Molecular dynamics simulation analyses of viral fusion peptides in membranes prone to phase transition: effects on membrane curvature, phase behavior and lipid-water interface destabilization

Manami  Nishizawa; Kazuhisa  Nishizawa

doi:10.4236/jbpc.2010.11003

Manami Nishizawa, Kazuhisa Nishizawa^*

Abstract: To gain insight into the atomistic details of membrane fusion induced by fusogenic peptides, molecular dynamic simulations of synthetic peptides, derived from viral fusion proteins, contained in lipid bilayers were performed. A 20 amino acid peptide from the N-terminus of the influenza HA fusion peptide (WT20) assumed the oblique orientation at the interface between water and the membrane made up of dipalmitoylphosphatidylcholine (DPPC)/palmitic acid (PA), as reported previously for different membranes. Simulations of WT20 embedded in bilayer membranes made up of dioleoylphos-phatidylethanolamine (DOPE) and DPPC/PA showed a positive curvature-inducing effect, whereas WT20 showed a negative curvature-inducing effect on a DPPC bilayer. In phase re-constitution analyses starting from a random mixture of DPPC, PA and water molecules, WT20 weakly stabilized an inverted hexagonal phase. In the latter analyses WT20 preferentially assumed a transmembrane orientation as opposed to the interfacial orientation, regardless of the phase to which the system settled (lamellar vs. inverted hexagonal). In another set of analyses using systems containing a water layer between the apposed DPPC/PA (and DOPE) monolayers, the behavior of WT20 during the formation of an intermembrane connection (or stalk) was examined. Comparison among the mutants supports a view that the oblique orientation of WT20 facilitates the perturbation of the lipid-water interface and the stalk formation. Taken together, these results imply that the influenza HA fusion peptide can have substantial effects on the membrane curvature and can assume a wide range of orientation/position in membranes depending on the local environment of the lipid/water system. Its movability and oblique orientation appear to be associated with its ability to perturb membrane/water interfaces.

Keywords: Molecular Simulation; Fusion Peptide; Stalk Formation; Lipid Mixing; Hemifusion

Cite this paper: nullNishizawa, M. and Nishizawa, K. (2010) Molecular dynamics simulation analyses of viral fusion peptides in membranes prone to phase transition: effects on membrane curvature, phase behavior and lipid-water interface destabilization. Journal of Biophysical Chemistry, 1, 19-32. doi: 10.4236/jbpc.2010.11003.

References

[1] Wilson, I.A., Skehel, J.J. and Wiley, D.C. (1981) Struc-ture of the haemagglutinin membrane glycoprotein of in-fluenza virus at 3 A resolution. Nature, 289(5796), 366-373.

[2] Carr, C.M. and Kim, P.S. (1993) A spring-loaded me-chanism for the conformational change of influenza he-magglutinin. Cell, 73(4), 823-832.

[3] Skehel, J.J. and Wiley, D.C. (2000) Receptor binding and membrane fusion in virus entry: The influenza hemag-glutinin. Annual Review Biochemistry, 69, 531-569.

[4] Tamm, L.K., Crane, J. and Kiessling, V. (2003) Mem-brane fusion: A structural perspective on the interplay of lipids and proteins. Current Opinion in Structural Biology, 13, 453-466.

[5] Earp, L.J., Delos, S.E., Park, H.E. and White, J.M. (2005) The many mechanisms of viral membrane fusion proteins. Current Topics in Microbiology and Immunology, 285, 25-66.

[6] Chan, D.C., Fass, D., Berger, J.M. and Kim, P.S. (1997) Core structure of gp41 from the HIV envelope glyco-protein. Cell, 89(2), 263-273.

[7] Gething, M.J., Doms, R.W., York, D. and White, J. (1986) Studies on the mechanism of membrane fusion: Site- specific mutagenesis of the hemagglutinin of influenza virus. The Journal of Cell Biology, 102(1), 11-23.

[8] Cross, K.J., Wharton, S.A., Skehel, J.J., Wiley, D.C. and Steinhauer, D.A. (2001) Studies on influenza haemagglu-tinin fusion peptide mutants generated by reverse genetics. EMBO Journal, 20, 4432-4442.

[9] Chen, J., Skehel, J.J. and Wiley, D.C. (1999) N- and C-terminal residues combine in the fusion-pH influenza hemagglutinin HA(2) subunit to form an N cap that ter-minates the triple-stranded coiled coil. Proceedings of the National Academy of Sciences USA, 96, 8967-8972.

[10] Gallaher, W.R. (1987) Detection of a fusion peptide se-quence in the transmembrane protein of human immu-nodeficiency virus. Cell, 50(3), 327-328.

[11] Durell, S.R., Martin, I., Ruysschaert, J.M., Shai, Y. and Blumenthal, R. (1997) What studies of fusion peptides tell us about viral envelope glycoprotein-mediated membrane fusion. Molecular Membrane Biology, 14(3), 97- 112.

[12] Bosch, M.L., Earl, P.L., Fargnoli, K., Picciafuoco, S., Giombini, F., Wong-Staal, F. and Franchini, G. (1989) Identification of the fusion peptide of primate immuno-deficiency viruses. Science, 244(4905), 694-697.

[13] Dürrer, P., Galli, C., Hoenke, S., Corti, C., Glück, R., Vorherr, T. and Brunner, J. (1996) H+-induced membrane insertion of influenza virus hemagglutinin involves the HA2 amino-terminal fusion peptide but not the coiled coil region. The Journal of Biological Chemistry, 271(23), 13417-13421.

[14] Harter, C., James, P., B?chi, T., Semenza, G. and Brunner, J. (1989) Hydrophobic binding of the ectodomain of in-fluenza hemagglutinin to membranes occurs through the “fusion peptide”. The Journal of Biological Chemistry, 264(11), 6459-6464.

[15] Stegmann, T., Delfino, J.M., Richards, F.M. and Helenius, A. (1991) The HA2 subunit of influenza hemagglutinin inserts into the target membrane prior to fusion. The Journal of Biological Chemistry, 266, 18404-18410.

[16] Lear, J.D. and DeGrado, W.F. (1987) Membrane binding and conformational properties of peptides representing the NH2 terminus of influenza HA-2. The Journal of Bi-ological Chemistry, 262(14), 6500-6505.

[17] Murata, M., Takahashi, S., Kagiwada, S., Suzuki, A. and Ohnishi, S. (1992) pH-dependent membrane fusion and vesiculation of phospholipid large unilamellar vesicles induced by amphiphilic anionic and cationic peptides. Biochemistry, 31(7), 1986-1992.

[18] Wharton, S.A., Martin, S.R., Ruigrok, R.W., Skehel, J.J. and Wiley, D.C. (1988) Membrane fusion by peptide analogues of influenza virus haemagglutinin. Journal of General Virology, 69, 1847-1857.

[19] Burger, K.N., Wharton, S.A., Demel, R.A. and Verkleij, A.J. (1991) The interaction of synthetic analogs of the N-terminal fusion sequence of influenza virus with a lipid monolayer. Comparison of fusion-active and fu-sion-defective analogs. Biochimica et Biophysica Acta, 1065(2), 121-129.

[20] Soltesz, S.A. and Hammer, D.A. (1997) Lysis of large unilamellar vesicles induced by analogs of the fusion peptide of influenza virus hemagglutinin. Journal of Colloid and Interface Science, 186(2), 399-409.

[21] Epand, R.F., Macosko, J.C., Russel, C.J., Shin, Y.-K. and Epand, R.M. (1999) The ectodomain of HA2 of influenza virus promotes rapid pH dependent membrane fusion. Journal of Molecular Biology, 286(2), 489-503.

[22] Tamm, L.K. and Han, X. (2000) Viral fusion peptides: A tool set to disrupt and connect biological membranes. Bioscience Reports, 20(6), 501-518.

[23] Zhelev, D.V., Stoicheva, N., Scherrer, P. and Needham, D. (2001) Interaction of synthetic HA2 influenza fusion peptide analog with model membranes. Biophysical Journal, 81(1), 285-304.

[24] Nieva, J.L. and Agirre, A. (2003) Are fusion peptides a good model to study viral cell fusion? Biochimica et Bi-ophysica Acta, 1614(1), 104-115.

[25] Rafalski, M., Lear, J.D. and DeGrado, W.F. (1990) Phospholipid interactions of synthetic peptides representing the N-terminus of HIV gp41. Biochemistry, 29(34), 7917-7922.

[26] Nieva, J.L., Nir, S., Muga, A., Goni, F.M. and Wilschut, J. (1994) Interaction of the HIV-1 fusion peptide with phospholipid vesicles: Different structural requirements for fusion and leakage. Biochemistry, 33(11), 3201-3209.

[27] Brasseur, R., Lorge, P., Goormaghtigh, E., Ruysschaert, J.M., Espion, D. and Burny, A. (1998) The mode of in-sertion of the paramyxovirus F1 N-terminus into lipid matrix, an initial step in host cell/virus fusion. Virus Genes, 1(4), 325-332.

[28] Martin, I., Dubois, M.C., Defrise-Quertain, F., Saermark, T., Burny, A., Brasseur, R. and Ruysschaert, J.M. (1994) Correlation between fusogenicity of synthetic modified peptides corresponding to the NH2-terminal extremity of simian immunodeficiency virus gp32 and their mode of insertion into the lipid bilayer: An infrared spectroscopy study. The Journal of Virology, 68, 1139-1148.

[29] Martin, I., Schaal, H., Scheid, A. and Ruysschaert, J.M. (1996) Lipid membrane fusion induced by the human immunodeficiency virus type 1 gp41 N-terminal extremity is determined by its orientation in the lipid bilayer. The Journal of Virology, 70, 298-304.

[30] Lüneberg, J., Martin, I., Nüssler, F., Ruysschaert, J.M. and Herrmann, A. (1995) Structure and topology of the influenza virus fusion peptide in lipid bilayers. The Journal of Biological Chemistry, 270(46), 27606-27614.

[31] Han, X., Bushweller, J.H., Cafiso, D.S. and Tamm, L.K. (2001) Membrane structure and fusion-triggering con-formational change of the fusion domain from influenza hemagglutinin. Nature Structural Biology, 8(8), 715-720.

[32] Han, X. and Tamm, L.K. (2000) A host-guest system to study structure-function relationships of membrane fusion peptides. Proceedings of the National Academy of Sciences USA, 97(24), 13097-13102.

[33] Li, Y., Han, X., Lai, A.L., Bushweller, J.H., Cafiso, D.S. and Tamm, L.K. (2005) Membrane structures of the he-mifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemag-glutinin suggest a mechanism for pore opening in mem-brane fusion. The Journal of Virology, 79(18), 12065- 12076..

[34] Lai, A.L., Park, H., White, J.M. and Tamm, L.K. (2006) Fusion peptide of influenza hemagglutinin requires a fixed angle boomerang structure for activity. The Journal of Biological Chemistry, 281(9), 5760-5770.

[35] Sáez-Cirión, A., Nir, S., Lorizate, M., Agirre, A., Cruz, A., Pérez-Gil, J. and Nieva, J.L. (2002) Sphingomyelin and cholesterol promote HIV-1 gp41 pretransmembrane sequence surface aggregation and membrane restructuring. The Journal of Biological Chemistry, 277(24), 21776- 21785.

[36] Lorizate, M., Huarte, N., Sáez-Cirión, A. and Nieva, J.L. (2008) Interfacial pre-transmembrane domains in viral proteins promoting membrane fusion and fission. Bio-chimica et Biophysica Acta, 1778(7-8), 1624-1639.

[37] Charloteaux, B., Lorin, A., Brasseur, R. and Lins, L. (2009) The “Tilted Peptide Theory” links membrane in-sertion properties and fusogenicity of viral fusion peptides. Protein and Peptide Letters, 2009; 16(7), 718-725.

[38] Efremov, R.G., Nolde, D.E., Volynsky, P.E., Chernyavsky, A.A., Dubovskii, P.V. and Arseniev, A.S. (1999) Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin. FEBS Letters, 462(1-2), 205-210.

[39] Gray, C., Tatulian, S.A., Wharton, S.A. and Tamm, L.K. (1996) Effect of the N-terminal glycine on the secondary structure, orientation, and interaction of the influenza hemagglutinin fusion peptide with lipid bilayers. Bio-physical Journal, 70(5), 2275-2286.

[40] Marrink, S.-J., de Vries, A.H. and Tieleman, D.P. (2009) Lipids on the move: Simulation of membrane pores, do-mains, stalks and curves. Biochimica et Biophysica Acta, 1788(1), 149-168.

[41] Marrink, S.-J. and Tieleman, D.P. (2001) Molecular dy-namics simulation of a lipid diamond cubic phase. Journal of the American Chemical Society, 123(49), 12383- 12391.

[42] Knecht, V., Mark, A.E. and Marrink, S.-J. (2006) Phase behaviour of a phospholipid/fatty acid/water mixture stu-died in atomic detail. Journal of the American Chemical Society, 128(6), 2030-2034.

[43] Marrink, S.-J. and Mark, A.E. (2004) Molecular view of hexagonal phase formation in phospholipid membranes. Biophysical Journal, 87(6), 3894-3900.

[44] Nielsen, S.O., Lopez, C.F., Ivanov, I., Moore, P.B., Shel-ley, J.C. and Klein, M.L. (2004) Transmembrane pep-tide-induced lipid sorting and mechanism of Lal-pha-to-inverted phase transition using coarse-grain mo-lecular dynamics. Biophysical Journal, 87(4), 2107-2115.

[45] Kamath, S. and Wong, T.C. (2002) Membrane structure of the Human Immunodeficiency Virus gp41 fusion domain by molecular dynamics simulation. Biophysical Journal, 83(1), 135-143.

[46] Vaccaro, L., Cross, K.J., Kleinjung, J., Straus, S.K., Thomas, D.J., Wharton, S.A., Skehel, J.J. and Fraternali, F. (2005) Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers. Bio-physical Journal, 88(1), 25-36.

[47] Huang, Q., Chen, C.L. and Herrmann, A. (2004) Bilayer conformation of fusion peptide of influenza virus he-magglutinin: A molecular dynamics simulation study. Biophysical Journal, 87(1), 14-22.

[48] Lagüe, P., Roux, B. and Pastor, R.W. (2005) Molecular dynamics simulations of the influenza hemagglutinin fu-sion peptide in micelles and bilayers: Conformational analysis of peptide and lipids. Journal of Molecular Bi-ology, 354(5), 1129-1141.

[49] Sammalkorpi, M. and Lazaridis, T. (2007) Configuration of influenza hemagglutinin fusion peptide monomers and oligomers in membranes. Biochimica et Biophysica Acta, 1768(1), 30-38.

[50] De Vries, A.H., Mark, A.E. and Marrink, S.J. (2004) The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study. The Journal of Physical Che-mistry B, 108(7), 2454-2463.

[51] Seddon, J.M., Templer, R.H., Warrender, N.A., Huang, Z., Cevc, G. and Marsh, D. (1997) Phosphatidylcholine–fatty acid membranes: Effects of headgroup hydration on the phase behaviour and structural parameters of the gel and inverse hexagonal (HII) phases. Biochimica et Biophysica Acta, 1327, 131-147.

[52] Lindahl, E., Hess, B. and van der Spoel, D. (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 7(8), 306-317.

[53] Berger, O., Edholm, O. and J?hnig, F. (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoyl-phosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophysical Journal, 72(5), 2002-2013.

[54] Sun, Z.Y., Oh, K.J., Kim, M., Yu, J., Brusic, V., Song, L., Qiao, Z., Wang, J.H., Wagner, G. and Reinherz, E.L. (2008) HIV-1 broadly neutralizing antibody extracts its epitope from a kinked gp41 ectodomain region on the viral membrane. Immunity, 28(1), 52-63.

[55] Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J. (1981) Intermolecular forces, interaction models for water in relation to protein hydration. D. Reidel Publishing, Dordrecht, The Netherlands.

[56] Hess, B., Bekker, H., Berendsen, H.J.C. and Fraaije, J.G.E.M. (1997) LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemi-stry, 18(12), 1463-1472.

[57] Miyamoto, S. and Kollman, P.A. (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Che-mistry, 13(8), 952-962.

[58] Darden, T., York, D. and Pedersen, L. (1993) Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089- 10092.

[59] Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81(8), 3684-3690.

[60] Zhou, Z., Macosko, J.C., Hughes, D.W., Sayer, B.G., Hawes, J. and Epand, R.M. (2000) 15N NMR study of the ionization properties of the influenza virus fusion peptide in zwitterionic phospholipid dispersions. Bio-physics Journal, 78(5), 2418-2425.

[61] Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recongnition of hydro-gen-bond and geometrical features. Biopolymers, 2, 2577-2637.

[62] Humphery, W., Dalke, A. and Schulten, K. (1996) VMD--visual molecular dynamics. Journal of Molecular Graphics, 14, 33-38.

[63] Epand, R.M. and Epand, R.F. (1994) Relationship be-tween the infectivity of influenza virus and the ability of its fusion peptide to perturb bilayers. Biochemical and Biophysical Research Communications, 202(3), 1420-1425.

[64] Colotto, A. and Epand, R.M. (1997) Structural study of the relationship between the rate of membrane fusion and the ability of the fusion peptide of influenza virus to per-turb bilayers. Biochemistry, 36(25), 7644-7651.

[65] Siegel, D.P. and Epand, R.M. (2000) Effect of influenza hemagglutinin fusion peptide on lamellar/inverted phase transitions in dipalmitoleoylphosphatidylethanolamine: implications for membrane fusion mechanisms. Biochi-mica et Biophysica Acta, 1468(1-2), 87-98.

[66] Han, X. and Tamm, L.K. (2000) pH-dependent self- as-sociation of influenza hemagglutinin fusion peptides in lipid bilayers. Journal of Molecular Biology, 304(5), 953-965.

[67] Qiao, H., Armstrong, R.T., Melikyan, G.B., Cohen, F.S. and White, J.M. (1999) A specific point mutant at position 1 of the influenza hemagglutinin fusion peptide displays a hemifusion phenotype. Molecular Biology Cell, 10(8), 2759-2769.

[68] Kasson, P.M., Kelley, N.W., Singhal, N., Vrljic, M., Brunger, A.T. and Pande, V.S. (2006) Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proceedings of the National Academy Sciences USA, 103(32), 11916-11921.

[69] Peisajovich, S.G. and Shai, Y. (2003) Viral fusion proteins: multiple regions contribute to membrane fusion. Biochimica et Biophysica Acta, 1614(1), 122-129.

[70] Lau, W.L., Ege, D.S., Lear, J.D., Hammer, D.A. and De-Grado, W.F. (2004) Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization. Biophysics Journal, 86(1), 272- 284.

[71] Kim, J.H., Hartley, T.L., Curran, A.R. and Engelman, D.M. (2009) Molecular dynamics studies of the trans-membrane domain of gp41 from HIV-1. Biochimica et Biophysica Acta, 1788(9), 1804-1812.