7058-7068.
44. Li, H.,;, Poulos, T. L., Acta Crystallogr Sect D 1995, 51, 21-32.
45. Ost, T. W.,;, Munro, A. W.,;, Mowat, C. G.,;, Taylor, P. R.,;, Pesseguiero, A.,;, Fulco, A. J.,;, Cho, A. K.,;, Cheesman, M. A.,;, Walkinshaw, M. D.,;, Chapman, S. K., Biochemistry 2001, 40, 13430-13438.
46. Chen, Z.,;, Ost, T. W.,;, Schelvis, J. P., Biochemistry 2004, 43, 1798-1808.
47. Balabin, I. A.,;, Onuchic, J. N., Science 2000, 290, 114-117.
48. Jones, M. L.,;, Kurnikov, I. V.,;, Beratan, D. N., J Phys Chem A 2002, 106, 2002-2006.
49. Balabin, I. A.,;, Beratan, D. N.,;, Skourtis, S. S., Phys Rev Lett 2008, 101, 158102.
50. Beratan, D. N.,;, Skourtis, S. S.,;, Balabin, I. A.,;, Balaeff, A.,;, Keinan, S.,;, Venkatramani, R.,;, Xiao, D., Acc Chem Res 2009, 42, 1669-1678.
51. Skourtis, S. S.,;, Waldeck, D. H.,;, Beratan, D. N., Annu Rev Phys Chem 2010, 61, 461-485.
52. Sevrioukova, I.,;, Peterson, J. A., Biochimie 1996, 78, 744-751.
53. Aigrain, L.,;, Fatemi, F.,;, Frances, O.,;, Lescop, E.,;, Truan, G., Int J Mol Sci 2012, 13, 15012-15041.