PDB-based protein loop prediction: Parameters for selection and methods for optimization

Journal of Molecular Biology

Volumn 267, Issue 4, 1997, Pages 975-1001

  Van Vlijmen, Herman W T ^a   Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Energy mimimization; Homology modeling; Protein loops; Structural database search; Structure prediction

Indexed keywords

ANTIBODY;

ACCURACY; ARTICLE; CRYSTAL STRUCTURE; DATA BASE; ENERGY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

EID: 0031564640     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0857     Document Type: Article

References (70)

1. Allen M. P., Tildesley D. J. Computer Simulations of Liquids. 1987;Clarendon Press, Oxford.
2. Bajorath J., Sheriff S. Comparison of an antibody model with an X-ray structure: the variable fragment of BR96. Proteins: Struct. Funct. Genet. 24:1996;152-157.
3. 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. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
4. Borchert T. V., Abagyan R., Jaenicke R., Wierenga R. K. Design, creation, and characterization of a stable, monomeric, triosephosphate isomerase. Proc. Natl Acad. Sci. USA. 91:1994;1515-1518.
5. Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comp. Chem. 4:1983;187-217.
6. Bruccoleri R. E., Karplus M. Chain closure with bond angle variations. Macromolecules. 18:1985;2767-2773.
7. Bruccoleri R. E., Karplus M. Conformational sampling using high-temperature molecular dynamics. Biopolymers. 29:1990;1847-1862.
8. Bruccoleri R. E., Haber E., Novotny J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature. 335:1988;564-568.
9. Carlacci L., Englander S. W. The loop problem in proteins: a Monte Carlo simulated annealing approach. Biopolymers. 33:1993;1271-1286.
10. Casari G., Sippl M. J. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 224:1992;725-732.
11. Chothia C., Lesk A. M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196:1987;901-917.
12. Chothia C., Lesk A. M., Tramontano A., Levitt M., Smith-Gill S. J., Air G., Sheriff S., Padlan E. A., Davies D., Tulip W. R., Colman P. M., Spinelli S., Alzari P. M., Poljak R. J. Conformations of immunoglobulin hypervariable regions. Nature. 342:1989;877-883.
13. Hsegments. J. Mol. Biol. 227:1992;799-817.
14. Claessens M., Van Cutsem E., Lasters I., Wodak S. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng. 2:1989;335-345.
15. Collura V., Higo J., Garnier J. Modelling of protein loops by simulated annealing. Protein Sci. 2:1993;1502-1510.
16. Collura V. P., Greaney P. J., Robson B. A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603. Protein Eng. 7:1994;221-233.
17. Coleman J. E., Williams K. R., King G. C., Prigodich R. V., Shamoo Y., Konigsberg W. H. Mapping the functional domains in single-strand {DNA}-binding proteins Gene5 and Gene32. Protein Engineering. 1987;Alan R. Liss, Inc. New York.
18. Creighton T. E. Protein Folding. 1993;W. H. Freeman and Company, New York.
19. Crippen G. M., Viswanadhan V. N. Sidechain and backbone potential function for conformational analysis of proteins. Int. J. Peptide Protein Res. 25:1985;487-509.
20. Dudek M., Scheraga H. A. Protein structure prediction using a combination of sequence homology and global energy minimization. I. Global energy minimization of surface loops. J. Comp. Chem. 11:1990;121-151.
21. Dunbrack R. L., Jr, Karplus M. A backbone dependent rotamer library for proteins: application to side-chain prediction. J. Mol. Biol. 230:1993;543-574.
22. Fidelis K., Stern P. S., Bacon D., Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7:1994;953-960.
23. Fine R. M., Wang H., Shenkin P. S., Yarmush D. L., Levinthal C. Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins: Struct. Funct. Genet. 1:1986;342-362.
24. Finkelstein A. V., Reva B. A. Search for the stable state of a short chain in a molecular field. Protein Eng. 5:1992;617-624.
25. Gerber P. R. Peptide mechanics: a force field for peptides and proteins working with entire residues as smallest units. Biopolymers. 32:1992;1003-1017.
26. Gonnet G. H., Cohen M. A., Benner S. A. Exhaustive matching of the entire protein sequence database. Science. 256:1992;1443-1445.
27. Greer J. Model for haptoglobin heavy chain based upon structural homology. Proc. Natl Acad. Sci. USA. 77:1980;3393-3397.
28. Henikoff S., Henikoff J. G. Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA. 89:1992;10915-10919.
29. Jones T. A., Thirup S. Using known substructures in protein model building and crystallography. EMBO J. 5:1986;819-822.
30. Joseph D., Petsko G. A., Karplus M. Anatomy of a protein conformational change: hinged ''lid'' motion of the triosephosphate isomerase loop. Science. 249:1990;1425-1428.
31. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A. 32:1976;922-923.
32. Kolinski A., Skolnick J. Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides. J. Chem. Phys. 97:1992;9412-9426.
33. Kolinski A., Godzik A., Skolnick J. A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: application to designed helical proteins. J. Chem. Phys. 98:1993;7420-7432.
34. Leszczynski J. F., Rose G. D. Loops in globular proteins: a novel category of secondary structure. Science. 234:1986;849-855.
35. Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:1976;59-107.
36. Martin A. C. R., Cheetham J. C., Rees A. R. Modelling antibody hypervariable loops: a combined algorithm. Proc. Natl Acad. Sci. USA. 86:1989;9268-9272.
37. Mattos C., Petsko G. A., Karplus M. Analysis of two-residue turns in proteins. J. Mol. Biol. 238:1994;733-747.
38. McGarrah D. B., Judson R. S. Analysis of the genetic algorithm method of molecular conformation determination. J. Comp. Chem. 14:1993;1385-1395.
39. Metropolis N., Rosenbluth A. W., Rosenbluth M. N., Teller A. H., Teller E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1953;1087-1092.
40. Mosimann S., Meleshko R., James M. N. G. A critical assessment of comparative molecular modelling of tertiary structures of proteins. Proteins: Struct. Funct. Genet. 23:1995;301-317.
41. Moult J., James M. N. G. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins: Struct. Funct. Genet. 1:1986;146-163.
42. Niefind K., Schomburg D. Amino acid similarity coefficients for protein modelling and sequence alignment derived from main-chain folding angles. J. Mol. Biol. 219:1991;481-497.
43. Orengo C. A., Jones D. T., Thornton J. M. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634.
44. Pascarella S., Argos P. A data bank merging related protein structures and sequences. Protein Eng. 5:1992;121-137.
45. Press W. H., Flannery B. P., Teukolsky S. A., Vetterling W. T. Numerical Recipes. The Art of Scientific Computing. 1986;Cambridge University Press, Cambridge.
46. Reczko M., Martin A. C. R., Bohr H., Suhai S. Prediction of hypervariable CDR-H3 loop structures in antibodies. Protein Eng. 8:1995;389-395.
47. Ring C. S., Cohen F. E. Conformational sampling of loop structures using genetic algorithms. Isr. J. Chem. 34:1994;245-252.
48. Ring C. S, Kneller D. G., Langridge R., Cohen F. E. Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 224:1992;685-699.
49. Risler J. L., Delorme M. O., Delacroix H., Henaut A. Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix. J. Mol. Biol. 204:1988;1019-1029.
50. Rosenbach D., Rosenfeld R. Simulations modelling of multiple loops in proteins. Protein Sci. 4:1995;496-505.
51. Šali A. Modelling mutations and homologous proteins. Curr. Opin. Struct. Biol. 6:1995;437-451.
52. Šali A., Blundell T. L. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212:1990;403-428.
53. Šali A., Overington J. P. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3:1994;1582-1596.
54. Shenkin P. S., Yarmush D. L., Fine R. M., Wang H., Levinthal C. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers. 26:1987;2053-2085.
55. Sibanda B. L., Blundell T. L., Thornton J. M. Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. Mol. Biol. 206:1989;759-777.
56. Skolnick J., Kolinski A., Brooks C. L., III, Godzik A., Rey A. A method for predicting protein structure from sequence. Curr. Biol. 3:1993;414-423.
57. Smith K. C., Honig B. Evaluation of the conformational free energies of loops in proteins. Proteins: Struct. Funct. Genet. 18:1994;119-132.
58. Steipe B., Plückthun A., Huber R. Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant. J. Mol. Biol. 225:1992;739-753.
59. idimer database. Protein Sci. 4:1995;1412-1420.
60. Summers N. L., Karplus M. Modelling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro < > non-Pro mutations. J. Mol. Biol. 216:1990;991-1016.
61. Sun S. Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci. 2:1993;762-785.
62. Tanner J. J., Nell L. J., McCammon J. A. Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent. Biopolymers. 32:1992;23-31.
63. Tramontano A., Lesk A. M. Common features of the conformations of antigen-binding loops in immunoglobulins and application to modelling loop conformations. Proteins: Struct. Funct. Genet. 13:1992;231-245.
64. Vajda S., DeLisi C. Determining minimum energy conformations of polypeptides by dynamic programming. Biopolymers. 29:1990;1755-1772.
65. Wlodawer A., Miller M., Jakolski M., Sathyanarayana B. K., Baldwin E., Weber I. T., Selk L. M., Clawson L., Schneider J., Kent S. B. H. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science. 245:1989;616-621.
66. Wu S., Cygler M. Conformation of complementarity determining region L1 loop in murine IgG 1 light chain extends the repertoire of canonical forms. J. Mol. Biol. 229:1993;597-601.
67. Zhen Q., Kyle D. J. Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings. Proteins: Struct. Funct. Genet. 24:1996;209-217.
68. Zheng Q., Rosenfeld R., Vajda S., DeLisi C. Loop closure via bond scaling and relaxation. J. Comp. Chem. 14:1993a;556-565.
69. Zheng Q., Rosenfeld R., Vajda S., DeLisi C. Determining protein loop conformation using scaling-relaxation techniques. Protein Sci. 2:1993b;1242-1248.
70. Zheng Q., Rosenfeld R., DeLisi C., Kyle D. J. Multiple copy sampling in protein loop modelling: computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci. 3:1994;493-506.