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Volumn 60, Issue 4, 2005, Pages 606-616

Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes

Author keywords

Bioinformatics; Genome wide analysis; Hydrophobicity scale; Membrane protein; Prediction; Transmembrane helices

Indexed keywords

ARGININE; LYSINE; MEMBRANE PROTEIN;

EID: 24644490119     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20583     Document Type: Article
Times cited : (105)

References (45)
  • 1
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7:1029-1038.
    • (1998) Protein Sci , vol.7 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 2
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane protein superfolds exist?
    • Jones DT. Do transmembrane protein superfolds exist? FEBS Lett 1998;423:281-285.
    • (1998) FEBS Lett , vol.423 , pp. 281-285
    • Jones, D.T.1
  • 4
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567-580.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 5
    • 0037472764 scopus 로고    scopus 로고
    • Comprehensive analysis of transmembrane topologies in prokaryotic genomes
    • Arai M, Ikeda M, Shimizu T. Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene 2003;304:77-86.
    • (2003) Gene , vol.304 , pp. 77-86
    • Arai, M.1    Ikeda, M.2    Shimizu, T.3
  • 6
    • 0001911218 scopus 로고    scopus 로고
    • State-of-the-art in membrane protein prediction
    • Chen CP, Rost B. State-of-the-art in membrane protein prediction. Appl Bioinformatics 2002;1:21-35.
    • (2002) Appl Bioinformatics , vol.1 , pp. 21-35
    • Chen, C.P.1    Rost, B.2
  • 7
    • 0024442722 scopus 로고
    • Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues
    • von Heijne G. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature 1989;341:456-458.
    • (1989) Nature , vol.341 , pp. 456-458
    • Von Heijne, G.1
  • 8
    • 0000651660 scopus 로고
    • The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology
    • von Heijne G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology. EMBO J 1986;5:3021-3027.
    • (1986) EMBO J , vol.5 , pp. 3021-3027
    • Von Heijne, G.1
  • 9
    • 0027264995 scopus 로고
    • Predicting the topology of eukaryotic membrane proteins
    • Sipos L, von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur J Biochem 1993;213:1333-1340.
    • (1993) Eur J Biochem , vol.213 , pp. 1333-1340
    • Sipos, L.1    Von Heijne, G.2
  • 10
    • 0025896455 scopus 로고
    • The 'positive-inside rule' applies to thylakoid membrane proteins
    • Gavel Y, Steppuhn J, Herrmann R, von Heijne G. The 'positive-inside rule' applies to thylakoid membrane proteins. FEBS Lett 1991;282:41-46.
    • (1991) FEBS Lett , vol.282 , pp. 41-46
    • Gavel, Y.1    Steppuhn, J.2    Herrmann, R.3    Von Heijne, G.4
  • 11
    • 0026609104 scopus 로고
    • The distribution of charged amino acids in mitochondrial inner-membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins
    • Gavel Y, von Heijne G. The distribution of charged amino acids in mitochondrial inner-membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins. Eur J Biochem 1992;205:1207-1215.
    • (1992) Eur J Biochem , vol.205 , pp. 1207-1215
    • Gavel, Y.1    Von Heijne, G.2
  • 12
    • 0026716643 scopus 로고
    • Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
    • von Heijne G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 1992;225:487-494.
    • (1992) J Mol Biol , vol.225 , pp. 487-494
    • Von Heijne, G.1
  • 13
    • 0028568176 scopus 로고
    • TopPred II: An improved software for membrane protein structure predictions
    • Claros MG, von Heijne G. TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci 1994;10:685-686.
    • (1994) Comput Appl Biosci , vol.10 , pp. 685-686
    • Claros, M.G.1    Von Heijne, G.2
  • 14
    • 0000092577 scopus 로고    scopus 로고
    • Free energy determinants of peptide association with lipid bilayers
    • Simon S, McIntosh T, editors. San Diego: Academic Press
    • Kessel A, Ben-Tal N. Free energy determinants of peptide association with lipid bilayers. In: Simon S, McIntosh T, editors. Peptide-lipid interactions. San Diego: Academic Press; 2002.
    • (2002) Peptide-Lipid Interactions
    • Kessel, A.1    Ben-Tal, N.2
  • 15
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 1984;179:125-142.
    • (1984) J Mol Biol , vol.179 , pp. 125-142
    • Eisenberg, D.1    Schwarz, E.2    Komaromy, M.3    Wall, R.4
  • 16
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman DM, Steitz TA, Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem 1986;15:321-353.
    • (1986) Annu Rev Biophys Biophys Chem , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 17
    • 0000448982 scopus 로고
    • Prediction of protein antigenic determinants from amino acid sequences
    • Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 1981;78:3824-3828.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 3824-3828
    • Hopp, T.P.1    Woods, K.R.2
  • 18
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 19
    • 0035812599 scopus 로고    scopus 로고
    • Energetics, stability, and prediction of transmembrane helices
    • Jayasinghe S, Hristova K, White SH. Energetics, stability, and prediction of transmembrane helices. J Mol Biol 2001;312:927-934.
    • (2001) J Mol Biol , vol.312 , pp. 927-934
    • Jayasinghe, S.1    Hristova, K.2    White, S.H.3
  • 20
    • 0022484922 scopus 로고
    • Prediction of protein structure
    • Argos P, Rao JK. Prediction of protein structure. Methods Enzymol 1986;130:185-207.
    • (1986) Methods Enzymol , vol.130 , pp. 185-207
    • Argos, P.1    Rao, J.K.2
  • 21
    • 0037633968 scopus 로고    scopus 로고
    • Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method
    • Zhou H, Zhou Y. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Sci 2003;12:1547-1555.
    • (2003) Protein Sci , vol.12 , pp. 1547-1555
    • Zhou, H.1    Zhou, Y.2
  • 22
    • 0034495418 scopus 로고    scopus 로고
    • A collection of well characterised integral membrane proteins
    • Möller S, Kriventseva EV, Apweiler R. A collection of well characterised integral membrane proteins. Bioinformatics 2000;16:1159-1160.
    • (2000) Bioinformatics , vol.16 , pp. 1159-1160
    • Möller, S.1    Kriventseva, E.V.2    Apweiler, R.3
  • 23
    • 0035109170 scopus 로고    scopus 로고
    • A database of membrane protein topology
    • Jayasinghe S, Hristova K, White S. A database of membrane protein topology. Protein Sci 2001;10:455-458.
    • (2001) Protein Sci , vol.10 , pp. 455-458
    • Jayasinghe, S.1    Hristova, K.2    White, S.3
  • 24
    • 0037249645 scopus 로고    scopus 로고
    • TMPDB: A database of experimentally-characterized transmembrane topologies
    • Ikeda M, Arai M, Okuno T, Shimizu T. TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res 2003;31:406-409.
    • (2003) Nucleic Acids Res , vol.31 , pp. 406-409
    • Ikeda, M.1    Arai, M.2    Okuno, T.3    Shimizu, T.4
  • 26
    • 0042622443 scopus 로고    scopus 로고
    • DSSPcont: Continuous secondary structure assignments for proteins
    • Carter P, Andersen CA, Rost B. DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res 2003;31:3293-3295.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3293-3295
    • Carter, P.1    Andersen, C.A.2    Rost, B.3
  • 29
    • 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
  • 32
    • 0033342531 scopus 로고    scopus 로고
    • Recent advances in the understanding of membrane protein assembly and structure
    • von Heijne G. Recent advances in the understanding of membrane protein assembly and structure. Quart Rev Biophys 2000;32:285-307.
    • (2000) Quart Rev Biophys , vol.32 , pp. 285-307
    • Von Heijne, G.1
  • 34
    • 0342351613 scopus 로고
    • Predicting the orientation of eukaryotic membrane-spanning proteins
    • Hartmann E, Rapoport TA, Lodish HF. Predicting the orientation of eukaryotic membrane-spanning proteins. Proc Natl Acad Sci USA 1989;86:5786-5790.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 5786-5790
    • Hartmann, E.1    Rapoport, T.A.2    Lodish, H.F.3
  • 35
    • 0028834958 scopus 로고
    • Properties of N-terminal tails in G-protein coupled receptors: A statistical study
    • Wallin E, von Heijne G. Properties of N-terminal tails in G-protein coupled receptors: a statistical study. Protein Eng 1995;8:693-698.
    • (1995) Protein Eng , vol.8 , pp. 693-698
    • Wallin, E.1    Von Heijne, G.2
  • 36
    • 0036557845 scopus 로고    scopus 로고
    • Basic charge clusters and predictions of membrane protein topology
    • Juretic D, Zoranic L, Zucic D. Basic charge clusters and predictions of membrane protein topology. J Chem Inf Comput Sci 2002;42:620-632.
    • (2002) J Chem Inf Comput Sci , vol.42 , pp. 620-632
    • Juretic, D.1    Zoranic, L.2    Zucic, D.3
  • 37
    • 0023676242 scopus 로고
    • Topogenic signals in integral membrane proteins
    • von Heijne G, Gavel Y. Topogenic signals in integral membrane proteins. Eur J Biochem 1988;174:671-678.
    • (1988) Eur J Biochem , vol.174 , pp. 671-678
    • Von Heijne, G.1    Gavel, Y.2
  • 38
    • 0026521552 scopus 로고
    • The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins
    • Nakashima H, Nishikawa K. The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Lett 1992;303:141-146.
    • (1992) FEBS Lett , vol.303 , pp. 141-146
    • Nakashima, H.1    Nishikawa, K.2
  • 39
    • 0026557830 scopus 로고
    • The functions of tryptophan residues in membrane proteins
    • Schiffer M, Chang CH, Stevens FJ. The functions of tryptophan residues in membrane proteins. Protein Eng 1992;5:213-214.
    • (1992) Protein Eng , vol.5 , pp. 213-214
    • Schiffer, M.1    Chang, C.H.2    Stevens, F.J.3
  • 40
    • 0029738872 scopus 로고    scopus 로고
    • Experimentally determined hydrophobicity scale for proteins at membrane interfaces
    • Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 1996;3:842-848.
    • (1996) Nat Struct Biol , vol.3 , pp. 842-848
    • Wimley, W.C.1    White, S.H.2
  • 41
    • 0034732952 scopus 로고    scopus 로고
    • Analysis of the role of interfacial tryptophan residues in controlling the topology of membrane proteins
    • Ridder AN, Morein S, Stam JG, Kuhn A, de Kruijff B, Killian JA. Analysis of the role of interfacial tryptophan residues in controlling the topology of membrane proteins. Biochemistry 2000;39:6521-6528.
    • (2000) Biochemistry , vol.39 , pp. 6521-6528
    • Ridder, A.N.1    Morein, S.2    Stam, J.G.3    Kuhn, A.4    De Kruijff, B.5    Killian, J.A.6
  • 42
    • 1542313960 scopus 로고    scopus 로고
    • Sec61p contributes to signal sequence orientation according to the positive-inside rule
    • Goder V, Junne T, Spiess M. Sec61p contributes to signal sequence orientation according to the positive-inside rule. Mol Biol Cell 2004;15:1470-1478.
    • (2004) Mol Biol Cell , vol.15 , pp. 1470-1478
    • Goder, V.1    Junne, T.2    Spiess, M.3
  • 43
    • 0030791975 scopus 로고    scopus 로고
    • Anionic phosholipids are determinants of membrane protein topology
    • van Klompenburg W, Nilsson IM, von Heijne G, de Kruijff B. Anionic phosholipids are determinants of membrane protein topology. EMBO J 1997;16:4261-4266.
    • (1997) EMBO J , vol.16 , pp. 4261-4266
    • Van Klompenburg, W.1    Nilsson, I.M.2    Von Heijne, G.3    De Kruijff, B.4
  • 44
    • 0028364507 scopus 로고
    • Membrane protein topology: Effects of delta mu H+ on the translocation of charged residues explain the 'positive inside' rule
    • Andersson H, von Heijne G. Membrane protein topology: effects of delta mu H+ on the translocation of charged residues explain the 'positive inside' rule. EMBO J 1994;13:2267-2272.
    • (1994) EMBO J , vol.13 , pp. 2267-2272
    • Andersson, H.1    Von Heijne, G.2
  • 45


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.