Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site

Journal of Physical Chemistry A

Volumn 115, Issue 41, 2011, Pages 11248-11255

  Berka, Karel ^a   Hendrychová, Tereza ^a   Anzenbacher, Pavel ^a   Otyepka, Michal ^a  

^a PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ATOMISTIC MODELS; CATALYTIC DOMAINS; CYTOCHROME P450; CYTOCHROMES P450; CYTOPLASMIC DOMAINS; DIOLEOYLPHOSPHATIDYLCHOLINE; DRUG METABOLISMS; ENERGY MINIMA; EXPERIMENTAL DATA; EXPLICIT WATER; MICROSOMAL PROTEINS; MOLECULAR DYNAMICS SIMULATIONS; N-TERMINALS; TIME-SCALES; TRANSMEMBRANES; WATER PHASE;

COMPUTER SIMULATION; METABOLISM; MOLECULAR DYNAMICS; PHASE INTERFACES;

MEMBRANES;

1,2 OLEOYLPHOSPHATIDYLCHOLINE; 1,2-OLEOYLPHOSPHATIDYLCHOLINE; CYP2C9 PROTEIN, HUMAN; IBUPROFEN; PHOSPHATIDYLCHOLINE; UNSPECIFIC MONOOXYGENASE;

ARTICLE; ARTIFICIAL MEMBRANE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; SURFACE PROPERTY; X RAY CRYSTALLOGRAPHY;

ARYL HYDROCARBON HYDROXYLASES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HUMANS; IBUPROFEN; MEMBRANES, ARTIFICIAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PHOSPHATIDYLCHOLINES; SURFACE PROPERTIES;

EID: 80054709526     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp204488j     Document Type: Article

References (67)

1. Ortiz de Montellano, P. R. Cytochrome P450: Structure, Mechanism, and Biochemistry, 3 rd ed.; Kluwer Academic/Plenum Publishers: New York, 2005.
2. Anzenbacher, P.; Anzenbacherova, E. Cell. Mol. Life Sci. 2001, 58 (5-6) 737-47
3. Coon, M. J. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 1-25
4. Graham, S. E.; Peterson, J. A. Arch. Biochem. Biophys. 1999, 369 (1) 24-9
5. Cojocaru, V.; Winn, P. J.; Wade, R. C. Biochim. Biophys. Acta 2007, 1770 (3) 390-401
6. Hendrychova, T.; Anzenbacherova, E.; Hudecek, J.; Skopalik, J.; Lange, R.; Hildebrandt, P.; Otyepka, M.; Anzenbacher, P. Biochim. Biophys. Acta 2011, 1814 (1) 58-68
7. Otyepka, M.; Skopalik, J.; Anzenbacherova, E.; Anzenbacher, P. Biochim. Biophys. Acta 2007, 1770 (3) 376-389
8. Skopalik, J.; Anzenbacher, P.; Otyepka, M. J. Phys. Chem. B 2008, 112 (27) 8165-73
9. Pochapsky, T. C.; Kazanis, S.; Dang, M. Antioxid. Redox Signaling 2010, 13 (8) 1273-96
10. Fishelovitch, D.; Hazan, C.; Shaik, S.; Wolfson, H. J.; Nussinov, R. J. Am. Chem. Soc. 2007, 129 (6) 1602-11
11. Sakaguchi, M.; Mihara, K.; Sato, R. EMBO J. 1987, 6 (8) 2425-31
12. Black, S. D. FASEB J. 1992, 6 (2) 680-5
13. Black, S. D.; Martin, S. T.; Smith, C. A. Biochemistry 1994, 33 (22) 6945-51
14. Szklarz, G. D.; Halpert, J. R. Life Sci. 1997, 61 (26) 2507-20
15. Cosme, J.; Johnson, E. F. J. Biol. Chem. 2000, 275 (4) 2545-53
16. Nakayama, K.; Puchkaev, A.; Pikuleva, I. A. J. Biol. Chem. 2001, 276 (33) 31459-65
17. Fernando, H.; Halpert, J. R.; Davydov, D. R. Biochemistry 2006, 45 (13) 4199-209
18. Lepesheva, G. I.; Seliskar, M.; Knutson, C. G.; Stourman, N. V.; Rozman, D.; Waterman, M. R. Arch. Biochem. Biophys. 2007, 464 (2) 221-7
19. Bayburt, T. H.; Sligar, S. G. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (10) 6725-30
20. Shank-Retzlaff, M. L.; Raner, G. M.; Coon, M. J.; Sligar, S. G. Arch. Biochem. Biophys. 1998, 359 (1) 82-8
21. Hudecek, J.; Anzenbacher, P. Biochim. Biophys. Acta 1988, 955 (3) 361-70
22. Friedman, F. K.; Robinson, R. C.; Dai, R. Front. Biosci. 2004, 9, 2796-806
23. Lomize, A. L.; Pogozheva, I. D.; Lomize, M. A.; Mosberg, H. I. Protein Sci. 2006, 15 (6) 1318-33
24. Scott, E. E.; He, Y. Q.; Halpert, J. R. Chem. Res. Toxicol. 2002, 15 (11) 1407-13
25. Williams, P. A.; Cosme, J.; Sridhar, V.; Johnson, E. F.; McRee, D. E. Mol. Cell 2000, 5 (1) 121-131
26. Conner, K. P.; Woods, C. M.; Atkins, W. M. Arch. Biochem. Biophys. 2011, 507 (1) 56-65
27. Rydberg, P.; Rod, T. H.; Olsen, L.; Ryde, U. J. Phys. Chem. B 2007, 111 (19) 5445-5457
28. Evans, W. E.; Relling, M. V. Science 1999, 286 (5439) 487-91
29. Williams, P. A.; Cosme, J.; Ward, A.; Angove, H. C.; Matak Vinkovic, D.; Jhoti, H. Nature 2003, 424 (6947) 464-8
30. Larkin, M. A.; Blackshields, G.; Brown, N. P.; Chenna, R.; McGettigan, P. A.; McWilliam, H.; Valentin, F.; Wallace, I. M.; Wilm, A.; Lopez, R.; Thompson, J. D.; Gibson, T. J.; Higgins, D. G. Bioinformatics 2007, 23 (21) 2947-8
31. Waterhouse, A. M.; Procter, J. B.; Martin, D. M.; Clamp, M.; Barton, G. J. Bioinformatics 2009, 25 (9) 1189-91
32. von Wachenfeldt, C.; Johnson, E. F. Structures of Eukaryotic Cytochrome P450 Enzymes-Membrane Topology. In Cytochrome P450: Structure, Mechanism and Biochemistry, 2 nd ed.; Plenum Press: New York, 1995; pp 183-223.
33. DeLano, W. L. The PyMOL Molecular Graphics System, 0.99rc6; DeLano Scientific: Palo Alto, CA, 2002.
34. van Meer, G.; Voelker, D. R.; Feigenson, G. W. Nat. Rev. Mol. Cell Biol. 2008, 9 (2) 112-24
35. Siu, S. W.; Vacha, R.; Jungwirth, P.; Bockmann, R. A. J. Chem. Phys. 2008, 128 (12) 125103
36. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 2004, 25 (13) 1656-76
37. Berger, O.; Edholm, O.; Jahnig, F. Biophys. J. 1997, 72 (5) 2002-13
38. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4 (3) 435-447
39. Petrek, M.; Kosinova, P.; Koca, J.; Otyepka, M. Structure 2007, 15 (11) 1357-63
40. Petrek, M.; Otyepka, M.; Banas, P.; Kosinova, P.; Koca, J.; Damborsky, J. BMC Bioinf. 2006, 7, 316
41. Porubsky, P. R.; Battaile, K. P.; Scott, E. E. J. Biol. Chem. 2010, 285 (29) 22282-90
42. Schuttelkopf, A. W.; van Aalten, D. M. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60 (Pt 8) 1355-63
43. Hub, J. S.; de Groot, B. L.; van der Spoel, D. J. Chem. Theory Comput. 2010, 6 (12) 3713-3720
44. Ruan, K. H.; So, S. P.; Zheng, W.; Wu, J.; Li, D.; Kung, J. Biochem. J. 2002, 368 (Pt 3) 721-8
45. Bond, P. J.; Wee, C. L.; Sansom, M. S. Biochemistry 2008, 47 (43) 11321-31
46. Ohta, Y.; Kawato, S.; Tagashira, H.; Takemori, S.; Kominami, S. Biochemistry 1992, 31 (50) 12680-7
47. Ozalp, C.; Szczesna-Skorupa, E.; Kemper, B. Biochemistry 2006, 45 (14) 4629-37
48. Headlam, M. J.; Wilce, M. C.; Tuckey, R. C. Biochim. Biophys. Acta 2003, 1617 (1-2) 96-108
49. Pikuleva, I. A.; Mast, N.; Liao, W. L.; Turko, I. V. Lipids 2008, 43 (12) 1127-32
50. Mast, N.; Liao, W. L.; Pikuleva, I. A.; Turko, I. V. Arch. Biochem. Biophys. 2009, 483 (1) 81-9
51. Schoch, G. A.; Yano, J. K.; Wester, M. R.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. J. Biol. Chem. 2004, 279 (10) 9497-9503
52. Hu, G.; Johnson, E. F.; Kemper, B. Drug Metab. Dispos. 2010, 38 (11) 1976-83
53. Szczesna-Skorupa, E.; Mallah, B.; Kemper, B. J. Biol. Chem. 2003, 278 (33) 31269-76
54. Nussio, M. R.; Voelcker, N. H.; Miners, J. O.; Lewis, B. C.; Sykes, M. J.; Shapter, J. G. Chem. Phys. Lipids 2010, 163 (2) 182-9
55. Kida, Y.; Ohgiya, S.; Mihara, K.; Sakaguchi, M. Arch. Biochem. Biophys. 1998, 351 (2) 175-9
56. Bridges, A.; Gruenke, L.; Chang, Y. T.; Vakser, I. A.; Loew, G.; Waskell, L. J. Biol. Chem. 1998, 273 (27) 17036-49
57. Wade, R. C.; Motiejunas, D.; Schleinkofer, K.; Sudarko; Winn, P. J.; Banerjee, A.; Kaniakin, A.; Jung, C. Biochim. Biophys. Acta 2005, 1754 (1-2) 239-244
58. Williams, P. A.; Cosme, J.; Sridhar, V.; Johnson, E. F.; McRee, D. E. J. Inorg. Biochem. 2000, 81 (3) 183-90
59. Zhao, Y.; White, M. A.; Muralidhara, B. K.; Sun, L.; Halpert, J. R.; Stout, C. D. J. Biol. Chem. 2006, 281 (9) 5973-81
60. Schleinkofer, K.;, Sudarko; Winn, P. J.; Ludemann, S. K.; Wade, R. C. EMBO Rep. 2005, 6 (6) 584-589
61. Li, W. H.; Shen, J.; Liu, G. X.; Tang, Y.; Hoshino, T. Proteins: Struct., Funct., Bioinf. 2011, 79 (1) 271-281
62. Fishelovitch, D.; Shaik, S.; Wolfson, H. J.; Nussinov, R. J. Phys. Chem. B 2009, 113 (39) 13018-25
63. Ekroos, M.; Sjogren, T. Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (37) 13682-7
64. Boggara, M. B.; Krishnamoorti, R. Biophys. J. 2010, 98 (4) 586-95
65. McMullen, T. P. W.; Lewis, R. N. A. H.; McElhaney, R. N. Curr. Opin. Colloid Interface Sci. 2004, 8 (6) 459-468
66. Orsi, M.; Essex, J. W. Soft Matter 2010, 6 (16) 3797-3808
67. Watkinson, R. M.; Herkenne, C.; Guy, R. H.; Hadgraft, J.; Oliveira, G.; Lane, M. E. Skin Pharmacol. Physiol. 2009, 22 (1) 15-21