Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool

Journal of Molecular Biology

Volumn 267, Issue 5, 1997, Pages 1268-1282

  Bower, Michael J ^a   Cohen, Fred E ^a   Dunbrack Jr , Roland L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Backbone dependent rotamer library; Homology modeling; Protein structure; Side chain prediction

Indexed keywords

POLYPEPTIDE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; DATA BASE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STEREOCHEMISTRY;

EID: 0031576989     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0926     Document Type: Article

References (58)

1. Bamborough P., Cohen F. E. Modeling protein-ligand complexes. Curr. Opin. Struct. Biol. 6:1996;236-241.
2. Benedetti E., Morelli G., Nemethy G., Scheraga H. A. Statistical and energetic analysis of side-chain conformations in oligopeptides. Int. J. Peptide Protein Res. 22:1983;1-15.
3. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. J., 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. Bhat T. N., Sasisekharan V., Vijayan M. An analysis of side-chain conformation in proteins. Int. J. Peptide Prot. Res. 13:1979;170-184.
5. Blundell T. L., Sibanda B. L., Sternberg M. J. E., Thornton J. M. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 326:1987;347-352.
6. 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. Comput. Chem. 4:1983;187-217.
7. Browne W. J., North A. C., Phillips D. C. A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. J. Mol. Biol. 42:1969;65-86.
8. Chandrasekaran R., Ramachandran G. N. Studies on the conformation of amino acids, XI. Analysis of the observed side group conformations in proteins. Int. J. Protein Res. 2:1970;223-233.
9. Chung S. Y., Subbiah S. A structural explanation for the twilight zone of protein sequence homology. Structure. 4:1996;1123-1127.
10. Clopper C. J., Pearson E. S. The use of confidence or fiducial limits illustrated in the case of the binomial. Biometrika. 26:1934;404.
11. Compton D. A. C., Montero S., Murphy W. F. Low-frequency Raman spectrum and asymmetric potential function for internal rotation of gaseous n-butane. J. Phys. Chem. 84:1980;3587-3591.
12. David C. Sprouting side-chain conformations in X-PLOR simulations of peptides. J. Comput. Chem. 14:1993;715-717.
13. Defay T., Cohen F. E. Evaluation of current techniques for ab initio protein structure prediction. Proteins: Struct. Funct. Genet. 23:1995;431-445.
14. Desmet J., De Maeyer M., Hazes B., Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature. 356:1992;539-542.
15. Dunbrack R. L., Jr, Karplus M. Backbone-dependent rotamer library for proteins: Application to side-chain prediction. J. Mol. Biol. 230:1993;543-574.
16. Dunbrack R. L., Jr, Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein side-chains. Nature Struct. Biol. 1:1994;334-340.
17. Durig J. R., Compton D. A. C. Analysis of torsional spectra of molecules with two internal C3v rotors. 12. Low frequency vibrational spectra, methyl torsional potential function, and internal rotation of n-butane. J. Phys. Chem. 83:1979;265-268.
18. Eisenmenger F., Argos P., Abagyan R. A method to configure protein side-chains from the main-chain trace in homology modeling. J. Mol. Biol. 231:1993;849-860.
19. Faber H. R., Matthews B. W. A mutated T4 lysozyme displays five different crystal conformations. Nature. 348:1990;263-266.
20. Gelin B. R., Karplus M. Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment. Biochemistry. 18:1979;1256-1268.
21. Glantz S. A. Primer of Biostatistics. 1992;McGraw-Hill, New York.
22. Holm L., Sander C. Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: application to model building by homology. Proteins: Struct. Funct. Genet. 14:1992;213-223.
23. Hwang J. K., Liao W. F. Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng. 8:1995;363-370.
24. James M. N. G., Sielecki A. R. Structure and refinement of penicillopepsin at 1.8 Å resolution. J. Mol. Biol. 163:1983;299-361.
25. Janin J., Wodak S., Levitt M., Maigret B. Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125:1978;357-386.
26. Kishan K. V., Zeelen J. P., Noble M. E., Borchert T. V., Wierenga R. K. Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms. Protein Sci. 3:1994;779-787.
27. Koehl P., Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:1994;249-275.
28. Kono H., Doi J. Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry. Proteins: Struct. Funct. Genet. 19:1994;244-255.
29. Kossiakoff A. A., Randal M., Guenot J., Eigenbrot C. Variability of conformations at crystal contacts in BPTI represent true low-energy structures. Proteins: Struct. Funct. Genet. 14:1992;65-74.
30. Lasters I., Desmet J. The fuzzy-end elimination theorem: Correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem. Protein Eng. 6:1993;717-722.
31. Laughton C. A. Prediction of protein side-chain conformations from local three-dimensional homology relationships. J. Mol. Biol. 235:1994;1088-1097.
32. Lee C., Subbiah S. Prediction of protein side-chain conformation by packing optimization. J. Mol. Biol. 217:1991;373-388.
33. Levitt M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226:1992;507-533.
34. McGregor M. J., Islam S. A., Sternberg M. J. E. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198:1987;295-310.
35. Morris A. L., MacArthur M. W., Hutchinson E. G., Thornton J. M. Stereochemical quality of protein structure coordinates. Proteins: Struct. Funct. Genet. 12:1992;345-364.
36. Pearlman, D. A. Case, D. A. Caldwell, J. W. Ross, W. S. Cheatham III, T. E. Ferguson, D. M. Seibel, G. L. Singh, U. C. Weiner, P. K. Kollman, P. A. 1995, AMBER 4.1, University of California, San Francisco.
37. Pearson W. R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183:1990;63-98.
38. Pearson W. R., Lipman D. J. Improved tools for biological sequence analysis. Proc. Natl Acad. Sci. USA. 85:1988;2444-2448.
39. Ponder J. W., Richards F. M. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193:1987;775-791.
40. Ring C. S., Cohen F. E. Modeling protein structures: construction and their applications. FASEB J. 7:1993;783-790.
41. Sasisekharan V., Ponnuswamy P. K. Backbone and side-chain conformations of amino acids and amino acid residues in peptides. Biopolymers. 9:1970;1249-1256.
42. Sasisekharan V., Ponnuswamy P. K. Studies on the conformation of amino acids. X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit. Biopolymers. 10:1971;583-592.
43. Schrauber H., Eisenhaber F., Argos P. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J. Mol. Biol. 230:1993;592-612.
44. Schulz G. E., Schirmer R. H. Principles of Protein Structure. Springer Advanced Texts in Chemistry. 1979;Springer-Verlag, New York.
45. Shenkin P. S., Farid H., Fetrow J. S. Prediction and evaluation of side-chain conformations for protein backbone structures. Proteins: Struct. Funct. Genet. 26:1996;323-352.
46. Summers N. L., Karplus M. Construction of side-chains in homology modeling. Application to the C-terminal lobe of rhizopuspepsin. J. Mol. Biol. 210:1989;785-811.
47. Summers N. L., Carlson W. D., Karplus M. Analysis of side-chain orientations in homologous proteins. J. Mol. Biol. 196:1987;175-198.
48. Sutcliffe M. J., Haneef I., Carney D., Blundell T. L. Knowledge based modeling of homologous proteins, Part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1:1987a;377-384.
49. Sutcliffe M. J., Hayes F. R., Blundell T. L. Knowledge based modeling of homologous proteins, Part II: rules for the conformations of substituted side-chains. Protein Eng. 1:1987b;385-392.
50. Swanson E. PSSHOW Users Guide. 1994.
51. Tanimura R., Kidera A., Nakamura H. Determinants of protein side-chain packing. Protein Sci. 3:1994;2358-2365.
52. Tuffery P., Etchebest C., Hazout S., Lavery R. A new approach to the rapid determination of protein side-chain conformations. J. Biomol. Struct. Dynam. 8:1991;1267-1289.
53. Tuffery P., Etchebest C., Hazout S., Lavery R. A critical comparison of search algorithms applied to the optimization of protein side-chain conformations. J. Comput. Chem. 14:1993;790-798.
54. Vasquez M. An evaluation of discrete and continuum search techniques for conformational analysis of side-chains in proteins. Biopolymers. 36:1995;53-70.
55. Vasquez M. Modeling side-chain conformation. Curr. Opin. Struct. Biol. 6:1996;217-221.
56. Wiberg K. B., Murcko M. A. Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions. J. Am. Chem. Soc. 110:1988;8029-8038.
57. Wilson C., Gregoret L. M., Agard D. A. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J. Mol. Biol. 229:1993;996-1006.
58. Zhang G., Kazanietz M. G., Blumberg P. M., Hurley J. H. Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester. Cell. 81:1995;917-924.