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Volumn 18, Issue 6, 2008, Pages 467-476

Prediction of sites under adaptive evolution in cytochrome P450 sequences and their relationship to substrate recognition sites

Author keywords

Adaptive evolution; Cytochrome P450; Positive darwinian selection; Selection; Substrate recognition site

Indexed keywords

CYTOCHROME P450; CYTOCHROME P450 2B; CYTOCHROME P450 2C; CYTOCHROME P450 2D; CYTOCHROME P450 3A;

EID: 44649143137     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/FPC.0b013e3282f9b68e     Document Type: Article
Times cited : (12)

References (42)
  • 1
    • 27944474033 scopus 로고    scopus 로고
    • Selectionism and neutralism in molecular evolution
    • Nei M. Selectionism and neutralism in molecular evolution. Mol Biol Evol 2005; 22:2318-2342.
    • (2005) Mol Biol Evol , vol.22 , pp. 2318-2342
    • Nei, M.1
  • 2
    • 0033800170 scopus 로고    scopus 로고
    • Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites
    • Yang Z, Swanson WJ, Vacquier VD. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Mol Biol Evol 2000; 17:1446-1455.
    • (2000) Mol Biol Evol , vol.17 , pp. 1446-1455
    • Yang, Z.1    Swanson, W.J.2    Vacquier, V.D.3
  • 3
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 1998; 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 4
    • 0020383449 scopus 로고
    • Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide
    • Gojobori T, Ishii K, Nei M. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol 1982; 18:414-423.
    • (1982) J Mol Evol , vol.18 , pp. 414-423
    • Gojobori, T.1    Ishii, K.2    Nei, M.3
  • 5
    • 0030750055 scopus 로고    scopus 로고
    • Long term trends in the evolution of H(3) HA1 human influenza type A
    • Fitch WM, Bush RM, Bender CA, Cox NJ. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci U S A 1997; 94:7712-7718.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , pp. 7712-7718
    • Fitch, W.M.1    Bush, R.M.2    Bender, C.A.3    Cox, N.J.4
  • 6
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • Yang Z, Nielsen R, Hasegawa M. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol 1998; 15:1600-1611.
    • (1998) Mol Biol Evol , vol.15 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Hasegawa, M.3
  • 7
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000; 17:32-43.
    • (2000) Mol Biol Evol , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 8
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen AM. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000; 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.4
  • 9
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 2002; 19:908-917.
    • (2002) Mol Biol Evol , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 11
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997; 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 13
    • 0036890399 scopus 로고    scopus 로고
    • The cytochrome P450 superfamily: Biochemistry, evolution and drug metabolism in humans
    • Danielson PB. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab 2002; 3:561-597.
    • (2002) Curr Drug Metab , vol.3 , pp. 561-597
    • Danielson, P.B.1
  • 14
    • 0037225752 scopus 로고    scopus 로고
    • Study of P450 function using gene knockout and transgenic mice
    • Gonzalez FJ, Kimura S. Study of P450 function using gene knockout and transgenic mice. Arch Biochem Biophys 2003; 409:153-158.
    • (2003) Arch Biochem Biophys , vol.409 , pp. 153-158
    • Gonzalez, F.J.1    Kimura, S.2
  • 17
    • 0023598348 scopus 로고
    • Evolution of cytochrome P-450 proteins
    • Nelson DR, Strobel HW. Evolution of cytochrome P-450 proteins. Mol Biol Evol 1987; 4:572-593.
    • (1987) Mol Biol Evol , vol.4 , pp. 572-593
    • Nelson, D.R.1    Strobel, H.W.2
  • 18
    • 0027078402 scopus 로고
    • Human cytochromes P450: Evolution and cDNA-directed expression
    • Gonzalez FJ, Gelboin HV. Human cytochromes P450: evolution and cDNA-directed expression. Environ Health Perspect 1992; 98:81-85.
    • (1992) Environ Health Perspect , vol.98 , pp. 81-85
    • Gonzalez, F.J.1    Gelboin, H.V.2
  • 19
    • 0026542989 scopus 로고
    • Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences
    • 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.
    • (1992) J Biol Chem , vol.267 , pp. 83-90
    • Gotoh, O.1
  • 20
    • 0034961867 scopus 로고    scopus 로고
    • Cytochrome P450 (CYP) mutants and substrate-specificity alterations: Segment-directed mutagenesis applied to human CYP1A1
    • Urban P, Jobert AS, Laine R, Pompon D. Cytochrome P450 (CYP) mutants and substrate-specificity alterations: segment-directed mutagenesis applied to human CYP1A1. Biochem Soc Trans 2001; 29:128-135.
    • (2001) Biochem Soc Trans , vol.29 , pp. 128-135
    • Urban, P.1    Jobert, A.S.2    Laine, R.3    Pompon, D.4
  • 23
    • 0037307413 scopus 로고    scopus 로고
    • Signatures of natural selection in the human genome
    • Bamshad M, Wooding SP. Signatures of natural selection in the human genome. Nat Rev Genet 2003; 4:99-111.
    • (2003) Nat Rev Genet , vol.4 , pp. 99-111
    • Bamshad, M.1    Wooding, S.P.2
  • 24
    • 33744911365 scopus 로고    scopus 로고
    • A revised evolutionary history of the CYP1A Subfamily: Gene duplication, gene conversion, and positive selection
    • Goldstone HM, Stegeman JJ. A revised evolutionary history of the CYP1A Subfamily: gene duplication, gene conversion, and positive selection. J Mol Evol 2006; 62:708-719.
    • (2006) J Mol Evol , vol.62 , pp. 708-719
    • Goldstone, H.M.1    Stegeman, J.J.2
  • 25
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. 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.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 27
    • 44649088626 scopus 로고    scopus 로고
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876-4882.
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL
  • 28
    • 33747847779 scopus 로고    scopus 로고
    • PAL2 NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • Suyama M, Torrents D, Bork P. PAL2 NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 2006; 34:W609-W612.
    • (2006) Nucleic Acids Res , vol.34
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 29
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 30
    • 0035957018 scopus 로고    scopus 로고
    • Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals
    • Swanson WJ, Yang Z, Wolfner MF, Aquadro CF. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc Natl Acad Sci U S A 2001; 98:2509-2514.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 2509-2514
    • Swanson, W.J.1    Yang, Z.2    Wolfner, M.F.3    Aquadro, C.F.4
  • 31
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 34
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 1977; 6:151-176.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 35
    • 0029968922 scopus 로고    scopus 로고
    • The contour-buildup algorithm to calculate the analytical molecular surface
    • Totrov M, Abagyan R. The contour-buildup algorithm to calculate the analytical molecular surface. J Struct Biol 1996; 116:138-143.
    • (1996) J Struct Biol , vol.116 , pp. 138-143
    • Totrov, M.1    Abagyan, R.2
  • 36
    • 0036724899 scopus 로고    scopus 로고
    • DNA sequence variation in a 3.7-kb noncoding sequence 5′ of the CYP1A2 gene: Implications for human population history and natural selection
    • Wooding SP, Watkins WS, Bamshad MJ, Dunn DM, Weiss RB, Jorde LB. DNA sequence variation in a 3.7-kb noncoding sequence 5′ of the CYP1A2 gene: implications for human population history and natural selection. Am J Hum Genet 2002; 71:528-542.
    • (2002) Am J Hum Genet , vol.71 , pp. 528-542
    • Wooding, S.P.1    Watkins, W.S.2    Bamshad, M.J.3    Dunn, D.M.4    Weiss, R.B.5    Jorde, L.B.6
  • 38
    • 33845624599 scopus 로고    scopus 로고
    • Structural divergence and adaptive evolution in mammalian cytochromes P450 2C
    • da Fonseca RR, Antunes A, Melo A, Ramos MJ. Structural divergence and adaptive evolution in mammalian cytochromes P450 2C. Gene 2007; 387:58-66.
    • (2007) Gene , vol.387 , pp. 58-66
    • da Fonseca, R.R.1    Antunes, A.2    Melo, A.3    Ramos, M.J.4
  • 40
    • 44649181845 scopus 로고    scopus 로고
    • Yang Z. Phylogenetic Analysis by Maximum Likelihood version 4. 2007;
    • Yang Z. Phylogenetic Analysis by Maximum Likelihood version 4. 2007; http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf
  • 41
    • 0036548404 scopus 로고    scopus 로고
    • Cytochromes P450 and experimental models of drug metabolism
    • Zuber R, Anzenbacherova E, Anzenbacher P. Cytochromes P450 and experimental models of drug metabolism. J Cell Mol Med 2002; 6:189-198.
    • (2002) J Cell Mol Med , vol.6 , pp. 189-198
    • Zuber, R.1    Anzenbacherova, E.2    Anzenbacher, P.3
  • 42
    • 29144526714 scopus 로고    scopus 로고
    • Protein structure prediction: Inroads to biology
    • Petrey D, Honig B. Protein structure prediction: inroads to biology. Mol Cell 2005; 20:811-819.
    • (2005) Mol Cell , vol.20 , pp. 811-819
    • Petrey, D.1    Honig, B.2


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