Htp: A neural network-based method for predicting the topology of helical transmembrane domains in proteins

Bioinformatics

Volumn 12, Issue 1, 1996, Pages 41-48

  Fariselli, Piero ^a   Casadio, Rita ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER PROGRAM; MEMBRANE STRUCTURE; MICROCOMPUTER; PREDICTION; PRIORITY JOURNAL;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; DATABASES, FACTUAL; EVALUATION STUDIES; HUMANS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; NEURAL NETWORKS (COMPUTER); PROTEIN STRUCTURE, SECONDARY; SOFTWARE; SOFTWARE DESIGN;

EID: 0029978247     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.1.41     Document Type: Article

References (49)

1. Akyama, Y. and Ito, K. (1987) Topology analysis of the SecY protein, an integral membrane protein involved in protein export in Escherichia coli. EMBO J., 6, 3465-3470.
2. Bairoch, A. and Boeckmann, B. (1992) The SWISS-PROT protein sequence data bank. Nucleic Acids. Res., 20, 2019-2022.
3. Bernstein, F.C, Koetzle.T.F., Williams.G.J.B., Meyer, E.F., Brice.M.D., Rodgers, J.R., Kennard.O., Shimanouchi.T. and Tasumi.M. (1977) The protein data bank: a computer-based archival file for macro-molecular structures. J. Mol. Biol., 112, 535-542.
4. Chothia, C. (1992) One thousand families for the molecular biologist. Nature, 357, 543-544.
5. Cornette, J.L., Cease.K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and De Lisi, C. (1987) Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol., 195, 659-685.
6. Cowan.S.W., Schirmer.T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R.A., Jansonius.J.N. and Rosenbusch, J.P. (1992) Crystal structures explain functional properties of two E. coli porins. Nature, 358, 727— 733.
7. Degli Esposti, M., Crimi, M. and Venturoli.G. (1990) A critical evaluation of the hydropathy profile of membrane proteins. Eur. J. Biochem.. 190, 207-219.
8. Deisenhofer, J., Epp.O., Miki, K., Huber, R. and Michel, H. (1985) Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 A resolution. Nature, 318, 618-624.
9. Edelman.J. (1993) Quadratic minimization of predictors for protein secondary structure: application to transmembrane a-helixes. J. Mol. Biol., 232, 165-191.
10. Eisenberg.D., Schwarz, E., Komaromy.M. and Wall.R. (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol., 179, 125-142.
11. Engelman, D.M., Steitz.T.A. and Goldman, A. (1986) Identifying non-polar transbilayer helixes in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem., 15, 321-353.
12. Fariselli, P., Compiani, M. and Casadio, R. (1993) Predicting secondary structures of membrane proteins with neural networks. Eur. Biophys. J., 22, 41-51.
13. Fasman.G.D. (1989) The development of the prediction of protein structure. In Fasman.G.D. (ed.), Prediction of Protein Structure and the Principles of Protein Conformation. Plenum Press, New York, pp. 193-316.
14. Fasman, G.D. and Gilbert, W. A. (1990) The prediction of transmembrane protein sequences and their conformation: an evaluation. Trends Biochem. Sci., 15, 89-92.
15. Feher, G., Allen.J.P., Okamura, M.Y. and Recs, D.C. (1989) Structure and function of bacterial photosynthetic reaction centers. Nature, 339, 111-116.
16. Henderson.R., Baldwin,.J.M., Ceska, T.A., Zemlin, F., Beckmann, E. and Downing, K.H. (1990) Model for the structure of bacteriorhodopsin based on high resolution electron cryo-microscopy. J. Mol. Biol., 213, 899-929.
17. Hirst, J.D. and Sternberg.J.E. (1992) Prediction of structural and functional features of proteins and nucleic acid sequences by artificial neural networks. Biochemistry, 31, 7211-7218.
18. Jones.D.T., Taylor.W.R. and Thornton,.J.M. (1994) A model recognifition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 33, 3038-3049.
19. Khorana.H.G. (1992) Rhodopsin, photoreceptor of the rod cell. J. Biol. Chem., 267, 1-4.
20. Klein, P., Kanehisa.M. and De Lisi, C. (1985) The detection and classification of membrane-spanning protein. Biochim. Biophys. Acta, 815, 468-476.
21. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydrophobic character of a protein. J. Mol. Biol., 157, 103-132.
22. Kuhlbrandt, W., Wang, D.N. and Fujiyoshi, Y. (1994) Atomic model of plant light-harvesting complex by electron crystallography. Nature, 367, 614-621.
23. Kuhn, L.A., Leigh.J.S. (1985) A statistical technique for predicting membrane protein structure. Biochim. Biophys. Acta, 828, 351-361.
24. Lipman, D.J. and Pearson.W.L. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
25. Manoil.C. and Beckwith.J. (1986) A genetic approach to analyzing membrane protein topology. Science, 233, 1403-1408.
26. Matthews.B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophvs. Acta, 405, 442-451.
27. McDermott, G., Prince, S.M., Freer, A.A., Hawthornthwaite-Lawless, A.M., Papiz, M.Z., Cogdell, R.J. and isaacs, N.W. (1995) Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. Nature, 374, 517-521.
28. McGovern.K.., Ehrmann, M.and Beckwith, J. (1991) Decoding signals for membrane proteins using alkaline phosphatase fusions. EMBO J., 10. 2773-2782.
29. Michel, H. (1993) Crystallization of membrane proteins. Trends Biochem Sci., 8, 56-59.
30. Michel, H., Weyer, K.A., Gruenberg.H., Dunger.I., Osterhelt.D. and Lottspeich, F. (1986) The light and medium subunits of the photosynthetic reaction center from Rhodopseudomonas viridis: isolation of the genes, nucleotide and amino acid sequence. EMBO J., 5, 1149-1158.
31. Parodi.L.A., Granatir.C.A. and Maggiora.G.M. (1994) A consensus procedure for predicting the location of o-helical transmembrane segments in proteins. Comput. Applic. Biosci., 5, 527-535.
32. Persson.B. and Argos.P. (1994) Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J. Mol. Biol., 237, 182-192.
33. Presnell, S.R. and Cohen.F.E. (1993) Artificial neural networks for pattern recognition in biochemical sequences. Annu. Rev. Biophvs. Biomol. Struct., 22, 283-298.
34. Qian.N. and Sejnowski.T.G. (1988) Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol., 202, 865-884.
35. Rao.J.K.M. and Argos.P. (1986) A conformational preference parameter to predict helices in integral membrane proteins. Biochim. Biophvs. Acta, 869, 197-214.
36. Rost, B. and Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
37. Rost, B., Sander, C. and Schneider.R. (1994) Redefining the goals of protein secondary structure prediction. J. Mol. Biol., 235, 13-26.
38. Rost.B., Casadio, R., Fariselli, P. and Sander, C. (1995) Transmembrane helices predicted at 95% accuracy. Prot. Sci., 4, 521-533.
39. Rumelhart, D.E., Hinton, G.E. and Williams, R.J. (1986) Learning representation by back-propagation errors. Nature, 323, 533-536.
40. Schertler.G.F.X., Villa, C. and Henderson, R. (1993) Projection structure of rhodopsin. Nature, 362, 770-772.
41. Schultz, G.E. (1988) A critical evaluation of methods for prediction of protein secondary structures. Annu. Rev. Biophvs. Biophys. Chem., 17, 1-21.
42. Strosberg.A.D. (1991) Structure/function relationship of proteins belonging to the family of receptors coupled to GTP-binding proteins. Eur. J. Biochem., 29, 11009-11023.
43. Traxler, B., Boyd, D. and Beckwith, J. (1993) The topological analysis of integral membrane proteins. J. Membrane Biol., 132, 1 — 11.
44. Turner, R.J. and Weiner, J.H. (1993) Evaluation of transmembrane helix prediction methods using the recently defined NMR structures of the coat proteins from bacteriophages M13 and Pfl. Biochim. Biophys. Acta, 1202, 161-168.
45. Vivarelli, F., Giusti, G., Villani, M., Campanini, R., Fariselli, P., Compiani, M. and Casadio, R. (1995) LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins. Comput. Applic. Biosci.. 11, 253-260.
46. von Heijne, G. (1992) Hydrophobicity analysis and the positive-inside rule. J. Mot. Biol., 225, 487-494.
47. von Heijne.G. (1994) Membrane proteins: from sequence to structure. Annu. Rev. Biophvs. Biomol. Struct., 23, 167-192.
48. Weiss.M.S., Kreush.A., Shiltz, E., Nestel.U.. Welte.W.. Weckesser, J. and SchulZjG.E. (1991) The structure of porin from Rhodobacler capsulalus at 1.8 A resolution. FEBS Lett., 280, 379-382.
49. White.S.H. (1994) Hydrophaty plots and the prediction of membrane protein topology. In White, S.H. (ed.). Membrane Protein Structure. Oxford University Press, New York, pp. 97-124.