A global taxonomy of loops in globular proteins

Journal of Molecular Biology

Volumn 259, Issue 4, 1996, Pages 855-872

  Kwasigroch, Jean Marc ^a   Chomilier, Jacques ^a   Mornon, Jean Paul ^a  

^a SORBONNE UNIVERSITÉ   (France)

Author keywords

Loops; Molecular modeling; Proteins; Structural biology; Taxonomy

Indexed keywords

AMINO ACID; GLOBULAR PROTEIN; LYSINE;

AMINO ACID SEQUENCE; ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; TAXONOMY;

EID: 0030596489     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0363     Document Type: Article

References (60)

1. Adzhubei, A. A., Eisenmenger, F., Tumanyan, V. G., Zinke, M., Brodzinski, S. & Esipova, N. G. (1987). Approaching a complete classification of protein secondary structure. J. Biomol. Struct. Dynam. 5, 689-704.
2. Bernstein, F. C, Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
3. Bruccoleri, R. E., Haber, E. & Novotny, J. (1988). Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature, 335, 564-568.
4. Casari, G., Sander, C. & Valencia, A. (1995). A method to predict functional residues in proteins. Struct. Biol. 2, 171-178.
5. Chan, A. W. E., Hutchinson, E. G., Harris, D. & Thornton, J. M. (1993). Identification, classification, and analysis of beta bulges in proteins. Protein Sci. 2, 1574-159.
6. Chelvanayagam, G., Roy, G. & Argos, P. (1994). Easy adaptation of protein structure to sequence. Protein Eng. 7, 173-184.
7. Claessens, M., van Cutsem, E., Lasters, I. & Wodak, S. (1989). Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng. 2, 335-345.
8. Cohen, B. I., Presnell, S. R. & Cohen, F. E. (1993). Origins of structural diversity within sequentially identical hexapeptides. Protein Sci. 2, 2134-2145.
9. Colloc'h, N. & Cohen, F. (1991). β-Breakers: an aperiodic secondary struture. J. Mol. Biol. 221, 603-613.
10. Colloc'h, N., Etchebest, C., Thoreau, E., Henrissat, B. & Mornon, J.-P. (1993). Comparison of three algorithms for the assignment of secondary structures in proteins: the advantages of a consensus assignment. Protein Eng. 6, 377-382.
11. Collura, V., Higo, J. & Garnier, J. (1993). Modeling of protein loops by simulated annealing. Protein Sci. 2, 1502-1510.
12. Edwards, M. S., Sternberg, M. J. E. & Thornton, J. M. (1987). Structural and sequence patterns in the loops of βαβ units. Protein Eng. 1, 173-181.
13. Efimov, A. V. (1986). Standard conformations of a polypeptide chain in irregular regions of proteins. Mol. Biol. (USSR), 20, 250-260.
14. Efimov, A. V. (1991). Structure of α-α-hairpins with short connections. Protein Eng. 4, 245-250.
15. Efimov, A. V. (1993). Standard structures in proteins. Prog. Biophys. Mol. Biol. 60, 201-239.
16. Fechteler, T., Dengler, U. & Schomburg, D. (1995). Prediction of protein three dimensional structures in insertion and deletion regions; a procedure for searching data bases of representative protein fragments using geometric scoring criteria. J. Mol. Biol. 253, 114-131.
17. Fetrow, J. S. (1995). Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J. 9, 708-717.
18. Fidelis, K., Stern, P. S., Bacon, D. & Moult, J. (1994). Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7, 953-960.
19. Fine, R. M., Wang, H., Shenkin, P. S., Yarmush, D. L. & Levinthal, C. (1986). Predicting antibody hypervariable loop conformations II: minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins: Struct Funct. Genet. 1, 342-362.
20. Greer, J. (1990). Comparative modeling methods: application to the family of the mammalian serine proteases. Proteins: Struct. Funct. Genet. 7, 317-334.
21. Henikoff, S. & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
22. Higo, J., Collura, V. & Garnier, J. (1992). Development of an extended simulated annealing method: application to the modeling of complementary determining regions of immunoglobulins. Biopolymers, 32, 33-43.
23. Hutchinson, E. G. & Thornton, J. M. (1994). A revised set of potentials for β-turn formation in proteins. Protein Sci. 3, 2207-2216.
24. Jain, A. K. & Dubes, R. C. (1988). Algorithms for Clustering Data. Prentice Hall, Englewood Cliffs, New Jersey.
25. Jones, T. A. & Thirup, S. (1986). Using known substructures in protein model building and crystallography. EMBO J. 5, 819-822.
26. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers, 22, 2577-2637.
27. Koehl, P. & Delarue, M. (1995). A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Struct. Biol. 2, 163-169.
28. Laskowski, R., Moss, D. S. & Thornton, J. M. (1993). Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231, 1049-1067.
29. Leszczynski, J. F. & Rose, G. D. (1986). Loops in globular proteins: a novel category of secondary structure. Science, 234, 849-855.
30. Lewis, P. N., Momany, F. A. & Sheraga, H. (1973). Chain reversals in proteins. Biochim. Biophys. Acta, 303, 211-229.
31. Luthy, R., McLachlan, A. D. & Eisenberg, D. (1991). Secondary structure based profiles: use of structure conserving scoring tables in searching protein sequence databases for structural similarities. Proteins: Struct. Funct. Genet. 10, 229-239.
32. Mas, M. T., Smith, K. C., Yarmush, D. L., Aisaka, K. & Fine, R. M. (1992). Modeling the anti CEA antibody combining site by homology and conformational search. Proteins: Struct. Funct. Genet. 14, 483-498.
33. Mattos, C., Petsko, G. A. & Karplus, M. (1994). Analysis of two residue turns in proteins. J. Mol. Biol. 238, 733-747.
34. Milner-White, E. J. & Poet, R. (1986). Four classes of β-hairpins in proteins. Biochem. J. 240, 289-292.
35. Moult, J. & James, M. N. G. (1986). An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins: Struct. Funct. Genet. 1, 146-163.
36. Peitsch, M. C. (1995). Protein modeling by e-mail. Biotechnology, 13, 658-660.
37. Rice, P. A., Goldman, A. & Steitz, T. A. (1990). A helixturn-strand structural motif common in α-β proteins. Proteins: Struct. Funct. Genet. 8, 334-340.
38. Richards, F. M. & Kundrot, C. E. (1988). Identification of structural motifs from protein coordinate data: secondary structure and first level supersecondary structure. Proteins: Struct. Funct. Genet. 3, 71-84.
39. Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34, 167-339.
40. Richardson, J. S. & Richardson, D. C. (1988). Amino acid preferences for specific locations at the ends of a helices. Science, 240, 1648-1652.
41. Ring, C. S., Kneller, D. G., Langridge, R. & Cohen, F. E. (1992). Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 224, 685-699.
42. Rooman, M., Rodriguez, J. & Wodak, S. (1990). Automatic definition of recurrent local structure motifs in proteins. J. Mol. Biol. 213, 327-336.
43. Šali, A., Potterton, L., Yuan, F., van Vlijmen, H. & Karplus, M. (1995). Evaluation of comparative protein modeling by MODELLER. Proteins: Struct. Funct. Genet. 23, 318-326.
44. Sander, C. & Schneider, R. (1991). Database of homology derived protein structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet. 9, 56-68.
45. Scheerlinck, J.-P. Y., Lasters, I., Claessens, M., De Maeyer, M., Pio, F., Delhaise, P. & Wodak, S. J. (1992). Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features. Proteins: Struct. Funct. Genet. 12, 299-313.
46. Sibanda, B. L. & Thornton, J. M. (1985). β-Hairpin families in globular proteins. Nature, 316, 170-174.
47. Sibanda, B. L. & Thornton, J. M. (1991). Conformation of β hairpins in protein structures: classification and diversity in homologous structures. Methods Enzymol. 202, 59-82.
48. Sklenar, H., Etchebest, C. & Lavery, R. (1989). Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins: Struct. Funct. Genet. 6, 46-60.
49. Sudarsanam, S., DuBose, R. F., March, C. J. & Srinivasan, S. (1995). Modeling protein loops using a Φi + 1, ψi dimer database. Protein Sci. 4, 1412-1420.
50. Swindells, M. B., MacArthur, M. W. & Thornton, J. M. (1995). Intrinsic Φ,ψ propensities of amino acids, derived from the coil regions of known structures. Nature Struct. Biol. 2, 596-603.
51. Topham, C. M., McLeod, A., Eisenmenger, F., Overington, J. P., Johnson, M. S. & Blundell, T. L. (1993). Fragment ranking in modeling of protein structure. J. Mol. Biol. 229, 194-220.
52. Tramontane, A. & Lesk, A. M. (1992). Common features of the conformations of antigen binding loops in immunoglobulins and application to modeling loop conformations. Proteins: Struct. Funct. Genet. 13, 231-245.
53. Unger, R., Harel, D., Wherland, S. & Sussman, J. L. (1989). A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins: Struct. Funct. Genet. 5, 355-373.
54. Venkatachalam, C. M. (1968). Stereochemical criteria for polypeptides and proteins. Conformation of a system of three linked peptide units. Biopolymers, 6, 1425-1436.
55. Wilmot, C. M. & Thornton, J. M. (1988). Analysis and prediction of the different types of β turn in proteins. J. Mol. Biol. 203, 221-232.
56. Wilmot, C. M. & Thornton, J. M. (1990). β Turns and their distortions: a proposed new nomenclature. Protein Eng. 3, 479-493.
57. Wintjens, R. T., Rooman, M. J. & Wodak, S. J. (1996). Automatic classification and analysis of αα turn motifs in proteins. J. Mol. Biol. 255(235-253).
58. Woodcock, S., Mornon, J.-P. & Henrissat, B. (1992). Detection of secondary structure elements in proteins by hydrophobic cluster analysis. Protein Eng. 5, 629-635.
59. Zheng, Q., Rosenfeld, R., Vajda, S. & DeLisi, C. (1993). Loop closure via bond scaling and relaxation. J. Comput. Chem. 14, 556-565.
60. Zheng, Q., Rosenfeld, R., DeLisi, C. & Kyle, D. J. (1994). Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci. 3, 493-506.