Environmental features are important in determining protein secondary structure

Protein Science

Volumn 10, Issue 6, 2001, Pages 1172-1177

  Macdonald, J Randy ^a   Johnson Jr , W Curtis ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

Prediction secondary structure; Protein folding

Indexed keywords

AMINO ACID; PROTEIN; SOLVENT;

ALGORITHM; ALPHA HELIX; ARTICLE; BETA SHEET; ENVIRONMENT; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; AMINO ACIDS; MODELS, CHEMICAL; MODELS, STATISTICAL; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

EID: 0035018354     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.420101     Document Type: Article

References (23)

1. Chou, P.Y. and Fasman, G.D. 1978. Empirical predictions of protein conformation. Ann. Rev. Biochem. 47: 251-276.
2. Connolly, M.L. 1983. Analytical molecular surface calculation. J. Appl. Cryst. 16: 548-558.
3. Cuff, J.A. and Barton, G.J. 1999. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins Struct. Funct. Genet. 34: 508-519.
4. Garnier, J., Osguthorpe, D.J., and Robson, B. 1978. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120: 97-120.
5. Garnier, J., Levin, J.M., Gibrat, J.F., and Biou, V. 1994. Secondary structure prediction and protein design. Biochem. Soc. Symp. 57: 11-24.
6. Garnier, J., Gibrat, J.F., and Robson B. 1996. GOR method for predicting protein secondary structure from amino acid sequence. Meth. Enzymol. 266: 540-553.
7. Hobohm, U. and Sander, C. 1994. Enlarged representative set of protein structures. Protein Sci. 3: 522-524.
8. Holley, L.H. and Karplus, M. 1989. Protein secondary structure prediction with a neural network. Proc. Natl. Acad. Sci. 86: 152-156.
9. King, S.M. and Johnson, W.C. 1999. Assigning secondary structure from protein coordinate data. Proteins Struct. Funct. Genet. 35: 313-320.
10. Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graphics 14: 51-55.
11. Krittanai, C. and Johnson, W.C., Jr. 2000. The relative order of helical propensity of amino acids changes with solvent environment. Proteins Struct. Funct. Genet. 39: 132-141.
12. Levin, J.M., Robson, B., and Gamier, J. 1986. An algorithm for secondary structure determination in proteins based on sequence simulation. FASEB Lett. 205: 303-308.
13. Myers, J.K., Pace, C.N., and Scholtz, J.M. 1997. A direct comparison of helix propensity in proteins and peptides. Proc. Natl. Acad. Sci. 94: 2833-2837.
14. Nishikawa, K. and Ooi, T. 1986. Amino acid sequence homolog applied to the prediction of protein secondary structure, and joint prediction with existing methods. Biochim. Biophys. Acta 871: 45-54.
15. Pongor, S. and Szaley, A.A. 1985. Prediction of homology and divergence in the secondary structure of polypeptides. Proc. Natl. Acad. Sci. 82: 366-370.
16. Qian, N. and Sejnowski, T.J. 1988. Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol. 202: 865-884.
17. Rost, B. and Sander, C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232: 584-599.
18. Stolorz, P., Lapedes, A., and Xia, Y. 1992. Predicting protein secondary structure using neural net and statistical methods. J. Mol. Biol. 225: 363-377.
19. Sweet, R.M. 1986. Evolutionary similarity among peptide segments is a basis for prediction of protein folding. Biopolymers 25: 1565-1577.
20. Waterhous, D.V. and Johnson, W.C., Jr. 1994. Importance of environment in determining secondary structure in proteins. Biochemistry 33: 2121-2128.
21. Williams, R.W., Chang, A., Juretic, D., and Loughran, S. 1987. Secondary structure predictions and medium range interactions. Biochim. Biophys. Acta 916: 200-204.
22. Zhong, L. and Johnson, W.C., Jr. 1992. Environment affects amino acid preference for secondary structure. Proc. Natl. Acad. Sci. 89: 4462-4465.
23. Zvelebil, M.J., Barton, G.J., Taylor, W.R., and Sternberg, M.J.E. 1987. Prediction of protein secondary structure and active sites using alignment of homologous sequence. J. Mol. Biol. 194: 957-961.