Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship

Protein Science

Volumn 11, Issue 12, 2002, Pages 2871-2886

  De Brevern, Alexandre G ^a   Valadié, Hélène ^a   Hazout, Serge ^a   Etchebest, Catherine ^a  

^a INSERM   (France)

Author keywords

3D local structure prediction; 3D overlapping motifs; 3D protein topology; Probabilistic approach; Sequence structure relationship; Structural alphabet

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; BAYES THEOREM; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYMOLOGY; METHODOLOGY; MOLECULAR GENETICS; THERMODYNAMICS; THERMUS THERMOPHILUS;

METHIONINE TRANSFER RNA LIGASE; PEPTIDE FRAGMENT;

AMINO ACID SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; METHIONINE-TRNA LIGASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; THERMODYNAMICS; THERMUS THERMOPHILUS;

EID: 0036893073     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0220502     Document Type: Article

References (73)

1. Aurora, R. and Rose, G.D. 1998. Helix capping. Protein Sci. 7: 21-38.
2. Baker, D. and Sali, A. 2001. Protein structure prediction and structural genomics. Science 294: 93-96.
3. Barlow, D.J. and Thornton, J.M. 1988. Helix geometry in proteins. J. Mol. Biol. 201: 601-619.
4. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The protein data bank. Nucleic Acids Res. 28: 235-242.
5. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, Jr., 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 macromolecular structures. J. Mol. Biol. 112: 535-540.
6. Bonneau, R. and Baker, D. 2001. Ab initio protein structure prediction: Progress and prospects. Annu. Rev. Biophys. Biomol. Struct. 30: 173-189.
7. Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C.E.M., and Baker, D. 2001. Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins 37(S5): 119-126.
8. Boutonnet, N.S., Kajava, A.V., and Rooman, M.J. 1998. Structural classification of αββ and ββα supersecondary structure units in proteins. Proteins 30: 193-212.
9. Brenner, S.E., Koehl, P., and Levitt, M. 2000. The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Res. 28: 254-256.
10. Bystroff, C. and Baker, D. 1998. Prediction of local structure in proteins using a library of sequence-structure motif. J. Mol. Biol. 281: 565-577.
11. Bystroff, C., Thorsson, V., and Baker, D. 2000. HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins. J. Mol. Biol. 301: 173-190.
12. Camproux, A.C., Tuffery, P., Chevrolat, J.P., Boisvieux, J.F., and Hazout, S. 1999. Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng. 12: 1063-1073.
13. Camproux, A.C., de Brevern, A.G., Hazout, S., and Tuffery, P. 2001. Exploring the use of a structural alphabet for a structural prediction of protein loops. Theor. Chem. Acc. 106(1/2): 28-35.
14. Chan, A.W., Hutchinson, E.G., Harris, D., and Thornton, J.M. 1993. Identification, classification, and analysis of β-bulges in proteins. Protein Sci. 2: 1574-1590.
15. Chandonia, J.M. and Karplus, M. 1999. New methods for accurate prediction of protein secondary structure. Proteins 35: 293-306.
16. Chou, K.C. 1997. Prediction and classification of a-turn types. Biopolymers 42: 837-853.
17. Colloc'h, N., Etchebest, C., Thoreau, E., Henrissat, B., and Mornon, J.-P. 1993. Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment. Protein Eng. 6: 377-382.
18. Cuff, J.A. and Barton, G.J. 1999. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 34: 508-519.
19. de Brevern, A.G. and Hazout, S. 2000. Hybrid Protein Model (HPM): A method to compact protein 3D-structures information and physicochemical properties. IEEE Comp Soc. S1: 49-54.
20. -. 2001. Compacting local protein folds by a "Hybrid Protein Model." Theor. Chem. Acc. 106(1/2): 36-47.
21. -. 2002. Improvement of "Hybrid Protein Model" to define an optimal repertory of contiguous 3D protein structure fragments. Bioinformatics (in press).
22. de Brevern, A.G., Etchebest, C., and Hazout, S. 2000. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 41: 271-287.
23. de Brevern, A.G., Camproux, A.C., Hazout, S., Etchebest, C., and Tuffery, P. 2001. Beyond the secondary structures: The structural alphabets. In Recent Advances In Protein Engineering (ed. S.G. Pandalai), Vol. 1, pp. 319-331. Research Signpost, Trivandrum, India.
24. Dunbrack Jr., L. 2001. http://www.fccc.edu/research/labs/dunbrack/pisces/culledpdb.html
25. Fetrow, J.S. 1995. Omega loops: Nonregular secondary structures significant in protein function and stability. FASEB J. 9: 708-717.
26. Fetrow, J.S., Palumbo, M.J., and Berg, G. 1997. Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 27: 249-271.
27. Fiser, A. and Sali, A. 2001. MODELLER: Generation and refinement of homology models. Methods Enzymol. (in press).
28. Frishman, D. and Argos, P. 1995. Knowledge-based protein secondary structure assignment. Proteins 23: 566-579.
29. Genome International Sequencing Consortium. 2000. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
30. Hobohm, U. and Sander, C. 1994. Enlarged representative set of protein structures. Protein Sci. 3: 522-524.
31. Hobohm, U., Scharf, M., Schneider, R., and Sander, C. 1992. Selection of a representative set of structures from the Brookhaven Protein Data bank. Protein Sci. 1: 409-417.
32. Humphrey, W., Dalke, A. and Schulten, K. 1996, VMD - Visual molecular dynamics. J. Mol. Graph. 14: 33-38.
33. Hutchinson, E.G. and Thornton, J.M. 1994. A revised set of potentials for β-turn formation in proteins. Protein Sci. 3: 2207-2216.
34. Jaroszewski, L., Rychlewski, L., Zhang, B., and Godzik, A. 1998. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 7: 1431-1440.
35. Jones, D.T., Tress, M., Bryson, K., and Hadley, C. 1999. Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins S3: 104-111.
36. Kelley, L.A., MacCallum R.M., and Sternberg, M.J. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520.
37. Kohonen, T. 1982 Self-organized formation of topologically correct feature maps. Biol. Cybern. 43: 59-69.
38. -. 2001. Self-organizing Maps, 3rd Ed., chapters 2-4. Springer-Verlag, Berlin, Germany.
39. Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55.
40. Kumar, S. and Bansal, M. 1998. Geometrical and sequence characteristics of α-helices in globular proteins. Biophys J. 75: 1935-1944.
41. Kwasigroch, J.-M., Chomilier, J., and Momon, J.-P. 1996. A global taxonomy of loops in globular proteins. J. Mol. Biol. 259: 855-872.
42. Labesse, G., Colloc'h, N., Pothier, J., and Momon, J.-P. 1997. P-SEA: A new efficient assignment of secondary structure from Cα trace of proteins. Comput. Appl. Biosci. 13: 291-295.
43. Leszczynski, J.F. and Rose, G.D. 1986. Loops in globular proteins: A novel category of secondary structure. Science 14: 849-855.
44. Meller, J. and Elber, R. 2001. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins 45: 241-261.
45. Milner-White, E.J. 1988. Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with α-helices and β-bulge loops. J. Mol. Biol. 199: 503-511.
46. Murzin A.G., Brenner S.E., Hubbard T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
47. Noguchi, T., Matsuda, H., and Akiyama, Y. 2001. PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB). Nucleic Acids Res. 29: 219-220.
48. Orengo, C.A., Bray, J.E., Hubbard, T., LoConte, L., and Sillitoe, I. 1999. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 37: 149-170.
49. Ouali, M. and King, R.D. 2000. Cascaded multiple classifiers for secondary structure prediction. Protein Sci. 9: 1162-1176.
50. Pavone, V., Gaeta, G., Lombardi, A., Nastri, F., Maglio, O., Isernia, C., and Saviano, M. 1996. Discovering protein secondary structures: Classification and description of isolated α-turns. Biopolymers 38: 705-721.
51. Petersen, T.N., Lundegaard, C., Nielsen, M., Bohr, H., Bohr, J., Brunak, S., Gippert, G.P., and Lund, O. 2000. Prediction of protein secondary structure at 80% accuracy. Proteins 41: 17-20.
52. Pollastri, G., Przybylski, D., Rost, B., and Baldi, P. 2002. Improving the prediction of secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47: 228-235.
53. Rabiner, L.R. 1989. A tutorial on Hidden Markov Models and selected applications in speech recognition. Proc. IEEE 77: 257-285.
54. Rajashankar, K.R. and Ramakumar, S. 1996. π turns in proteins and peptides: Classification, conformation, occurrence, hydratation and sequence. Protein Sci. 5: 932-946.
55. Richardson, J.S. 1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34: 167-339.
56. Richardson, J.S., Getzoff, E.D., and Richardson, D.C. 1978. The β bulge: A common small unit of nonrepetitive protein structure. Proc. Natl. Acad. Sci. 75: 2574-2578.
57. Ring, C.S., Kneller, D.G., Langridge, R., and Cohen, F.E. 1992. Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 224: 685-699.
58. 10-helix/coil transitions in isolated peptides. Protein Sci. 5: 1689-1696.
59. Rooman, M.J., Rodriguez, J., and Wodak, S.J. 1990. Automatic definition of recurrent local structure motifs in proteins. J. Mol. Biol. 213: 327-336.
60. Rose, G.D., Gierasch, L.M., and Smith, J.A. 1985. Turns in peptides and proteins. Adv. Protein Chem. 37: 1-109.
61. Rost, B. 2001. Review: Protein secondary structure prediction continues to rise. J. Struct. Biol. 134: 204-218.
62. Rost, B. and Sander, C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232: 584-599.
63. Salamov, A.A. and Solovyev, V.V. 1997. Protein secondary structure prediction using local alignments. J. Mol. Biol. 268: 31-36.
64. Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
65. Schuchhardt, J., Schneider, G., Reichelt, J., Schomburg, D., and Wrede, P. 1996. Local structural motifs of protein backbones are classified by self-organizing neural networks. Protein Eng. 9: 833-842.
66. Sibanda, B.L. and Thornton, J.M. 1991. Conformation of β hairpins in protein structures: Classification and diversity in homologous structures. Methods Enzymol. 202: 59-82.
67. Simons, K.T., Kooperberg, C., Huang, E. and Baker, D. 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268: 209-225.
68. Simons, K., Bonneau, R., Ruczinski, I., and Baker, D. 1999. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 37: 171-176.
69. Unger, R., Harel, D., Wherland, S., and Sussman, J.L. 1989. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 5: 355-373.
70. Wilmot, C.M. and Thornton, J.M. 1988. Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 5: 221-232.
71. Wintjens, R.T., Rooman, M.J., and Wodak, S.J. 1996. Automatic classification and analysis of α α-turn motifs in proteins. J. Mol. Biol. 255: 235-253.
72. Wojick, J., Mornon, J.-P., and Chomilier, J. 1999. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J. Mol. Biol. 289: 1469-1490.
73. Xu, Y. and Xu, D. 2000. Protein threading using PROSPECT: Design and evaluation. Proteins 40: 343-354.