Prediction of transmembrane regions of β-barrel proteins using ANN- and SVM-based methods

Proteins: Structure, Function and Genetics

Volumn 56, Issue 1, 2004, Pages 11-18

  Natt, Navjyot K ^a   Kaur, Harpreet ^a   Raghava, G P S ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

barrels; Artificial neural networks; LOOCV; Multiple sequence alignment; Physicochemical parameters; Support vector machine; Transmembrane proteins

Indexed keywords

BETA BARREL PROTEIN; CARRIER PROTEIN; MALTOPORIN; MEMBRANE PROTEIN; OUTER MEMBRANE PROTEIN; PHOSPHOLIPASE A; PHOSPHOPORIN; PORIN; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; CELL METABOLISM; ESCHERICHIA COLI; HYDROPHILICITY; HYDROPHOBICITY; LEARNING; MACHINE; METHODOLOGY; MODEL; NEISSERIA MENINGITIDIS; NONHUMAN; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SALMONELLA TYPHIMURIUM; SUPPORT VECTOR MACHINE;

ALGORITHMS; BACTERIAL PROTEINS; CELL MEMBRANE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HYDROPHOBICITY; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MEMBRANE PROTEINS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PLIABILITY; PROTEIN STRUCTURE, SECONDARY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SOLVENTS; THERMODYNAMICS;

EID: 2642587355     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20092     Document Type: Article

References (55)

1. Wallin E, Von Heijne G. Genome wide analysis of integral membrane proteins eubacterial, archaean and eukaryotic organisms. Protein Sci 1998;7:1029-1038.
2. Jones DT. Do transmembrane protein superfolds exist? FEBS Lett 1998;423:281-285.
3. Cowan SW, Rosenbusch JP. Folding pattern diversity of integral membrane proteins. Science 1994;264:914-916.
4. Schulz GE. Porins: general to specific, native to engineered passive pores. Curr Opin Struct Biol 1996;10:485-490.
5. Schulz GE. β-Barrel membrane proteins. Curr Opin Struct Biol 2000;10:443-447.
6. Jenkins JA, Karlson R, Konig N, Paupit RA, Jasonius JN, Rizkallah PJ, Rosenbusch JP, Rummel G, Schirmer T. The structure of OmpF porin in a tetragonal crystal form. Structure 1995;3:1041-1050.
7. Zeth K, Deiderichs K, Welte W, Engelhardt H. Crystal structure of Omp32, the anion selective porin from Comamonas acidovorans in complex with a periplasmic peptide at 2.1 Å resolution. Structure 2000;8:981-992.
8. Buchman SK, Smith BS, Venkatramani L, Xia D Esser L, Palnitkar M, Chakraborty R, VanderHalm D, Deisenhofer J. Crystal structure of the outer membrane active transporter FepA from Escherchia coli. Nat Struct Biol 1999;6:56-63.
9. Cowan SW, Garavito RM, Jasonius JN, Fergusson AD, Hofmann E, Coulton JW, Diedericks K, Welte W. Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysacharride. Science 1998;282:2215-2220.
10. Ferguson AD, Braun V, Fielder HP, Coulton JW, Diederichs K, Welte W. Crystal structure of the antibiotic albomycin in complex with the outer membrane protein FhuA. Protein Sci 2000;9:956-9639.
11. Tusnady GE, Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 1998;283:489-506.
12. Rost B, Farseilli P, Sander C. Transmembrane helices predicted at 95% accuracy Protein Sci 1995;4:521-533.
13. Rost B, Farseilli P, Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci 1996;5: 1704-1718.
14. Casadio R, Jacoboni I, Messina A, Pinto V. A 3-D model of the voltage-dependent anion channel (VDAC). FEBS Lett 2002;520: 1-7.
15. Rost B, Chen CP, Kernytsky A. Transmembrane helix predictions revisited. Prot Sci 2002;11:2774-2791.
16. Jacoboni I, Martelli PL, Farselli P, De Pinto V, Casadio R. Prediction of the transmembrane regions of the β-barrel membrane proteins with neural network-based predictor. Protein Sci 2001;10:779-787.
17. Martelli RL, Fariselli P, Krogh A, Casadio R. A sequence profile based HMM for predicting and discriminating β-barrel membrane proteins. Bioinformatics 2002;18:S46-S53.
18. Zhai Y, Saier MH Jr. The β-barrel finder (BBF) program, allowing identification of outer membrane β-barrel proteins encoded within prokaryotic genomes. Prot Sci 2002;11:2196-2207.
19. Gromiha MM, Majumdar R, Ponnuswamy PK. Identification of membrane spanning β-strands in bacterial porins. Protein Eng 1997;5:497-500.
20. Cuff JA, Barton GJ. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000;3:502-511.
21. Kaur H, Raghava GP. A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci 2003;5:923-929.
22. Kaur H, Raghava GP. Prediction of beta-turns in proteins from multiple alignment using neural network. Protein Sci 2003;3:627-634.
23. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 1997;25: 3389-3402.
24. Vapnik V, Chervonenkis A. Theory of Pattern recognition. (In Russian) Moscow: Nauka, 1974.
25. Joachims T. Text categorization with support vector machines: learning with many relevant features. Proceedings of the European conference on machine learning. Springer, Berlin.
26. Chou KC, Zhang CT. Prediction of protein structural classes. Crit Rev Biochem Mol Biol 1995;30:275-349.
27. Schulz GE. The structure of bacterial outer membrane proteins. Biochimica et Biophysica Acta 2002;1565:308-317.
28. Sansom SP, Ulmschineider MB. Amino acid distributions in integral membrane protein structures. Biochimica et Biophysica Acta 2001;1512:1-14.
29. Forst D, Welte W, Wacker T, Diederichs K. Structure of the sucrose specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Nat Struct Biol 1998;5:37-46.
30. Meyer JE, Hofnung M., Schulz GE. Structure of maltoporin from Salmonella typhimurium ligated with nitrophenyl maltotrioside. J Mol Biol 1997;226:761-775.
31. Wang YF, Dutzler R, Rizakallah PJ, Rosenbusch JP, Schirmer T. Channel specificity: Structural basis for sugar discrimination and differential flux rates in maltoporin. J Mol Biol 1997;272:56-63.
32. Pautsch A, Schulz GE. Structure of the outer membrane protein A transmembrane domain. Nat Str Biol 1998;5:1013-1017.
33. Vogt J, Schulz GE. The structure of the outer membrane protein OmpX from Escherichia coli reveals mechanisms of virulence. Structure 1999;7:1301-1309.
34. Kreusch A, Schulz GE. Refined structure of the porin from Rhodobacter blastica: comparison with the porin from Rhodobacter capsulatus. J Mol Biol 1994;243:891-905.
35. Weiss MS, Schulz GE. Structure of porin refined at 1.8 Å resolution. J Mol Biol 1992;227:493-509.
36. Cowan SW. Refined structure of OMF porin from E. Coli at 2.3 Å resolution. (unpublished).
37. Vandeputte-Rutten L, Kramer RA, Kroon J, Dekker N, Egmond MR, Gros P. Crystal structure of outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site. EMBO 2001;20:5033-5039.
38. Snijder HJ, Ubarretxena-Belandia I, Blaauw ML. Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature 1999;401:717-721.
39. Cowan SW, Schirmer T, Rummel G, Steirt M, Ghosh R, Paupit RA, Jasonius JN, Rosenbusch JP. Crystal structures explain functional properties of two E. coli porins. Nature 1992;358:727-733.
40. Prince SM, Actman M, Derrick JP. Crystal Structure of OpcA, integral membrane protein from Neisseria meningitis. Proc Natl Acad Sci USA 2002;99:3417-3421.
41. Manvalan P, Ponnuswamy PK. Hydrophobic character of amino acids in globular proteins. Nature 1978;275:673-674.
42. Ponnuswamy PK, Prabhakaran M, Manvalan P. Hydrophobic packing and spatial arrangement of amino acids in globular proteins. Biochimica et Biophysica Acta 1980;623:301-316.
43. Eisenberg D, Schwarz E, Komarony M, Wall R. Analysis of membrane and surface protein sequences with hydrophobic moment plot. J Mol Biol 1984;179:125-142.
44. Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 1981;78:3824-3828.
45. Kyte J, Doolittle RF. A simplest method for displaying the hydropathic character of the proteins. J Mol Biol 1982;157:105-132.
46. Parker JM, Guo D, Hodges RS. New hydrohilicity scale derived from high performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray derived accessible sites. Biochemistry 1986;25:5425-5432.
47. Jones DD. Amino acid properties and side chain orientation in proteins: a cross-correlation approach. J Theo Biol 1975;50:167-183.
48. Janin J, Wodak S. Conformation of amino acid side chains in proteins. J Mol Biol 1978;125:357-386.
49. Bhaskaran, Ponnuswamy PK. Possible flexibilities of amino acid residues in globular proteins. Int J Peptide Protein Res 1988;32: 241-255.
50. Karplus PA, Schulz GE. Naturwissens-chaften 1985;72:212-219.
51. Ragone R, Facchiano F, Facchiano AM, Colonna G. Flexibility plot of proteins. Protein Engg 1989;2:497-504.
52. Bull HB, Breese K. Surface tension of amino acid solution-a hydrophobicity scale of the amino acid residues. Archi Bioch Biophy 1974; 161:665-670.
53. Chothia C. Principles that determine the structure of proteins. Annu Rev Biochem 1984;53:537-572.
54. Levitt M. Conformational Preferences of amino acids in globular proteins. Biochemistry 1978;17:4277-4285.
55. Barrel BG, Bankier AT, Drouin J. A different genetic code for human mitochondrial genome. Nature 1979;282:189-194.