TMPad: An integrated structural database for helix-packing folds in transmembrane proteins

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Lo, Allan ^a   Cheng, Cheng Wei ^a   Chiu, Yi Yuan ^a,b   Sung, Ting Yi ^a   Hsu, Wen Lian ^a  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID; MEMBRANE PROTEIN;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; INTERNET; LIGAND BINDING; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; RNA TRANSLATION; STATISTICAL ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS; TRANSMEMBRANE PROTEIN HELIX PACKING DATABASE;

BINDING SITES; DATABASES, PROTEIN; LIGANDS; LIPIDS; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; USER-COMPUTER INTERFACE;

EID: 78651331297     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1255     Document Type: Article

References (56)

1. Vinothkumar,K.R. and Henderson,R. (2010) Structures of membrane proteins. Q. Rev. Biophys., 43, 65-158.
2. 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.
3. Stevens,T.J. and Arkin,I.T. (2000) Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins, 39, 417-420.
4. White,S.H. (2009) Biophysical dissection of membrane proteins. Nature, 459, 344-346.
5. Popot,J.L. and Engelman,D.M. (1990) Membrane protein folding and oligomerization: the two-stage model. Biochemistry, 29, 4031-4037.
6. Popot,J.L. and Engelman,D.M. (2000) Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem., 69, 881-922.
7. Chothia,C., Levitt,M. and Richardson,D. (1981) Helix to helix packing in proteins. J. Mol. Biol., 145, 215-250.
8. Langosch,D. and Heringa,J. (1998) Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils. Proteins, 31, 150-159.
9. Gimpelev,M., Forrest,L.R., Murray,D. and Honig,B. (2004) Helical packing patterns in membrane and soluble proteins. Biophys. J., 87, 4075-4086.
10. Kim,S., Jeon,T.J., Oberai,A., Yang,D., Schmidt,J.J. and Bowie,J.U. (2005) Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. Proc. Natl Acad. Sci. USA, 102, 14278-14283.
11. Adamian,L. and Liang,J. (2002) Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers. Proteins, 47, 209-218.
12. Walters,R.F. and DeGrado,W.F. (2006) Helix-packing motifs in membrane proteins. Proc. Natl Acad. Sci. USA, 103, 13658-13663.
13. Beuming,T. and Weinstein,H. (2004) A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics, 20, 1822-1835.
14. Yin,H., Slusky,J.S., Berger,B.W., Walters,R.S., Vilaire,G., Litvinov,R.I., Lear,J.D., Caputo,G.A., Bennett,J.S. and DeGrado,W.F. (2007) Computational design of peptides that target transmembrane helices. Science, 315, 1817-1822.
15. Tusnady,G.E., Dosztanyi,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.
16. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
17. Tusnady,G.E., Dosztanyi,Z. and Simon,I. (2005) TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics, 21, 1276-1277.
18. 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.
19. Tusnady,G.E., Kalmar,L. and Simon,I. (2008) TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res., 36, D234-D239.
20. Burba,A.E., Lehnert,U., Yu,E.Z. and Gerstein,M. (2006) Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins. Bioinformatics, 22, 2735-2738.
21. Rose,A., Goede,A. and Hildebrand,P.W. (2010) MPlot-a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins. Nucleic Acids Res., 38(Suppl.), W602-W608.
22. 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.
23. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
24. Andreeva,A., Howorth,D., Chandonia,J.M., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425.
25. Laskowski,R.A. (2009) PDBsum new things. Nucleic Acids Res., 37, D355-D359.
26. Reichert,J. and Suhnel,J. (2002) The IMB Jena Image Library of Biological Macromolecules: 2002 update. Nucleic Acids Res., 30, 253-254.
27. The UniProt Consortium. (2009) The Universal Protein Resource (UniProt). Nucleic Acids Res., 37, D169-D174.
28. Bansal,M., Kumar,S. and Velavan,R. (2000) HELANAL: a program to characterize helix geometry in proteins. J. Biomol. Struct. Dyn., 17, 811-819.
29. Lo,A., Chiu,H.S., Sung,T.Y., Lyu,P.C. and Hsu,W.L. (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J. Proteome Res., 7, 487-496.
30. Bernsel,A., Viklund,H., Hennerdal,A. and Elofsson,A. (2009) TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res., 37, W465-W468.
31. Jones,D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics, 23, 538-544.
32. Lee,J. and Im,W. (2007) Implementation and application of helix-helix distance and crossing angle restraint potentials. J. Comput. Chem., 28, 669-680.
33. Pappu,R.V., Marshall,G.R. and Ponder,J.W. (1999) A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat. Struct. Biol., 6, 50-55.
34. Lee,B. and Richards,F.M. (1971) The interpretation of protein structures: estimation of static accesibility. J. Mol. Biol., 55, 379-400.
35. Hubbard,S.J. and Thornton,J.M. (1993) 'NACCESS' Computer Program. Department of Biochemistry and Molecular Biology, University of College London.
36. Wishart,D.S., Knox,C., Guo,A.C., Cheng,D., Shrivastava,S., Tzur,D., Gautam,B. and Hassanali,M. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 36, D901-906.
37. The jQuery JavaScript Library. http://jquery.com (29 November 2010, date last accessed).
38. The MySQL database. http://www.mysql.com (29 November 2010, date last accessed).
39. DeLano,W.L. (2002) The PyMOL Molecular Graphics System on World Wide Web. http://www.pymol.org (29 November 2010, date last accessed).
40. Jmol. an open-source Java viewer for chemical structures in 3D. http://www.jmol.org (29 November 2010, date last accessed).
41. Harries,W.E., Akhavan,D., Miercke,L.J., Khademi,S. and Stroud,R.M. (2004) The channel architecture of aquaporin 0 at a 2.2-A resolution. Proc. Natl Acad. Sci. USA, 101, 14045-14050.
42. Sui,H., Han,B.G., Lee,J.K., Walian,P. and Jap,B.K. (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature, 414, 872-878.
43. Ho,J.D., Yeh,R., Sandstrom,A., Chorny,I., Harries,W.E., Robbins,R.A., Miercke,L.J. and Stroud,R.M. (2009) Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance. Proc. Natl Acad. Sci. USA, 106, 7437-7442.
44. Horsefield,R., Norden,K., Fellert,M., Backmark,A., Tornroth- Horsefield,S., Terwisscha van Scheltinga,A.C., Kvassman,J., Kjellbom,P., Johanson,U. and Neutze,R. (2008) High-resolution x-ray structure of human aquaporin 5. Proc. Natl Acad. Sci. USA, 105, 13327-13332.
45. Lee,J.K., Kozono,D., Remis,J., Kitagawa,Y., Agre,P. and Stroud,R.M. (2005) Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A. Proc. Natl Acad. Sci. USA, 102, 18932-18937.
46. Savage,D.F. and Stroud,R.M. (2007) Structural basis of aquaporin inhibition by mercury. J. Mol. Biol., 368, 607-617.
47. Fischer,G., Kosinska-Eriksson,U., Aponte-Santamaria,C., Palmgren,M., Geijer,C., Hedfalk,K., Hohmann,S., de Groot,B.L., Neutze,R. and Lindkvist-Petersson,K. (2009) Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol., 7, e1000130.
48. Nyblom,M., Frick,A., Wang,Y., Ekvall,M., Hallgren,K., Hedfalk,K., Neutze,R., Tajkhorshid,E. and Tornroth-Horsefield,S. (2009) Structural and functional analysis of SoPIP2;1 mutants adds insight into plant aquaporin gating. J. Mol. Biol., 387, 653-668.
49. Tajkhorshid,E., Nollert,P., Jensen,M.O., Miercke,L.J., O'Connell,J., Stroud,R.M. and Schulten,K. (2002) Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science, 296, 525-530.
50. Gonen,T. and Walz,T. (2006) The structure of aquaporins. Q. Rev. Biophys., 39, 361-396.
51. Moretti,S., Armougom,F., Wallace,I.M., Higgins,D.G., Jongeneel,C.V. and Notredame,C. (2007) The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res., 35, W645-W648.
52. Hub,J.S. and de Groot,B.L. (2008) Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc. Natl Acad. Sci. USA, 105, 1198-1203.
53. Im,W., Lee,J., Kim,T. and Rui,H. (2009) Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. J. Comput. Chem., 30, 1622-1633.
54. Barth,P., Wallner,B. and Baker,D. (2009) Prediction of membrane protein structures with complex topologies using limited constraints. Proc. Natl Acad. Sci. USA, 106, 1409-1414.
55. Harrington,S.E. and Ben-Tal,N. (2009) Structural determinants of transmembrane helical proteins. Structure, 17, 1092-1103.
56. Ye,J., Fang,L., Zheng,H., Zhang,Y., Chen,J., Zhang,Z., Wang,J., Li,S., Li,R. and Bolund,L. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res., 34, W293-W297.