Prediction of local structure in proteins using a library of sequence-structure motifs

Journal of Molecular Biology

Volumn 281, Issue 3, 1998, Pages 565-577

  Bystroff, Christopher ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Clustering; I sites library; Initiation sites; Protein folding; Sequence patterns

Indexed keywords

PROLINE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0032555696     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1943     Document Type: Article

References (49)

1. Aurora R., Srinivasan R., Rose G.D. Rules for alpha-helix termination by glycine. Science. 264:1994;1126-1130
2. Bernstein F.C., Koetzle T.F., Williams G.J., 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. Eur. J. Biochem. 80:1977;319-324
3. Blanco F.J., Serrano L. Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem. 230:1995;34-649
4. Blanco F.J., Rivas G., Serrano L. A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nature Struct. Biol. 1:1994;584-590
5. Bystroff C., Baker D. Blind ab initio local structure predictions using a library of sequence-structure motifs. Proteins: Struct. Funct. Genet. Suppl. 1:1997;167-171
6. Chain A.W., Hutchinson E.G., Harris D., Thornton J.M. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci. 2:1993;1574-1590
7. de Alba E., Jiménez M.A., Rico M., Nieto J.L. Conformational investigation of designed short linear peptides able to fold into β-hairpin structures in aqueous solution. Folding Des. 1:1996;133-144
8. Donnelly D., Overington J.P., Blundell T.L. The prediction and orientation of alpha-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules. Protein Eng. 7:1994;645-653
9. Duda R.O., Hart P.E. Pattern Classification and Scene Analysis. 1973;John Wiley & Sons, New York
10. Efimov A.V. Standard structures in proteins. Prog. Biophys. Mol. Biol. 60:1993;201-239
11. elMasry N.F., Fersht A.R. Mutational analysis of the N-capping box of the alpha-helix of chymotrypsin inhibitor 2. Protein Eng. 7:1994;777-782
12. Everitt B. Cluster Analysis. 1993;Halsted Press, New York
13. Fischer D., Eisenberger D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955
14. Gribskov M., Luthy R., Eisenberg D. Profile analysis. Methods Enzymol. 183:1990;146-259
15. Han K.F., Baker D. Recurring local sequence motifs in proteins. J. Mol. Biol. 251:1995;176-187
16. Han K.F., Baker D. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc. Natl Acad. Sci. USA. 93:1996;5814-5818
17. Han K.F., Bystroff C., Baker D. Three dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Sci. 6:1997;1587-1590
18. Hobohm U., Scharf M., Schneider R., Sander C. Selection of representative protein data sets. Protein Sci. 1:1992;409-417
19. Hutchinson E.G., Thornton J.M. A revised set of potentials for beta-turn formation in proteins. Protein Sci. 3:1994;2207-2216
20. Ilyina E., Milius R., Mayo K.H. Synthetic peptides probe folding initiation sites in platelet factor-4 stable chain reversal found within the hydrophobic sequence LIATLKNGRKISL. Biochemistry. 33:1994;13436-13444
21. Itzhaki L.S., Neira J.L., Ruiz Sanz J., de Prat Gay G., Fersht A.R. Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2. J. Mol. Biol. 254:1995;289-304
22. Jiménez M.A., Muñoz V., Rico M., Serrano L. Helix stop and start signals in peptides and proteins. The capping box does not necessarily prevent helix elongation. J. Mol. Biol. 242:1994;487-496
23. Kabsch W., Sander C. Dictionary of protein secondary structure pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637
24. Lesk A.M. CASP2 report on ab initio predictions. Proteins: Struct. Funct. Genet. 1997;151-166
25. Muñoz V., Serrano L. Analysis of i,i+5 and i,i+8 i-hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif. Biochemistry. 34:1995;15301-15306
26. Muñoz V., Blanco F.J., Serrano L. The hydrophobic-staple motif and a role for loop-residues in alpha-helix stability and protein folding. Nature Struct. Biol. 2:1995;380-385
27. Oliva B., Bates P.A., Querol E., Avilés F.X., Sternberg M.J.E. An automated classification of the structure of protein loops. J. Mol. Biol. 266:1997;814-830
28. Rooman M.J., Rodriguez J., Wodak S.J. Automatic definition of recurrent local structure motifs in proteins. J. Mol. Biol. 213:1990;327-336
29. Rooman M.J., Kocher J.P., Wodak S.J. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J. Mol. Biol. 221:1991;961-979
30. Rooman M.J., Kocher J.P., Wodak S.J. Extracting information on folding from the amino acid sequence accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry. 31:1992;10226-10238
31. Rost B., Sander C. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl Acad. Sci. USA. 90:1993;7558-7562
32. Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232:1993;584-599
33. Rost B., Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins: Struct. Funct. Genet. 19:1994;55-72
34. Rost B., Sander C., Schneider R. PHD an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10:1994;53-60
35. Sander C., Schneider R. The HSSP database of protein structure-sequence alignments. Nucl. Acids Res. 22:1994;3597-3599
36. Schellman C. The aL conformation at the ends of helices. Jaenicke R. Protein Folding Proceedings of the 28th Conference of the German Biochemical Society, University of Regensburg, Regensburg, West Germany, September 10-12, 1979. 1980;53-61 Elsevier/North-Holland Biomedical Press, Amsterdam
37. Schneider R., Sander C. The HSSP database of protein structure sequence alignments. Nucl. Acids Res. 24:1996;201-205
38. Searle M.S., Williams D.H., Packman L.C. A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin. Nature Struct. Biol. 2:1995;999-1006
39. Sieber V., Moe G.R. Interactions contributing to the formation of a beta-hairpin-like structure in a small peptide. Biochemistry. 35:1996;181-188
40. Unger R., Sussman J.L. The importance of short structural motifs in protein structure analysis. J. Comput. Aided Mol. Des. 7:1993;457-472
41. Unger R., Harel D., Wherland S., Sussman J.L. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins: Struct. Funct. Genet. 5:1989;355-373
42. Viguera A.R., Serrano L. Experimental analysis of the Schellman motif. J. Mol. Biol. 251:1995;150-160
43. Viguera A.R., Jiménez a M., Rico M., Serrano L. Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain. J. Mol. Biol. 255:1996;507-521
44. Vingron M., Argos P. A fast and sensitive multiple sequence alignment algorithm. Comput. Appl. Biol. Sci. 5:1989;115-121
45. West M.W., Hecht M.H. Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Protein Sci. 4:1995;2032-2039
46. Yang A.S., Hitz B., Honig B. Free energy determinants of secondary structure formation. III. Beta-turns and their role in protein folding. J. Mol. Biol. 259:1996;873-882
47. Yang J.J., Buck M., Pitkeathly M., Kotik M., Haynie D.T., Dobson C.M., Radford S.E. Conformational properties of four peptides spanning the sequence of hen lysozyme. J. Mol. Biol. 252:1995;483-491
48. Yi Q., Bystroff C., Rajagopal P., Klevit R.E., Baker D. Prediction and structural charcterization of an independently folding substructure in the src SH3 domain. J. Mol. Biol. 1998;. In the press
49. Zhu Z.Y., Blundell T.L. The use of amino acid patterns of classified helices and strands in secondary structure prediction. J. Mol. Biol. 260:1996;261-276