Expediting topology data gathering for the TOPDB database

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D283-D289

  Dobson, Laszlo ^a   Langó, Tamás ^a   Reményi, István ^a   Tusnády, Gabor E ^a  

^a INSTITUTE OF ENZYMOLOGY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; INFORMATION PROCESSING; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN GLYCOSYLATION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; RELIABILITY; TOPOLOGY DATA BANK OF TRANSMEMBRANE PROTEINS DATABASE; CHEMISTRY; PROTEIN CONFORMATION;

MEMBRANE PROTEIN;

DATABASES, PROTEIN; MEMBRANE PROTEINS; PROTEIN CONFORMATION;

EID: 84941351784     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1119     Document Type: Article

References (60)

1. Tusnády, G. E., Dosztányi, Z. and Simon, I. (2004) Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics, 20, 2964-2972.
2. Tusnády, G., Dosztányi, Z. and Simon, I. (2005) PDB TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 33, D275-D278.
3. Kozma, D., Simon, I. and Tusnády, G. E. (2013) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res., 41, D524-D529.
4. Manoil, C. and Beckwith, J. (1985) TnphoA: a transposon probe for protein export signals. Proc. Natl. Acad. Sci. U. S. A., 82, 8129-8133.
5. Miller, J. (1972) Experiments in Molecular Genetics. Cold Spring Harlbor, NY.
6. Broome-Smith, J. K., Tadayyon, M. and Zhang, Y. (1990) Beta-lactamase as a probe of membrane protein assembly and protein export. Mol. Microbiol., 4, 1637-1644.
7. Sengstag, C., Stirling, C., Schekman, R. and Rine, J. (1990) Genetic and biochemical evaluation of eucaryotic membrane protein topology: multiple transmembrane domains of Saccharomyces cerevisiae 3-hydroxy-3-methylglutaryl coenzyme A reductase. Mol. Cell. Biol., 10, 672-680.
8. Waldo, G. S., Standish, B. M., Berendzen, J. and Terwilliger, T. C. (1999) Rapid protein-folding assay using green fuorescent protein. Nat. Biotechnol., 17, 691-695.
9. Brach, T., Soyk, S., Müller, C., Hinz, G., Hell, R., Brandizzi, F. and Meyer, A. J. (2009) Non-invasive topology analysis of membrane proteins in the secretory pathway. Plant J., 57, 534-541.
10. Anderson, D. J., Blobel, G., Tzartos, S., Gullick, W. and Lindstrom, J. (1983) Transmembrane orientation of an early biosynthetic form of acetylcholine receptor delta subunit determined by proteolytic dissection in conjunction with monoclonal antibodies. J. Neurosci., 3, 1773-1784.
11. Charbit, A., Ronco, J., Michel, V., Werts, C. and Hofnung, M. (1991) Permissive sites and topology of an outer membrane protein with a reporter epitope. J. Bacteriol., 173, 262-275.
12. Anand, R., Bason, L., Saedi, M. S., Gerzanich, V., Peng, X. and Lindstrom, J. (1993) Reporter epitopes: a novel approach to examine transmembrane topology of integral membrane proteins applied to the alpha 1 subunit of the nicotinic acetylcholine receptor. Biochemistry, 32, 9975-9984.
13. Kast, C., Canfeld, V., Levenson, R. and Gros, P. (1996) Transmembrane organization of mouse P-glycoprotein determined by epitope insertion and immunofuorescence. J. Biol. Chem., 271, 9240-9248.
14. Kast, C. and Gros, P. (1997) Topology mapping of the amino-terminal half of multidrug resistance-associated protein by epitope insertion and immunofuorescence. J. Biol. Chem., 272, 26479-26487.
15. Kast, C. and Gros, P. (1998) Epitope insertion favors a six transmembrane domain model for the carboxy-terminal portion of the multidrug resistance-associated protein. Biochemistry, 37, 2305-2313.
16. Nilsson, I. M. and von Heijne, G. (1993) Determination of the distance between the oligosaccharyltransferase active site and the endoplasmic reticulum membrane. J. Biol. Chem., 268, 5798-5801.
17. Sokolowska, I., Ngounou Wetie, A. G., Roy, U., Woods, A. G. and Darie, C. C. (2013) Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins. Biochim. Biophys. Acta, 1834, 1474-1483.
18. Trinidad, J. C., Schoepfer, R., Burlingame, A. L. and Medzihradszky, K. F. (2013) N- and O-glycosylation in the murine synaptosome. Mol. Cell. Proteomics, 12, 3474-3488.
19. Wang, G., Wu, Y., Zhou, T., Guo, Y., Zheng, B., Wang, J., Bi, Y., Liu, F., Zhou, Z., Guo, X. et al. (2013) Mapping of the N-linked glycoproteome of human spermatozoa. J. Proteome Res., 12, 5750-5759.
20. Han, D., Moon, S., Kim, Y., Min, H. and Kim, Y. (2014) Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry. BMC Genomics, 15, 95.
21. Loo, T. W. and Clarke, D. M. (1999) Determining the structure and mechanism of the human multidrug resistance P-glycoprotein using cysteine-scanning mutagenesis and thiol-modification techniques. Biochim. Biophys. Acta, 1461, 315-325.
22. Farrell, K. B., Tusnady, G. E. and Eiden, M. V. (2009) New structural arrangement of the extracellular regions of the phosphate transporter SLC20A1, the receptor for gibbon ape leukemia virus. J. Biol. Chem., 284, 29979-29987.
23. Zhu, Q., Lee, D. W. K. and Casey, J. R. (2003) Novel topology in C-terminal region of the human plasma membrane anion exchanger, AE1. J. Biol. Chem., 278, 3112-3120.
24. Lee, A. G. (2003) Lipid-protein interactions in biological membranes: a structural perspective. Biochim. Biophys. Acta, 1612, 1-40.
25. Tusnády, G. E., Dosztányi, Z. and Simon, I. (2005) TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics, 21, 1276-1277.
26. Lomize, A. L., Pogozheva, I. D., Lomize, M. A. and Mosberg, H. I. (2007) The role of hydrophobic interactions in positioning of peripheral proteins in membranes. BMC Struct. Biol., 7, 44.
27. Lomize, M. A., Pogozheva, I. D., Joo, H., Mosberg, H. I. and Lomize, A. L. (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res., 40, D370-D376.
28. Schramm, C. A., Hannigan, B. T., Donald, J. E., Keasar, C., Saven, J. G., Degrado, W. F. and Samish, I. (2012) Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure, 20, 924-935.
29. Lomize, M. A., Lomize, A. L., Pogozheva, I. D. and Mosberg, H. I. (2006) OPM: orientations of proteins in membranes database. Bioinformatics, 22, 623-625.
30. Bagos, P. G., Liakopoulos, T. D. and Hamodrakas, S. J. (2006) Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics, 7, 189.
31. Tusnády, G. E. and Simon, I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
32. Käll, L., Krogh, A. and Sonnhammer, E. L. L. (2007) Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res., 35, W429-W432.
33. Melén, K., Krogh, A. and von Heijne, G. (2003) Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol., 327, 735-744.
34. Bernsel, A. and von Heijne, G. (2005) Improved membrane protein topology prediction by domain assignments. Protein Sci., 14, 1723-1728.
35. Xu, E. W., Kearney, P. and Brown, D. G. (2006) The use of functional domains to improve transmembrane protein topology prediction. J. Bioinform. Comput. Biol., 4, 109-123.
36. Rapp, M., Drew, D., Daley, D. O., Nilsson, J., Carvalho, T., Melén, K., De Gier, J.-W. and Von Heijne, G. (2004) Experimentally based topology models for E.coli inner membrane proteins. Protein Sci., 13, 937-945.
37. Dobson, L., Reményi, I. and Tusnády, G. E. (2014) The Human Transmembrane Proteome. PLoS One, in press.
38. Tusnády, G. E., Kalmár, L., Hegyi, H., Tompa, P. and Simon, I. (2008) TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. Bioinformatics, 24, 1469-1470.
39. Tusnády, G. E. and Simon, I. (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 283, 489-506.
40. Shen, H. and Chou, J. J. (2008) MemBrain: improving the accuracy of predicting transmembrane helices. PLoS One, 3, e2399.
41. Nugent, T. and Jones, D. T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics, 10, 159.
42. Viklund, H. and Elofsson, A. (2008) OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics, 24, 1662-1668.
43. Reynolds, S. M., Käll, L., Riffe, M. E., Bilmes, J. A. and Noble, W. S. (2008) Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput. Biol., 4, e1000213.
44. Viklund, H. and Elofsson, A. (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci., 13, 1908-1917.
45. Bernsel, A., Viklund, H., Falk, J., Lindahl, E., von Heijne, G. and Elofsson, A. (2008) Prediction of membrane-protein topology from first principles. Proc. Natl. Acad. Sci. U. S. A., 105, 7177-7181.
46. Sonnhammer, E. L., von Heijne, G. and Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
47. Chen, R., Jiang, X., Sun, D., Han, G., Wang, F., Ye, M., Wang, L. and Zou, H. (2009) Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. J. Proteome Res., 8, 651-661.
48. Kaji, H., Shikanai, T., Sasaki-Sawa, A., Wen, H., Fujita, M., Suzuki, Y., Sugahara, D., Sawaki, H., Yamauchi, Y., Shinkawa, T. et al. (2012) Large-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB. J. Proteome Res., 11, 4553-4566.
49. Wollscheid, B., Bausch-Fluck, D., Henderson, C., O'Brien, R., Bibel, M., Schiess, R., Aebersold, R. and Watts, J. D. (2009) Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol., 27, 378-386.
50. Hennerdal, A. and Elofsson, A. (2011) Rapid membrane protein topology prediction. Bioinformatics, 27, 1322-1323.
51. Nugent, T. and Jones, D. T. (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc. Natl. Acad. Sci. U. S. A., 109, E1540-E1547.
52. Drew, D., Sjöstrand, D., Nilsson, J., Urbig, T., Chin, C., de Gier, J.-W. and von Heijne, G. (2002) Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc. Natl. Acad. Sci. U. S. A., 99, 2690-2695.
53. Daley, D. O., Rapp, M., Granseth, E., Melén, K., Drew, D. and von Heijne, G. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science, 308, 1321-1323.
54. Kim, H., Melén, K., Osterberg, M. and von Heijne, G. (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc. Natl. Acad. Sci. U. S. A., 103, 11142-11147.
55. Klammer, M., Messina, D. N., Schmitt, T. and Sonnhammer, E. L. (2009) MetaTM - a consensus method for transmembrane protein topology prediction. BMC Bioinformatics, 10, 314.
56. Marsico, A., Scheubert, K., Tuukkanen, A., Henschel, A., Winter, C., Winnenburg, R. and Schroeder, M. (2010) MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. Nucleic Acids Res., 38, D181-D189.
57. Goudenège, D., Avner, S., Lucchetti-Miganeh, C. and Barloy-Hubler, F. (2010) CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC Microbiol., 10, 88.
58. Lo, A., Cheng, C.-W., Chiu, Y.-Y., Sung, T.-Y. and Hsu, W.-L. (2011) TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. Nucleic Acids Res., 39, D347-D355.
59. Butler, E. K., Davis, R. M., Bari, V., Nicholson, P. A. and Ruiz, N. (2013) Structure-function analysis of MurJ reveals a solvent-exposed cavity containing residues essential for peptidoglycan biogenesis in Escherichia coli. J. Bacteriol., 195, 4639-4649.
60. Kozma, D., Simon, I. and Tusnády, G. E. (2012) CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods. Nucleic Acids Res., 40, W329-W333.