Deciphering protein sequence information through hydrophobic cluster analysis (HCA): Current status and perspectives

Cellular and Molecular Life Sciences

Volumn 53, Issue 8, 1997, Pages 621-645

  Callebaut, I ^a   Labesse, G ^a   Durand, P ^a   Poupon, A ^a   Canard, L ^a   Chomilier, J ^a   Henrissat, B ^b   Mornon, J P ^a  

^a LMCP   (France)

^b CENTRE DE RECHERCHES SUR LES MACROMOLÉCULES VÉGÉTALES CERMAV CNRS   (France)

Author keywords

HCA; Helical net; Protein folding; Sequence analysis

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; CLUSTER ANALYSIS; DATA ANALYSIS; PROTEIN FOLDING; PROTEIN STABILITY; REVIEW; SEQUENCE HOMOLOGY;

ALPHA 1-ANTITRYPSIN; AMINO ACID SEQUENCE; CHEMISTRY, PHYSICAL; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEINS; SEQUENCE ANALYSIS;

EID: 0030690133     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s000180050082     Document Type: Review

References (76)

1. Lemesle-Varloot L., Henrissat B., Gaboriaud C., Bissery V., Morgat A. and Mornon J.-P. (1990) Hydrophobic cluster analysis: procedures to derive structural and functional information from 2D representation of protein sequences. Biochimie 72: 555-574
2. Chothia C. (1992) One thousand families for the molecular biologist. Nature 357: 543-544
3. Li H., Helling R., Tang C. and Wingreen N. (1996) Emergence of preferred structures in a simple model of protein folding. Science 273: 666-669
4. Kardar M. (1996) Which came first, protein sequence or structure? Science 273: 610-611
5. Allschul S., Gish W., Miller W., Myers E. and Lipman D. (1990) Basic local alignment search tool. J. Molec. Biol. 215: 403-410
6. Pearson W. R. and Lipman D. J. (1988) Improved tools for biological comparison. Proc. Natl Acad. Sci. USA 85: 2444-2448
7. Koonin E. V., Tatusov R. L. and Rudd K. E. (1996) Protein sequence comparison at genome scale. Meth. Enzymol. 266: 295-322
8. Bork P. and Gibson T. J. (1996) Searching motif and profile searches. Meth. Enzymol. 266: 162-184
9. Gaboriaud C., Bissery V., Benchetrit T. and Mornon J.-P. (1987) Hydrophobic cluster analysis. An efficient new way to compare and analyse amino-acid sequences. FEBS Lett. 224: 149-155
10. Woodcock S., Mornon J.-P. and Henrissat B. (1992) Detection of secondary structure elements in proteins by Hydrophobic Cluster Analysis. Prot. Eng. 5: 629-635
11. Dunhill P. (1968) The use of helical net diagrams to represent protein sequences. Biophys. J. 8: 865-875
12. Lim V. I. (1974) Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. J. Molec. Biol. 88: 857-872
13. Lim V. A. (1974) Algorithm for prediction of x-helical and β-structural regions in globular proteins. J. Molec. Biol. 88: 873-894
14. Hobohm U. and Sander C. (1992) Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci. 1: 409-417
15. Labesse G., Colloc'h N., Pothier J. and Mornon J.-P. (1997) P-SEA: a program for secondary structure assignment from Cx. Comp. Appl. Biosci. 13: 291-295
16. Bourat G., Thoreau E. and Mornon J.-P. (1994) 2D-helical Hydrophobic clusters: statistics and morphology. J. Pharmacol. Belg. 49: 226-235
17. Vazquez S., Thomas C., Lew R. A. and Humphreys R. E. (1993) Favored and suppressed patterns of Hydrophobic and nonhydrophobic amino acids in protein sequences. Proc. Natl Acad Sci. USA 90: 9100-9104
18. West M. W. and Hecht M. H. (1995) Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci. 4: 2032-2039
19. Pauling L., Corey R. B. and Branson H. R. (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl Acad. Sci. USA 37: 205-211
20. Pan K.-M., Baldwin M. A., Nguyen J., Gasset M., Serban A., Groth D. et al. (1993) Conversion of x-helices into β-sheets features in the formation of the scrapie prion proteins. Proc. Natl Acad. Sci. USA 90: 10962-10966
21. Callcbaut I., Tasso A., Brasseur R., Burny A., Portetelle D. and Mornon J.-P. (1994) Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and in viral fusion peptides. Do prions possess a fusogenic peptide? J. Comp. Aided Molec. Design 8: 175-191
22. Forloni G., Angeretti N., Chiesa R., Monzani E., Salmona M., Bugiani O. et al. (1993) Neurotoxicity of a prion protein fragment. Nature 362: 543-546
23. De Gioia L., Selvaggini C., Ghibaudi E., Diomede L., Bugiani O., Forloni G. et al. (1994) Conformational polymorphism of the amyloidogenic and neurotoxic peptide homologous to residues 106-126 of the prion protein. J. Biol. Chem. 269: 7859-7862
24. Heller J., Kolbert A. C., Larsen R., Ernst M., Bekker T., Baldwin M. et al. (1996) Solid-state NMR studies of the prion protein HI fragment. Protein Sci. 5: 1655-1661
25. Rick R., Hornemann S., Wider G., Billeter M., Glockshuber R. and Wüthrich K. (1996) NMR structure of the mouse prion protein domain PrP(121-231). Nature 382: 180-182
26. Callebaut I. and Mornon J.-P. (1997) From BRCA1 to RAP1: a widespread BRCT module closely associated to DNA repair. FFBS Lett. 400: 25-30
27. Thoreau E., Petridou B., Kelly P. A., Djiane J. and Mornon J.-P. (1991) Structural symmetry of the extra-cellular domain of the Cytokine Growth hormone Prolactin receptor family and interferon receptors revealed by Hydrophobic Cluster Analysis. FFBS Lett. 282: 26-31
28. de Vos A. M., Ultsch M. and Kossiakoff A. A. (1992) Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 255: 306-312
29. Altschul S. F., Bokusi M. S., Gish W. and Wotton J. C. (1994) Issues in searching molecular sequence databases. Nature Genet. 6: 119-129
30. Durand P., Canard L. and Mornon J.-P. (1997) Visual Blast and Visual FastA: graphic workbenches for interactive analysis of full Blast and FastA outputs under Microsoft Windows 95 NT. Comput. Appl. Biosci. 13: 407-413
31. Labesse G. (1997) MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis. Comput. Appl. Biosci. 12: 463-467
32. Tatusov R. L., Altschul S. F. and Koonin E. V. (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA 91: 12091-12095
33. Hegyi H. and Pongor S. (1993) Predicting potential domain homologies from FASTA search results. Comput. Appl. Biosci. 9: 371-372
34. Tatusov R. L. and Koonin E. V. (1994) A simple tool to search for sequence motifs that are conserved in BLAST outputs. Comput. Appl. Biosci. 10: 457-459
35. Worley K. C., Wiese B. A. and Smith R. F. (1995) BEAUTY: An enhanced BLAST-based search tool that integrates multiple biological information ressources into sequence similarity search results. Genome Res. 5: 173-184
36. Turkenburg J. P. and Dodson E. J. (1996) Modern developments in molecular replacement. Curr. Opin. Struct. Biol. 6: 604-610
37. Tong X., Drapkin R., Yalamanchill R., Mosialos G. and Kieff F. (1995) The Epstein-Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interacr with TFIIF. Molec. Cell. Biol. 15: 4735-4744
38. Callebaut I. and Mornon J.-P. (1997) The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. Biochem. J. 321: 125-132
39. Murzin A. G. (1993) OB (oligonucleotide oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12: 861-867
40. Ponting C. P. (1997) Tudor domains in proteins that interact with RNA. Trends Biochem. Sci. 22: 51-52
41. Crooke E. and Wickner W. (1987) Trigger factor: a soluble protein that folds proOmpA into a membrane-assembly-competent form. Proc. Natl Acad. Sci. USA 84: 5216-5220
42. Crooke E., Brundage L., Rice M. and Wickner W. (1988) ProOmpA spontaneously folds in a membrane assembly competent state which trigger factor stabilizes. EMBO J. 7: 1831-1835
43. Crooke E., Guthrie B., Lecker S., Lill R. and Wickner W. (1988) ProOmpA is stabilized for membrane translocation by either purified E. coli trigger factor or canine signal recognition particle. Cell 54: 1003-1011
44. Lecker S., Lill R., Ziegelhoffer T., Georgopoulos C., Bassford P. J., Kumamoto C. A. et al. (1989) Three pure chaperone proteins of Escherichia coli SecB, trigger factor and GroEL form soluble complexes with precursor proteins in vitro. EMBO J. 8: 2703-2709
45. Callebaut I. and Mornon J.-P. (1995) Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. FEBS Lett. 374: 211-215
46. Stoller G., Rücknagel K. P., Nierhaus K. H., Schmid F. X., Fischer G. and Rahfeld J.-U. (1995) A ribosome-associated peptidyl-prolyl cis-trans isomerase identified as the trigger factor. EMBO J. 14: 4939-4948
47. Stoller G., Tradler T., Rücknagel J.-U. and Fischer G. (1996) A 11.8 kDa proteolytic fragment of the E. coli trigger factor represents the domain carrying the peptidyl-prolyl cis-trans isomerase activity. FEBS Lett. 384: 117-122
48. Hesterkamp T. and Bukau B. (1996) Identification of the prolyl isomerase domain of Escherichia trigger factor. FEBS Lett. 385: 67-71
49. Valent Q. A., Kendall D. A., High S., Kusters R., Oudega B. and Luirink J. (1995) Early events in proprotein recognition in E. coli: interaction of SRP and trigger factor with nascent polypeptides. EMBO J. 14: 5494-5505
50. Hesterkamp T., Hauser S., Lutcke H. and Bukau B. (1996) Escherichia coli trigger factor is a prolyl isomerase that associates with nascent polypeptide chains. Proc. Natl Acad. Sci. USA 93: 4437-4441
51. Krandror O., Sherman M., Rhode M. and Goldberg A. L. (1995) Trigger factor is involved in GroEL-dependent protein degradation in Escherichia coli and promotes binding of GroEL to unfolded proteins. EMBO J. 14: 6021-6027
52. Scholtz C., Stoller C., Zarnt T., Fischer G. and Schmid F. X. (1997) Cooperation of enzymatic and chaperone functions of trigger factor in the catalysis of protein folding. EMBO J. 16: 54-58
53. Miki Y., Swensen J., Shattuck-Eidens D., Futreal P. A., Harshman K., Tavtigian S. et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCAI. Science 66: 66-71
54. Holt J. T., Thompson M. E., Szabo C., Robinson-Benion C., Arteaga C. L., King M.-C. et al. (1996) Growth retardation and tumor inhibition by BRCAI. Nature Genet. 12: 298-302
55. Chapman M. S. and Verma I. M. (1996) Transcriptional activation by BRCAI. Nature 382: 678-679
56. Koonin E. V., Altschul S. F. and Bork P. (1996) BRCAI protein products: functional motifs. Nature Genet. 13: 266-267
57. Bork P., Hofmann K., Bucher P., Neuwald A. F., Altschul S. F. and Koonin E. V. (1997) A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J. 11: 68-76
58. Callebaut I., Courvalin J.-C., Worman H. J. and Mornon J.-P. (1997) Hydrophobic Cluster Analysis reveals a third chromodomain in the Tetrahymena Pdd1p protein of the chromo superfamily. Biochem. Biophys. Res. Commun. 235: 103-107
59. Mornon J.-P., Thoreau E., Rowlands D., Callebaut I. and Moreau G. (1994) Putative dimeric organization of nuclear receptor hormone-binding domains, as suggested by Hydrophobic Cluster Analysis. C. R. Acad. Sci. Paris, Life Sci. 317: 597-606
60. Renaud J.-P., Rochel N., Ruff M., Vivat V., Chambon P., Gronemeyer H. et al. (1995) Crystal structure of the RAR-; ligand-binding domain bound to all-trans retinoic acid. Nature 378: 681-689
61. Wagner R. L., Apriletti J. W., McGrath M. E., West B. L., Baxter J. D. and Flettcrick R. J. (1995) A structural role for hormone in the thyroid hormone receptor. Nature 378: 690-697
62. Lewis D. F. V. and Lae B. G. (1993) Interaction of some peroxisome proliferators with the mouse liver peroxisome proliferator-activated receptor (PPAR) a molecular modelling and quantitative structure-activity relationship (QSAR) study. Xenobiotica 23: 73-96
63. Goldstein R. A., Katzenellenbogen J. A., Luthey-Schulten Z. A., Seielstad D. A. and Wolynes P. G. (1993) Three-dimensional model for the hormone binding domains of steroid receptors. Proc. Natl Acad. Sci. USA 90: 9949-9953
64. Höltje H. D. and Dall N. (1993) A molecular modelling study on the hormone binding site of the estrogen receptor. Pharmazie 48: 243-249
65. McPhie P., Parkison C., Lee B. K. and Cheng S. Y. (1993) Structure of the hormone binding domain of human β1 thyroid hormone nuclear receptor. Is it an x. β barrel? Biochemistry 32: 7460-7465
66. Ojasoo T. and Doré J.-C. (1996) Taxonomy of nuclear receptors and serpins by multivariate analysis of amino-acid composition. J. Steroid Biochem. Molec. Biol. 58: 167-181
67. Flaherty K. M., DeLuca-Flaherty C. and McKay D. (1990) Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein. Nature 346: 623-628
68. Braig K., Otwinowski Z., Hedge R., Boisvert D. C., Joachimiak A., Horwich A. L. et al. (1994) The crystal structure of the bacterial chaperonin GroEl at 2.8 Å. Nature 371: 578-586
69. Flaherty K. M., McKay D., Kabsch W. and Holmes K. (1991) Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc. Natl Acad. Sci. USA 88: 5041-5045
70. Callebaut I., Catelli M. G., Portetelle D., Burny A., Baulieu E. E. and Mornon J.-P. (1994) Structural similarities between chaperone molecules of the HSP60 and HSP70 families deduced from Hydrophobic Cluster Analysis. FEBS Lett. 342: 242-248
71. Callebaut I., Catelli M. G., Portetelle D., Meng X., Cadepond F., Burny A. et al. (1994) Redox mechanism for the chaperone activity of the heat shock protein HSP60, 70 and 90 as suggested by Hydrophobic Cluster Analysis: hypothesis. C.R. Acad. Sci. Paris, Life Sci. 317: 721-729
72. Henikoff S. (1996) Scores for sequence searches and alignments. Curr. Opin. Struct. Biol. 6: 353-360
73. Doolittle R. F. (1981) Similar amino acid sequences: chance or common ancestry. Science 214: 149-159
74. Lipman D. J., Wilbur W. J., Smith T. F. and Waterman M. S. (1984) On the statistical significance of nucleic acid similarities. Nucl. Acids Res. 12: 215-226
75. Landès C., Hénaut A. and Risler J.-L. (1992) A comparison of several similarity indices used in the classification of protein sequences. A multivariate analysis. Nucl. Acids Res. 20: 3631-3637
76. Karlin S. and Altschul S. F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA 87: 2264-2268