Tools for Predicting Binding and Insertion of CPPs into Lipid Bilayers

  • Paulo F. Almeida
Part of the Methods in Molecular Biology book series (MIMB, volume 683)


The ability to predict properties such as peptide binding and insertion into membranes is an important and time-saving asset in the design of new cell-penetrating peptides (CPPs). Methods to predict those properties are described here, which make use of calculations performed with the Wimley–White hydrophobicity scales. In addition, electrostatic effects can be estimated in a way that provides acceptably close approximations in many cases. Finally, an estimate of the probability of insertion is also discussed. These procedures are illustrated by comparing the calculations with experiments on a few CPPs.

Key words

Binding thermodynamics Membrane insertion Interfacial hydrophobicity scale Octanol hydrophobicity scale Protein transduction domains Amphipathic peptides 



This work was supported by National Institutes of Health grant No. GM072507. I thank Steve White and Bill Wimley for their comments on the manuscript.


  1. 1.
    White, S. H., and Wimley, W. C. (1999). Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28, 319–365.CrossRefPubMedGoogle Scholar
  2. 2.
    Jaysinghe, S., Hristova, K., Wimley, W., Snider, C., and White, S. H. (2009) Membrane Protein Explorer (MPEx).
  3. 3.
    Wimley, W. C., Creamer, T. P., and White, S. H. (1996) Solvation energies of amino acid side chains and backbone in a family of host–guest pentapeptides. Biochemistry 35, 5109–5124.CrossRefPubMedGoogle Scholar
  4. 4.
    Wimley, W. C., and White, S. H. (1996) Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3, 842–848.CrossRefPubMedGoogle Scholar
  5. 5.
    Hristova, K., and White, S. H. (2005) An experiment-based algorithm for predicting the partitioning of unfolded peptides into phosphatidylcholine bilayer interfaces. Biochemistry 44, 12614–12619.CrossRefPubMedGoogle Scholar
  6. 6.
    Ladokhin, A. S., and White, S. H. (1999) Folding if amphipathic α-helices on membranes: energetics of helix formation by melittin. J. Mol. Biol. 285, 1363–1369.CrossRefPubMedGoogle Scholar
  7. 7.
    Wimley, W. C., Hristova, K., Ladokhin, A. S., Silvestro, L., Axelsen, P. H., and White, S. H. (1998) Folding of β-sheet membrane proteins: A hydrophobic hexapeptide model. J. Mol. Biol. 277, 1091–1110.CrossRefPubMedGoogle Scholar
  8. 8.
    Wieprecht, T., Apostolov, O., Beyermann, M., and Seelig, J. (1999) Thermodynamics of the R-helix-coil transition of amphipathic peptides in a membrane environment: Implications for the peptide-membrane binding equilibrium. J. Mol. Biol. 294, 785–794.CrossRefPubMedGoogle Scholar
  9. 9.
    Wieprecht, T., Apostolov, O., Beyermann, M., and Seelig, J. (2000) Interaction of a mitochondrial presequence with lipid membranes: Role of helix formation for membrane binding and perturbation. Biochemistry 39, 15297–15305.CrossRefPubMedGoogle Scholar
  10. 10.
    Klocek, G., Schulthess, T., Shai, Y., and Seelig, J. (2009) Thermodynamics of melittin binding to lipid bilayers. Aggregation and pore formation. Biochemistry 48, 2586–2596.Google Scholar
  11. 11.
    Fernandez-Vidal, M., Jayasinghe, S., Ladokhin, A. S., and White, S. H. (2007) Folding amphipathic helices into membranes: Amphiphilicity trumps hydrophobicity. J. Mol. Biol. 370, 459–470.CrossRefPubMedGoogle Scholar
  12. 12.
    Almeida, P. F., and Pokorny, A. (2009) Mechanisms of antimicrobial, cytolytic, and cell-penetrating peptides: From kinetics to thermodynamics. Biochemistry 48, 8083–8093.CrossRefPubMedGoogle Scholar
  13. 13.
    Jayasinghe, S., Hristova, K., and White, S. H. (2001) Energetics, stability, and prediction of transmembrane helices. J. Mol. Biol. 312, 927–934.CrossRefPubMedGoogle Scholar
  14. 14.
    Kim, J., Mosior, M, Chung, L., Wu, H., and McLaughlin, S. (1991) Binding of peptides with basic residues to membranes containing acidic phospholipids. Biophys. J. 60, 135–148.CrossRefPubMedGoogle Scholar
  15. 15.
    Ben-Tal, N., Honig, B., Peitzsch, R. M., Denisov, G., and McLaughlin, S. (1996) Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results. Biophys. J. 71, 561–575.CrossRefPubMedGoogle Scholar
  16. 16.
    Murray, D., Arbuzova, A., Hangyás-Mihályné, G., Gambhir, A., Ben-Tal, N., Honig, B., and McLaughlin, S. (1999) Electrostatic properties of membranes containing acidic lipids and adsorbed basic peptides: theory and experiment. Biophys. J. 77, 3176–3188.CrossRefPubMedGoogle Scholar
  17. 17.
    Mosior, M, and McLaughlin, S. (1992) Binding of basic peptides to acidic lipids in membranes: effects of inserting alanine(s) between the basic residues. Biochemistry 31, 1767–1773.CrossRefPubMedGoogle Scholar
  18. 18.
    Gregory, S. M., Cavenaugh, A., Journigan, V., Pokorny, A., and Almeida, P. F. F. (2008) A quantitative model for the all-or-none permeabilization of phospholipid vesicles by the antimicrobial peptide cecropin A. Biophys. J. 94, 1667–1680.CrossRefPubMedGoogle Scholar
  19. 19.
    Gregory, S. M., Pokorny, A., and Almeida, P. F. F (2009) Magainin 2 revisited: a test of the quantitative model for the all-or-none permeabilization of phospholipid vesicles. Biophys. J. 96, 116–131.CrossRefPubMedGoogle Scholar
  20. 20.
    Yandek, L. E., Pokorny, A., and Almeida. P. F. F. (2008) Small changes in the primary structure of transportan 10 alter the thermodynamics and kinetics of its interaction with phospholipid vesicles. Biochemistry 47, 3051–3060.CrossRefPubMedGoogle Scholar
  21. 21.
    Ladokhin, A. S., and White, S. H. (2001). Protein chemistry at membrane interfaces: non-additivity of electrostatic and hydrophobic interactions. J. Mol. Biol. 309, 543–552.CrossRefPubMedGoogle Scholar
  22. 22.
    Persson, D., Thorén, P. E., Herner, M., Lincoln, P., Nordén, B. (2003) Application of a novel analysis to measure the binding of the membrane-translocating peptide penetratin to negatively charged liposomes. Biochemistry 42, 421–429.CrossRefPubMedGoogle Scholar
  23. 23.
    Thorén, P. E. G., Persson, D., Esbjorner, E. K., Goksor, M., Lincoln, P., and Nordén, B. (2004) Membrane binding and translocation of cell-penetrating peptides. Biochemistry 43, 3471–3489.CrossRefPubMedGoogle Scholar
  24. 24.
    Ziegler, A., Blatter, X. L., Seelig, A., and Seelig, J. (2003) Protein transduction domains of HIV-1 and SIV TAT interact with charged lipid vesicles. Binding mechanism and thermodynamic analysis. Biochemistry 42, 9185–9194.CrossRefPubMedGoogle Scholar
  25. 25.
    Yandek, L. E., Pokorny, A., Florén, A., Knoelke, K., Langel, U., and Almeida, P. F. F. (2007) Mechanism of the cell-penetrating peptide transportan 10 permeation of lipid bilayers. Biophys. J. 92, 2434–2444.CrossRefPubMedGoogle Scholar
  26. 26.
    Magzoub, M., Eriksson, L. E. G., and Gräslund, A. (2002) Conformational states of the cell-penetrating peptide penetratin when interacting with phospholipid vesicles: effects of surface charge and peptide concentration. Biochim. Biophys. Acta 1563, 53–63.CrossRefPubMedGoogle Scholar
  27. 27.
    Binder, H., and Lindblom, G. (2003) Charge-dependent translocation of the trojan peptide penetratin across lipid membranes. Biophys. J. 85, 982–995.CrossRefPubMedGoogle Scholar
  28. 28.
    Tanford, C. (1991). The hydrophobic effect: formation of micelles and biological membranes. 2nd Ed., Krieger, Malabar, FL.Google Scholar
  29. 29.
    Mitchell, D. J., Kim, D. T., Steinman, L., Fathman, C. G., and Rothbard, J. B. (2000) Polyarginine enters cell more efficiently than other polycationic homopolymers. J. Pept. Res. 56, 318–325.CrossRefPubMedGoogle Scholar
  30. 30.
    Sakai, N., and Matile, S. (2003) Anion-mediated transfer of polyarginine across liquid and bilayer membranes. J. Am. Chem. Soc. 125, 14348–14356.CrossRefPubMedGoogle Scholar
  31. 31.
    Sakai, N., Takeuchi, T., Futaki, S., and Matile, S. (2005) Direct observation of anion mediated translocation of fluorescent oligoarginine carriers into and across bulk liquid and anionic bilayer membranes. ChemBioChem 6, 114–122.CrossRefPubMedGoogle Scholar
  32. 32.
    Rothbard, J. B., Jessop, T. C., Lewis, R. S., Murray, B. A., and Wender, P. A. (2004) Role of membrane potential and hydrogen bonding in the mechanism of translocation of guanidinium-rich peptides into cells. J. Am. Chem. Soc. 126, 9506–9507.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Paulo F. Almeida
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of North Carolina WilmingtonWilmingtonUSA

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