Structural basis for the mutation-induced dysfunction of human CYP2J2: A computational study

Journal of Chemical Information and Modeling

Volumn 53, Issue 6, 2013, Pages 1350-1357

  Cong, Shan ^a,b   Ma, Xiao Tu ^a   Li, Yi Xue ^a,b,c,d   Wang, Jing Fang ^a,d  

^a Shanghai Jiao Tong University   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASES; ENDOTHELIAL CELLS; HYDROGEN BONDS; METABOLISM; MOLECULES; REACTION INTERMEDIATES; UNSATURATED FATTY ACIDS;

AB INITIO MODELING; COMPUTATIONAL MODEL; COMPUTATIONAL STUDIES; CORONARY ARTERY DISEASE; EPOXYEICOSATRIENOIC ACIDS; ESSENTIAL FATTY ACIDS; INFLAMMATORY REACTION; SUBSTRATE RECOGNITION;

THREE DIMENSIONAL COMPUTER GRAPHICS;

ARACHIDONATE EPOXYGENASE; ARACHIDONIC ACID; CYTOCHROME P450;

CHEMISTRY; GENETICS; HUMAN; METABOLISM; MOLECULAR DYNAMICS; POINT MUTATION; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS; ARTICLE;

ARACHIDONIC ACID; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; MOLECULAR DYNAMICS SIMULATION; POINT MUTATION; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS;

EID: 84879596358     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400003p     Document Type: Article

References (60)

1. Sprecher, H. Metabolism of highly unsaturated n-3 and n-6 fatty acids Biochim. Biophys. Acta 2000, 1486, 219-231
2. MacDonald, J. I.; Sprecher, H. Phospholipid fatty acid remodeling in mammalian cells Biochim. Biophys. Acta 1991, 1084, 105-121
3. Funk, C. D. Prostaglandins and leukotrienes: advances in eicosanoid biology Science 2001, 294, 1871-1875
4. Harris, W. S.; Mozaffarian, D.; Rimm, E.; Kris-Etherton, P.; Rudel, L. L.; Appel, L. J.; Engler, M. M.; Engler, M. B.; Sacks, F. Omega-6 fatty acids and risk for cardiovascular disease: a science advisory from the American Heart Association Nutrition Subcommittee of the Council on Nutrition, Physical Activity, and Metabolism; Council on Cardiovascular Nursing; and Council on Epidemiology and Prevention Circulation 2009, 119, 902-907
5. Ferrucci, L.; Cherubini, A.; Bandinelli, S.; Bartali, B.; Corsi, A.; Lauretani, F.; Martin, A.; Andres-Lacueva, C.; Senin, U.; Guralnik, J. M. Relationship of plasma polyunsaturated fatty acids to circulating inflammatory markers J. Clin. Endocrinol. Metab. 2006, 91, 439-446
6. Zeldin, D. C. Epoxygenase pathways of arachidonic acid metabolism J. Biol. Chem. 2001, 276, 36059-36062
7. Fleming, I. Vascular cytochrome p450 enzymes: physiology and pathophysiology Trends. Cardiovasc. Med. 2008, 18, 20-25
8. Spector, A. A. Arachidonic acid cytochrome P450 epoxygenase pathway J. Lipid Res. 2009, 50, S52-S56
9. Wang, H.; Lin, L.; Jiang, J.; Wang, Y.; Lu, Z. Y.; Bradbury, J. A.; Lih, F. B.; Wang, D. W.; Zeldin, D. C. Up-regulation of endothelial nitric-oxide synthase by endothelium-derived hyperpolarizing factor involves mitogen-activated protein kinase and protein kinase C signaling pathways J. Pharmacol. Exp. Ther. 2003, 307, 753-764
10. Loot, A. E.; Popp, R.; Fisslthaler, B.; Vriens, J.; Nilius, B.; Fleming, I. Role of cytochrome P450-dependent transient receptor potential V4 activation in flow-induced vasodilatation Cardiovasc. Res. 2008, 80, 445-452
11. Node, K.; Huo, Y.; Ruan, X.; Yang, B.; Spiecker, M.; Ley, K.; Zeldin, D. C.; Liao, J. K. Anti-inflammatory properties of cytochrome P450 epoxygenase-derived eicosanoids Science 1999, 285, 1276-1279
12. Spiecker, M.; Liao, J. K. Vascular protective effects of cytochrome p450 epoxygenase-derived eicosanoids Arch. Biochem. Biophys. 2005, 433, 413-420
13. Gainer, J. V.; Bellamine, A.; Dawson, E. P.; Womble, K. E.; Grant, S. W.; Wang, Y.; Cupples, L. A.; Guo, C. Y.; Demissie, S.; O'Donnell, C. J.; Brown, N. J.; Waterman, M. R.; Capdevila, J. H. Functional variant of CYP4A11 20-hydroxyeicosatetraenoic acid synthase is associated with essential hypertension Circulation 2005, 111, 63-69
14. Imig, J. D.; Hammock, B. D. Soluble epoxide hydrolase as a therapeutic target for cardiovascular diseases Nat. Rev. Drug Discovery 2009, 8, 794-805
15. Laffer, C. L.; Laniado-Schwartzman, M.; Wang, M. H.; Nasjletti, A.; Elijovich, F. Differential regulation of natriuresis by 20- hydroxyeicosatetraenoic Acid in human salt-sensitive versus salt-resistant hypertension Circulation 2003, 107, 574-578
16. Wu, S.; Moomaw, C. R.; Tomer, K. B.; Falck, J. R.; Zeldin, D. C. Molecular cloning and expression of CYP2J2, a human cytochrome P450 arachidonic acid epoxygenase highly expressed in heart J. Biol. Chem. 1996, 271, 3460-3468
17. Spiecker, M.; Darius, H.; Hankeln, T.; Soufi, M.; Sattler, A. M.; Schaefer, J. R.; Node, K.; Borgel, J.; Mugge, A.; Lindpaintner, K.; Huesing, A.; Maisch, B.; Zeldin, D. C.; Liao, J. K. Risk of coronary artery disease associated with polymorphism of the cytochrome P450 epoxygenase CYP2J2 Circulation 2004, 110, 2132-2136
18. King, L. M.; Ma, J.; Srettabunjong, S.; Graves, J.; Bradbury, J. A.; Li, L.; Spiecker, M.; Liao, J. K.; Mohrenweiser, H.; Zeldin, D. C. Cloning of CYP2J2 gene and identification of functional polymorphisms Mol. Pharmacol. 2002, 61, 840-852
19. Strushkevich, N.; Usanov, S. A.; Plotnikov, A. N.; Jones, G.; Park, H. W. Structural analysis of CYP2R1 in complex with vitamin D3 J. Mol. Biol. 2008, 380, 95-106
20. Blundell, T. L.; Sibanda, B. L.; Sternberg, M. J.; Thornton, J. M. Knowledge-based prediction of protein structures and the design of novel molecules Nature 1987, 326, 347-352
21. Jones, T. A.; Thirup, S. Using known substructures in protein model building and crystallography EMBO J. 1986, 5, 819-822
22. Wang, J. F.; Wei, D. Q.; Lin, Y.; Wang, Y. H.; Du, H. L.; Li, Y. X.; Chou, K. C. Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP Biochem. Biophys. Res. Commun. 2007, 359, 323-329
23. Wang, J. F.; Chou, K. C. Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics Protein Eng. Des. Sel. 2010, 23, 663-666
24. Wang, J. F.; Chou, K. C. Insights from modeling the 3D structure of New Delhi metallo-beta-lactamse and its binding interactions with antibiotic drugs PLoS One 2011, 6, e18414
25. Wang, J. F.; Wei, D. Q.; Li, L.; Zheng, S. Y.; Li, Y. X.; Chou, K. C. 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design Biochem. Biophys. Res. Commun. 2007, 355, 513-519
26. Wang, J. F.; Wei, D. Q.; Chen, C.; Li, Y.; Chou, K. C. Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design Protein Pept. Lett. 2008, 15, 27-32
27. Wang, J. F.; Wei, D. Q.; Chou, K. C. Drug candidates from traditional Chinese medicines Curr. Top. Med. Chem. 2008, 8, 1656-1665
28. Wang, J. F.; Wei, D. Q.; Chou, K. C. Pharmacogenomics and personalized use of drugs Curr. Top. Med. Chem. 2008, 8, 1573-1579
29. Wu, S.; Skolnick, J.; Zhang, Y. Ab initio modeling of small proteins by iterative TASSER simulations BMC Biol. 2007, 5, 17
30. Labute, P. The generalized Born/volume integral implicit solvent model: estimation of the free energy of hydration using London dispersion instead of atomic surface area J. Comput. Chem. 2008, 29, 1693-1698
31. Rocchia, W.; Alexov, E.; Honing, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions J. Phys. Chem. B 2001, 105, 6507-6514
32. Ponder, J. W.; Case, D. A. Force fields for protein simulations Adv. Protein Chem. 2003, 66, 27-85
33. Schoneboom, J. C.; Lin, H.; Reuter, N.; Thiel, W.; Cohen, S.; Ogliaro, F.; Shaik, S. The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations J. Am. Chem. Soc. 2002, 124, 8142-8151
34. Case, D. A.; Cheatham, T. E., 3rd; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs J. Comput. Chem. 2005, 26, 1668-1688
35. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
36. Lian, P.; Wei, D. Q.; Wang, J. F.; Chou, K. C. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes PLoS One 2011, 6, e18587
37. Wang, Y.; Wei, D. Q.; Wang, J. F. Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism J. Chem. Inf. Model. 2010, 50, 875-878
38. Wang, Y.; Wu, X. L.; Wei, D. Q.; Li, Y. X.; Wang, J. F. Autoinhibitory mechanism for the mutation-induced impaired FGF9 signaling J. Chem. Inf. Model. 2012, 52, 2422-2429
39. Wang, Y. J.; Wang, J. F.; Ping, J.; Yu, Y.; Wang, Y.; Lian, P.; Li, X.; Li, Y. X.; Hao, P. Computational studies on the substrate interactions of influenza A virus PB2 subunit PLoS One 2012, 7, e44079
40. Perdih, A.; Bren, U.; Solmajer, T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase J. Mol. Model. 2009, 15, 983-996
41. Bren, U.; Janežič, D. Individual degrees of freedom and the salvation properties of water J. Chem. Phys. 2012, 137, 024108
42. Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26
43. Wang, J. F.; Zhang, C. C.; Chou, K. C.; Wei, D. Q. Structure of cytochrome p450s and personalized drug Curr. Med. Chem. 2009, 16, 232-244
44. Li, J.; Wei, D. Q.; Wang, J. F.; Li, Y. X. A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations J. Chem. Inf. Model. 2011, 51, 3217-3225
45. Ping, J.; Wang, Y. J.; Wang, J. F.; Li, X.; Li, Y. X.; Hao, P. Negatively cooperative binding properties of human cytochrome P450 2E1 with monocyclic substrates Curr. Drug Metab. 2012, 13, 1024-1031
46. Bren, U.; Oostenbrink, C. Cytochrome P450 3A4 inhibition by ketoconazole: trackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations J. Chem. Inf. Model 2012, 52, 1573-1582
47. Imai, M.; Shimada, H.; Watanabe, Y.; Matsushima-Hibiya, Y.; Makino, R.; Koga, H.; Horiuchi, T.; Ishimura, Y. Uncoupling of the cytochrome P-450cam monooxygenase reaction by a single mutation, threonine-252 to alanine or valine: possible role of the hydroxy amino acid in oxygen activation Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 7823-7827
48. Wang, J. F.; Chou, K. C. Molecular modeling of cytochrome P450 and drug metabolism Curr. Drug Metab. 2010, 11, 342-346
49. Wu, S.; Zhang, Y. LOMETS: a local meta-threading-server for protein structure prediction Nucleic Acids Res. 2007, 35, 3375-3382
50. Laskowski, R. A.; Moss, D. S.; Thornton, J. M. Main-chain bond lengths and bond angles in protein structures J. Mol. Biol. 1993, 231, 1049-1067
51. Benkert, P.; Tosatto, S. C.; Schomburg, D. QMEAN: A comprehensive scoring function for model quality assessment Proteins 2008, 71, 261-277
52. Colovos, C.; Yeates, T. O. Verification of protein structures: patterns of nonbonded atomic interactions Protein Sci. 1993, 2, 1511-1519
53. Luthy, R.; Bowie, J. U.; Eisenberg, D. Assessment of protein models with three-dimensional profiles Nature 1992, 356, 83-85
54. Gotoh, O. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences J. Biol. Chem. 1992, 267, 83-90
55. Meunier, B.; de Visser, S. P.; Shaik, S. Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes Chem. Rev. 2004, 104, 3947-3980
56. Chen, Q.; Zhang, T.; Wang, J. F.; Wei, D. Q. Advances in human cytochrome p450 and personalized medicine Curr. Drug Metab. 2011, 12, 436-444
57. Gonzalez-Diaz, H.; Prado-Prado, F.; Garcia-Mera, X.; Alonso, N.; Abeijon, P.; Caamano, O.; Yanez, M.; Munteanu, C. R.; Pazos, A.; Dea-Ayuela, M. A.; Gomez-Munoz, M. T.; Garijo, M. M.; Sansano, J.; Ubeira, F. M. MIND-BEST: Web Server for Drugs and Target Discovery; Design, Synthesis, and Assay of MAO-B Inhibitors and Theoretical-Experimental Study of G3PDH Protein from Trichomonas gallinae J. Proteome Res. 2011, 10, 1698-1718
58. Gonzalez-Diaz, H.; Prado-Prado, F.; Sobarzo-Sanchez, E.; Haddad, M.; Chevalley, S. M.; Valentin, A.; Quetin-Leclercq, J.; Dea-Ayuela, M. A.; Teresa Gomez-Munos, M.; Munteanu, C. R.; Jose Torres-Labandeira, J.; Garcia-Mera, X.; Tapia, R. A.; Ubeira, F. M. NL MIND-BEST: A web server for ligands and proteins discovery-Theoretic-experimental study of proteins of Giardia lamblia and new compounds active against Plasmodium falciparum J. Theor. Biol. 2011, 276, 229-249
59. González-Díaz, H.; Vilar, S.; Santana, L.; Uriarte, E. Medicinal Chemistry and Bioinformatics-Current Trends in Drugs Discovery with Networks Topological Indices Curr. Top. Med. Chem. 2007, 7, 1025-39
60. González-Díaz, H.; González-Díaz, Y.; Santana, L.; Ubeira, F. M.; Uriarte, E. Proteomics, networks and connectivity indices Proteomics 2008, 8, 750-778 Education Scholars