Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 2000 Nov;79(5):2322–2330. doi: 10.1016/S0006-3495(00)76478-2

Calculations suggest a pathway for the transverse diffusion of a hydrophobic peptide across a lipid bilayer.

A Kessel 1, K Schulten 1, N Ben-Tal 1
PMCID: PMC1301120  PMID: 11053112

Abstract

Alamethicin is a hydrophobic antibiotic peptide 20 amino acids in length. It is predominantly helical and partitions into lipid bilayers mostly in transmembrane orientations. The rate of the peptide transverse diffusion (flip-flop) in palmitoyl-oleyl-phosphatidylcholine vesicles has been measured recently and the results suggest that it involves an energy barrier, presumably due to the free energy of transfer of the peptide termini across the bilayer. We used continuum-solvent model calculations, the known x-ray crystal structure of alamethicin and a simplified representation of the lipid bilayer as a slab of low dielectric constant to calculate the flip-flop rate. We assumed that the lipids adjust rapidly to each configuration of alamethicin in the bilayer because their motions are significantly faster than the average peptide flip-flop time. Thus, we considered the process as a sequence of discrete peptide-membrane configurations, representing critical steps in the diffusion, and estimated the transmembrane flip-flop rate from the calculated free energy of the system in each configuration. Our calculations indicate that the simplest possible pathway, i.e., the rotation of the helix around the bilayer midplane, involving the simultaneous burial of the two termini in the membrane, is energetically unfavorable. The most plausible alternative is a two-step process, comprised of a rotation of alamethicin around its C-terminus residue from the initial transmembrane orientation to a surface orientation, followed by a rotation around the N-terminus residue from the surface to the final reversed transmembrane orientation. This process involves the burial of one terminus at a time and is much more likely than the rotation of the helix around the bilayer midplane. Our calculations give flip-flop rates of approximately 10(-7)/s for this pathway, in accord with the measured value of 1.7 x 10(-6)/s.

Full Text

The Full Text of this article is available as a PDF (208.3 KB).

Selected References

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

  1. Ashcroft R. G., Coster H. G., Smith J. R. The molecular organisation of bimolecular lipid membranes. The dielectric structure of the hydrophilic/hydrophobic interface. Biochim Biophys Acta. 1981 Apr 22;643(1):191–204. doi: 10.1016/0005-2736(81)90232-7. [DOI] [PubMed] [Google Scholar]
  2. Banerjee U., Chan S. I. Structure of alamethicin in solution: nuclear magnetic resonance relaxation studies. Biochemistry. 1983 Jul 19;22(15):3709–3713. doi: 10.1021/bi00284a026. [DOI] [PubMed] [Google Scholar]
  3. Barranger-Mathys M., Cafiso D. S. Collisions between helical peptides in membranes monitored using electron paramagnetic resonance: evidence that alamethicin is monomeric in the absence of a membrane potential. Biophys J. 1994 Jul;67(1):172–176. doi: 10.1016/S0006-3495(94)80466-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Barranger-Mathys M., Cafiso D. S. Membrane structure of voltage-gated channel forming peptides by site-directed spin-labeling. Biochemistry. 1996 Jan 16;35(2):498–505. doi: 10.1021/bi951985d. [DOI] [PubMed] [Google Scholar]
  5. Ben-Shaul A., Ben-Tal N., Honig B. Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes. Biophys J. 1996 Jul;71(1):130–137. doi: 10.1016/S0006-3495(96)79208-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ben-Tal N., Ben-Shaul A., Nicholls A., Honig B. Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophys J. 1996 Apr;70(4):1803–1812. doi: 10.1016/S0006-3495(96)79744-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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. 1996 Aug;71(2):561–575. doi: 10.1016/S0006-3495(96)79280-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ben-Tal N., Sitkoff D., Bransburg-Zabary S., Nachliel E., Gutman M. Theoretical calculations of the permeability of monensin-cation complexes in model bio-membranes. Biochim Biophys Acta. 2000 Jun 1;1466(1-2):221–233. doi: 10.1016/s0005-2736(00)00156-5. [DOI] [PubMed] [Google Scholar]
  9. Biggin P. C., Breed J., Son H. S., Sansom M. S. Simulation studies of alamethicin-bilayer interactions. Biophys J. 1997 Feb;72(2 Pt 1):627–636. doi: 10.1016/s0006-3495(97)78701-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cafiso D. S. Alamethicin: a peptide model for voltage gating and protein-membrane interactions. Annu Rev Biophys Biomol Struct. 1994;23:141–165. doi: 10.1146/annurev.bb.23.060194.001041. [DOI] [PubMed] [Google Scholar]
  11. Engelman D. M., Steitz T. A., Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 1986;15:321–353. doi: 10.1146/annurev.bb.15.060186.001541. [DOI] [PubMed] [Google Scholar]
  12. Engelman D. M., Steitz T. A. The spontaneous insertion of proteins into and across membranes: the helical hairpin hypothesis. Cell. 1981 Feb;23(2):411–422. doi: 10.1016/0092-8674(81)90136-7. [DOI] [PubMed] [Google Scholar]
  13. Esposito G., Carver J. A., Boyd J., Campbell I. D. High-resolution 1H NMR study of the solution structure of alamethicin. Biochemistry. 1987 Feb 24;26(4):1043–1050. doi: 10.1021/bi00378a010. [DOI] [PubMed] [Google Scholar]
  14. Essmann U., Berkowitz M. L. Dynamical properties of phospholipid bilayers from computer simulation. Biophys J. 1999 Apr;76(4):2081–2089. doi: 10.1016/S0006-3495(99)77364-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fattal D. R., Ben-Shaul A. A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch. Biophys J. 1993 Nov;65(5):1795–1809. doi: 10.1016/S0006-3495(93)81249-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Fox R. O., Jr, Richards F. M. A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution. Nature. 1982 Nov 25;300(5890):325–330. doi: 10.1038/300325a0. [DOI] [PubMed] [Google Scholar]
  17. Huang H. W., Wu Y. Lipid-alamethicin interactions influence alamethicin orientation. Biophys J. 1991 Nov;60(5):1079–1087. doi: 10.1016/S0006-3495(91)82144-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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. 1989 Apr 18;28(8):3421–3437. doi: 10.1021/bi00434a042. [DOI] [PubMed] [Google Scholar]
  19. Jayasinghe S., Barranger-Mathys M., Ellena J. F., Franklin C., Cafiso D. S. Structural features that modulate the transmembrane migration of a hydrophobic peptide in lipid vesicles. Biophys J. 1998 Jun;74(6):3023–3030. doi: 10.1016/S0006-3495(98)78010-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jähnig F. Thermodynamics and kinetics of protein incorporation into membranes. Proc Natl Acad Sci U S A. 1983 Jun;80(12):3691–3695. doi: 10.1073/pnas.80.12.3691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kessel A., Cafiso D. S., Ben-Tal N. Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys J. 2000 Feb;78(2):571–583. doi: 10.1016/S0006-3495(00)76617-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lewis J. R., Cafiso D. S. Correlation between the free energy of a channel-forming voltage-gated peptide and the spontaneous curvature of bilayer lipids. Biochemistry. 1999 May 4;38(18):5932–5938. doi: 10.1021/bi9828167. [DOI] [PubMed] [Google Scholar]
  23. Milik M., Skolnick J. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins. 1993 Jan;15(1):10–25. doi: 10.1002/prot.340150104. [DOI] [PubMed] [Google Scholar]
  24. North C. L., Barranger-Mathys M., Cafiso D. S. Membrane orientation of the N-terminal segment of alamethicin determined by solid-state 15N NMR. Biophys J. 1995 Dec;69(6):2392–2397. doi: 10.1016/S0006-3495(95)80108-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schwarz G., Stankowski S., Rizzo V. Thermodynamic analysis of incorporation and aggregation in a membrane: application to the pore-forming peptide alamethicin. Biochim Biophys Acta. 1986 Sep 25;861(1):141–151. doi: 10.1016/0005-2736(86)90573-0. [DOI] [PubMed] [Google Scholar]
  26. Tank D. W., Wu E. S., Meers P. R., Webb W. W. Lateral diffusion of gramicidin C in phospholipid multibilayers. Effects of cholesterol and high gramicidin concentration. Biophys J. 1982 Nov;40(2):129–135. doi: 10.1016/S0006-3495(82)84467-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tieleman D. P., Berendsen H. J., Sansom M. S. Surface binding of alamethicin stabilizes its helical structure: molecular dynamics simulations. Biophys J. 1999 Jun;76(6):3186–3191. doi: 10.1016/S0006-3495(99)77470-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Tieleman D. P., Sansom M. S., Berendsen H. J. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. Biophys J. 1999 Jan;76(1 Pt 1):40–49. doi: 10.1016/S0006-3495(99)77176-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. White S. H., Wimley W. C. Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct. 1999;28:319–365. doi: 10.1146/annurev.biophys.28.1.319. [DOI] [PubMed] [Google Scholar]
  30. Wilson M. A., Pohorille A. Mechanism of unassisted ion transport across membrane bilayers. J Am Chem Soc. 1996 Jul 17;118(28):6580–6587. doi: 10.1021/ja9540381. [DOI] [PubMed] [Google Scholar]
  31. Yang A. S., Honig B. Free energy determinants of secondary structure formation: I. alpha-Helices. J Mol Biol. 1995 Sep 22;252(3):351–365. doi: 10.1006/jmbi.1995.0502. [DOI] [PubMed] [Google Scholar]
  32. Yee A. A., O'Neil J. D. Uniform 15N labeling of a fungal peptide: the structure and dynamics of an alamethicin by 15N and 1H NMR spectroscopy. Biochemistry. 1992 Mar 31;31(12):3135–3143. doi: 10.1021/bi00127a014. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES