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Proc Natl Acad Sci U S A. Jan 1984; 81(1): 140–144.
PMCID: PMC344626

The hydrophobic moment detects periodicity in protein hydrophobicity.

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.

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Selected References

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  • Schiffer M, Edmundson AB. 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. [PMC free article] [PubMed]
  • Ptitsyn OB, Rashin AA. A model of myoglobin self-organization. Biophys Chem. 1975 Feb;3(1):1–20. [PubMed]
  • Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature. 1982 Sep 23;299(5881):371–374. [PubMed]
  • Salemme FR. Conformational and geometrical properties of beta-sheets in proteins. III. Isotropically stressed configurations. J Mol Biol. 1981 Feb 15;146(1):143–156. [PubMed]
  • McLachlan AD, Stewart M. The 14-fold periodicity in alpha-tropomyosin and the interaction with actin. J Mol Biol. 1976 May 15;103(2):271–298. [PubMed]
  • Bear RS, Adams JB, Poulton JW. 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. [PubMed]
  • KAUZMANN W. Some factors in the interpretation of protein denaturation. Adv Protein Chem. 1959;14:1–63. [PubMed]
  • Kuntz ID. Protein folding. J Am Chem Soc. 1972 May 31;94(11):4009–4012. [PubMed]
  • Rose GD. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature. 1978 Apr 13;272(5654):586–590. [PubMed]
  • Argos P, Rao JK, Hargrave PA. Structural prediction of membrane-bound proteins. Eur J Biochem. 1982 Nov 15;128(2-3):565–575. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, 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. [PubMed]
  • Chou PY, Fasman GD. Empirical predictions of protein conformation. Annu Rev Biochem. 1978;47:251–276. [PubMed]
  • Cohen FE, Richmond TJ, Richards FM. 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. [PubMed]
  • Chothia C, Levitt M, Richardson D. Helix to helix packing in proteins. J Mol Biol. 1981 Jan 5;145(1):215–250. [PubMed]
  • Richardson JS, Getzoff ED, Richardson DC. The beta bulge: a common small unit of nonrepetitive protein structure. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2574–2578. [PMC free article] [PubMed]
  • Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. [PubMed]
  • Terwilliger TC, Eisenberg D. The structure of melittin. I. Structure determination and partial refinement. J Biol Chem. 1982 Jun 10;257(11):6010–6015. [PubMed]
  • Terwilliger TC, Eisenberg D. The structure of melittin. II. Interpretation of the structure. J Biol Chem. 1982 Jun 10;257(11):6016–6022. [PubMed]

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