Voltage-dependent energetics of alamethicin monomers in the membrane

Biophysical Chemistry

Volumn 122, Issue 1, 2006, Pages 50-57

  Mottamal, Madhusoodanan ^a   Lazaridis, Themis ^a  

^a CITY COLLEGE OF NEW YORK   (United States)

Author keywords

Alamethicin; Implicit membrane model; Transmembrane potential; Voltage dependent gating

Indexed keywords

ALAMETHICIN; MONOMER;

AMINO TERMINAL SEQUENCE; ARTICLE; CHANNEL GATING; MEMBRANE BINDING; MEMBRANE MODEL; MEMBRANE POTENTIAL; PRIORITY JOURNAL; PROTEIN FUNCTION;

ALAMETHICIN; COMPUTER SIMULATION; LIPID BILAYERS; MEMBRANE LIPIDS; MEMBRANE POTENTIALS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 33745002504     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.02.005     Document Type: Article

References (47)

1. Sansom M.S. The biophysics of peptide models of ion channels. Prog. Biophys. Mol. Biol. 55 (1991) 139-235
2. Cafiso D.S. Alamethicin: a peptide model for voltage gating and protein membrane interactions. Annu. Rev. Biophys. Biomol. Struct. 23 (1994) 141-165
3. Fox Jr. R.O., and Richards F.M. A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5 A resolution. Nature 300 (1982) 325-330
4. Banerjee U., Zidovetzki R., Birge R.R., and Chan S.I. Interaction of alamethicin with lecithin bilayers: a 31P and 2H NMR study. Biochemistry 24 (1985) 7621-7627
5. North C.L., Barranger-Mathys M., and Cafiso D.S. Membrane orientation of the N-terminal segment of alamethicin determined by solid-state 15N NMR. Biophys. J. 69 (1995) 2392-2397
6. Huang H.W., and Wu Y. Lipid-alamethicin interactions influence alamethicin orientation. Biophys. J. 60 (1991) 1079-1087
7. Sansom M.S., Kerr I.D., and Mellor I.R. Ion channels formed by amphipathic helical peptides, a molecular modeling study. Eur. Biophys. J. 20 (1991) 229-240
8. Duclohier H., and Wroblewski H. Voltage-dependent pore formation and antimicrobial activity by alamethicin and analogues. J. Membr. Biol. 184 (2001) 1-12
9. Sansom M.S., Tieleman D.P., and Berendsen H.J. The mechanism of channel formation by alamethicin as viewed by molecular dynamics simulations. Novartis Found. Symp. 225 (1999) 128-141 (discussion 141-145)
10. Sansom M.S., Tieleman D.P., Forrest L.R., and Berendsen H.J. Molecular dynamics simulation of membranes with embedded proteins and peptides: porin, alamethicin and influenza virus M2. Biochem. Soc. Trans. 26 (1998) 438-443
11. Tieleman D.P., Berendsen H.J., and Sansom M.S. Surface binding of alamethicin stabilizes its helical structure: molecular dynamics simulations. Biophys. J. 76 (1999) 3186-3191
12. Tieleman D.P., Berendsen H.J., and Sansom M.S. An alamethicin channel in a lipid bilayer: molecular dynamics simulations. Biophys. J. 76 (1999) 1757-1769
13. Tieleman D.P., Berendsen H.J., and Sansom M.S. Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces. Biophys. J. 80 (2001) 331-346
14. Tieleman D.P., Borisenko V., Sansom M.S.P., and Woolley G.A. Understanding pH dependent selectivity of alamethicin K18 channels by computer simulation. Biophys. J. 84 (2003) 1464-1469
15. Tieleman D.P., Breed J., Berendsen H.J., and Sansom M.S. Alamethicin channels in membrane: molecular dynamics simulations. Faraday Discuss. 111 (1998) 209-223 (discussion 225-246)
16. Tieleman D.P., Forrest L.R., Sansom M.S., and Berendsen H.J. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations. Biochemistry 37 (1998) 17554-17561
17. Tieleman D.P., Hess B., and Sansom M.S. Analysis and evaluation of channel models: simulations of alamethicin. Biophys. J. 83 (2002) 2393-2407
18. Tieleman D.P., Sansom M.S., and Berendsen H.J. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. Biophys. J. 76 (1999) 40-49
19. Kessel A., Cafiso D.S., and Ben-Tal N. Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys. J. 78 (2000) 571-583
20. Lazaridis T. Effective energy function for proteins in lipid membranes. Proteins 52 (2003) 176-192
21. Lazaridis T., and Karplus M. Effective energy function for proteins in solution. Proteins 35 (1999) 133-152
22. Lazaridis T., and Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278 (1997) 1928-1931
23. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4 (1983) 187-217
24. Neria E., Fischer S., and Karplus M. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105 (1996) 1902-1921
25. Lazaridis T., and Karplus M. Thermodynamics of protein folding: a microscopic view. Biophys. Chem. 100 (2003) 367-395
26. Masunov A., and Lazaridis T. Potentials of mean force between ionizable amino acid sidechains in aqueous solution. J. Am. Chem. Soc. 125 (2003) 1722-1730
27. Wimley W.C., and White S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3 (1996) 842-848
28. Radzicka A., and Wolfenden R. Comparing the polarities of the amino acids: sidechain distribution coefficients between the vapor phase, cyclohexane, 1-octanol and neutral aqueous solution. Biochemistry 27 (1988) 1664-1670
29. Weiner M.C., and White S.H. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of X-ray and neutron diffraction data II. Distribution and packing of terminal methyl groups. Biophys. J. 61 (1992) 428-433
30. Lazaridis T. Implicit solvent simulations of peptide interactions with anionic lipid membranes. Proteins 58 (2005) 518-527
31. Lazaridis T. Structural determinants of transmembrane beta-barrels. J. Chem. Theory Comput. 1 (2005) 716-722
32. Roux B. Influence of membrane potential on the free energy of an intrinsic protein. Biophys. J. 73 (1997) 2980-2989
33. Stankowski S., and Schwarz G. Lipid dependence of peptide-membrane interactions. FEBS Lett. 250 (1989) 556-560
34. Biggin P.C., Breed J., Son H.S., and Sansom M.S. Simulation studies of alamethicin bilayer interactions. Biophys. J. 72 (1997) 627-636
35. Schwarz G., Stankowski S., and Rizzo V. Thermodynamic analysis of incorporation and aggregation in a membrane: application to the pore-forming peptide alamethicin. Biochim. Biophys. Acta 861 (1986) 141-151
36. Chen F., Lee M., and Huang H.W. Sigmoidal concentration dependence of antimicrobial peptide activities: a case study on alamethicin. Biophys. J. 82 (2002) 908-914
37. Barranger-Mathys M., and Cafiso D.S. Membrane structure of voltage-gated channel forming peptides by site-directed spin-labeling. Biochemistry 35 (1996) 498-505
38. Bak M., Bywater R.P., Hohwy M., Thomsen J.K., Adelhorst K., Jakobsen H.J., Sorensen O.W., and Nielsen N.C. Conformation of alamethicin in oriented phospholipid bilayers by 15N solid-state nuclear magnetic resonance. Biophys. J. 81 (2001) 1684-1698
39. Dave P.C., Billington E., Pan Y.-L., and Straus S.K. Interaction of alamethicin with ether-linked phospholipid bilayers: oriented circular dichroism, 31P solid-state NMR, and differential scanning calorimetry studies. Biophys. J. 89 (2005) 2434-2442
40. Bechinger B., Skladnev D.A., Orgel A., Li X., Rogozhkina E.V., Ovchinnikova T.V., O'Neil J.D.J., and Raap J. 15N and 31P solid-state NMR investigations on the orientation of zervamicin II and alamethicin in phosphatidylcholine membranes. Biochemistry 40 (2001) 9428-9437
41. Chen F.-Y., Lee M.-T., and Huang H.W. Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation. Biophys. J. 84 (2003) 3751-3758
42. Lewis J.R., and Cafiso D.S. Correlation between the free energy of a channel-forming voltage gated peptide and the spontaneous curvature of bilayer lipids. Biochemistry 38 (1999) 5932-5938
43. Bransburg-Zabary S., Kessel A., Gutman M., and Ben-Tal N. Stability of an ion channel in lipid bilayers: implicit solvent model calculations with gramicidin. Biochemistry 41 (2002) 6946-6954
44. Vodyanoy I., Hall J.E., and Balasubramaniam T.M. Alamethicin-induced current-voltage curve asymmetry in lipid bilayers. Biophys. J. 42 (1983) 71-82
45. Molle G., Dugast J.-Y., Spach G., and Duclohier H. Ion channel stabilization of synthetic alamethicin analogs by rings of inter-helix h-bonds. Biophys. J. 70 (1996) 1669-1675
46. Kessel A., Tieleman D.P., and Ben-Tal N. Implicit solvent model estimates the stability of model structures of the alamethicin channel. Eur. Biophys. J. 33 (2004) 16-28
47. Huang H.W. Deformation free energy of bilayer membrane and its effect on gramicidin channel lifetime. Biophys. J. 50 (1986) 1061-1071