Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase

Journal of Physical Chemistry B

Volumn 116, Issue 32, 2012, Pages 9580-9594

  Fu, Gang ^a   Liu, Haining ^a   Doerksen, Robert J ^a,b  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b UNIVERSITY OF MISSISSIPPI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CRYSTAL STRUCTURE; DEGRADATION; MOLECULAR DYNAMICS; MOLECULAR MODELING; PIGMENTS; PORPHYRINS; REACTION KINETICS; SUBSTRATES;

BINDING AFFINITIES; BINDING FREE ENERGY; BINDING MODES; CATALYTIC MECHANISMS; CELLULAR RESPONSE; COFACTORS; ELECTRON DONORS; HEME DEGRADATION; HUMAN BILIVERDINS; HYDRIDE TRANSFERS; INDUCED FIT; INHIBITOR DESIGN; KEY ENZYMES; MD SIMULATION; MECHANISTIC STUDIES; MOLECULAR DYNAMICS SIMULATIONS; POISSON BOLTZMANN SURFACE AREAS (PBSA); PYRROLIC NITROGEN; REACTION ENERGY; REDUCTION PRODUCTS; SUBSTRATE BINDING; TERNARY COMPLEX; X-RAY STRUCTURE;

ENZYME ACTIVITY;

EID: 84865131634     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp301456j     Document Type: Article

References (63)

1. McDonagh, A. F. Seminars in Fetal and Neonatal Medicine 2010, 15, 141-147
2. McDonagh, A. F. Nat. Struct. Biol. 2001, 8, 198-200
3. Pirone, C.; Martin E Quirke, J.; Priestap, H. A.; Lee, D. W. J. Am. Chem. Soc. 2009, 131, 2830
4. Sedlak, T. W. Pediatrics 2004, 113, 1776-1782
5. Wang, J.; Evans, J. P.; Ogura, H.; La Mar, G. N.; Ortiz de Montellano, P. R. Biochemistry 2006, 45, 61-73
6. Fujiwara, R.; Chen, S.; Karin, M.; Tukey, R. H. Gastroenterology 2012, 142, 109-118.e102
7. Pereira, P. J. B.; Maceddo-Ribeiro, S.; Parraga, A.; Perez-Luque, R.; Cunningham, O.; Darcy, K.; Mantle, T. J.; Coll, M. Nat. Struct. Biol. 2001, 8, 215-220
8. Wang, J.; Evans, J. P.; Ogura, H.; LaMar, G. N.; Ortiz de Montellano, P. R. Biochemistry 2006, 45, 61-73
9. Baranano, D. E.; Rao, M.; Ferries, C. D.; Snyder, S. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16093-16098
10. Maines, M. D. Physiology 2005, 20, 382-389
11. Kapitulnik, J.; Maines, M. D. Trends Pharmacol. Sci. 2009, 30, 129-137
12. Lerner-Marmarosh, N.; Shen, J.; Torno, M. D.; Kravets, A.; Hu, Z.; Maines, M. D. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7109-7114
13. Barbara, W.; David, G.; Csizmadia, E.; Roger, T.; Kaczmarek, E.; Harris, C.; Zuckerbraun, B. S.; Otterbein, L. E. Proc. Natl. Acad. Sci. U.S.A., Early Ed. 2011, 1-6
14. Kim, S. Y.; Kang, H. T.; Choi, H. R.; Park, S. C. Exp. Mol. Med. 2011, 43, 15-23
15. Ding, B.; Gibbs, P. E. M.; Brookes, P. S.; Maines, M. D. FASEB J. 2011, 25, 301-313
16. Barone, E.; Di Domenico, f.; Cenini, G.; Sultana, R.; Coccia, R.; Preziosi, P.; Perluigi, M.; Mancuso, C.; Butterfield, D. A. J. Alzheimers Dis. 2011, 25, 623-633
17. Maines, M. D. Curr. Drug Targets 2010, 11, 1586-1594
18. Kikuchi, A.; Park, S.; Miyatake, H.; Sun, D.; Sato, M.; Yoshida, T.; Shiro, Y. Nat. Struct. Biol. 2001, 8, 221-225
19. Franklin, E.; Browne, S.; Hayes, J.; Boland, C.; Dunne, A.; Elliot, G.; Mantle, T. J. Biochem. J. 2007, 405, 61-67
20. Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. J. Am. Chem. Soc. 2001, 123, 5221-5230
21. Li, W.; Ode, H.; Hoshino, T.; Liu, H.; Tang, Y.; Jiang, H. J. Chem. Theory Comput. 2009, 5, 1411-1420
22. Smith, L. J.; Browne, S.; Mulholland, A. J.; Mantle, T. J. Biochem. J. 2008, 411, 475-484
23. Whitby, F. G.; Philips, J. D.; Hill, C. P.; McCoubrey, W.; Maines, M. D. J. Mol. Biol. 2002, 319, 1199-1210
24. Prime, version 2.2 ed.; Schrödinger, LLC: New York, 2010.
25. Cunningham, O.; Dunne, A.; Sabido, P.; Lightner, D.; Mantle, T. J. J. Biol. Chem. 2000, 275, 19009-19017
26. Mora, M. E.; Bari, S. E.; Awruch, J.; Delfino, J. M. Bioorg. Med. Chem. 2003, 11, 4661-4672
27. Marai, C. N. J.; Chass, G. A.; Doust, A. B.; Scholes, G. D. J. Mol. Struct.: THEOCHEM 2004, 680, 219-225
28. Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R. J. Med. Chem. 2006, 49, 534-553
29. Glide, version 5.6 ed.; Schrödinger, LLC: New York, 2010.
30. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Gaussian 03, revision C.02 ed.; Gaussian, Inc.: Wallingford, CT, 2004.
31. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280
32. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668-1688
33. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. J. Comput. Chem. 2003, 24, 1999-2012
34. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157-1174
35. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
36. Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; AMBER9; University of California: San Francisco, CA, 2006.
37. Pastor, R. W.; Brooks, B. R.; Szabo, A. Mol. Phys. 1988, 65, 1409-1419
38. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T. J. Chem. Phys. 1995, 103, 8577-9593
39. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341
40. Gilson, M. K.; Sharp, K. A.; Honig, B. H. J. Comput. Chem. 1987, 9, 327-335
41. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988
42. Villa, J.; Strajbl, M.; Glennon, T. M.; Sham, Y. Y.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 11899-11904
43. Kuhn, B.; Kollman, P. A. J. Med. Chem. 2000, 43, 3786-3791
44. Gohlke, H.; Kiel, C.; Case, D. A. J. Mol. Biol. 2003, 330, 891-913
45. Qsite, version 5.0 ed.; Schrödinger, LLC: New York, 2008.
46. Becke, A. D. J. Chem. Phys. 1993, 98, 1372-1377
47. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
48. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789
49. Friesner, R. A. Drug Discovery Today: Technol. 2004, 1, 253-260
50. Friesner, R. A.; Guallar, V. Annu. Rev. Phys. Chem. 2005, 56, 389-427
51. Lin, H.; Truhlar, D. Theor. Chem. Acc. 2007, 117, 185-199
52. Senn, H. M.; Thiel, W. Curr. Opin. Chem. Biol. 2007, 11, 182-187
53. Gherman, B. F.; Goldberg, S. D.; Cornish, V. W.; Friesner, R. A. J. Am. Chem. Soc. 2004, 126, 7652-7664
54. Gherman, B. F.; Lippard, S. J.; Friesner, R. A. J. Am. Chem. Soc. 2005, 127, 1025-1037
55. Guallar, V.; Friesner, R. A. J. Am. Chem. Soc. 2004, 126, 8501-8508
56. Guallar, V.; Jacobson, M.; McDermott, A.; Friesner, R. A. J. Mol. Biol. 2004, 337, 227-239
57. Kravitz, J. Y.; Pecoraro, V. L.; Carlson, H. A. J. Chem. Theory Comput. 2005, 1, 1265-1274
58. Philipp, D. M.; Friesner, R. A. J. Comput. Chem. 1999, 20, 1468-1494
59. Rinaldo, D.; Philipp, D. M.; Lippard, S. J.; Friesner, R. A. J. Am. Chem. Soc. 2007, 129, 3135-3147
60. Tian, L.; Friesner, R. A. J. Chem. Theory Comput. 2009, 5, 1421-1431
61. Wirstam, M.; Lippard, S. J.; Friesner, R. A. J. Am. Chem. Soc. 2003, 125, 3980-3987
62. Jaguar, version 7.7 ed.; Schrödinger, LLC: New York, 2010.
63. Cho, K.-B.; Derat, E.; Shaik, S. J. Am. Chem. Soc. 2007, 129, 3182-3188