On the deduction and analysis of singlet and two-state gating-models from the static structures of mammalian CYP450

Journal of Structural Biology

Volumn 173, Issue 2, 2011, Pages 282-293

  Zawaira, Alexander ^a   Coulson, Lauren ^a   Gallotta, Marco ^b   Karimanzira, Owen ^a   Blackburn, Jonathan ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Cytochrome P450; Gating residues; Molecular dynamics; Random expulsion molecular dynamics; Tunnels

Indexed keywords

ALIPHATIC COMPOUND; AROMATIC COMPOUND; CYTOCHROME P450; CYTOCHROME P450 2C5; CYTOCHROME P450 2C8; CYTOCHROME P450 2C9; CYTOCHROME P450 3A4; CYTOCHROME P450 3A6; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CHANNEL GATING; HYDROPHOBICITY; MAMMAL; MOLECULAR DYNAMICS; POLARIZATION; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ARYL HYDROCARBON HYDROXYLASES; CYTOCHROME P-450 CYP3A; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, SECONDARY;

MAMMALIA;

EID: 78751580308     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.09.026     Document Type: Article

References (34)

1. Boddupalli S.S., Hasemann C.A., Ravichandran K.G., Lu J.Y., Goldsmith E.J., Deisenhofer J., Peterson J.A. Crystallization and preliminary x-ray diffraction analysis of P450terp and the hemoprotein domain of P450BM-3, enzymes belonging to two distinct classes of the cytochrome P450 superfamily. Proc. Natl Acad. Sci. USA 1992, 89:5567-5571.
2. Bridges A., Gruenke L., Chang Y.T., Vakser I.A., Loew G., Waskell L. Identification of the binding site on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase. J. Biol. Chem. 1998, 273:17036-17049.
3. Cojocaru V., Winn P.J., Wade R.C. The ins and outs of cytochrome P450s. Biochim. Biophys. Acta 2007, 1770:390-401.
4. Cupp-Vickery J.R., Poulos T.L. Structure of cytochrome P450eryF involved in erythromycin biosynthesis. Nat. Struct. Biol. 1995, 2:144-153.
5. Fishelovitch D., Shaik S., Wolfson H.J., Nussinov R. Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J. Phys. Chem. B 2009, 113:13018-13025.
6. Fulco A.J. P450BM-3 and other inducible bacterial P450 cytochromes: biochemistry and regulation. Annu. Rev. Pharmacol. Toxicol. 1991, 31:177-203.
7. 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.
8. Haines D.C., Tomchick D.R., Machius M., Peterson J.A. Pivotal role of water in the mechanism of P450BM-3. Biochemistry 2001, 40:13456-13465.
9. Hasemann C.A., Kurumbail R.G., Boddupalli S.S., Peterson J.A., Deisenhofer J. Structure and function of cytochromes P450: a comparative analysis of three crystal structures. Structure 1995, 3:41-62.
10. Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., Gibson T.J. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 1998, 23:403-405.
11. Lamb D.C., Lei L., Warrilow A.G., Lepesheva G.I., Mullins J.G., Waterman M.R., Kelly S.L. The first virally encoded cytochrome p450. J. Virol. 2009, 83:8266-8269.
12. Ludemann S.K., Carugo O., Wade R.C. Substrate access to cytochrome P450cam: a comparison of thermal motion pathway analysis with molecular dynamics simulation data. J. Mol. Model. 1997, 3:369-374.
13. Ludemann S.K., Lounnas V., Wade R.C. How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J. Mol. Biol. 2000, 303:797-811.
14. Ludemann S.K., Lounnas V., Wade R.C. How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. J. Mol. Biol. 2000, 303:813-830.
15. Park S.Y., Shimizu H., Adachi S., Shiro Y., Iizuka T., Nakagawa A., Tanaka I., Shoun H., Hori H. Crystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome P450nor. FEBS Lett. 1997, 412:346-350.
16. Park S.Y., Shimizu H., Adachi S., Nakagawa A., Tanaka I., Nakahara K., Shoun H., Obayashi E., Nakamura H., Iizuka T., Shiro Y. Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum. Nat. Struct. Biol. 1997, 4:827-832.
17. Petrek M., Otyepka M., Banas P., Kosinova P., Koca J., Damborsky J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinf. 2006, 7:316.
18. Pupko T., Bell R.E., Mayrose I., Glaser F., Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002, 18(Suppl. 1):S71-S77.
19. Sansen S., Yano J.K., Reynald R.L., Schoch G.A., Griffin K.J., Stout C.D., Johnson E.F. Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2. J. Biol. Chem. 2007, 282:14348-14355.
20. Schleinkofer K., Sudarko P.J., Winn P.J., Ludemann S.K., Wade R.C. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?. EMBO Rep. 2005, 6:584-589.
21. Schoch G.A., Yano J.K., Wester M.R., Griffin K.J., Stout C.D., Johnson E.F. Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J. Biol. Chem. 2004, 279:9497-9503.
22. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
23. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
24. Tina K.G., Bhadra R., Srinivasan N. PIC: Protein Interactions Calculator. Nucleic Acids Res. 2007, 35:W473-W476.
25. Valdar W.S. Scoring residue conservation. Proteins 2002, 48:227-241.
26. Valencia A. Automatic annotation of protein function. Curr. Opin. Struct. Biol. 2005, 15:267-274.
27. Wade R.C., Winn P.J., Schlichting I., Sudarko P.J. A survey of active site access channels in cytochromes P450. J. Inorg. Biochem. 2004, 98:1175-1182.
28. Wade R.C., Motiejunas D., Schleinkofer K., Sudarko P.J., Winn P.J., Banerjee A., Kariakin A., Jung C. Multiple molecular recognition mechanisms. Cytochrome P450 - a case study. Biochim. Biophys. Acta 2005, 1754:239-244.
29. Werck-Reichhart, D., Feyereisen, R., 2000. Cytochromes P450: a success story. Genome Biol 1: REVIEWS3003.
30. Wester M.R., Yano J.K., Schoch G.A., Yang C., Griffin K.J., Stout C.D., Johnson E.F. The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution. J. Biol. Chem. 2004, 279:35630-35637.
31. Winn P.J., Ludemann S.K., Gauges R., Lounnas V., Wade R.C. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine. Proc. Natl Acad. Sci. USA 2002, 99:5361-5366.
32. Yano J.K., Wester M.R., Schoch G.A., Griffin K.J., Stout C.D., Johnson E.F. The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution. J. Biol. Chem. 2004, 279:38091-38094.
33. Zawaira A., Matimba A., Masimirembwa C. Prediction of sites under adaptive evolution in cytochrome P450 sequences and their relationship to substrate recognition sites. Pharmacogenet. Genomics 2008, 18:467-476.
34. Zawaira A., Gallotta M., Beeton-Kempen N., Coulson L., Marais P., Kuttel M., Blackburn J. Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins. Comput. Biol. Chem. 2010, 34:42-52.