메뉴 건너뛰기




Volumn 12, Issue 14, 2012, Pages 2282-2294

A guideline to proteome-wide α-helical membrane protein topology predictions

Author keywords

Helical; Bioinformatics; Genome analysis; Membrane; Membrane proteins; Topology predictors

Indexed keywords

G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN; PROTEOME; SIGNAL PEPTIDE;

EID: 84864560730     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100495     Document Type: Article
Times cited : (27)

References (47)
  • 1
    • 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
  • 2
    • 0034177573 scopus 로고    scopus 로고
    • Membrane heredity and early chloroplast evolution
    • Cavalier-Smith, T., Membrane heredity and early chloroplast evolution. Trends Plant Sci. 2000, 5, 174-182.
    • (2000) Trends Plant Sci. , vol.5 , pp. 174-182
    • Cavalier-Smith, T.1
  • 3
    • 34249683488 scopus 로고    scopus 로고
    • Membrane protein structure: prediction versus reality
    • Elofsson, A., von Heijne, G., Membrane protein structure: prediction versus reality. Annu. Rev. Biochem. 2007, 76, 125-140.
    • (2007) Annu. Rev. Biochem. , vol.76 , pp. 125-140
    • Elofsson, A.1    von Heijne, G.2
  • 4
    • 0033525788 scopus 로고    scopus 로고
    • Mitochondrial evolution
    • Gray, M. W., Burger, G., Lang, B. F., Mitochondrial evolution. Science 1999, 283, 1476-1481.
    • (1999) Science , vol.283 , pp. 1476-1481
    • Gray, M.W.1    Burger, G.2    Lang, B.F.3
  • 5
    • 18444373540 scopus 로고    scopus 로고
    • The Protein Data Bank: unifying the archive
    • Westbrook, J., Feng, Z., Jain, S., Bhat, T. et al., The Protein Data Bank: unifying the archive. Nucleic Acids Res. 2002, 30, 245-248.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 245-248
    • Westbrook, J.1    Feng, Z.2    Jain, S.3    Bhat, T.4
  • 6
    • 0000929505 scopus 로고
    • The hydrophobic moment detects periodicity in protein hydrophobicity
    • Eisenberg, D., Weiss, R. M., Terwilliger, T. C., The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA 1984, 81, 140-144.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 140-144
    • Eisenberg, D.1    Weiss, R.M.2    Terwilliger, T.C.3
  • 7
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J., Doolittle, R., 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.2
  • 8
    • 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
  • 9
    • 0033538499 scopus 로고    scopus 로고
    • N-terminal tail export from the mitochondrial matrix. Adherence to the prokaryotic "positive-inside" rule of membrane protein topology
    • Rojo, E. E., Guiard, B., Neupert, W., Stuart, R. A., N-terminal tail export from the mitochondrial matrix. Adherence to the prokaryotic "positive-inside" rule of membrane protein topology. J. Biol. Chem. 1999, 274, 19617-19622.
    • (1999) J. Biol. Chem. , vol.274 , pp. 19617-19622
    • Rojo, E.E.1    Guiard, B.2    Neupert, W.3    Stuart, R.A.4
  • 10
    • 0032747993 scopus 로고    scopus 로고
    • Insertion of leader peptidase into the thylakoid membrane during synthesis in a chloroplast translation system
    • Houben, E., de Gier, J. W., van Wijk, K. J., Insertion of leader peptidase into the thylakoid membrane during synthesis in a chloroplast translation system. Plant Cell. 1999, 11, 1553-1564.
    • (1999) Plant Cell. , vol.11 , pp. 1553-1564
    • Houben, E.1    de Gier, J.W.2    van Wijk, K.J.3
  • 11
    • 44449083478 scopus 로고    scopus 로고
    • Prediction of membrane-protein topology from first principles
    • Bernsel, A., Viklund, H., Falk, J., Lindahl, E. et al., Prediction of membrane-protein topology from first principles. Proc. Natl. Acad. Sci. USA 2008, 105, 7177-7181.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 7177-7181
    • Bernsel, A.1    Viklund, H.2    Falk, J.3    Lindahl, E.4
  • 12
    • 0028568176 scopus 로고
    • TopPred II: an improved software for membrane protein structure predictions
    • Claros, M., 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.1    von Heijne, G.2
  • 13
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones, D., Taylor, W., Thornton, J., A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 1994, 33, 3038-3049.
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.1    Taylor, W.2    Thornton, J.3
  • 14
    • 0030038634 scopus 로고    scopus 로고
    • Topology prediction for helical transmembrane proteins at 86% accuracy
    • Rost, B., Fariselli, P., Casadio, R., Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 1996, 5, 1704-1718.
    • (1996) Protein Sci. , vol.5 , pp. 1704-1718
    • Rost, B.1    Fariselli, P.2    Casadio, R.3
  • 15
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • Jones, D., Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 2007, 23, 538-544.
    • (2007) Bioinformatics , vol.23 , pp. 538-544
    • Jones, D.1
  • 16
    • 67649472570 scopus 로고    scopus 로고
    • Transmembrane protein topology prediction using support vector machines
    • May 26.
    • Nugent, T., Jones, D., Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics 2009, May 26.
    • (2009) BMC Bioinformatics
    • Nugent, T.1    Jones, D.2
  • 17
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnády, G. E., Simon, I., The HMMTOP transmembrane topology prediction server. Bioinformatics 2001, 17, 849-850.
    • (2001) Bioinformatics , vol.17 , pp. 849-850
    • Tusnády, G.E.1    Simon, I.2
  • 19
    • 33847155026 scopus 로고    scopus 로고
    • Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins
    • Bagos, P. G., Liakopoulos, T. D., Hamodrakas, S. J., Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics 2006, 7, 189.
    • (2006) BMC Bioinformatics , vol.7 , pp. 189
    • Bagos, P.G.1    Liakopoulos, T.D.2    Hamodrakas, S.J.3
  • 20
    • 3042579686 scopus 로고    scopus 로고
    • Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • Viklund, H., Elofsson, A., Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci. 2004, 13, 1908-1917.
    • (2004) Protein Sci. , vol.13 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2
  • 21
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • Kall, L., Krogh, A., Sonnhammer, E., A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 2004, 338, 1027-1036.
    • (2004) J. Mol. Biol. , vol.338 , pp. 1027-1036
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.3
  • 22
    • 29144483361 scopus 로고    scopus 로고
    • An HMM posterior decoder for sequence feature prediction that includes homology information
    • Kall, L., Krogh, A., Sonnhammer, E., An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 2005, 21, i251-i257.
    • (2005) Bioinformatics , vol.21
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.3
  • 23
    • 34547584314 scopus 로고    scopus 로고
    • Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server
    • Käll, L., Krogh, A., Sonnhammer, E. L. L., Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res. 2007, 35, W429-W432.
    • (2007) Nucleic Acids Res. , vol.35
    • Käll, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 24
    • 57149112523 scopus 로고    scopus 로고
    • Transmembrane topology and signal peptide prediction using dynamic bayesian networks
    • Reynolds, S. M., Käll, L., Riffle, M. E., Bilmes, J. A. et al., Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput. Biol. 2008, 4, e1000213.
    • (2008) PLoS Comput. Biol. , vol.4
    • Reynolds, S.M.1    Käll, L.2    Riffle, M.E.3    Bilmes, J.A.4
  • 25
    • 48249151108 scopus 로고    scopus 로고
    • OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
    • Viklund, H., Elofsson, A., OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 2008, 24, 1662-1668.
    • (2008) Bioinformatics , vol.24 , pp. 1662-1668
    • Viklund, H.1    Elofsson, A.2
  • 26
    • 57249083976 scopus 로고    scopus 로고
    • SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
    • Viklund, H., Bernsel, A., Skwark, M., Elofsson, A., SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 2008, 24, 2928-2929.
    • (2008) Bioinformatics , vol.24 , pp. 2928-2929
    • Viklund, H.1    Bernsel, A.2    Skwark, M.3    Elofsson, A.4
  • 28
    • 3242891271 scopus 로고    scopus 로고
    • ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability
    • Arai, M., Mitsuke, H., Ikeda, M., Xia, J. et al., ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res. 2004, 32, W390-W393.
    • (2004) Nucleic Acids Res. , vol.32
    • Arai, M.1    Mitsuke, H.2    Ikeda, M.3    Xia, J.4
  • 29
  • 30
    • 0036947980 scopus 로고    scopus 로고
    • The presence of signal peptide significantly affects transmembrane topology prediction
    • Lao, D. M., Arai, M., Ikeda, M., Shimizu, T., The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics 2002, 18, 1562-1566.
    • (2002) Bioinformatics , vol.18 , pp. 1562-1566
    • Lao, D.M.1    Arai, M.2    Ikeda, M.3    Shimizu, T.4
  • 31
    • 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, E., 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.4
  • 32
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacerial, archaean, and eukaryotic organisms
    • Wallin, E., von Heijne, G., Genome-wide analysis of integral membrane proteins from eubacerial, 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
  • 33
  • 34
    • 0028040839 scopus 로고
    • Asparagine-linked oligosaccharides are localized to single extracytosolic segments in multi-span membrane glycoproteins
    • Landolt-Marticorena, C., Reithmeier, R. A., Asparagine-linked oligosaccharides are localized to single extracytosolic segments in multi-span membrane glycoproteins. Biochem. J. 1994, 302 (Pt 1), 253-260.
    • (1994) Biochem. J. , vol.302 , Issue.PART 1 , pp. 253-260
    • Landolt-Marticorena, C.1    Reithmeier, R.A.2
  • 35
    • 0029819510 scopus 로고    scopus 로고
    • Glycosylation of multiple extracytosolic loops in Band 3, a model polytopic membrane protein
    • Tam, L. Y., Landolt-Marticorena, C., Reithmeier, R. A., Glycosylation of multiple extracytosolic loops in Band 3, a model polytopic membrane protein. Biochem J. 1996, 318, 645-648.
    • (1996) Biochem J. , vol.318 , pp. 645-648
    • Tam, L.Y.1    Landolt-Marticorena, C.2    Reithmeier, R.A.3
  • 36
    • 64349089985 scopus 로고    scopus 로고
    • Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins
    • Wollscheid, B., Bausch-Fluck, D., Henderson, C., O'Brien, R. et al., Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol. 2009, 27, 378-386.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 378-386
    • Wollscheid, B.1    Bausch-Fluck, D.2    Henderson, C.3    O'Brien, R.4
  • 37
    • 19744376674 scopus 로고    scopus 로고
    • Global topology analysis of the Escherichia coli inner membrane proteome
    • Daley, D., Rapp, M., Granseth, E., Melén, K. et al., Global topology analysis of the Escherichia coli inner membrane proteome. Science 2005, 308, 1321-1323.
    • (2005) Science , vol.308 , pp. 1321-1323
    • Daley, D.1    Rapp, M.2    Granseth, E.3    Melén, K.4
  • 38
    • 33746616385 scopus 로고    scopus 로고
    • A global topology map of the Saccharomyces cerevisiae membrane proteome
    • Kim, H., Melén, K., Osterberg, M., Heijne, G. V., A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc. Natl. Acad. Sci. USA 2006, 103, 11142-11147.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 11142-11147
    • Kim, H.1    Melén, K.2    Osterberg, M.3    Heijne, G.V.4
  • 39
    • 79954493200 scopus 로고    scopus 로고
    • Rapid membrane protein topology prediction
    • Hennerdal, A., Elofsson, A., Rapid membrane protein topology prediction. Bioinformatics 2011, 27, 1322-1323.
    • (2011) Bioinformatics , vol.27 , pp. 1322-1323
    • Hennerdal, A.1    Elofsson, A.2
  • 40
    • 33745634395 scopus 로고    scopus 로고
    • CD-Hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W., Godzik, A., CD-Hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22, 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 41
    • 3042818018 scopus 로고    scopus 로고
    • The International Protein Index: an integrated database for proteomics experiments
    • Kersey, P., Duarte, J., Williams, A., Karavidopoulou, Y. et al., The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4, 1985-1988.
    • (2004) Proteomics , vol.4 , pp. 1985-1988
    • Kersey, P.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4
  • 42
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the Universal Protein Resource
    • Consortium, U., Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 2011, 39, D214-D219.
    • (2011) Nucleic Acids Res. , vol.39
    • Consortium, U.1
  • 44
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: discriminating signal peptides from transmembrane regions
    • Petersen, T., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8, 785-786.
    • (2011) Nat. Methods , vol.8 , pp. 785-786
    • Petersen, T.1    Brunak, S.2    von Heijne, G.3    Nielsen, H.4
  • 45
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S., Madden, T., Schaffer, A., Zhang, J. et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.1    Madden, T.2    Schaffer, A.3    Zhang, J.4
  • 46
    • 33644509247 scopus 로고    scopus 로고
    • A general model of G protein-coupled receptor sequences and its application to detect remote homologs
    • Wistrand, M., Kall, L., Sonnhammer, E., A general model of G protein-coupled receptor sequences and its application to detect remote homologs. Protein Sci. 2006, 15, 509-521.
    • (2006) Protein Sci. , vol.15 , pp. 509-521
    • Wistrand, M.1    Kall, L.2    Sonnhammer, E.3
  • 47
    • 74649086575 scopus 로고    scopus 로고
    • Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context
    • Hedin, L., Ojemalm, K., Bernsel, A., Hennerdal, A. et al., Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. J. Mol. Biol. 2010, 396, 221-229.
    • (2010) J. Mol. Biol. , vol.396 , pp. 221-229
    • Hedin, L.1    Ojemalm, K.2    Bernsel, A.3    Hennerdal, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.