Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations

Proteins: Structure, Function and Genetics

Volumn 30, Issue 3, 1998, Pages 228-231

  Sudarsanam, Sucha ^a,b  

^a AMGEN INC   (United States)

^b Aeiveos Corporation   (United States)

Author keywords

Fragment matching algorithms; Local vs. non local interactions; PDB; Protein folding; Secondary structure prediction

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

DATABASES, FACTUAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

EID: 0032519692     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980215)30:3<228::AID-PROT2>3.0.CO;2-G     Document Type: Article

References (15)

1. Bellew, R.M., Sabelko, J., Gruebele, M. Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. USA 93:5759-5764, 1996.
2. Minor, D.L., Kim, P.S. Context-dependent secondary structure formation of a designed protein sequence. Nature 380:730-734, 1996.
3. Moult, J. The current state of the art in protein structure prediction. Curr. Opin. Biotechnolo. 7:422-427, 1996.
4. Cohen, B.I., Presnell, S.R., Cohen, F.E. Origins of structural diversity within sequentially identical hexapeptides. Protein Sci. 2:2134-2145, 1993.
5. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rojers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
6. Gonnet, G.H., Cohen, M.A., Benner, S.A. Exhaustive matching of the entire protein sequence database. Science 256: 1443-1445, 1992.
7. Vogt, G., Etzold, T., Argos, P. An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited. J. Mol. Biol. 249:816-831, 1995.
8. Hobohm, U., Scharf, M., Schneider, R., Sander, C. Selection of representative protein data sets. Protein Sci. 2:409-417, 1992.
9. i dimer database. Protein Sci. 4:1412-1420, 1995.
10. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
11. Wilson, I.A., Haft, D.H., Getzoff, E.D., Tainer, J.A., Lerner, R.A., Brenner, S. Identical short peptide sequences in unrelated proteins can have different conformations: A testing ground for theories of immune recognition. Proc. Natl. Acad. Sci. USA 82:5255-5259, 1985.
12. Kabsch, W., Sander, C. On the use of sequence homologies to predict protein structure: Identical pentapeptides can have different conformations. Proc. Natl. Acad. Sci. USA 81:1075-1078, 1984.
13. 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 93:5814-5818, 1996.
14. Unger, R., Harel, D., Wherland, S., Sussman, J.L. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 5:355-373, 1989.
15. Rooman, M.J., Wodak, S.J. Identification of predictive sequence motifs limited by protein data base size. Nature 335:45-49, 1988.