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Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ

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Abstract

The three-dimensional modelling of proteins is a useful tool to fill the gap between the number of sequenced proteins and the number of experimentally known 3D structures. However, when the degree of homology between the protein and the available 3D templates is low, model building becomes a difficult task and the reliability of the results depends critically on the correctness of the sequence alignment. For this reason, we have undertaken the modelling of human cytochrome P450 1A2 starting by a careful analysis of several sequence alignment strategies (multiple sequence alignments and the TOPITS threading technique). The best results were obtained using TOPITS followed by a manual refinement to avoid unlikely gaps. Because TOPITS uses secondary structure predictions, several methods that are available for this purpose (Levin, Gibrat, DPM, NnPredict, PHD, SOPM and NNSP) have also been evaluated on cytochromes P450 with known 3D structures. More reliable predictions on α-helices have been obtained with PHD, which is the method implemented in TOPITS. Thus, a 3D model for human cytochrome P450 1A2 has been built using the known crystal coordinates of P450 BM3 as the template. The model was refined using molecular mechanics computations. The model obtained shows a consistent location of the substrate recognition segments previously postulated for the CYP2 family members. The interaction of caffeine and a carcinogenic aromatic amine (MeIQ), which are characteristic P450 1A2 substrates, has been investigated. The substrates were solvated taking into account their molecular electrostatic potential distributions. The docking of the solvated substrates in the active site of the model was explored with the AUTODOCK programme, followed by molecular mechanics optimisation of the most interesting complexes. Stable complexes were obtained that could explain the oxidation of the considered substrates by cytochrome P450 1A2 and could offer an insight into the role played by water molecules.

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References

  1. Black, S.D. and Coon, M.J., Adv. Enzymol., 60 (1987) 35.

    Google Scholar 

  2. Grant, D.M., Campbell, M.E., Tang, B.K. and Kallow, W., Biochem. Pharmacol., 36 (1987) 1251.

    Google Scholar 

  3. Segura, J., Roberts, D.J. and Tarrús, E., J. Pharm. Pharmacol., 41 (1988) 129.

    Google Scholar 

  4. Fuhr, V., Strobl, G., Manaut, F., Anders, E.-M., Sörgel, F., López-de-Briñas, E., Chu, D.T.W., Pernet, A.G., Mahr, G., Sanz, F. and Staib, H., Mol. Pharmacol., 43 (1993) 191.

    Google Scholar 

  5. Wakabayashi, K., Nagao, M., Esumi, H. and Sugimura, T., Cancer Res., 52 (Suppl.) (1992) 2092.

  6. Shimada, T., Iwasaki, M., Martin, M.V. and Guengerich, F.P., Cancer Res., 49 (1989) 3218.

    Google Scholar 

  7. Yamashita, K., Umemoto, A., Grivas, S., Kato, S., Sato, S. and Sugimura, T., Nucleic Acids Res., 19 (1988) 111.

    Google Scholar 

  8. Poulos, T.L., Finzel, B.C. and Howard, A.J., Biochemistry, 25 (1986) 5314.

    Google Scholar 

  9. Ravichandran, K.G., Boddupalli, S.S., Hasemann, C.A., Peterson, J.A. and Deisenhofer, J., Science, 261 (1993) 731.

    Google Scholar 

  10. Hasemann, C.A., Ravichandran, K.G., Peterson, J.A. and Deisenhofer, J., J. Mol. Biol., 236 (1994) 1169.

    Google Scholar 

  11. Cupp-Vickery, J.R. and Poulos, T.L., Nat. Struct. Biol., 2 (1995) 144.

    Google Scholar 

  12. Hasemann, C.A., Kurumbail, R.G., Boddupalli, S.S., Peterson, J.A. and Deisenhofer, J., Structure, 3 (1993) 41.

    Google Scholar 

  13. Laughton, C.A., Neidle, S., Zvelebil, M.J.J.M. and Sternberg, M.J.E., Biochem. Biophys. Res. Commun., 171 (1990) 1160.

    Google Scholar 

  14. Morris, G.M. and Richards, W.G., Biochem. Soc. Trans., 19 (1991) 793.

    Google Scholar 

  15. Zvelebil, M.J.J.M., Wolf, C.R. and Sternberg, M.J.E., Protein Eng., 4 (1991) 271.

    Google Scholar 

  16. Lewis, D.F.V. and Moereels, H., J. Comput.-Aided Mol. Design, 6 (1992) 235.

    Google Scholar 

  17. Vijayakumar, S. and Salerno, J.C., Biochim. Biophys. Acta, 1160 (1992) 281.

    Google Scholar 

  18. Laughton, C.A., Zvelebil, M.J.J.M. and Neidle, S., J. Steroid Biochem. Mol. Biol., 44 (1993) 399.

    Google Scholar 

  19. Koymans, L.M.H., Vermeulen, N.P.E., Baarslag, A. and Donné-Op den Kelder, G.M., J. Comput.-Aided Mol. Design, 7 (1993) 281.

    Google Scholar 

  20. Boscott, P.E. and Grant, G.H., J. Mol. Graph., 12 (1994) 185.

    Google Scholar 

  21. Szklarz, G.D., Ornstein, R.L. and Halpert, J.R., J. Biomol. Struct. Dyn., 12 (1994) 61.

    Google Scholar 

  22. Narhi, L.O. and Fulco, A.J., J. Biol. Chem., 262 (1987) 6683.

    Google Scholar 

  23. Nelson, D.R. and Strobel, H.W., Biochemistry, 28 (1989) 656.

    Google Scholar 

  24. Mosimann, S., Meleshko, R. and James, M.N.G., Proteins Struct. Funct. Genet., 23 (1995) 301.

    Google Scholar 

  25. Chang, Y.-T. and Loew, G.H., Protein Eng., 9 (1996) 755.

    Google Scholar 

  26. Sanz, F., López-de-Briñas, E., Rodríguez, J. and Manaut, F., Quant. Struct.-Act. Relatsh., 13 (1994) 281.

    Google Scholar 

  27. Lozano, J.J., López-de-Briñas, E., Manaut, F. and Sanz, F., In Sanz, F., Giraldo, J. and Manaut, F. (Eds.) QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, Prous Science, Barcelona, Spain, 1995, pp. 325–328.

    Google Scholar 

  28. Hasemann, C.A., Kurumbail, R.G., Boddupalli, S.S., Peterson, J.A. and Deisenhofer, J., Structure, 2 (1995) 41.

    Google Scholar 

  29. Thompson, J.D., Higgins, J.D. and Gibson, T.J., Nucleic Acids Res., 22 (1994) 4673.

    Google Scholar 

  30. PILEUP, Genetics Computer Group Inc., University Research Park, Madison, WI, U.S.A., 1995.

  31. Rost, B., In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S. (Eds.) Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, CA, U.S.A., 1995, pp. 314–321.

  32. Rost, B. and Sander, C., J. Mol. Biol., 232 (1993) 584.

    Google Scholar 

  33. Levin, J.M., Robson, B. and Garnier, J., FEBS Lett., 205 (1986) 303.

    Google Scholar 

  34. Gibrat, J.F., Garnier, J. and Robson, B., J. Mol. Biol., 198 (1987) 425.

    Google Scholar 

  35. Deleage, G. and Roux, B., Protein Eng., 1 (1987) 289.

    Google Scholar 

  36. Kneller, G., Cohe, F.E. and Langridge, R., J. Mol. Biol., 214 (1990) 171.

    Google Scholar 

  37. Geourjon, C. and Deleage, G., Protein Eng., 7 (1994) 157.

    Google Scholar 

  38. Salamov, A.A. and Solovyev, V.V., J. Mol. Biol., 247 (1995) 11.

    Google Scholar 

  39. Deleage, G., Clerc, F.F., Roux, B. and Gautheron, D.C., Comput. Appl. Biosci., 4 (1988) 351.

    Google Scholar 

  40. SOPM, http://www.ibcp.fr.

  41. NnPredict, http://www.cmpharm.ucsf.edu.

  42. PHDsec, http://www.embl-heidelberg.de.

  43. NNSP, http://www.bcm.tcm.edu.

  44. Kabsch, W. and Sander, C., Biopolymers, 22 (1983) 2577.

    Google Scholar 

  45. Vriend, G., J. Mol. Graph., 8 (1990) 52.

    Google Scholar 

  46. HOMOLOGY (v. 95.0) from Biosym/MSI, San Diego, CA, U.S.A., 1995.

  47. Hobohm, U., Scharf, M., Schneider, R. and Sander, C., Protein Sci., 1 (1992) 409.

    Google Scholar 

  48. Hobohm, U. and Sander, C., Protein Sci., 3 (1994) 522.

    Google Scholar 

  49. DISCOVER (v. 2.9.5) from Biosym/MSI, San Diego, CA, U.S.A., 1995.

  50. Dauber-Osguthorpe, P., Roberst, V.A. and Wolff, J., Proteins Struct. Funct. Genet., 4 (1988) 31.

    Google Scholar 

  51. INSIGHT II (v. 95.0) from Biosym/MSI, San Diego, CA, U.S.A., 1995.

  52. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M., J. Appl. Crystallogr., 26 (1993) 283.

    Google Scholar 

  53. Hooft, R.W.W., Vriend, G., Sander, C. and Abola, E.E., Nature, 381 (1996) 272.

    Google Scholar 

  54. GAUSSIAN 94, Gaussian Inc., Pittsburgh, PA, U.S.A.

  55. Sanz, F., Manaut, F., José, J., Segura, J., Carbó, M. and De la Torre, R., J. Mol. Struct. (THEOCHEM), 170 (1988) 171.

    Google Scholar 

  56. Sanz, F., Manaut, F., Rodríguez, J., Lozoya, E. and López-de-Briñas, E., J. Comput.-Aided Mol. Design, 7 (1993) 337.

    Google Scholar 

  57. Morris, G.M., Goodsell, D., Huey, R. and Olson, A.J., J. Comput.-Aided Mol. Design, 10 (1996) 293.

    Google Scholar 

  58. Degtyarenko, K.N. and Archakov, A.I., FEBS Lett., 322 (1993) 1.

    Google Scholar 

  59. Valencia, A., Kjeldgaard, M., Pai, E.F. and Sander, C., Proc. Natl. Acad. Sci. USA, 88 (1991) 5443.

    Google Scholar 

  60. Gotoh, O., J. Biol. Chem., 267 (1992) 83.

    Google Scholar 

  61. Arnold, G.E. and Ornstein, R.L., Proteins Struct. Funct. Genet., 18 (1994) 19.

    Google Scholar 

  62. Guenot, J.M. and Kollman, P.A., Protein Sci., 1 (1992) 1185.

    Google Scholar 

  63. Guenot, J.M. and Kollman, P.A., J. Comput. Chem., 14 (1993) 295.

    Google Scholar 

  64. Vriend, G. and Sander, C., J. Appl. Crystallogr., 26 (1993) 47.

    Google Scholar 

  65. Furuya, H., Shimizu, T., Hirano, K., Hatano, M. and Fujii-Kuriyama, Y., Biochemistry, 28 (1989) 6848.

    Google Scholar 

  66. Shimizu, T., Sadeque, A.J.M., Sadeque, G.N., Hatano, M. and Fujii-Kuriyama, Y., Biochemistry, 30 (1991) 1490.

    Google Scholar 

  67. Tuck, F.S., Hiroya, K., Shimizu, T., Hatano, M. and Ortiz de Montellano, P.R., Biochemistry, 32 (1993) 2548.

    Google Scholar 

  68. Mayuzumi, H., Shimizu, T., Sambongi, C., Hiroya, K. and Hatano, M., Arch. Biochem. Biophys., 310 (1994) 367.

    Google Scholar 

  69. Edwards, R.J., Singleton, A.M., Murray, B.P., Murray, S., Boobis, A.R. and Davies, D.S., Biochem. J., 278 (1991) 749.

    Google Scholar 

  70. Edwards, R.J., Sesardic, D., Murray, B.P., Singleton, A.M., Davies, D.S. and Boobis, A.R., Biochem. Pharmacol., 43 (1992) 1737.

    Google Scholar 

  71. Shen, S. and Strobel, H.W., Arch. Biochem. Biophys., 294 (1992) 83.

    Google Scholar 

  72. Cvrk, T., Hodek, P. and Strobel, H.W., Arch. Biochem. Biophys., 330 (1996) 142.

    Google Scholar 

  73. Poulos, T.L., Finzel, B.C. and Howard, A.J., J. Mol. Biol., 195 (1987) 687.

    Google Scholar 

  74. Poulos, T.L. and Howard, A.J., Biochemistry, 26 (1987) 8165.

    Google Scholar 

  75. Raag, R., Li, H., Jones, B.C. and Poulos, T.L., Biochemistry, 32 (1993) 4571.

    Google Scholar 

  76. Poulos, T.L., Finzel, B.C., Gunsalus, I.C., Wagner, G.C. and Kraut, J., J. Biol. Chem., 260 (1985) 16122.

    Google Scholar 

  77. Fuhr, U., Dohmer, J., Battula, N., Wölfel, C., Kudla, C., Keita, Y. and Staib, H., Biochem. Pharmacol., 43 (1992) 225.

    Google Scholar 

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Lozano, J., López-de-Briñas, E., Centeno, N. et al. Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ. J Comput Aided Mol Des 11, 395–408 (1997). https://doi.org/10.1023/A:1007947411145

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