Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1984 Jan;81(1):140–144. doi: 10.1073/pnas.81.1.140

The hydrophobic moment detects periodicity in protein hydrophobicity.

D Eisenberg, R M Weiss, T C Terwilliger
PMCID: PMC344626  PMID: 6582470

Abstract

Periodicities in the polar/apolar character of the amino acid sequence of a protein can be examined by assigning to each residue a numerical hydrophobicity and searching for periodicity in the resulting one-dimensional function. The strength of each periodic component is the quantity that has been termed the hydrophobic moment. When proteins of known three-dimensional structure are examined, it is found that sequences that form alpha helices tend to have, on average, a strong periodicity in the hydrophobicity of 3.6 residues, the period of the alpha helix. Similarly, many sequences that form strands of beta sheets tend to have a periodicity in their hydrophobicity of about 2.3 residues, the period typical of beta structure. Also, the few sequences known to form 3(10) helices display a periodicity of about 2.5 residues, not far from the period of 3 for an ideal 3(10) helix. This means that many protein sequences tend to form the periodic structure that maximizes their amphiphilicity. This observation suggests that the periodicity of the hydrophobicity of the protein primary structure is a factor in the formation of secondary structures. Moreover, the observation that many protein sequences tend to form segments of maximum amphiphilicity suggests that segments of secondary structure fold at a hydrophobic surface, probably formed from other parts of the folding protein.

Full text

PDF
140

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Argos P., Rao J. K., Hargrave P. A. Structural prediction of membrane-bound proteins. Eur J Biochem. 1982 Nov 15;128(2-3):565–575. doi: 10.1111/j.1432-1033.1982.tb07002.x. [DOI] [PubMed] [Google Scholar]
  2. Bear R. S., Adams J. B., Poulton J. W. Disclosure by Fourier methods of a long-range pattern of non-polar residues in the alpha1(I) sequence of collagen. J Mol Biol. 1978 Jan 5;118(1):123–126. doi: 10.1016/0022-2836(78)90248-6. [DOI] [PubMed] [Google Scholar]
  3. 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. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  4. Chothia C., Levitt M., Richardson D. Helix to helix packing in proteins. J Mol Biol. 1981 Jan 5;145(1):215–250. doi: 10.1016/0022-2836(81)90341-7. [DOI] [PubMed] [Google Scholar]
  5. Chou P. Y., Fasman G. D. Empirical predictions of protein conformation. Annu Rev Biochem. 1978;47:251–276. doi: 10.1146/annurev.bi.47.070178.001343. [DOI] [PubMed] [Google Scholar]
  6. Cohen F. E., Richmond T. J., Richards F. M. Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J Mol Biol. 1979 Aug 15;132(3):275–288. doi: 10.1016/0022-2836(79)90260-2. [DOI] [PubMed] [Google Scholar]
  7. Eisenberg D., Weiss R. M., Terwilliger T. C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature. 1982 Sep 23;299(5881):371–374. doi: 10.1038/299371a0. [DOI] [PubMed] [Google Scholar]
  8. KAUZMANN W. Some factors in the interpretation of protein denaturation. Adv Protein Chem. 1959;14:1–63. doi: 10.1016/s0065-3233(08)60608-7. [DOI] [PubMed] [Google Scholar]
  9. Kuntz I. D. Protein folding. J Am Chem Soc. 1972 May 31;94(11):4009–4012. doi: 10.1021/ja00766a060. [DOI] [PubMed] [Google Scholar]
  10. McLachlan A. D., Stewart M. The 14-fold periodicity in alpha-tropomyosin and the interaction with actin. J Mol Biol. 1976 May 15;103(2):271–298. doi: 10.1016/0022-2836(76)90313-2. [DOI] [PubMed] [Google Scholar]
  11. Ptitsyn O. B., Rashin A. A. A model of myoglobin self-organization. Biophys Chem. 1975 Feb;3(1):1–20. doi: 10.1016/0301-4622(75)80033-0. [DOI] [PubMed] [Google Scholar]
  12. Richardson J. S., Getzoff E. D., Richardson D. C. The beta bulge: a common small unit of nonrepetitive protein structure. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2574–2578. doi: 10.1073/pnas.75.6.2574. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
  14. Rose G. D. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature. 1978 Apr 13;272(5654):586–590. doi: 10.1038/272586a0. [DOI] [PubMed] [Google Scholar]
  15. Salemme F. R. Conformational and geometrical properties of beta-sheets in proteins. III. Isotropically stressed configurations. J Mol Biol. 1981 Feb 15;146(1):143–156. doi: 10.1016/0022-2836(81)90370-3. [DOI] [PubMed] [Google Scholar]
  16. Schiffer M., Edmundson A. B. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys J. 1967 Mar;7(2):121–135. doi: 10.1016/S0006-3495(67)86579-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Terwilliger T. C., Eisenberg D. The structure of melittin. I. Structure determination and partial refinement. J Biol Chem. 1982 Jun 10;257(11):6010–6015. doi: 10.2210/pdb1mlt/pdb. [DOI] [PubMed] [Google Scholar]
  18. Terwilliger T. C., Eisenberg D. The structure of melittin. II. Interpretation of the structure. J Biol Chem. 1982 Jun 10;257(11):6016–6022. [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES