메뉴 건너뛰기




Volumn 8, Issue 10, 2013, Pages

Classification of α-Helical Membrane Proteins Using Predicted Helix Architectures

Author keywords

[No Author keywords available]

Indexed keywords

APC PROTEIN; G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN;

EID: 84886429768     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0077491     Document Type: Article
Times cited : (5)

References (54)
  • 1
    • 0022348605 scopus 로고
    • Structure of the protein subunits in the photosynthetic reaction centre of rhodopseudomonas viridis at 3 A resolution
    • Deisenhofer J, Epp O, Miki K, Huber R, Michel H, (1985) Structure of the protein subunits in the photosynthetic reaction centre of rhodopseudomonas viridis at 3 A resolution. Nature 318: 618-624.
    • (1985) Nature , vol.318 , pp. 618-624
    • Deisenhofer, J.1    Epp, O.2    Miki, K.3    Huber, R.4    Michel, H.5
  • 2
    • 33845343261 scopus 로고    scopus 로고
    • Membrane-protein topology
    • von Heijne G, (2006) Membrane-protein topology. Nat Rev Mol Cell Biol 7: 909-918.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 909-918
    • von Heijne, G.1
  • 3
    • 0025292355 scopus 로고
    • Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy
    • Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, et al. (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213: 899-929.
    • (1990) J Mol Biol , vol.213 , pp. 899-929
    • Henderson, R.1    Baldwin, J.M.2    Ceska, T.A.3    Zemlin, F.4    Beckmann, E.5
  • 4
    • 0025782832 scopus 로고
    • Proline kinks in transmembrane alpha-helices
    • von Heijne G, (1991) Proline kinks in transmembrane alpha-helices. J Mol Biol 218: 499-503.
    • (1991) J Mol Biol , vol.218 , pp. 499-503
    • von Heijne, G.1
  • 5
    • 0026537558 scopus 로고
    • Proline residues in transmembrane helices of channel and transport proteins: a molecular modeling study
    • Sansom MS, (1992) Proline residues in transmembrane helices of channel and transport proteins: a molecular modeling study. Protein Eng 5: 53-60.
    • (1992) Protein Eng , vol.5 , pp. 53-60
    • Sansom, M.S.1
  • 6
    • 0037122805 scopus 로고    scopus 로고
    • X-ray structure of a Clc chloride channel at 3 A reveals the molecular basis of anion selectivity
    • Dutzler R, Campbell EB, Cadene M, Chait BT, MacKinnon R, (2002) X-ray structure of a Clc chloride channel at 3 A reveals the molecular basis of anion selectivity. Nature 415: 287-294.
    • (2002) Nature , vol.415 , pp. 287-294
    • Dutzler, R.1    Campbell, E.B.2    Cadene, M.3    Chait, B.T.4    MacKinnon, R.5
  • 7
    • 12344330612 scopus 로고    scopus 로고
    • A study of the membrane-water interface region of membrane proteins
    • Granseth E, von Heijne G, Elofsson A, (2005) A study of the membrane-water interface region of membrane proteins. J Mol Biol 346: 377-385.
    • (2005) J Mol Biol , vol.346 , pp. 377-385
    • Granseth, E.1    von Heijne, G.2    Elofsson, A.3
  • 8
    • 33746361201 scopus 로고    scopus 로고
    • Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes
    • Viklund H, Granseth E, Elofsson A, (2006) Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol 361: 591-603.
    • (2006) J Mol Biol , vol.361 , pp. 591-603
    • Viklund, H.1    Granseth, E.2    Elofsson, A.3
  • 9
    • 34249683488 scopus 로고    scopus 로고
    • Membrane protein structure: prediction versus reality
    • Elofsson A, von Heijne G, (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76: 125-140.
    • (2007) Annu Rev Biochem , vol.76 , pp. 125-140
    • Elofsson, A.1    von Heijne, G.2
  • 10
    • 79251519929 scopus 로고    scopus 로고
    • Topology prediction of helical transmembrane proteins: how far have we reached?
    • Tusnady GE, Simon I, (2010) Topology prediction of helical transmembrane proteins: how far have we reached? Curr Protein Pept Sci 11: 550-561.
    • (2010) Curr Protein Pept Sci , vol.11 , pp. 550-561
    • Tusnady, G.E.1    Simon, I.2
  • 12
    • 33846033844 scopus 로고    scopus 로고
    • The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
    • Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, et al. (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35: D291-297.
    • (2007) Nucleic Acids Res , vol.35
    • Greene, L.H.1    Lewis, T.E.2    Addou, S.3    Cuff, A.4    Dallman, T.5
  • 13
    • 77951217658 scopus 로고    scopus 로고
    • Current status of membrane protein structure classification
    • Neumann S, Fuchs A, Mulkidjanian A, Frishman D, (2010) Current status of membrane protein structure classification. Proteins 78: 1760-1773.
    • (2010) Proteins , vol.78 , pp. 1760-1773
    • Neumann, S.1    Fuchs, A.2    Mulkidjanian, A.3    Frishman, D.4
  • 14
    • 77955823082 scopus 로고    scopus 로고
    • Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns
    • Fuchs A, Frishman D, (2010) Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns. Proteins 78: 2587-2599.
    • (2010) Proteins , vol.78 , pp. 2587-2599
    • Fuchs, A.1    Frishman, D.2
  • 15
    • 84856771753 scopus 로고    scopus 로고
    • Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
    • Neumann S, Hartmann H, Martin-Galiano AJ, Fuchs A, Frishman D, (2012) Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins. Proteins 80: 839-857.
    • (2012) Proteins , vol.80 , pp. 839-857
    • Neumann, S.1    Hartmann, H.2    Martin-Galiano, A.J.3    Fuchs, A.4    Frishman, D.5
  • 16
    • 13444280419 scopus 로고    scopus 로고
    • PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank
    • Tusnady GE, Dosztanyi Z, Simon I, (2005) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 33: D275-278.
    • (2005) Nucleic Acids Res , vol.33
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 17
    • 10244252813 scopus 로고    scopus 로고
    • Transmembrane proteins in the Protein Data Bank: identification and classification
    • Tusnady GE, Dosztanyi Z, Simon I, (2004) Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics 20: 2964-2972.
    • (2004) Bioinformatics , vol.20 , pp. 2964-2972
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 18
    • 33748449674 scopus 로고    scopus 로고
    • Defining the fold space of membrane proteins: the CAMPS database
    • Martin-Galiano AJ, Frishman D, (2006) Defining the fold space of membrane proteins: the CAMPS database. Proteins 64: 906-922.
    • (2006) Proteins , vol.64 , pp. 906-922
    • Martin-Galiano, A.J.1    Frishman, D.2
  • 19
    • 61449245515 scopus 로고    scopus 로고
    • Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks
    • Fuchs A, Kirschner A, Frishman D, (2009) Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks. Proteins 74: 857-871.
    • (2009) Proteins , vol.74 , pp. 857-871
    • Fuchs, A.1    Kirschner, A.2    Frishman, D.3
  • 22
    • 38549172064 scopus 로고    scopus 로고
    • TOPDB: topology data bank of transmembrane proteins
    • Tusnady GE, Kalmar L, Simon I, (2008) TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res 36: D234-239.
    • (2008) Nucleic Acids Res , vol.36
    • Tusnady, G.E.1    Kalmar, L.2    Simon, I.3
  • 24
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 26
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 27
    • 47049099111 scopus 로고    scopus 로고
    • Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration
    • Bauer S, Grossmann S, Vingron M, Robinson PN, (2008) Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24: 1650-1651.
    • (2008) Bioinformatics , vol.24 , pp. 1650-1651
    • Bauer, S.1    Grossmann, S.2    Vingron, M.3    Robinson, P.N.4
  • 29
    • 33745698481 scopus 로고    scopus 로고
    • A limited universe of membrane protein families and folds
    • Oberai A, Ihm Y, Kim S, Bowie JU, (2006) A limited universe of membrane protein families and folds. Protein Sci 15: 1723-1734.
    • (2006) Protein Sci , vol.15 , pp. 1723-1734
    • Oberai, A.1    Ihm, Y.2    Kim, S.3    Bowie, J.U.4
  • 33
    • 0038024615 scopus 로고    scopus 로고
    • The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
    • Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB, (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63: 1256-1272.
    • (2003) Mol Pharmacol , vol.63 , pp. 1256-1272
    • Fredriksson, R.1    Lagerstrom, M.C.2    Lundin, L.G.3    Schioth, H.B.4
  • 34
  • 37
    • 77449124225 scopus 로고    scopus 로고
    • Membrane transport proteins: surprises in structural sameness
    • Theobald DL, Miller C, (2010) Membrane transport proteins: surprises in structural sameness. Nat Struct Mol Biol 17: 2-3.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 2-3
    • Theobald, D.L.1    Miller, C.2
  • 38
    • 0032570779 scopus 로고    scopus 로고
    • Do transmembrane protein superfolds exist?
    • Jones DT, (1998) Do transmembrane protein superfolds exist? FEBS Lett 423: 281-285.
    • (1998) FEBS Lett , vol.423 , pp. 281-285
    • Jones, D.T.1
  • 39
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • Wallin E, von Heijne G, (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7: 1029-1038.
    • (1998) Protein Sci , vol.7 , pp. 1029-1038
    • Wallin, E.1    von Heijne, G.2
  • 40
    • 0033664559 scopus 로고    scopus 로고
    • Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs
    • Remm M, Sonnhammer E, (2000) Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Res 10: 1679-1689.
    • (2000) Genome Res , vol.10 , pp. 1679-1689
    • Remm, M.1    Sonnhammer, E.2
  • 41
    • 0037472764 scopus 로고    scopus 로고
    • Comprehensive analysis of transmembrane topologies in prokaryotic genomes
    • Arai M, Ikeda M, Shimizu T, (2003) Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene 304: 77-86.
    • (2003) Gene , vol.304 , pp. 77-86
    • Arai, M.1    Ikeda, M.2    Shimizu, T.3
  • 42
    • 19744376674 scopus 로고    scopus 로고
    • Global topology analysis of the Escherichia coli inner membrane proteome
    • Daley DO, Rapp M, Granseth E, Melen K, Drew D, et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-1323.
    • (2005) Science , vol.308 , pp. 1321-1323
    • Daley, D.O.1    Rapp, M.2    Granseth, E.3    Melen, K.4    Drew, D.5
  • 43
    • 33746616385 scopus 로고    scopus 로고
    • A global topology map of the Saccharomyces cerevisiae membrane proteome
    • Kim H, Melen K, Osterberg M, von Heijne G, (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci U S A 103: 11142-11147.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 11142-11147
    • Kim, H.1    Melen, K.2    Osterberg, M.3    von Heijne, G.4
  • 44
    • 0035379645 scopus 로고    scopus 로고
    • The internal repeats in the Na+/Ca2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies
    • Saaf A, Baars L, von Heijne G, (2001) The internal repeats in the Na+/Ca2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. The Journal of biological chemistry 276: 18905-18907.
    • (2001) The Journal of Biological Chemistry , vol.276 , pp. 18905-18907
    • Saaf, A.1    Baars, L.2    von Heijne, G.3
  • 45
    • 0041353145 scopus 로고    scopus 로고
    • Structure and mechanism of the lactose permease of Escherichia coli
    • Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, et al. (2003) Structure and mechanism of the lactose permease of Escherichia coli. Science 301: 610-615.
    • (2003) Science , vol.301 , pp. 610-615
    • Abramson, J.1    Smirnova, I.2    Kasho, V.3    Verner, G.4    Kaback, H.R.5
  • 46
    • 0037783318 scopus 로고    scopus 로고
    • Tracing pathways of transport protein evolution
    • Saier MH Jr, (2003) Tracing pathways of transport protein evolution. Mol Microbiol 48: 1145-1156.
    • (2003) Mol Microbiol , vol.48 , pp. 1145-1156
    • Saier Jr., M.H.1
  • 47
    • 2342578691 scopus 로고    scopus 로고
    • Internal gene duplication in the evolution of prokaryotic transmembrane proteins
    • Shimizu T, Mitsuke H, Noto K, Arai M, (2004) Internal gene duplication in the evolution of prokaryotic transmembrane proteins. J Mol Biol 339: 1-15.
    • (2004) J Mol Biol , vol.339 , pp. 1-15
    • Shimizu, T.1    Mitsuke, H.2    Noto, K.3    Arai, M.4
  • 48
    • 40549125974 scopus 로고    scopus 로고
    • Common occurrence of internal repeat symmetry in membrane proteins
    • Choi S, Jeon J, Yang JS, Kim S, (2008) Common occurrence of internal repeat symmetry in membrane proteins. Proteins 71: 68-80.
    • (2008) Proteins , vol.71 , pp. 68-80
    • Choi, S.1    Jeon, J.2    Yang, J.S.3    Kim, S.4
  • 49
    • 78649662610 scopus 로고    scopus 로고
    • Internal duplications in alpha-helical membrane protein topologies are common but the nonduplicated forms are rare
    • Hennerdal A, Falk J, Lindahl E, Elofsson A, (2010) Internal duplications in alpha-helical membrane protein topologies are common but the nonduplicated forms are rare. Protein science: a publication of the Protein Society 19: 2305-2318.
    • (2010) Protein Science: A Publication of the Protein Society , vol.19 , pp. 2305-2318
    • Hennerdal, A.1    Falk, J.2    Lindahl, E.3    Elofsson, A.4
  • 50
    • 0031920140 scopus 로고    scopus 로고
    • Estimation of structural similarity of membrane proteins by hydropathy profile alignment
    • Lolkema JS, Slotboom DJ, (1998) Estimation of structural similarity of membrane proteins by hydropathy profile alignment. Mol Membr Biol 15: 33-42.
    • (1998) Mol Membr Biol , vol.15 , pp. 33-42
    • Lolkema, J.S.1    Slotboom, D.J.2
  • 51
    • 0037432531 scopus 로고    scopus 로고
    • Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis
    • Lolkema JS, Slotboom DJ, (2003) Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis. J Mol Biol 327: 901-909.
    • (2003) J Mol Biol , vol.327 , pp. 901-909
    • Lolkema, J.S.1    Slotboom, D.J.2
  • 52
    • 58949087902 scopus 로고    scopus 로고
    • The major amino acid transporter superfamily has a similar core structure as Na+-galactose and Na+-leucine transporters
    • Lolkema JS, Slotboom DJ, (2008) The major amino acid transporter superfamily has a similar core structure as Na+-galactose and Na+-leucine transporters. Mol Membr Biol 25: 567-570.
    • (2008) Mol Membr Biol , vol.25 , pp. 567-570
    • Lolkema, J.S.1    Slotboom, D.J.2
  • 53
    • 80055018057 scopus 로고    scopus 로고
    • Membrane topology screen of secondary transport proteins in structural class ST[3] of the MemGen classification. Confirmation and structural diversity
    • Ter Horst R, Lolkema JS, (2012) Membrane topology screen of secondary transport proteins in structural class ST[3] of the MemGen classification. Confirmation and structural diversity. Biochim Biophys Acta 1818: 72-81.
    • (2012) Biochim Biophys Acta , vol.1818 , pp. 72-81
    • Ter Horst, R.1    Lolkema, J.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.