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Experimentally determined hydrophobicity scale for proteins at membrane interfaces

Abstract

The partitioning of membrane-active oligopeptides into membrane interfaces promotes the formation of secondary structure. A quantitative description of the coupling of structure formation to partitioning, which may provide a basis for understanding membrane protein folding and insertion, requires an appropriate free energy scale for partitioning. A complete interfacial hydrophobicity scale that includes the contribution of the peptide bond was therefore determined from the partitioning of two series of small model peptides into the interfaces of neutral (zwitterionic) phospholipid membranes. Aromatic residues are found to be especially favoured at the interface while charged residues, and the peptide bond, are disfavoured about equally. Reduction of the high cost of partitioning the peptide bond through hydrogen bonding may be important in the promotion of structure formation in the membrane interface.

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References

  1. 1

    Shai, Y. Pardaxin: Channel formation by a shark repellant peptide from fish. Toxicology 87, 109–129 (1994).

    CAS  Article  Google Scholar 

  2. 2

    Maloy, W.L. & Kari, U.P. Structure-activity studies on magainins and other host defense peptides. Biopolymers 37, 105–122 (1995).

    CAS  Article  Google Scholar 

  3. 3

    Gierasch, L.M. Signal sequences. Biochemistry 28, 923–929 (1989).

    CAS  Article  Google Scholar 

  4. 4

    Wickner, W. Mechanisms of membrane assembly: general lessons from the study of M13 coat protein and escherichia coli leader peptidase. Biochemistry 27, 1081–1086 (1988).

    CAS  Article  Google Scholar 

  5. 5

    Schatz, G. & Dobberstein, B. Common principles of protein translocation across membranes. Science 271, 1519–1526 (1996).

    CAS  Article  Google Scholar 

  6. 6

    Jacobs, R.E. & White, S.H. The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices. Biochemistry 28, 3421–3437 (1989).

    CAS  Article  Google Scholar 

  7. 7

    Wimley, W.C., Creamer, T.P. & White, S.H. Solvation energies of amino acid sidechains and backbone in a family of host-guest pentapeptides. Biochemistry 35, 5109–5124 (1996).

    CAS  Article  Google Scholar 

  8. 8

    Wimley, W.C., Gawrisch, K., Creamer, T.P. & White, S.H. A direct measurement of salt-bridge solvation energies using a peptide model system: Implications for protein stability. Proc. Natl. Acad. Sci. USA 93, 2985–2990 (1996).

    CAS  Article  Google Scholar 

  9. 9

    Fauchère, J.-L. & Pliska, V. Hydrophobic parameters of pi amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. Chim. Ther. 18, 369–375 (1983).

    Google Scholar 

  10. 10

    Radzicka, A. & Wolfenden, R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, l-octanol, and neutral aqueous solution. Biochemistry 27, 1664–1670 (1988).

    CAS  Article  Google Scholar 

  11. 11

    Kim, A. & Szoka, F.C. Amino acid side-chain contributions to free energy of transfer of tripeptides from water to octanol. Pharm. Res. 9, 504–514 (1992).

    CAS  Article  Google Scholar 

  12. 12

    Wiener, M.C. & White, S.H. Structure of a fluid dioleoylphospha tidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. Biophys. J. 61, 434–447 (1992).

    CAS  Article  Google Scholar 

  13. 13

    Brown, J.W. & Huestis, W.H. Structure and orientation of a bilayer-bound model tripeptide: A 1H NMR study. J. Phys. Chem. 97, 2967–2973 (1993).

    CAS  Article  Google Scholar 

  14. 14

    Roseman, M.A. Hydrophobicity of the peptide C=O…H-N Hydrogen-bonded Group. J. Mol. Biol. 201, 621–625 (1988).

    CAS  Article  Google Scholar 

  15. 15

    Wimley, W.C. & White, S.H. Quantitation of electrostatic and hydrophobic membrane interactions by equilibrium dialysis and reverse-phase HPLC. Anal. Biochem. 213, 213–217 (1993).

    CAS  Article  Google Scholar 

  16. 16

    Wimley, W.C. & White, S.H. Membrane partitioning: Distinguishing bilayer effects from the hydrophobic effect. Biochemistry 32, 6307–6312 (1993).

    CAS  Article  Google Scholar 

  17. 17

    Segrest, J.P. et al. The amphipathic helix in the exchangeable apolipoproteins - A review of secondary structure and function. J. Lipid Res. 33, 141–166 (1992).

    CAS  PubMed  Google Scholar 

  18. 18

    Schwyzer, R. Conformations and orientations of amphiphilic peptides induced by artificial lipid membranes: Correlations with biological activity. Chemtracts-Biochem. Mol. Biol. 3, 347–379 (1992).

    CAS  Google Scholar 

  19. 19

    Killian, J.A., Timmermans, J.W., Keur, S. & DeKruiff, B. The tryptophans of gramicidin are essential for the lipid structure modulating effect of the peptide. Biochim. Biophys. Acta 820, 154–156 (1985).

    CAS  Article  Google Scholar 

  20. 20

    Hu, W., Lee, K.C. & Cross, T.A. Tryptophans in membrane proteins -indole ring orientations and functional implications in the gramicidin channel. Biochemistry 32, 7035–7047 (1993).

    CAS  Article  Google Scholar 

  21. 21

    Koeppe, R.E., Killian, J.A. & Greathouse, D.V. Orientations of the tryptophan 9 and 11 side chains of the gramicidin channel based on deuterium nuclear magnetic resonance spectroscopy. Biophys. J. 66, 14–24 (1994).

    CAS  Article  Google Scholar 

  22. 22

    Landolt-Marticorena, C., Williams, K.A., Deber, C.M. & Reithmeier, R.A.F. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229, 602–608 (1993).

    CAS  Article  Google Scholar 

  23. 23

    Schiffer, M., Chang, C.H. & Stevens, F.J. The functions of tryptophan residues in membrane proteins. Protein Eng. 5, 213–214 (1992).

    CAS  Article  Google Scholar 

  24. 24

    Kyte, J. & Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–132 (1982).

    CAS  Article  Google Scholar 

  25. 25

    Engelman, D.M., Steitz, T.A. & Goldman, A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys, Biophys. Chem. 15, 321–353 (1986).

    CAS  Article  Google Scholar 

  26. 26

    Eisenberg, D. & McLachlan, A.D. Solvation energy in protein folding and binding. Nature 319, 199–203 (1986).

    CAS  Article  Google Scholar 

  27. 27

    Ben-Tal, N., Ben-Shaul, A., Nicholls, A. & Honig, B. Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophys. J. 70, 1803–1812 (1996).

    CAS  Article  Google Scholar 

  28. 28

    Jähnig, F. Thermodynamics and kinetics of protein incorporation into membranes. Proc. Natl. Acad. Sci. USA 80, 3691–3695 (1983).

    Article  Google Scholar 

  29. 29

    Ben-Shaul, A., Ben-Tal, N. & Honig, B. Statistical thermodynamic analysis of protein insertion into lipid membranes. Biophys. J. 71, 130–137 (1996).

    CAS  Article  Google Scholar 

  30. 30

    Peitzsch, R.M. & McLaughlin, S. Binding of acylated peptides and fatty acids to phospholipid vesicles - pertinence to myristoylated proteins. Biochemistry 32, 10436–10443 (1993).

    CAS  Article  Google Scholar 

  31. 31

    Flewelling, R.F. & Hubbell, W.L. Hydrophobic ion interactions with membranes. Thermodynamic analysis of tetraphenylphosphonium binding to vesicles. Biophys. J. 49, 531–540 (1986).

    CAS  Article  Google Scholar 

  32. 32

    Franks, N.P., Abraham, M.H. & Lieb, W.R. Molecular organization of liquid n-octanol - an x-ray diffraction analysis. J. Pharm. Sci. 82, 466–470 (1993).

    CAS  Article  Google Scholar 

  33. 33

    von Heijne, G. & Blomberg, C. Trans-membrane translocation of proteins: The direct transfer model. Eur. J. Biochem. 97, 175–181 (1979).

    CAS  Article  Google Scholar 

  34. 34

    Roseman, M.A. Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J. Mol. Biol. 200, 513–523 (1988).

    CAS  Article  Google Scholar 

  35. 35

    Thorgeirsson, T.E., Russell, C.J., King, D.S. & Shin, Y.-K. Direct determination of the membrane affinities of individual amino acids. Biochemistry 35, 1803–1809 (1996).

    CAS  Article  Google Scholar 

  36. 36

    Thorgeirsson, T.E., Yu, Y.G. & Shin, Y.-K. A limiting law for the electrostatics of the binding of polypeptides to phospholipid bilayers. Biochemistry 34, 5518–5522 (1995).

    CAS  Article  Google Scholar 

  37. 37

    Selsted, M.E., Novotny, M.J., Morris, W.L., Tang, Y.-Q., Smith, W. & Cullor, J.S. Indolicidin, a novel bactericidal tridecapeptide amide from neutrophils. J. Biol. Chem. 267, 4292–4295 (1992).

    CAS  PubMed  Google Scholar 

  38. 38

    Ladokhin, A.S., Selsted, M.E. & White, S.H. Bilayer interactions of indolicidin, a small antimicrobial peptide rich in tryptophan, proline, and basic amino acids. Biophys. J, submitted.

  39. 39

    Tretyachenko-Ladokhina, V.G., Ladokhin, A.S., Wang, L.M., Steggles, A.W. & Holloway, P.W. Amino acid substitutions in the membrane-binding domain of cytochrome b(5) alter its membrane-binding properties. Biochim. Biophys. Acta 1153, 163–169 (1993).

    CAS  Article  Google Scholar 

  40. 40

    Nakajima, K. et al. Membrane-assisted receptor subtype selection: Synthesis, membrane structure, and opioid receptor affinity of [Phe8,12]-and [Phe8,12,Lys10]-Dynorphin-(1-13)-tridecapeptide. Tetrahedron 44, 721–732 (1988).

    CAS  Article  Google Scholar 

  41. 41

    Li, S.C. & Deber, C.M. A measure of helical propensity for amino acids in membrane environments. Nature Struct. Biol. 1, 368–373 (1994).

    CAS  Article  Google Scholar 

  42. 42

    Deber, C.M. & Li, S.-C. Peptides in membranes: Helicity and hydrophobicity. Biopolymers 37, 295–318 (1995).

    CAS  Article  Google Scholar 

  43. 43

    Ben-Tal, N., Honig, B., Peitzsch, R.M., Denisov, G. & McLaughlin, S. Binding of small basic peptides to membranes containing acidic lipids: Theoretical models and experimental results. Biophys. J. 71, 561–575 (1996).

    CAS  Article  Google Scholar 

  44. 44

    Engelman, D.M. & Steitz, T.A. The spontaneous insertion of proteins into and across membranes: The helical hairpin hypothesis. Cell 23, 411–422 (1981).

    CAS  Article  Google Scholar 

  45. 45

    Mayer, L.D., Hope, M.J. & Cullis, P.R. Vesicles of variable sizes produced by a rapid extrusion procedure. Biochim. Biophys. Acta 858, 161–168 (1986).

    CAS  Article  Google Scholar 

  46. 46

    Park, K., Perczel, A. & Fasman, G.D. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. Protein Sci. 1, 1032–1049 (1992).

    CAS  Article  Google Scholar 

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Wimley, W., White, S. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Mol Biol 3, 842–848 (1996). https://doi.org/10.1038/nsb1096-842

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