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Hydrophobic Moments as Tools for Analyzing Protein Sequences and Structures

  • David Eisenberg
  • Morgan Wesson
  • William Wilcox

Abstract

This chapter deals with the two main themes of this book—prediction of protein structure from sequence and principles of protein conformation—but from a narrow point of view. The point of view is that the interaction with water of the amino acid side chains is a major determinant of protein structure. Charged and polar side chains seek contact with water, and apolar side chains avoid water, preferring to cluster together beneath the surface of the protein. This avoidance of water is the hydrophobic interaction, first described in detail by Kauzmann (1959). In this point of view, it is the simultaneous attraction of some amino acid side chains to water and the avoidance of water by others that is a major factor in dictating the conformation taken by the polypeptide backbone.

Keywords

Amino Acid Side Chain Triose Phosphate Isomerase Amino Acid Analogue Hydrophobicity Scale Polar Side Chain 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Argiolas, A., and Pisano, J. J., 1985, Bombolitins: A new class of mast cell degranulating peptides from the venom of the bumblebee Megabombus pennsylvanicus, J. Biol. Chem. 260(3):1437–444.PubMedGoogle Scholar
  2. Banner, D. W., Bloomer, A. C., Petsko, G. A., Phillips, D. C., and Wilson, 1976, Atomic coordinates for triose phosphate isomerase from chicken muscle, Biochem. Biophys. Res. Commun. 72(1): 146–155.PubMedCrossRefGoogle Scholar
  3. Blake, C. C. F., Geisow, M. J., Oatley, S. J., Rerat, B., Rerat, C., 1978, Structure of pre albumin: Secondary, tertiary, and quaternary interactions determined by Fourier refinement at 1.8 Å, J. Mol. Biol. 121(3):339–356.PubMedCrossRefGoogle Scholar
  4. Chothia, C., 1976, The nature of the accessible and buried surfaces in proteins, J. Mol. Biol. 105(1):1–12.PubMedCrossRefGoogle Scholar
  5. Cohn, E. J., and Edsall, J. T., 1943, Proteins, Amino Acids, and Peptides as Ions and Dipolar Ions, Reinhold, New York, pp. 206–212.Google Scholar
  6. DeGrado, W. F., Kezdy, F. J., and Kaiser, E. T., 1981, Design, synthesis, and characterization of a cytotoxic peptide with melittin-like activity, J. Am. Chem. Soc. 103(3):679–681.CrossRefGoogle Scholar
  7. Edsall, J. T., and McKenzie, H. A., 1978, Water and proteins: I. The significance and structure of water: Its interaction with electrolytes and non-electrolytes, Adv. Biophys. 10: 137–207.PubMedGoogle Scholar
  8. Eisenberg, D., 1984, Three-dimensional structure of membrane and surface proteins, Annu. Rev. Biochem. 53: 595–623.PubMedCrossRefGoogle Scholar
  9. Eisenberg, D., and McLachlan, A. D., 1986, Solvation energy in protein folding and binding, Nature (London) 319(6050): 199–203.CrossRefGoogle Scholar
  10. Eisenberg, D., and Wesson, M., Hydrophobic moment analysis identifies two possible surface-seeking alpha helices in HIV gp41, in preparation.Google Scholar
  11. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1982a, The helical hydrophobic moment: A measure of the amphiphilicity of a helix, Nature (London) 299(5881):371–374.CrossRefGoogle Scholar
  12. Eisenberg, D., Weiss, R. M., Terwilliger, T. C., and Wilcox, W., 1982b, Hydrophobic moments and protein structure, Faraday Symp. Chem. Soc. 17:109–120.CrossRefGoogle Scholar
  13. Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R., 1984a, Analysis of membrane and surface protein sequences with the hydrophobic moment plot, J. Mol. Biol. 179(1):125–142.PubMedCrossRefGoogle Scholar
  14. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1984b, The hydrophobic moment detects periodicity in protein hydrophobicity, Proc. Natl. Acad. Sci. U.S.A. 81(1):140–144.PubMedCrossRefGoogle Scholar
  15. Eisenberg, D., Wilcox, W., Eshita, S. M., Pryciak, P. M., Ho, S. P., and DeGrado, W. F., 1986a, The design, synthesis, and crystallization of an alphahelical peptide, Proteins: Struct. Funct. Genet. 1(1):16–22.CrossRefGoogle Scholar
  16. Eisenberg, D., Wilcox, W., and McLachlan, A. D., 1986b, Hydrophobicity and amphiphilicity in protein structure, J. Cell. Biochem. 31(1):11–17.PubMedCrossRefGoogle Scholar
  17. Fauchère, J. L., and Pliška, V., 1983, Hydrophobic parameters π of amino acid side chains from the partitioning of N-acetyl-arnino acid arnides, Eur. J. Med. Chem.-Chim. Ther. 18(4):369–375.Google Scholar
  18. Finer-Moore, J., and Stroud, R. M., 1984, Amphipathic analysis and possible formation of the ion channel in an acetylcholine receptor, Proc. Natl. Acad. Sci. U.S.A. 81(1):155–159.PubMedCrossRefGoogle Scholar
  19. Fitton, J. E., Dell, A., and Shaw, W. V., 1980, The amino acid sequence of the delta hemolysin of Staphylococcus aureus, FEBS Lett. 115(2):209–212.PubMedCrossRefGoogle Scholar
  20. Frömmel, C., 1984, The apolar surface area of amino acids and its empirical correlation with hydrophobic free energy, J. Theor. Biol. 111(2):247–260.PubMedCrossRefGoogle Scholar
  21. Guy, H. R., 1985, Amino acid side-chain partition energies and distribution of residues in soluble proteins, Biophys. J. 47(1):61–70.PubMedCrossRefGoogle Scholar
  22. Habermann, E., 1972, Bee and wasp venoms, Science 177(4046):314–322.PubMedCrossRefGoogle Scholar
  23. Hopp, T. P., and Woods, K. R., 1981, Prediction of protein antigenic determinants from amino acid sequences, Proc. Natl. Acad. Sci. U.S.A. 78(6):3824–3828.PubMedCrossRefGoogle Scholar
  24. Janin, J., 1979, Surface and inside volumes in globular proteins, Nature (London) 277(5696): 491–492.CrossRefGoogle Scholar
  25. Kaiser, E. T., and Kezdy, F. J., 1983, Secondary structures of proteins and peptides in amphiphilic environments (A review), Proc. Natl. Acad. Sci. U.S.A. 80(4):1137–1143.PubMedCrossRefGoogle Scholar
  26. Kauzmann, W., 1959, Some factors in the interpretation of protein denaturation, Adv. Protein Chem. 14:1–63.PubMedCrossRefGoogle Scholar
  27. Kreil, G., 1973, Structure of melittin isolated from two species of honey bees, FEBS Lett. 33(2):241–244.CrossRefGoogle Scholar
  28. Kyte, J., and Doolittle, R. F., 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157(1):105–132.PubMedCrossRefGoogle Scholar
  29. Novotny, J., Bruccoleri, R., and Karplus, M., 1984, An analysis of incorrectly folded protein models: Implications for structure predictions, J. Mol. Biol. 177(4):787–818.PubMedCrossRefGoogle Scholar
  30. Nozaki, Y., and Tanford, C., 1971, Solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions: Establishment of a hydrophobicity scale, J. Biol. Chem. 246(7):2211–2217.PubMedGoogle Scholar
  31. Perutz, M. F., Kendrew, J. C., and Watson, H. C., 1965, Structure and function of hemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence, J. Mol. Biol. 13:669–678.CrossRefGoogle Scholar
  32. Rees, D. C., Lewis, M., and Lipscomb, W. N., 1983, Refined crystal structure of carboxypeptidase A at 1.54 Å resolution, J. Mol. Biol. 168(2): 367–387.PubMedCrossRefGoogle Scholar
  33. Richardson, J. S., 1981, The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34:167–339.PubMedCrossRefGoogle Scholar
  34. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H., 1985, Hydrophobicity of amino acid residues in globular proteins Science 229(4716):834–838.PubMedCrossRefGoogle Scholar
  35. Schiffer, M., and Edmundson, A. B., 1967, Use of helical wheels to represent the structures of proteins and to identify segments with helical potential, Biophys. J. 7(2):121–135.PubMedCrossRefGoogle Scholar
  36. Steiner, H., Hultmark, D., Engstroem, A., Bennich, H., and Boman, H. G., 1981, Sequence and specificity of two antibacterial proteins involved in insect immunity, Nature (London) 292(5820):246–248.CrossRefGoogle Scholar
  37. Sweet, R. M., and Eisenberg, D., 1983, Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure, J. Mol. Biol. 171(4):479–488.PubMedCrossRefGoogle Scholar
  38. Terwilliger, T. C., and Eisenberg, D., 1982a, The structure of melittin: I. Structure determination and partial refinement, J. Biol. Chem. 257(11):6010–6015.PubMedGoogle Scholar
  39. Terwilliger, T. C., and Eisenberg, D., 1982b, The structure of melittin: II. Interpretation of the structure, J. Biol. Chem. 257(11):6016–6022.PubMedGoogle Scholar
  40. Terwilliger, T. C., Weissman, L., and Eisenberg, D., 1982, The structure of melittin in the form I crystals and its implication for melittin’s lytic and surface activities, Biophys. J. 37(1):353–361.PubMedCrossRefGoogle Scholar
  41. Von Heijne, G., and Blomberg, C., 1979, Trans-membrane translocation of proteins: The direct transfer model, Eur. J. Biochem. 97(1):175–181.CrossRefGoogle Scholar
  42. Wolfenden, R., Andersson, L., Cullis, P. M., and Southgate, C. C. B., 1981, Affinities of amino acid side chains for solvent water, Biochemistry 20(4):849–855.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1989

Authors and Affiliations

  • David Eisenberg
    • 1
  • Morgan Wesson
    • 1
  • William Wilcox
    • 1
  1. 1.Molecular Biology Institute, and Departments of Chemistry and BiochemistryUniversity of California, Los AngelesLos AngelesUSA

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