Journal of Biosciences

, Volume 8, Issue 1–2, pp 15–23 | Cite as

A critique of the utility of the prediction of protein secondary structure

  • Gerald D. Fasman


The Chou-Fasman predictive algorithm for determining the secondary structure of proteins from the primary sequence is reviewed. Many examples of its use are presented which illustrate its wide applicability, such as predicting (a) regions with the potential for conformational change, (b) sequences which are capable of assuming several conformations in different environments, (c) effects of single amino acid mutations, (d) amino acid replacements in synthesis of peptides to bring about a change in conformation, (e) guide to the synthesis of polypeptides with definitive secondary structure,e.g. signal sequences, (f) conformational homologues from varying sequences and (g) the amino acid requirements for amphiphilicα-helical peptides.


Protein structure prediction secondary structures structure secondary proteins 

Abbreviations used


Parathyroid hormone


rough endoplasmic reticulum


corticotropin releasing factor


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  1. Anfinsen, C. B., Haber, E., Sela, M. and White, F. H., Jr. (1961)Proc. Natl. Acad. Sci. USA,47, 1309.CrossRefGoogle Scholar
  2. Bentley, G., Dodson, E., Dodson, G., Hodgkin, D. and Mercola, D. (1976)Nature (London),261, 166.CrossRefGoogle Scholar
  3. Bourgeois, S. and Pfahl, M. (1976)Adv. Prot. Chem.,30, 1.Google Scholar
  4. Briggs, M. S. and Gierasch, L. M. (1984)Biochemistry,23, 3111.CrossRefGoogle Scholar
  5. Chou, P. Y., Adler, A. J. and Fasman, G. D. (1975)J. Mol. Biol.,96, 29.CrossRefGoogle Scholar
  6. Chou, P. Y. and Fasman, G. D. (1974a)Biochemistry,13, 211.CrossRefGoogle Scholar
  7. Chou, P. Y. and Fasman, G. D. (1974b)Biochemistry,13, 222.CrossRefGoogle Scholar
  8. Chou, P. Y. and Fasman, G. D. (1975)Biochemistry,14, 2536.CrossRefGoogle Scholar
  9. Chou, P. Y. and Fasinan, G. D. (1977a)Peptides, Proceedings of the fifth American Peptide Symposium, (eds M. Goodman and J. Meinhofer) (New York: John Wiley and Sons), p. 284.Google Scholar
  10. Chou, P. Y. and Fasman, G. D. (1977b)J. Mol. Biol.,155, 135.CrossRefGoogle Scholar
  11. Chou, P. Y. and Fasman, G. D. (1978a)Adv. Enzymol., 47, 45.Google Scholar
  12. Chou, P. Y. and Fasman, G. D. (1978b)Ann. Rev. Biochem., 47, 251.CrossRefGoogle Scholar
  13. Chou, P. Y. and Fasman, G. D. (1979a)Biophys. J.,26, 367.CrossRefGoogle Scholar
  14. Chou, P. Y. and Fasman, G. D. (1979b)Biophys. J.,26, 385.CrossRefGoogle Scholar
  15. Cohen, F. E., Abarbanel, R. M., Kunz, I. D. and Fletterick, R. J. (1983)Biochemistry,22, 4894.CrossRefGoogle Scholar
  16. Cohen, F. E., Richmond, T. J., and Richards, F. M. J. (1979)J. Mol. Biol.,132, 275.CrossRefGoogle Scholar
  17. Cohen, F. E. and Sternberg, M. J. E. (1980)J. Mol. Biol.,137, 9.CrossRefGoogle Scholar
  18. Davis, B. D. and Tai, P. C. (1980)Nature (London) 283, 433.CrossRefGoogle Scholar
  19. DeGrado, W. F., Kezdy, E. J. and Kaiser, E. T. (1981)J. Am. Chem. Soc.,103, 679.CrossRefGoogle Scholar
  20. Edelman, G. M., Cunningham, B. A., Reeke, G. N., Jr., Becker, J. W., Waxdall, M. J. and Wang, J. L. (1972)Proc. Natl. Acad. Sci. USA,69, 2580.CrossRefGoogle Scholar
  21. Emr, S. D. and Silhavy, T. J. (1983)Proc. Natl. Acad. Sci. USA,80, 4599.CrossRefGoogle Scholar
  22. Epand, R. M. (1971)Can. J. Bio. Chem.,49, 166.Google Scholar
  23. Garnier, J., Osguthorpe, D. J. and Robson, B. (1978)J. Mol. Biol.,120, 97.CrossRefGoogle Scholar
  24. Gratzer, W. B., Bailey, E. and Beaven, G. H. (1967)Biochem. Biophys. Res. Commun.,28, 914.CrossRefGoogle Scholar
  25. Gutte, B., Daumigen, M. and Wittschieber, E. (1979)Nature (London),281, 650.CrossRefGoogle Scholar
  26. Hardman, K. D. and Ainsworth, C. F. (1972)Biochemistry,11, 4910.CrossRefGoogle Scholar
  27. Hüber, R., Kulka, D., Ruhlman, A. and Steigemann, W. (1972)Cold Spring Harbor Symp. Quant. Biol.,36, 141.CrossRefGoogle Scholar
  28. Lesk, A. M. and Chothia, C. (1984)J. Mol. Biol.,174, 175.CrossRefGoogle Scholar
  29. Levitt, M. and Greer, J. (1977)J. Mol. Biol.,114, 181.CrossRefGoogle Scholar
  30. Lilies, A. and Rossman, M. G. (1974)Ann. Rev. Biochem.,43, 475.CrossRefGoogle Scholar
  31. Matthews, B. (1976)Ann. Rev. Phys. Chem.,27, 493.CrossRefGoogle Scholar
  32. McCubbin, W. D., Oikawa, K. and Kay, C. M. (1971)Biochem. Biophys. Res. Commun.,43, 666.CrossRefGoogle Scholar
  33. Moran, E. C., Chou, P. Y. and Fasman, G. D. (1977)Biochem. Biophys. Res. Commun., 77, 1300.CrossRefGoogle Scholar
  34. Pallai, P. V., Mabilla, M., Goodman, M., Vale, W. and Rivier, J. (1983)Proc. Natl. Acad. Sci. USA,80, 6770.CrossRefGoogle Scholar
  35. Potts, Jr., J. T., Kronenberg, H. M. and Rosenblatt, M. (1982)Adv. Prot. Chem.,35, 323.Google Scholar
  36. Ptitsyn, O. B. and Finkelstein, A. V. (1980) inProtein Folding, (ed. R. Jaenicke) (Elsevier/North Holland), 101.Google Scholar
  37. Rawlings, N., Ashman, K. and Wittman-Leibold, B., (1983)Int. J. Pept. Protein Res.,22, 515.CrossRefGoogle Scholar
  38. Rosenblatt, M., Habener, J. F., Tyler, F. A., Shepard, G. L. and Potts, Jr., J. T. (1979)J. Biol. Chem.,254, 1414.PubMedGoogle Scholar
  39. Shotton, D. M. and Watson, H. C. (1970)Nature (London),225, 811.CrossRefGoogle Scholar
  40. Snell, C. R., and Smyth, D. G. (1975)J. Biol. Chem.,250, 6291.PubMedGoogle Scholar
  41. Srere, P. A. and Brooks, G. C. (1969)Arch. Biochem. Biophys.,129, 708.CrossRefGoogle Scholar
  42. Steenberg, J. E. and Cohen, F. E. (1982)Int. J. Biol. Macromol.,4, 137.CrossRefGoogle Scholar
  43. Sternberg, M. J. E., Cohen, F. E., Taylor, W. R. and Feldman, R. J. (1982)Philos. Trans. R. Soc., London Ser. B,239, 177.Google Scholar
  44. Venkatachalam, C. M. (1968)Biopolymers,6, 1425.CrossRefGoogle Scholar
  45. Visser, L. and Blout, E. R. (1971)Biochemistry,10, 743.CrossRefGoogle Scholar
  46. Wickner, W. (1979)Ann. Rev. Biochem.,48, 23.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 1985

Authors and Affiliations

  • Gerald D. Fasman
    • 1
  1. 1.Graduate Department of BiochemistryBrandeis UniversityWalthamUSA

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