Monte Carlo simulations of peptide-membrane interactions with the MCPep web server

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Gofman, Yana ^a,b   Haliloglu, Turkan ^c,d   Ben Tal, Nir ^b  

^a INSTITUTE OF MATERIALS RESEARCH   (Germany)

^b TEL AVIV UNIVERSITY   (Israel)

^c Polymer Research Center   (Turkey)

^d BOGAZICI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; MEMBRANE LIPID;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONFORMATIONAL TRANSITION; ENERGY; LIPID COMPOSITION; MONTE CARLO METHOD; PEPTIDE MEMBRANE INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN LIPID INTERACTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SIMULATION; SURFACE CHARGE; WEB SERVER;

AMINO ACIDS; COMPUTER SIMULATION; INTERNET; MEMBRANE LIPIDS; MONTE CARLO METHOD; PEPTIDES; PROTEIN CONFORMATION; SOFTWARE; USER-COMPUTER INTERFACE; VESICLE-ASSOCIATED MEMBRANE PROTEIN 2;

EID: 84864446755     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks577     Document Type: Article

References (36)

1. Singer, S.J. and Nicolson, G.L. (1972) The fluid mosaic model of the structure of cell membranes. Science, 175, 720-731.
2. Kessel, A. and Ben-Tal, N. (2010) Introduction to Proteins: Structure, Function and Motion. CRC Press, Boca Raton, Florida, pp. 450-463.
3. Lindahl, E. and Sansom, M.S. (2008) Membrane proteins: molecular dynamics simulations. Curr. Opin. Struct. Biol., 18, 425-431.
4. Roux, B. and Schulten, K. (2004) Computational studies of membrane channels. Structure, 12, 1343-1351.
5. Bond, P.J. and Khalid, S. (2010) Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations. Protein Pept. Lett., 17, 1313-1327.
6. Shental-Bechor, D., Haliloglu, T. and Ben-Tal, N. (2007) Interactions of cationic-hydrophobic peptides with lipid bilayers: a Monte Carlo simulation method. Biophys. J., 93, 1858-1871.
7. Gordon-Grossman, M., Gofman, Y., Zimmermann, H., Frydman, V., Shai, Y., Ben-Tal, N. and Goldfarb, D. (2009) A combined pulse EPR and Monte Carlo simulation study provides molecular insight on peptide-membrane interactions. J. Phys. Chem. B., 113, 12687-12695.
8. Gofman, Y., Linser, S., Rzeszutek, A., Shental-Bechor, D., Funari, S.S., Ben-Tal, N. and Willumeit, R. (2010) Interaction of an antimicrobial peptide with membranes: experiments and simulations with NKCS. J. Phys. Chem. B., 114, 4230-4237.
9. Dorosz, J., Gofman, Y., Kolusheva, S., Otzen, D., Ben-Tal, N., Nielsen, N.C. and Jelinek, R. (2010) Membrane interactions of novicidin, a novel antimicrobial peptide: phosphatidylglycerol promotes bilayer insertion. J. Phys. Chem. B., 114, 11053-11060.
10. Kessel, A., Shental-Bechor, D., Haliloglu, T. and Ben-Tal, N. (2003) Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta. Biophys. J., 85, 3431-3444.
11. Merklinger, E., Gofman, Y., Kedrov, A., Driessen, A.J.M., Ben-Tal, N., Shai, Y. and Rapaport, D. (2011) Membrane-integration of a mitochondrial signal-anchored protein does not require additional proteinaceous factors. Biochem. J., 442, 381-389.
12. Kessel, A. and Ben-Tal, N. (2002) In: Simon, S.A. and McInotosh, T.J. (eds), Current Topics in Membranes, Vol. 52. Academic Press, San Diego, CA, pp. 205-253.
13. Ben-Tal, N., Ben-Shaul, A., Nicholls, A. and Honig, B. (1996) Free-energy determinants of alpha-helix insertion into lipid bilayers. Biophys. J., 70, 1803-1812.
14. Bahar, I., Kaplan, M. and Jernigan, R.L. (1997) Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins, 29, 292-308.
15. Fattal, D.R. and Ben-Shaul, A. (1993) A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch. Biophys. J., 65, 1795-1809.
16. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H. and Teller, E. (1953) Equation of state calculations by fast computing machines. J. Chem. Phys., 21, 1087-1092.
17. Marsh, D. (2008) Energetics of hydrophobic matching in lipid-protein interactions. Biophys. J., 94, 3996-4013.
18. Krivov, G.G., Shapovalov, M.V. and Dunbrack, R.L. Jr (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77, 778-795.
19. Shental-Bechor, D., Kirca, S., Ben-Tal, N. and Haliloglu, T. (2005) Monte Carlo studies of folding, dynamics, and stability in alpha-helices. Biophys. J., 88, 2391-2402.
20. Takamori, S., Holt, M., Stenius, K., Lemke, E.A., Gronborg, M., Riedel, D., Urlaub, H., Schenck, S., Brugger, B., Ringler, P. et al. (2006) Molecular anatomy of a trafficking organelle. Cell, 127, 831-846.
21. Jahn, R. and Scheller, R.H. (2006) SNAREs-engines for membrane fusion. Nat. Rev. Mol. Cell. Biol., 7, 631-643.
22. Parpura, V. and Mohideen, U. (2008) Molecular form follows function: (un)snaring the SNAREs. Trends Neurosci., 31, 435-443.
23. Wiederhold, K. and Fasshauer, D. (2009) Is assembly of the SNARE complex enough to fuel membrane fusion? J. Biol. Chem., 284, 13143-13152.
24. Li, F., Pincet, F., Perez, E., Eng, W.S., Melia, T.J., Rothman, J.E. and Tareste, D. (2007) Energetics and dynamics of SNAREpin folding across lipid bilayers. Nat. Struct. Mol. Biol., 14, 890-896.
25. Marsh, D. (2006) Elastic curvature constants of lipid monolayers and bilayers. Chem. Phys. Lipids., 144, 146-159.
26. Haleva, E., Ben-Tal, N. and Diamant, H. (2004) Increased concentration of polyvalent phospholipids in the adsorption domain of a charged protein. Biophys. J., 86, 2165-2178.
27. May, S., Harries, D. and Ben-Shaul, A. (2000) Lipid demixing and protein-protein interactions in the adsorption of charged proteins on mixed membranes. Biophys. J., 79, 1747-1760.
28. Heimburg, T., Angerstein, B. and Marsh, D. (1999) Binding of peripheral proteins to mixed lipid membranes: effect of lipid demixing upon binding. Biophys. J., 76, 2575-2586.
29. Sitkoff, D., Ben-Tal, N. and Honig, B. (1996) Calculation of alkane to water solvation free energies using continuum solvent models. J. Phys. Chem., 100, 2744-2752.
30. Kessel, A., Cafiso, D.S. and Ben-Tal, N. (2000) Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects. Biophys. J., 78, 571-583.
31. Kessel, A., Schulten, K. and Ben-Tal, N. (2000) Calculations suggest a pathway for the transverse diffusion of a hydrophobic peptide across a lipid bilayer. Biophys. J., 79, 2322-2330.
32. Bechor, D. and Ben-Tal, N. (2001) Implicit solvent model studies of the interactions of the influenza hemagglutinin fusion peptide with lipid bilayers. Biophys. J., 80, 643-655.
33. Bransburg-Zabary, S., Kessel, A., Gutman, M. and Ben-Tal, N. (2002) Stability of an ion channel in lipid bilayers: implicit solvent model calculations with gramicidin. Biochemistry, 41, 6946-6954.
34. Petrey, D. and Honig, B. (2005) Protein structure prediction: inroads to biology. Mol. Cell., 20, 811-819.
35. Schushan, M. and Ben-Tal, N. (2010) Introduction to Protein Structure Prediction. John Wiley & Sons, Inc., Hoboken, NJ, pp. 369-401.
36. de Planque, M.R. and Killian, J.A. (2003) Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol. Membr. Biol., 20, 271-284.