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Resource for structure related information on transmembrane proteins

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Structural Bioinformatics of Membrane Proteins

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Abstract

Transmembrane proteins are involved in a wide variety of vital biological processes including transport of water-soluble molecules, flow of information and energy production. Despite significant efforts to determine the structures of these proteins, only a few thousand solved structures are known so far. Here, we review the various resources for structure-related information on these types of proteins ranging from the 3D structure to the topology and from the up-to-date databases to the various Internet sites and servers dealing with structure prediction and structure analysis. Abbreviations: 3D, three dimensional; PDB, Protein Data Bank; TMP, transmembrane protein.

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References

  • Ahram M, Litou ZI, Fang R, Al-Tawallbeh G (2006) Estimation of membrane proteins in the human proteome. In Silico Biol 6: 379–386

    Google Scholar 

  • Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, Mitchell AL, Moulton G, Nordle A, Paine K, Taylor P, Uddin A, Zygouri C (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res 31: 400–402

    Article  Google Scholar 

  • Bagos PG, Liakopoulos TD, Hamodrakas SJ (2006) Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinform 7: 189

    Article  Google Scholar 

  • Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LL (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res 33: D154–D159

    Article  Google Scholar 

  • Bakos É, Hegedűs T, Holló Z, Welker E, Tusnády G, Zaman G, Flens M, Váradi A, Sarkadi B (1996) Membrane topology and glycosylation of the human multidrug resistance-associated protein. J Biol Chem 271: 12322–12326

    Article  Google Scholar 

  • Bamberg K and Sachs G (1994) Topological analysis of H+,K(+)-ATPase using in vitro translation. J Biol Chem 269: 16909–16919

    Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28: 235–242

    Article  Google Scholar 

  • Bernsel A and von Heijne G (2005) Improved membrane protein topology prediction by domain assignments. Protein Sci 14: 1723–1728

    Article  Google Scholar 

  • Bogdanov M, Zhang W, Xie J, Dowhan W (2005) Transmembrane protein topology mapping by the substituted cysteine accessibility method (SCAM(TM)): application to lipid-specific membrane protein topogenesis. Methods 36: 148–171

    Article  Google Scholar 

  • Bond PJ and Sansom MSP (2006) Insertion and assembly of membrane proteins via simulation. J Am Chem Soc 128: 2697–2704

    Article  Google Scholar 

  • Boyd D, Traxler B, Beckwith J (1993) Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions. J Bacteriol 175: 553–556

    Google Scholar 

  • Broome-Smith JK, Tadayyon M, Zhang Y (1990) Beta-lactamase as a probe of membrane protein assembly and protein export. Mol Microbiol 4: 1637–1644

    Article  Google Scholar 

  • Chen CP and Rost B (2002) State-of-the-art in membrane protein prediction. Appl Bioinform 1: 21–35

    Google Scholar 

  • Chen CP, Kernytsky A, Rost B (2002) Transmembrane helix predictions revisited. Protein Sci 11: 2774–2791

    Article  Google Scholar 

  • Daley DO, Rapp M, Granseth E, Melén K, Drew D, von Heijne G (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321–1323

    Article  Google Scholar 

  • Elofsson A and von Heijne G (2007) Membrane protein structure: prediction versus reality. Ann Rev Biochem 76: 125–140

    Article  Google Scholar 

  • Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247–D251

    Article  Google Scholar 

  • van Geest M and Lolkema JS (2000) Membrane topology and insertion of membrane proteins: search for topogenic signals. Microbiol Mol Biol Rev 64: 13–33

    Article  Google Scholar 

  • Henrick K and Tornton JM (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358–361

    Article  Google Scholar 

  • Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM (2008) Remediation of the protein data bank archive. Nucleic Acids Res 36: D426–D433

    Article  Google Scholar 

  • Ikeda M, Arai M, Okuno T, Shimizu T (2003) TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res 31: 406–409

    Article  Google Scholar 

  • Jones DT (1998) Do transmembrane protein superfolds exist? FEBS Lett 423: 281–285

    Article  Google Scholar 

  • Käll L, Krogh A, Sonnhammer ELL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027–1036

    Article  Google Scholar 

  • Kast C, Canfield V, Levenson R, Gros P (1996) Transmembrane organization of mouse P-glycoprotein determined by epitope insertion and immunofluorescence. J Biol Chem 271: 9240–9248

    Article  Google Scholar 

  • Kim H, Melén K, von Heijne G (2003) Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J Biol Chem 278: 10208–10213

    Article  Google Scholar 

  • Kim H, Melén K, Osterberg M, von Heijne G (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Nat Acad Sci USA 103: 11142–11147

    Article  Google Scholar 

  • Klabunde T and Hessler G (2002) Drug design strategies for targeting G-protein-coupled receptors. Chembiochem: Eur J Chem Biol 3: 928–944

    Article  Google Scholar 

  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567–580

    Article  Google Scholar 

  • Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res 32: D142–D144

    Article  Google Scholar 

  • Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res 28: 257–259

    Article  Google Scholar 

  • Lomize AL, Pogozheva ID, Lomize MA, Mosberg HI (2006a) Positioning of proteins in membranes: a computational approach. Protein Sci 15: 1318–1333

    Article  Google Scholar 

  • Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006b) OPM: orientations of proteins in membranes database. Bioinformatics 22: 623–625

    Article  Google Scholar 

  • Melén K, Krogh A, von Heijne G (2003) Reliability measures for membrane protein topology prediction algorithms. J Mol Biol 327: 735–744

    Article  Google Scholar 

  • Miller J (1972) Experiments in molecular genetics. Cold Spring Harbor, New York

    Google Scholar 

  • Mitaku S, Ono M, Hirokawa T, Boon-Chieng S, Sonoyama M (1999) Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. Biophys Chem 82: 165–171

    Article  Google Scholar 

  • Möller S, Kriventseva EV, Apweiler R (2000) A collection of well characterised integral membrane proteins. Bioinformatics 16: 1159–1160

    Article  Google Scholar 

  • Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water permeation through aquaporin-1. Nature 407: 599–605

    Article  Google Scholar 

  • Oomen CJ, van Ulsen P, van Gelder P, Feijen M, Tommassen J, Gros P (2004) Structure of the translocator domain of a bacterial autotransporter. EMBO J 23: 1257–1266

    Article  Google Scholar 

  • Orengo CA, Martin AM, Hutchinson G, Jones S, Jones DT, Michie AD, Swindells MB, Tornton JM (1998) Classifying a protein in the CATH database of domain structures. Acta Crystallogr D, Biol Crystallogr 54: 1155–1167

    Article  Google Scholar 

  • Ostermeier C and Michel H (1997) Crystallization of membrane proteins. Curr Opin Struct Biol 7: 697–701

    Article  Google Scholar 

  • Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289: 739–745

    Article  Google Scholar 

  • Preusch PC, Norvell JC, Cassatt JC, Cassman M (1998) Progress away from ‘no crystals, no grant’. Nat Struct Biol 5: 12–14

    Article  Google Scholar 

  • Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B (2007) Membrane protein prediction methods. Methods 41: 460–474

    Article  Google Scholar 

  • Raman P, Cherezov V, Caffrey M (2006) The membrane protein data bank. Cell Mol Life Sci 63: 36–51

    Article  Google Scholar 

  • Rapp M, Drew D, Daley DO, Nilsson J, Carvalho T, Melén K, De Gier J, Von Heijne G (2004) Experimentally based topology models for E. coli inner membrane proteins. Protein Sci 13: 937–945

    Article  Google Scholar 

  • Sansom MSP, Scott K, Bond PJ (2008) Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochem Soc Trans 36: 27–32

    Article  Google Scholar 

  • Scott K, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MSP (2008) Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 16: 621–630

    Article  Google Scholar 

  • Sigrist CJA, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3: 265–274

    Article  Google Scholar 

  • Tusnády GE and Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849–850

    Article  Google Scholar 

  • Tusnády G and Simon I (2009) Shedding light on transmembrane topology. In: Protein structure prediction: method and algorithms. Wiley Book Series on Bioinformatics (in press)

    Google Scholar 

  • Tusnády G, Dosztányi Z, Simon I (2004) Transmembrane proteins in the protein data bank: identification and classification. Bioinformatics 20: 2964–2972

    Article  Google Scholar 

  • Tusnády GE, Dosztányi Z, Simon I (2005a) TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics 21: 1276–1277

    Article  Google Scholar 

  • Tusnády G, Dosztányi Z, Simon I (2005b) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res 33: D275–D278

    Article  Google Scholar 

  • Tusnády GE, Kalmár L, Simon I (2008) TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res 36: D234–D239

    Article  Google Scholar 

  • White S and Wimley W (1999) Membrane protein folding and stability: physical principles. Ann Rev Biophys Biomol Struct 28: 319–365

    Article  Google Scholar 

  • Xu EW, Kearney P, Brown DG (2006) The use of functional domains to improve transmembrane protein topology prediction. J Bioinform Comput Biol 4: 109–123

    Article  Google Scholar 

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Authors and Affiliations

  1. Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary

    Gábor E. Tusnády & István Simon

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  1. Gábor E. Tusnády
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  2. István Simon
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Tusnády, G.E., Simon, I. (2010). Resource for structure related information on transmembrane proteins. In: Structural Bioinformatics of Membrane Proteins. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0045-5_3

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  • DOI: https://doi.org/10.1007/978-3-7091-0045-5_3

  • Publisher Name: Springer, Vienna

  • Print ISBN: 978-3-7091-0044-8

  • Online ISBN: 978-3-7091-0045-5

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