Structural and Material Perturbations of Lipid Bilayers Due to HIV-1 Tat Peptide

  • Kiyotaka Akabori
Part of the Springer Theses book series (Springer Theses)


This chapter reports the effect on lipid bilayers of Tat, the transactivator of transcription, which is an important protein for HIV-1 infection. Synergistic use of low-angle X-ray scattering (LAXS) and atomistic molecular dynamic simulations (MD) revealed Tat peptides binding to lipid headgroups. This binding induced the local lipid phosphate groups to move closer to the center of the bilayer. The position of the positively charged guanidinium components of the arginines was also indicated. A single lipid component sample and samples consisting of mixtures of different lipids were studied. Generally, the Tat peptide decreased the bilayer bending modulus and increased the area/lipid. Although a mechanism for translation remains obscure, this study suggests that the peptide/lipid interaction makes the Tat peptide poised to translocate from the headgroup region.


Form Factor Molecular Dynamic Simulation Electron Density Profile Bilayer Thickness Headgroup Region 
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  1. 1.
    R. Fischer, M. Fotin-Mleczek, H. Hufnagel, R. Brock, Break on through to the other side: biophysics and cell biology shed light on cell-penetrating peptides. ChemBioChem 6(12), 2126–2142 (2005)CrossRefGoogle Scholar
  2. 2.
    A. Joliot, A. Prochiantz, Transduction peptides: from technology to physiology. Nat. Cell Biol. 6(3), 189–196 (2004)CrossRefGoogle Scholar
  3. 3.
    M. Lindgren, M. Hällbrink, A. Prochiantz, U. Langel, Cell-penetrating peptides. Trends Pharmacol. Sci. 21(3), 99–103 (2000)CrossRefGoogle Scholar
  4. 4.
    A.D. Frankel, C.O. Pabo, Cellular uptake of the Tat protein from human immunodeficiency virus. Cell 55(6), 1189–1193 (1988)CrossRefGoogle Scholar
  5. 5.
    M. Green, P.M. Loewenstein, Autonomous functional domains of chemically synthesized human immunodeficiency virus Tat trans-activator protein. Cell 55(6), 1179–1188 (1988)CrossRefGoogle Scholar
  6. 6.
    E. Vives, P. Brodin, B. Lebleu, HIV-1 Tat protein basic domain rapidly translocates through the plasma membrane and accumulates in the cell nucleus. J. Biolog. Chem. 272(25), 16010–16017 (1997)CrossRefGoogle Scholar
  7. 7.
    G. Ter-Avetisyan, G. Tünnemann, D. Nowak, M. Nitschke, A. Herrmann, M. Drab, M.C. Cardoso, Cell entry of arginine-rich peptides is independent of endocytosis. J. Biolog. Chem. 284(6), 3370–3378 (2009)CrossRefGoogle Scholar
  8. 8.
    F. Duchardt, M. Fotin-Mleczek, H. Schwarz, R. Fischer, R. Brock, A comprehensive model for the cellular uptake of cationic cell-penetrating peptides. Traffic 8(7), 848–866 (2007)CrossRefGoogle Scholar
  9. 9.
    G. Tünnemann, R.M. Martin, S. Haupt, C. Patsch, F. Edenhofer, M.C. Cardoso, Cargo-dependent mode of uptake and bioavailability of Tat-containing proteins and peptides in living cells. FASEB J. 20(11), 1775–1784 (2006)CrossRefGoogle Scholar
  10. 10.
    A. Ziegler, P. Nervi, M. Dürrenberger, J. Seelig, The cationic cell-penetrating peptide CPPTat derived from the HIV-1 protein Tat is rapidly transported into living fibroblasts: optical, biophysical, and metabolic evidence. Biochemistry 44(1), 138–148 (2005). PMID: 15628854.CrossRefGoogle Scholar
  11. 11.
    J.S. Wadia, R.V. Stan, S.F. Dowdy, Transducible Tat-HA fusogenic peptide enhances escape of Tat-fusion proteins after lipid raft macropinocytosis. Nat. Med. 10(3), 310–315 (2004)CrossRefGoogle Scholar
  12. 12.
    I.M. Kaplan, J.S. Wadia, S.F. Dowdy, Cationic Tat peptide transduction domain enters cells by macropinocytosis. J. Control. Release 102(1), 247–253 (2005)CrossRefGoogle Scholar
  13. 13.
    D.A. Mann, A.D. Frankel, Endocytosis and targeting of exogenous HIV-1 Tat protein. EMBO J. 10(7), 1733–420 (1991)Google Scholar
  14. 14.
    J.P. Richard, K. Melikov, H. Brooks, P. Prevot, B. Lebleu, L.V. Chernomordik, Cellular uptake of unconjugated Tat peptide involves clathrin-dependent endocytosis and heparan sulfate receptors. J. Biol. Chem. 280(15), 15300–15306 (2005)CrossRefGoogle Scholar
  15. 15.
    S.W. Jones, R. Christison, K. Bundell, C.J. Voyce, S. Brockbank, P. Newham, M.A. Lindsay, Characterisation of cell-penetrating peptide-mediated peptide delivery. Br. J. Pharmacol. 145(8), 1093–1102 (2005)CrossRefGoogle Scholar
  16. 16.
    A. Vendeville, F. Rayne, A. Bonhoure, N. Bettache, P. Montcourrier, B. Beaumelle, HIV-1 Tat enters T cells using coated pits before translocating from acidified endosomes and eliciting biological responses. Mol. Biol. Cell 15(5), 2347–2360 (2004)CrossRefGoogle Scholar
  17. 17.
    C. Foerg, U. Ziegler, J. Fernandez-Carneado, E. Giralt, R. Rennert, A.G. Beck-Sickinger, H.P. Merkle, Decoding the entry of two novel cell-penetrating peptides in HeLa cells: lipid raft-mediated endocytosis and endosomal escape. Biochemistry 44(1), 72–81 (2005)CrossRefGoogle Scholar
  18. 18.
    A. Fittipaldi, M. Giacca, Transcellular protein transduction using the Tat protein of HIV-1. Adv. Drug Deliv. Rev. 57(4), 597–608 (2005)CrossRefGoogle Scholar
  19. 19.
    Y. Liu, M. Jones, C.M. Hingtgen, G. Bu, N. Laribee, R.E. Tanzi, R.D. Moir, A. Nath, J.J. He, Uptake of HIV-1 Tat protein mediated by low-density lipoprotein receptor-related protein disrupts the neuronal metabolic balance of the receptor ligands. Nat. Med. 6(12), 1380–1387 (2000)CrossRefGoogle Scholar
  20. 20.
    V.P. Torchilin, R. Rammohan, V. Weissig, T.S. Levchenko, Tat peptide on the surface of liposomes affords their efficient intracellular delivery even at low temperature and in the presence of metabolic inhibitors. Proc. Natl. Acad. Sci. 98(15), 8786–8791 (2001)CrossRefADSGoogle Scholar
  21. 21.
    V.P. Torchilin, T.S. Levchenko, R. Rammohan, N. Volodina, B. Papahadjopoulos-Sternberg, G.G. D’Souza, Cell transfection in vitro and in vivo with nontoxic Tat peptide-liposome–DNA complexes. Proc. Natl. Acad. Sci. 100(4), 1972–1977 (2003)CrossRefADSGoogle Scholar
  22. 22.
    C. Rudolph, C. Plank, J. Lausier, U. Schillinger, R.H. Müller, J. Rosenecker, Oligomers of the arginine-rich motif of the HIV-1 Tat protein are capable of transferring plasmid DNA into cells. J. Biol. Chem. 278(13), 11411–11418 (2003)CrossRefGoogle Scholar
  23. 23.
    A. Chauhan, A. Tikoo, A.K. Kapur, M. Singh, The taming of the cell penetrating domain of the HIV Tat: myths and realities. J. Control. Release 117(2), 148–162 (2007)CrossRefGoogle Scholar
  24. 24.
    J. Sabatier, E. Vives, K. Mabrouk, A. Benjouad, H. Rochat, A. Duval, B. Hue, E. Bahraoui, Evidence for neurotoxic activity of Tat from human immunodeficiency virus type 1. J. Virol. 65(2), 961–967 (1991)Google Scholar
  25. 25.
    A. Mishra, V.D. Gordon, L.H. Yang, R. Coridan, G.C.L. Wong, HIV Tat forms pores in membranes by inducing saddle-splay curvature: potential role of bidentate hydrogen bonding. Angew. Chem.-Int. Ed. 47(16), 2986–2989 (2008)CrossRefGoogle Scholar
  26. 26.
    S.T. Yang, E. Zaitseva, L.V. Chernomordik, K. Melikov, Cell-penetrating peptide induces leaky fusion of liposomes containing late endosome-specific anionic lipid. Biophys. J. 99(8), 2525–2533 (2010)CrossRefADSGoogle Scholar
  27. 27.
    P.E.G. Thoren, D. Persson, E.K. Esbjorner, M. Goksor, P. Lincoln, B. Norden, Membrane binding and translocation of cell-penetrating peptides. Biochemistry 43(12), 3471–3489 (2004)CrossRefGoogle Scholar
  28. 28.
    S. Krämer, H. Wunderli-Allenspach, No entry for Tat (44–57) into liposomes and intact mdck cells: novel approach to study membrane permeation of cell-penetrating peptides. Biochim. Biophys. Acta (BBA)-Biomembr. 1609(2), 161–169 (2003)Google Scholar
  29. 29.
    C. Ciobanasu, J.P. Siebrasse, U. Kubitscheck, Cell-penetrating HIV-1 Tat peptides can generate pores in model membranes. Biophys. J. 99(1), 153–62 (2010)CrossRefADSGoogle Scholar
  30. 30.
    P.A. Gurnev, S.-T. Yang, K.C. Melikov, L.V. Chernomordik, S.M. Bezrukov, Cationic cell-penetrating peptide binds to planar lipid bilayers containing negatively charged lipids but does not induce conductive pores. Biophys. J. 104(9), 1933–1939 (2013)CrossRefADSGoogle Scholar
  31. 31.
    H.D. Herce, A.E. Garcia, J. Litt, R.S. Kane, P. Martin, N. Enrique, A. Rebolledo, V. Milesi, Arginine-rich peptides destabilize the plasma membrane, consistent with a pore formation translocation mechanism of cell-penetrating peptides. Biophys. J. 97(7), 1917–1925 (2009)CrossRefADSGoogle Scholar
  32. 32.
    Y.C. Su, A.J. Waring, P. Ruchala, M. Hong, Membrane-bound dynamic structure of an arginine-rich cell-penetrating peptide, the protein transduction domain of HIV Tat, from solid-state NMR. Biochemistry 49(29), 6009–6020 (2010)CrossRefGoogle Scholar
  33. 33.
    S. Shojania, J.D. O’Neil, HIV-1 Tat is a natively unfolded protein – the solution conformation and dynamics of reduced HIV-1 Tat-(1–72) by NMR spectroscopy. J. Biol. Chem. 281(13), 8347–8356 (2006)CrossRefGoogle Scholar
  34. 34.
    P. Bayer, M. Kraft, A. Ejchart, M. Westendorp, R. Frank, P. Rosch, Structural studies of HIV-1 Tat protein. J. Mol. Biol. 247(4), 529–535 (1995)Google Scholar
  35. 35.
    H.D. Herce, A.E. Garcia, Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 Tat peptide across lipid membranes. Proc. Natl. Acad. Sci. 104(52), 20805–20810 (2007)CrossRefADSGoogle Scholar
  36. 36.
    S. Yesylevskyy, S.J. Marrink, A.E. Mark, Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the Tat peptide with lipid bilayers. Biophys. J. 97(1), 40–49 (2009)CrossRefADSGoogle Scholar
  37. 37.
    E.D. Jarasch, C.E. Reilly, P. Comes, J. Kartenbeck, W.W. Franke, Isolation and characterization of nuclear membranes from calf and rat thymus. Hoppe Seylers Z. Physiol. Chem. 354(8), 974–86 (1973)CrossRefGoogle Scholar
  38. 38.
    S.A. Tristram-Nagle, Preparation of oriented, fully hydrated lipid samples for structure determination using X-ray scattering. Methods Mol. Biol. 400, 63–75 (2007)CrossRefGoogle Scholar
  39. 39.
    N. Kučerka, Y. Liu, N. Chu, H.I. Petrache, S. Tristram-Nagle, J.F. Nagle, Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys. J. 88(4), 2626–2637 (2005)CrossRefGoogle Scholar
  40. 40.
    S. Barna, M. Tate, S. Gruner, E. Eikenberry, Calibration procedures for charge-coupled device X-ray detectors. Rev. Sci. Instrum. 70(7), 2927–2934 (1999)CrossRefADSGoogle Scholar
  41. 41.
    Y. Lyatskaya, Y.F. Liu, S. Tristram-Nagle, J. Katsaras, J.F. Nagle, Method for obtaining structure and interactions from oriented lipid bilayers. Phys. Rev. E 63(1), 0119071–0119079 (2001)Google Scholar
  42. 42.
    Y.F. Liu, J.F. Nagle, Diffuse scattering provides material parameters and electron density profiles of biomembranes. Phys. Rev. E 69(4), 040901–040904(R) (2004)Google Scholar
  43. 43.
    Y. Liu, New method to obtain strcuture of biomembranes using diffuse X-ray scattering: application to fluid phase DOPC lipid bilayers. PhD thesis, Carnegie Mellon University, 2003Google Scholar
  44. 44.
    G. King, S. White, Determining bilayer hydrocarbon thickness from neutron diffraction measurements using strip-function models. Biophys. J. 49(5), 1047–1054 (1986)CrossRefADSGoogle Scholar
  45. 45.
    F. Heinrich, M. Lösche, Zooming in on disordered systems: Neutron reflection studies of proteins associated with fluid membranes. Biochim. Biophys. Acta (BBA) – Biomembr. 1838(9), 2341–2349 (2014). Interfacially active peptides and proteins.Google Scholar
  46. 46.
    P. Shekhar, H. Nanda, M. Lösche, F. Heinrich, Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques. J. Appl. Phys. 110(10), 102216 (2011)Google Scholar
  47. 47.
    T. Mitsui, X-ray diffraction studies of membranes. Adv. Biophys. 10, 97–135 (1978)Google Scholar
  48. 48.
    M.C. Wiener, R.M. Suter, J.F. Nagle, Structure of the fully hydrated gel phase of dipalmitoylphosphatidylcholine. Biophys. J. 55(2), 315–325 (1989)CrossRefADSGoogle Scholar
  49. 49.
    J.B. Klauda, N. Kučerka, B.R. Brooks, R.W. Pastor, J.F. Nagle, Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophys. J. 90(8), 2796–2807 (2006)CrossRefADSGoogle Scholar
  50. 50.
    N. Kučerka, J.F. Nagle, J.N. Sachs, S.E. Feller, J. Pencer, A. Jackson, J. Katsaras, Lipid bilayer structure determined by the simultaneous analysis of neutron and X-ray scattering data. Biophys. J. 95(5), 2356–2367 (2008)CrossRefADSGoogle Scholar
  51. 51.
    S. Tristram-Nagle, Y. Liu, J. Legleiter, J.F. Nagle, Structure of gel phase DMPC determined by X-ray diffraction. Biophys. J. 83(6), 3324–3335 (2002)CrossRefADSGoogle Scholar
  52. 52.
    A.R. Braun, J.N. Sachs, J.F. Nagle, Comparing simulations of lipid bilayers to scattering data: the gromos 43A1-S3 force field. J. Phys. Chem. B 117(17), 5065–5072 (2013)CrossRefGoogle Scholar
  53. 53.
  54. 54.
    B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, Gromacs 4: algorithms for highly efficient, load-balanced, scalable molecular simulation. J. Chem. Theory Comput. 4(3), 435–447 (2008)CrossRefGoogle Scholar
  55. 55.
    J.P.M. Jambeck, A.P. Lyubartsev, Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J. Phys. Chem. B 116(10), 3164–3179 (2012)CrossRefGoogle Scholar
  56. 56.
    J.P.M. Jambeck, A.P. Lyubartsev, An extension and further validation of an all-atomistic force field for biological membranes. J. Chem. Theory Comput. 8(8), 2938–2948 (2012)CrossRefGoogle Scholar
  57. 57.
    V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins Struct. Funct. Bioinform. 65(3), 712–725 (2006)CrossRefGoogle Scholar
  58. 58.
    W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79(2), 926–935 (1983)CrossRefADSGoogle Scholar
  59. 59.
    N. Kučerka, J. Katsaras, J. Nagle, Comparing membrane simulations to scattering experiments: Introducing the SIMtoEXP software. J. Membr. Biol. 235(1), 43–50 (2010)CrossRefGoogle Scholar
  60. 60.
    S. Miyamoto, P.A. Kollman, Settle: an analytical version of the shake and rattle algorithm for rigid water models. J. Comput. Chem. 13(8), 952–962 (1992)CrossRefGoogle Scholar
  61. 61.
    B. Hess, H. Bekker, H.J.C. Berendsen, J.G. E.M. Fraaije, Lincs: A linear constraint solver for molecular simulations. J. Comput. Chem. 18(12), 1463–1472 (1997)CrossRefGoogle Scholar
  62. 62.
    T. Darden, D. York, L. Pedersen, Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98(12), 10089–10092 (1993)CrossRefADSGoogle Scholar
  63. 63.
    G. Bussi, D. Donadio, M. Parrinello, Canonical sampling through velocity rescaling. J. Chem. Phys. 126(1), 014101–420 (2007)CrossRefADSGoogle Scholar
  64. 64.
    M. Parrinello, A. Rahman, Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52(12), 7182–7190 (1981)CrossRefADSGoogle Scholar
  65. 65.
    N. Kučerka, S. Tristram-Nagle, J.F. Nagle, Closer look at structure of fully hydrated fluid phase DPPC bilayers. Biophysical Journal 90(11), L83–L85 (2006)CrossRefADSGoogle Scholar
  66. 66.
    N. Kučerka, S. Tristram-Nagle, J.F. Nagle, Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. J. Membr. Biol. 208(3), 193–202 (2005)CrossRefGoogle Scholar
  67. 67.
    H. Petrache, S. Feller, J. Nagle, Determination of component volumes of lipid bilayers from simulations. Biophys. J. 72(5), 2237–2242 (1997)CrossRefADSGoogle Scholar
  68. 68.
    S. Tristram-Nagle, C.-P. Yang, J.F. Nagle, Thermodynamic studies of purple membrane. Biochim. Biophys. Acta (BBA)-Biomembr. 854(1), 58–66 (1986)Google Scholar
  69. 69.
  70. 70.
    A.C.V. Johansson, E. Lindahl, The role of lipid composition for insertion and stabilization of amino acids in membranes. J. Chem. Phys. 130(18), (2009)Google Scholar
  71. 71.
    S. Tristram-Nagle, J.F. Nagle, HIV-1 fusion peptide decreases bending energy and promotes curved fusion intermediates. Biophys. J. 93(6), 2048–2055 (2007)CrossRefADSGoogle Scholar
  72. 72.
    M. Vazdar, E. Wernersson, M. Khabiri, L. Cwiklik, P. Jurkiewicz, M. Hof, E. Mann, S. Kolusheva, R. Jelinek, P. Jungwirth, Aggregation of oligoarginines at phospholipid membranes: molecular dynamics simulations, time-dependent fluorescence shift, and biomimetic colorimetric assays. J. Phys. Chem. B 117(39), 11530–11540 (2013)CrossRefGoogle Scholar
  73. 73.
    Z. Wu, Q. Cui, A. Yethiraj, Why do arginine and lysine organize lipids differently? insights from coarse-grained and atomistic simulations. J. Phys. Chem. B 117(40), 12145–12156 (2013)CrossRefGoogle Scholar
  74. 74.
    L.B. Li, I. Vorobyov, T.W. Allen, Potential of mean force and pk(a) profile calculation for a lipid membrane-exposed arginine side chain. J. Phys. Chem. B 112(32), 9574–9587 (2008)CrossRefGoogle Scholar
  75. 75.
    I. Vorobyov, L.B. Li, T.W. Allen, Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane. J. Phys. Chem. B 112(32), 9588–9602 (2008)CrossRefGoogle Scholar
  76. 76.
    J.L. MacCallum, W.F.D. Bennett, D.P. Tieleman, Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94(9), 3393–3404 (2008)CrossRefADSGoogle Scholar
  77. 77.
    E.V. Schow, J.A. Freites, P. Cheng, A. Bernsel, G. von Heijne, S.H. White, D.J. Tobias, Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments. J. Membr. Biol. 239(1–2), 35–48 (2011)CrossRefGoogle Scholar
  78. 78.
    W.C. Wimley, T.P. Creamer, S.H. White, Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 35(16), 5109–5124 (1996)CrossRefGoogle Scholar
  79. 79.
    W.C. Wimley, S.H. White, Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3(10), 842–848 (1996)CrossRefGoogle Scholar
  80. 80.
    B. Roux, Lonely arginine seeks friendly environment. J. Gen. Physiol. 130(2), 233–236 (2007)CrossRefGoogle Scholar
  81. 81.
    W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12), 2577–637 (1983)CrossRefGoogle Scholar
  82. 82.
    D. Choi, J.H. Moon, H. Kim, B.J. Sung, M.W. Kim, G.Y. Tae, S.K. Satija, B. Akgun, C.J. Yu, H.W. Lee, D.R. Lee, J.M. Henderson, J.W. Kwong, K.L. Lam, K.Y.C. Lee, K. Shin, Insertion mechanism of cell-penetrating peptides into supported phospholipid membranes revealed by X-ray and neutron reflection. Soft Matter 8(32), 8294–8297 (2012)CrossRefADSGoogle Scholar
  83. 83.
    A. Ziegler, X.L. Blatter, A. Seelig, J. Seelig, Protein transduction domains of HIV-1 and SIV Tat interact with charged lipid vesicles. binding mechanism and thermodynamic analysis. Biochemistry 42(30), 9185–94 (2003)Google Scholar
  84. 84.
    K. Huang, A.E. Garcia, Free energy of translocating an arginine-rich cell-penetrating peptide across a lipid bilayer suggests pore formation. Biophys. J. 104(2), 412–420 (2013)CrossRefADSGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Kiyotaka Akabori
    • 1
  1. 1.Carnegie Mellon UniversityPittsburghUSA

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