Statistical analysis and exposure status classification of transmembrane beta barrel residues

Computational Biology and Chemistry

Volumn 35, Issue 2, 2011, Pages 96-107

  Hayat, Sikander ^a   Park, Yungki ^a   Helms, Volkhard ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

Exposure status; Propensity scales; Transmembrane beta barrel proteins

Indexed keywords

BI-LAYER; EXPOSURE STATUS; FREQUENCY PROFILES; HELICAL MEMBRANE; HYDROPHOBIC CORE; INNER MEMBRANES; INTERFACE REGIONS; MEMBRANE BILAYERS; OUTER MEMBRANE; PHYSICOCHEMICAL PROPERTY; PROPENSITY SCALES; PROTEIN STRUCTURES; STATISTICAL ANALYSIS; TRANSMEMBRANE BETA BARREL PROTEINS; TRANSMEMBRANES;

CHEMICAL PROPERTIES; COMPUTATIONAL METHODS; LIPID BILAYERS; MEMBRANES; OLIGOMERS;

PROTEINS;

MEMBRANE PROTEIN;

ARTICLE; CHEMICAL PHENOMENA; CHEMISTRY; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; PROTEIN SECONDARY STRUCTURE; STATISTICAL ANALYSIS;

COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MEMBRANE PROTEINS; PROTEIN STRUCTURE, SECONDARY;

EID: 79956371793     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2011.03.002     Document Type: Article

References (76)

1. L. Adamian, and J. Liang Prediction of transmembrane helix orientation in polytopic membrane proteins BMC Structural Biology 6 2006 13 30
2. M. Ali, and B. Imperiali Protein oligomerization: how and why Bioorganic and Medicinal Chemistry 13 2005 5013 5020 (Pubitemid 41043188)
3. T. Beuming, and H. Weinstein A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins Bioinformatics 20 2004 1822 1835 (Pubitemid 39199046)
4. S. Black, and D. Mould Development of hydrophobicity parameters to analyze proteins which bear post-or cotranslational modifications Analytical Biochemistry 193 1991 72 82
5. M. Bogdanov, and W. Dowhan Lipid-assisted protein folding Journal of Biological Chemistry 274 1999 36827 36830
6. J. Bowie Solving the membrane protein folding problem Nature 438 2005 581 589 (Pubitemid 41740561)
7. H. Bull, and K. Breese Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues Archives of Biochemistry and Biophysics 161 1974 665 670
8. A. Chamberlain, Y. Lee, S. Kim, and J. Bowie Snorkeling preferences foster an amino acid composition bias in transmembrane helices Journal of Molecular Biology 339 2004 471 479 (Pubitemid 38596964)
9. H. Cid, M. Bunster, M. Canales, and F. Gazitua Hydrophobicity and structural classes in proteins Protein Engineering 5 1992 373 375
10. D. Donnelly, J. Overington, S. Ruffle, J. Nugent, and T. Blundell Modeling α-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues Protein Science 2 1993 55 70 (Pubitemid 23029009)
11. H. Edelsbrunner The union of balls and its dual shape Discrete and Computational Geometry 13 1995 415 440
12. H. Edelsbrunner, M. Facello, P. Fu, and J. Liang Measuring proteins and voids in proteins Proceedings of the Hawaii International Conference on System Sciences 1995 IEEE Institute of Electrical and Electronics 256 264
13. D. Eisenberg, and A. McLachlan Solvation energy in protein folding and binding Nature 319 1986 199 203 (Pubitemid 16128783)
14. D. Eisenberg, R. Weiss, T. Terwilliger, and W. Wilcox Hydrophobic moments and protein structure Faraday Symposia of the Chemical Society 1982 Royal Society of Chemistry 109 120
15. D. Engelman, T. Steitz, and A. Goldman Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins Annual Review of Biophysics and Biophysical Chemistry 15 1986 321 353
16. E. Eppens, N. Nouwen, and J. Tommassen Folding of a bacterial outer membrane protein during passage through the periplasm The EMBO Journal 16 1997 4295 4301 (Pubitemid 27298182)
17. J. Fauchere, M. Charton, L. Kier, A. Verloop, and V. Pliska Amino acid side chain parameters for correlation studies in biology and pharmacology International Journal of Peptide and Protein Research 32 1988 269 278
18. J. Fauchere, and V. Pliska Hydrophobic parameters pi of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides European Journal of Medicinal Chemistry 18 1983 369 375
19. T. Freeman, and W. Wimley Jr. A highly accurate statistical approach for the prediction of transmembrane beta-barrels Bioinformatics 26 2010 1965
20. J. Friedman, T. Hastie, and R. Tibshirani The Elements of Statistical Learning 2001
21. M. Gimpelev, L. Forrest, D. Murray, and B. Honig Helical packing patterns in membrane and soluble proteins Biophysical Journal 87 2004 4075 4086 (Pubitemid 39602911)
22. E. Granseth, G. von Heijne, and A. Elofsson A study of the membrane-water interface region of membrane proteins Journal of Molecular Biology 346 2005 377 385 (Pubitemid 40128328)
23. R. Grantham Amino acid difference formula to help explain protein evolution Science 185 1974 862 864
24. K. Gunasekaran, H. Nagarajaram, C. Ramakrishnan, and P. Balaram Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals Journal of Molecular Biology 275 1998 917 932 (Pubitemid 28077704)
25. T. Hopp, and K. Woods Prediction of protein antigenic determinants from amino acid sequences Proceedings of the National Academy of Sciences of the United States of America 78 1981 3824 3828 (Pubitemid 11060471)
26. C. Hsu, and C. Lin A comparison of methods for multiclass support vector machines IEEE Transactions on Neural Networks 13 2002 415 425 (Pubitemid 34475042)
27. K. Illergrd, S. Callegari, and A. Elofsson MPRAP: an accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane BMC Bioinformatics 11 2010 333 344
28. R. Jackups, and J. Liang Interstrand pairing patterns in β-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction Journal of Molecular Biology 354 2005 979 993 (Pubitemid 41735517)
29. J. Janin Surface and inside volumes in globular proteins Nature 277 1979 491 492
30. J. Janin, S. WodakMichael, and B. Maigret Conformation of amino acid side-chains in proteins Journal of Molecular Biology 125 1978 357 386 (Pubitemid 9063908)
31. D. Jones Amino acid properties and side-chain orientation in proteins: a cross correlation approach Journal of Theoretical Biology 50 1975 167 183
32. S. Jones, and J. Thornton Analysis of protein-protein interaction sites using surface patches Journal of Molecular Biology 272 1997 121 132 (Pubitemid 27395542)
33. S. Jones, and J. Thornton Prediction of protein-protein interaction sites using patch analysis Journal of Molecular Biology 272 1997 133 143 (Pubitemid 27395543)
34. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 2004 2577 2637
35. S. Kawashima, P. Pokarowski, M. Pokarowska, A. Kolinski, T. Katayama, and M. Kanehisa AAindex: amino acid index database, progress report 2008 Nucleic Acids Research 36 2008 D202
36. J. Kleinschmidt Membrane protein folding on the example of outer membrane protein A of Escherichia coli Cellular and Molecular Life Sciences (CMLS) 60 2003 1547 1558 (Pubitemid 37041354)
37. S. Konishi, T. Nishio, and T. Shimizu Inner residues in the transmembrane helix bundle are more conservative Genome Informatics Series 2003 549 550
38. C. Lazdunski, and H. Benedetti Insertion and translocation of proteins into and though membranes FEBS Letters 268 1990 408 414
39. J. Liang, L. Adamian, and R. Jackups The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect Trends in Biochemical Sciences 30 2005 355 357 (Pubitemid 40942028)
40. M. Lomize, A. Lomize, I. Pogozheva, and H. Mosberg OPM: orientations of proteins in membranes database Bioinformatics 22 2006 623 625 (Pubitemid 43372827)
41. P. Manavalan, and P. Ponnuswamy Hydrophobic character of amino acid residues in globular proteins Nature 275 1978 673 674 (Pubitemid 9031478)
42. G. Meng, R. Fronzes, V. Chandran, H. Remaut, and G. Waksman Protein oligomerization in the bacterial outer membrane (Review) Molecular Membrane Biology 26 2009 136 145
43. S. Miyazawa, and R. Jernigan Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues Proteins Structure Function and Genetics 34 1999 49 68 (Pubitemid 29019531)
44. Y. Nozaki, and C. Tanford The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale Journal of Biological Chemistry 246 1971 2211 2217
45. Y. Ou, S. Chen, and M. Gromiha Prediction of membrane spanning segments and topology in β-barrel membrane proteins at better accuracy Journal of Computational Chemistry 31 2010 217 223
46. Y. Park, S. Hayat, and V. Helms Prediction of the burial status of transmembrane residues of helical membrane proteins BMC Bioinformatics 8 2007 302 316
47. Y. Park, and V. Helms How strongly do sequence conservation patterns and empirical scales correlate with exposure patterns of transmembrane Biopolymers 83 2006 389 399 (Pubitemid 44683083)
48. Y. Park, and V. Helms On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins Bioinformatics 23 2007 701 708 (Pubitemid 46554721)
49. J. Pei, and N. Grishin AL2CO: calculation of positional conservation in a protein sequence alignment Bioinformatics 17 2001 700 712 (Pubitemid 32851378)
50. N. Pfanner, N. Wiedemann, C. Meisinger, and T. Lithgow Assembling the mitochondrial outer membrane Nature Structural & Molecular Biology 11 2004 1044 1048 (Pubitemid 39453331)
51. V. Pliska, M. Schmidt, and J. Fauchre Partition coefficients of amino acids and hydrophobic parameters [pi] of their side-chains as measured by thin-layer chromatography Journal of Chromatography 216 1981 79 92 (Pubitemid 12217951)
52. P. Ponnuswamy Hydrophobic characteristics of folded proteins Progress in Biophysics and Molecular Biology 59 1993 57 103
53. H. Ponstingl, T. Kabir, D. Gorse, and J. Thornton Morphological aspects of oligomeric protein structures Progress in Biophysics and Molecular Biology 89 2005 9 35 (Pubitemid 40483213)
54. A. Radzicka, and R. Wolfenden Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution Biochemistry 27 1988 1664 1670
55. A. Randall, J. Cheng, M. Sweredoski, and P. Baldi TMBpro: secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins Bioinformatics 24 2008 513 520 (Pubitemid 351256295)
56. B. Robson, and D. Osguthorpe Refined models for computer simulation of protein folding: applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor Journal of Molecular Biology 132 1979 19 51
57. M. Roseman Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds Journal of Molecular Biology 200 1988 513 522
58. B. Rost, and C. Sander Third generation prediction of secondary structures Methods in Molecular Biology (Clifton, NJ) 143 2000 71 96
59. B. Rost, G. Yachdav, and J. Liu The predictprotein server Nucleic Acids Research 32 2004 W321
60. N. Ruiz, D. Kahne, and T. Silhavy Advances in understanding bacterial outer-membrane biogenesis Nature Reviews: Microbiology 4 2006 57 66 (Pubitemid 43135287)
61. E. Schleiff, and J. Soll Membrane protein insertion: mixing eukaryotic and prokaryotic concepts EMBO Reports 6 2005 1023 1027 (Pubitemid 41637645)
62. G. Schulz Porins: general to specific, native to engineered passive pores Current Opinion in Structural Biology 6 1996 485 490 (Pubitemid 26315842)
63. G. Schulz The structure of bacterial outer membrane proteins BBA-Biomembranes 1565 2002 308 317 (Pubitemid 35284483)
64. K. Seshadri, R. Garemyr, E. Wallin, G. Von Heijne, and A. Elofsson Architecture of β-barrel membrane proteins: analysis of trimeric porins Protein Science 7 1998 2026 2032 (Pubitemid 28432444)
65. L. Tamm, H. Hong, and B. Liang Folding and assembly of β-barrel membrane proteins BBA-Biomembranes 1666 2004 250 263 (Pubitemid 39425208)
66. R. Team R: A language and environment for statistical computing 2006 R Foundation for Statistical Computing Vienna, Austria
67. J. Thompson, D. Higgins, and T. Gibson CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 22 1994 4673 4680 (Pubitemid 24354800)
68. J. Tommassen, M. Struyvé, and H. Cock Export and assembly of bacterial outer membrane proteins Antonie van Leeuwenhoek 61 1992 81 85
69. M. Ulmschneider, and M. Sansom Amino acid distributions in integral membrane protein structures BBA-Biomembranes 1512 2001 1 14 (Pubitemid 32378779)
70. I. Valavanis, P. Bagos, and I. Emiris β-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties Computational Biology and Chemistry 30 2006 416 424 (Pubitemid 44792554)
71. G. von Heijne Principles of membrane protein assembly and structure Progress in Biophysics and Molecular Biology 66 1996 113 139 (Pubitemid 27208635)
72. J. Waldispuhl, B. Berger, P. Clote, and J. Steyaert transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels Nucleic Acids Research 34 2006 W189
73. S. White, and W. Wimley Membrane protein folding and stability: Physical Principles Annual Review of Biophysics and Biomolecular Structure 28 1999 319 365 (Pubitemid 29319262)
74. W. Wimley Toward genomic identification of ß-barrel membrane proteins: Composition and architecture of known structures Protein Science 11 2002 301 312 (Pubitemid 34075793)
75. Z. Yuan, F. Zhang, M. Davis, M. Boden, and R. Teasdale Predicting the solvent accessibility of transmembrane residues from protein sequence Journal of Proteome Research 5 2006 1063 1070 (Pubitemid 43727784)
76. J. Zimmerman, N. Eliezer, and R. Simha The characterization of amino acid sequences in proteins by statistical methods Journal of Theoretical Biology 21 1968 170 201