TopPTM: A new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Su, Min Gang ^a   Huang, Kai Yao ^a   Lu, Cheng Tsung ^a   Kao, Hui Ju ^a   Chang, Ya Han ^a   Lee, Tzong Yi ^a  

^a YUAN ZE UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CCR5; MEMBRANE PROTEIN;

ACETYLATION; AMINO TERMINAL SEQUENCE; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; ENZYME SUBSTRATE; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; SIGNAL TRANSDUCTION; CHEMISTRY; INTERNET; METABOLISM; PROTEIN DATABASE; CONTROLLED STUDY; DATA BASE; OPM DATABASE; PDBTM DATABASE; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN FOLDING; PROTEIN STABILITY; TMPAD DATABASE; TOPDB DATABASE; TOPPTM DATABASE; UNIPROTKB DATABASE;

DATABASES, PROTEIN; INTERNET; MEMBRANE PROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY;

EID: 84891814653     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1221     Document Type: Article

References (54)

1. Mann, M. and Jensen, O.N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol., 21, 255-261.
2. Farriol-Mathis, N., Garavelli, J.S., Boeckmann, B., Duvaud, S., Gasteiger, E., Gateau, A., Veuthey, A.L. and Bairoch, A. (2004) Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics, 4, 1537-1550.
3. Seo, J. and Lee, K.J. (2004) Post-translational modifications and their biological functions: proteomic analysis and systematic approaches. J. Biochem. Mol. Biol., 37, 35-44.
4. Wei, W. and Lin, H.K. (2012) The key role of ubiquitination and sumoylation in signaling and cancer: a research topic. Front. Oncol., 2, 187.
5. Hay, R.T. (2005) SUMO: a history of modification. Mol. Cell, 18, 1-12.
6. DiAntonio, A., Haghighi, A.P., Portman, S.L., Lee, J.D., Amaranto, A.M. and Goodman, C.S. (2001) Ubiquitination-dependent mechanisms regulate synaptic growth and function. Nature, 412, 449-452.
7. Lee, T.Y., Huang, H.D., Hung, J.H., Huang, H.Y., Yang, Y.S. and Wang, T.H. (2006) dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res., 34, D622-D627.
8. Lu, C.T., Huang, K.Y., Su, M.G., Lee, T.Y., Bretana, N.A., Chang, W.C., Chen, Y.J. and Huang, H.D. (2013) DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res., 41, D295-D305.
9. Vinothkumar, K.R. and Henderson, R. (2010) Structures of membrane proteins. Q. Rev. Biophys., 43, 65-158.
10. Wallin, E. and von Heijne, G. (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci., 7, 1029-1038.
11. Almen, M.S., Nordstrom, K.J., Fredriksson, R. and Schioth, H.B. (2009) Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol., 7, 50.
12. Fairman, J.W., Noinaj, N. and Buchanan, S.K. (2011) The structural biology of beta-barrel membrane proteins: a summary of recent reports. Curr. Opin. Struct. Biol., 21, 523-531.
13. Ikeda, M., Arai, M., Okuno, T. and Shimizu, T. (2003) TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res., 31, 406-409.
14. Kozma, D., Simon, I. and Tusnady, G.E. (2013) PDBTM: protein data bank of transmembrane proteins after 8 years. Nucleic Acids Res., 41, D524-D529.
15. 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.
16. Tusnady, GE., Kalmar, L. and Simon, I. (2008) TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res., 36, D234-D239.
17. Tusnady, GE., Kalmar, 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.
18. 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.
19. Freeman, T.C. Jr and Wimley, W.C. (2012) TMBB-DB: a transmembrane beta-barrel proteome database. Bioinformatics, 28, 2425-2430.
20. Seet, B.T., Dikic, I., Zhou, M.M. and Pawson, T. (2006) Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol., 7, 473-483.
21. Ackers, GK. and Smith, F.R. (1985) Effects of site-specific amino acid modification on protein interactions and biological function. Annu. Rev. Biochem., 54, 597-629.
22. Consortium, U. (2013) Update on activities at the universal protein resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
23. Tusnady, GE. and Simon, I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
24. Nugent, T. and Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics, 10, 159.
25. Hu, Z.Z., Narayanaswamy, M., Ravikumar, KE., Vijay-Shanker, K. and Wu, C.H. (2005) Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics, 21, 2759-2765.
26. Consortium, GO. (2013) Gene ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
27. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K, Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
28. Sigrist, C.J., de Castro, E., Cerutti, L., Cuche, BA., Hulo, N., Bridge, A., Bougueleret, L. and Xenarios, I. (2013) New and continuing developments at PROSITE. Nucleic Acids Res., 41, D344-D347.
29. Attwood, T.K, Coletta, A., Muirhead, G, Pavlopoulou, A., Philippou, P.B., Popov, I., Roma-Mateo, C, Theodosiou, A. and Mitchell, A.L. (2012) The PRINTS database: a fine-grained protein sequence annotation and analysis resource-its status in 2012. Database (Oxford), 2012, bas019.
30. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
31. Bru, C., Courcelle, E., Carrere, S., Beausse, Y., Dalmar, S. and Kahn, D. (2005) The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res., 33, D212-D215.
32. Ramasarma, T. (1996) Transmembrane domains participate in functions of integral membrane proteins. Indian J. Biochem. Biophys., 33, 20-29.
33. Wegener, K.L. and Campbell, I.D. (2008) Transmembrane and cytoplasmic domains in integrin activation and protein-protein interactions (review). Mol. Membr. Biol., 25, 376-387.
34. Cormier, E.G., Persuh, M., Thompson, D.A., Lin, S.W., Sakmar, T.P., Olson, W.C. and Dragic, T. (2000) Specific interaction of CCR5 amino-terminal domain peptides containing sulfotyrosines with HIV-1 envelope glycoprotein gp120. Proc. Natl Acad. Sci. USA, 97, 5762-5767.
35. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
36. Stein, A., Ceo, A. and Aloy, P. (2011) 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 39, D718-D723.
37. Herraez, A. (2006) Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Educ., 34, 255-261.
38. Lee, T.Y., Chen, Y.J., Lu, C.T., Ching, W.C., Teng, Y.C. and Huang, H.D. (2012) dbSNO: a database of cysteine S-nitrosylation. Bioinformatics, 28, 2293-2295.
39. Spudich, J.L., Yang, C.S., Jung, K.H. and Spudich, E.N. (2000) Retinylidene proteins: structures and functions from archaea to humans. Annu. Rev. Cell Dev. Biol., 16, 365-392.
40. Katre, N.V., Wolber, P.K., Stoeckenius, W. and Stroud, R.M. (1981) Attachment site(s) of retinal in bacteriorhodopsin. Proc. Natl Acad. Sci. USA, 78, 4068-4072.
41. Souda, P., Ryan, C.M., Cramer, W.A. and Whitelegge, J. (2011) Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry. Methods, 55, 330-336.
42. Arighi, C.N., Siu, A.Y., Tudor, C.O., Nchoutmboube, J.A., Wu, C.H. and Shanker, V.K. (2010) eFIP: a tool for mining functional impact of phosphorylation from literature. Methods Mol. Biol., 694, 63-75.
43. Farzan, M., Mirzabekov, T., Kolchinsky, P., Wyatt, R., Cayabyab, M., Gerard, N.P., Gerard, C., Sodroski, J. and Choe, H. (1999) Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell, 96, 667-676.
44. Schnur, E., Noah, E., Ayzenshtat, I., Sargsyan, H., Inui, T., Ding, F.X., Arshava, B., Sagi, Y., Kessler, N., Levy, R. et al. (2011) The conformation and orientation of a 27-residue CCR5 peptide in a ternary complex with HIV-1 gp120 and a CD4-mimic peptide. J. Mol. Biol., 410, 778-797.
45. Bannert, N., Craig, S., Farzan, M., Sogah, D., Santo, N.V., Choe, H. and Sodroski, J. (2001) Sialylated O-glycans and sulfated tyrosines in the NH2-terminal domain of CC chemokine receptor 5 contribute to high affinity binding of chemokines. J. Exp. Med., 194, 1661-1673.
46. Oppermann, M., Mack, M., Proudfoot, A.E. and Olbrich, H. (1999) Differential effects of CC chemokines on CC chemokine receptor 5 (CCR5) phosphorylation and identification of phosphorylation sites on the CCR5 carboxyl terminus. J. Biol. Chem., 274, 8875-8885.
47. Brandt, S.M., Mariani, R., Holland, A.U., Hope, T.J. and Landau, N.R. (2002) Association of chemokine-mediated block to HIV entry with coreceptor internalization. J. Biol. Chem., 277, 17291-17299.
48. Huttenrauch, F., Nitzki, A., Lin, F.T., Honing, S. and Oppermann, M. (2002) Beta-arrestin binding to CC chemokine receptor 5 requires multiple C-terminal receptor phosphorylation sites and involves a conserved Asp-Arg-Tyr sequence motif. J. Biol. Chem., 277, 30769-30777.
49. Pollok-Kopp, B., Schwarze, K., Baradari, V.K. and Oppermann, M. (2003) Analysis of ligand-stimulated CC chemokine receptor 5 (CCR5) phosphorylation in intact cells using phosphosite-specific antibodies. J. Biol. Chem., 278, 2190-2198.
50. Rahbar, R., Murooka, T.T., Hinek, A.A., Galligan, C.L., Sassano, A., Yu, C, Srivastava, K., Platanias, L.C. and Fish, E.N. (2006) Vaccinia virus activation of CCR5 invokes tyrosine phosphorylation signaling events that support virus replication. J. Virol., 80, 7245-7259.
51. Blanpain, C, Wittamer, V., Vanderwinden, J.M., Boom, A., Renneboog, B., Lee, B., Le Poul, E., El Asmar, L., Govaerts, C, Vassart, G. et al. (2001) Palmitoylation of CCR5 is critical for receptor trafficking and efficient activation of intracellular signaling pathways. J. Biol. Chem., 276, 23795-23804.
52. Kraft, K., Olbrich, H., Majoul, I., Mack, M., Proudfoot, A. and Oppermann, M. (2001) Characterization of sequence determinants within the carboxyl-terminal domain of chemokine receptor CCR5 that regulate signaling and receptor internalization. J. Biol. Chem., 276, 34408-34418.
53. Blanpain, C., Doranz, B.J., Bondue, A., Govaerts, C., De Leener, A., Vassart, G., Doms, R.W., Proudfoot, A. and Parmentier, M. (2003) The core domain of chemokines binds CCR5 extracellular domains while their amino terminus interacts with the transmembrane helix bundle. J. Biol. Chem., 278, 5179-5187.
54. Chen, S.A., Lee, T.Y. and Ou, Y.Y. (2010) Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. BMC Bioinformatics, 11, 536.