Topology prediction of membrane proteins: How distantly related homologs come into play

Structural Bioinformatics of Membrane Proteins

Volumn , Issue , 2010, Pages 61-82

  Casadio, Rita ^a   Martelli, Pier Luigi ^a   Bartoli, Lisa ^a   Fariselli, Piero ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84889804716     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-0045-5_4     Document Type: Chapter

References (50)

1. Aller SG, Yu J, Ward A, Weng Y, Chitt aboina S, Zhuo R, Harrell PM, Trinh YT, Zhang Q, Urbatsch IL, Chang G (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specifi c drug binding. Science 323: 1718-1722
2. Altschul SF and Koonin EV (1998) Iterated profi le searches with PSI-BLAST: a tool for discovery in protein databases. Trends Biochem Sci 23: 444-447
3. Amico M, Finelli M, Rossi I, Zauli A, Elofsson A, Viklund H, von Heijne G, Jones D, Krogh A, Fariselli P, Martelli PL, Casadio R (2006) PONGO: a web server for multiple predictions of all-Alpha transmembrane proteins. Nucleic Acids Res 34: W169-W172
4. Bartoli L, Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G, Maggi G, Casadio R (2009) The Bologna Annotation Resource: a non-hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis. J Proteome Res 8: 4362-4371
5. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: signalP 3.0. J Mol Biol 340: 783-795
6. Bishop CM (2006) Patt ern recognition and machine learning. Springer, New York
7. Casadio R, Jacoboni I, Messina A, De Pinto V (2002) A 3D model of the voltage-dependent anion channel (VDAC). FEBS Lett 520: 1-7
8. Casadio R, Fariselli P, Martelli PL (2003) In silico prediction of the structure of membrane proteins: is it feasible Brief Bioinform 4: 341-348
9. Chen CP, Kernytsky A, Rost B (2002) Transmembrane helix predictions revisited. Protein Sci 11: 2774-2791
10. Chen YJ, Pornillos O, Lieu S, Ma C, Chen AP, Chang G (2007) X-ray structure of EmrE supports dual topology model. Proc Nat Acad Sci USA 104: 18999-19004
11. Claros MG and Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779-786
12. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
13. Eswar N, Eramian D, Webb B, Shen MY, Sali A (2008) Protein structure modeling with MODELLER. Method Mol Biol 426: 145-159
14. Fariselli P, Compiani M, Casadio R. (1993) Predicting secondary structures of membrane proteins with neural networks. Eur Biophys J 22: 41-51
15. Fariselli P, Finocchiaro G, Casadio R (2003a) SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19: 2498-2499
16. Fariselli P, Finelli M, Marchignoli D, Martelli PL, Rossi I, Casadio R (2003b) MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics 19: 500-505
17. Fariselli P, Martelli PL, Casadio R (2005) A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinform 6: S12
18. Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM (2000) Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290: 481-486
19. Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433: 377-381
20. Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S (2009) Sequence-based feature prediction and annotation of proteins. Genome Biol 10: 206
21. Jones DT, Taylor WR, Th ornton JM (1994) A morel recognition approach to the prediction of all helical membrane protein structure and topology. Biochemistry 33: 3038-3049
22. Kl L, Krogh A, Sonnhammer ELL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027-1036
23. Kl L, Krogh A, Sonnhammer EL (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21: i251-i257
24. 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
25. Kyte J and Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132
26. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22: 623-625
27. Martelli PL, Fariselli P, Krogh A, Casadio R (2002) A sequence-profi le-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 18: S46-S53
28. Martelli PL, Fariselli P, Casadio R (2003) An ENSEMBLE machine learning approach for the prediction of all-Alpha membrane proteins. Bioinformatics 19: I205-I211
29. Martelli PL, Fariselli P, Casadio R (2004) Prediction of disulfi de-bonded cysteines in proteomes with a hidden neural network. Proteomics 4: 1665-1671
30. Mler S, Croning MD, Apweiler R (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646-653
31. Newby ZE, O'Connell J III, Robles-Colmenares Y, Khademi S, Miercke LJ, Stroud RM (2008) Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Nat Struct Mol Biol 15: 619-625
32. Newby ZE, O'Connell JD III, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM (2009) A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nat Protoc 4: 619-637
33. Nugent T and Jones DT (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinform 10: 159
34. Oberai A, Ihm Y, Kim S, Bowie JU (2006) A limited universe of membrane proteins and folds. Protein Sci 15: 1723-1734
35. 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 proteincoupled receptor. Science 289: 739-745
36. Pebay-Peyroula E, Rummel G, Rosenbusch JP, Landau EM (1997) X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277: 1676-1681
37. Pierleoni A, Martelli PL, Casadio R (2008) PredGPI: a GPI anchor predictor. BMC Bioinform 9: 392
38. Phillips R, Ursell T, Wiggins P, Sens P (2009) Emerging roles for lipids in shaping membrane-protein function. Nature 459: 379-385
39. Poisson G, Chauve C, Chen X, Bergeron A (2007) FragAnchor a large scale all Eukaryota predictor of Glycosylphosphatidylinositol-Anchor in protein sequences by qualitative scoring. Genomics Proteomics Bioinform 5: 121-130
40. Rost B and Sander C (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20: 216-26
41. Rost B, Casadio R, Fariselli P, Sander C (1995) Transmembrane helices predicted at 95% accuracy. Protein Sci 4: 521-533
42. Rost B, Fariselli P, Casadio R (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci 7: 1704-1718
43. Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6: 175-182
44. Tusny GE and Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850
45. Tusny GE, Dosztyi Z, Simon I (2004) Transmembrane proteins in the Protein Data Bank: identifi cation and classifi cation. Bioinformatics 20: 2964-2972
46. 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
47. Viklund H, Bernsel A, Skwark M, Elofsson A (2008) SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 24: 2928-2929
48. von Heijne G and Gavel Y (1988) Topogenic signals in integral membrane proteins. Eur J Biochem 174: 671-678
49. White SH (2009) Biophysical dissection of membrane proteins. Nature 459: 344-346
50. White SH and Wimley WC (1999) Membrane protein folding and stability: physical principles. Ann Rev Biophys Biomol Struct 28: 319-365