Molecular dynamics simulation of HIV-1 fusion domain-membrane complexes: Insight into the N-terminal gp41 fusion mechanism

Biophysical Chemistry

Volumn 170, Issue , 2012, Pages 9-16

  Promsri, Siriporn ^a   Ullmann, G Matthias ^b   Hannongbua, Supot ^a  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b UNIVERSITY OF BAYREUTH   (Germany)

Author keywords

DMPC; Fusion peptide; HIV 1 gp41; Membrane fusion; Molecular dynamics simulation; Order parameter

Indexed keywords

AMINO ACID; DIMYRISTOYLPHOSPHATIDYLCHOLINE; GLYCOPROTEIN GP 41; HYBRID PROTEIN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CELL MEMBRANE; HUMAN IMMUNODEFICIENCY VIRUS 1; LIPID MEMBRANE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

DIMYRISTOYLPHOSPHATIDYLCHOLINE; HIV ENVELOPE PROTEIN GP41; LIPID BILAYERS; MEMBRANE FUSION; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PEPTIDES;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84864823935     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2012.07.002     Document Type: Article

References (55)

1. R.M. Epand Fusion peptides and the mechanism of viral fusion Biochimica et Biophysica Acta 1614 2003 116 121
2. L.K. Tamm, J. Crane, and V. Kiessling Membrane fusion: a structural perspective on the interplay of lipids and proteins Current Opinion in Structural Biology 13 2003 453 466
3. J. Torres, T.J. Stevens, and M. Samso Membrane proteins: the "Wild West" of structural biology Trends in Biochemical Sciences 28 2003 137 144
4. R. Brasseur, T. Pillot, L. Lins, J. Vandekerckhove, and M. Rosseneu Peptides in membranes: tipping the balance of membrane stability Trends in Biochemical Sciences 22 1997 167 171
5. W. Qiang, J. Yang, and D.P. Weliky Solid-state nuclear magnetic resonance measurements of HIV fusion peptide to lipid distances reveal the intimate contact of [beta] strand peptide with membranes and the proximity of the Ala-14-Gly-16 Region with Lipid Headgroups Biochemistry 46 2007 4997 5008
6. C.M. Wasniewski, P.D. Parkanzky, M.L. Bodner, and D.P. Weliky Solid-state nuclear magnetic resonance studies of HIV and influenza fusion peptide orientations in membrane bilayers using stacked glass plate samples Chemistry and Physics of Lipids 132 2004 89 100
7. B. Barz, T.C. Wong, and I. Kosztin Membrane curvature and surface area per lipid affect the conformation and oligomeric state of HIV-1 fusion peptide: a combined FTIR and MD simulation study Biochimica et Biophysica Acta 1778 2008 945 953
8. X. Han, J.H. Bushweller, D.S. Cafiso, and L.K. Tamm Membrane structure and fusion-triggering conformational change of the fusion domain from influenza hemagglutinin Nature Structural Biology 8 2001 715 720
9. T. Korte, R.F. Epand, R.M. Epand, and R. Blumenthal Role of the Glu residues of the influenza hemagglutinin fusion peptide in the pH dependence of fusion activity Virology 289 2001 353 361
10. C.P. Jaroniec, J.D. Kaufman, S.J. Stahl, M. Viard, R. Blumenthal, P.T. Wingfield, and A. Bax Structure and dynamics of micelle-associated human immunodeficiency virus gp41 fusion domain Biochemistry 44 2005 16167 16180
11. B. Bechinger, L.M. Gierasch, M. Montal, M. Zaloff, and S.J. Opella Orientations of helical peptides in membrane bilayers by solid-state NMR spectroscopy Solid State Nuclear Magnetic Resonance Spectroscopy 7 1996 185 192
12. K.F. Morris, X. Gao, and T.C. Wong The interactions of the HIV gp41 fusion peptides with zwitterionic membrane mimics determined by NMR spectroscopy Biochimica et Biophysica Acta 1667 2004 67 81
13. Z. Zhou, J.C. Macosko, D.W. Hughes, B.G. Sayer, J. Hawes, and R.M. Epand 15N NMR study of the ionization properties of the influenza virus fusion peptide in zwitterionic phospholipid dispersions Biophysical Journal 78 2000 2418 2425
14. M.E. Haque, V. Koppaka, P.H. Axelsen, and B.R. Lentz Properties and structures of the influenza and HIV fusion peptides on lipid membranes: implications for a role in fusion Biophysical Journal 89 2005 3183 3194
15. A. Saez-Crion, and J.L. Nieva Conformational transitions of membrane-bound HIV-1 fusion peptide Biochim. Biophys. Acta - Biomembranes 1564 2002 57 65
16. J. Yang, M. Prorok, F.J. Castellino, and D.P. Weliky Oligomeric [beta]-structure of the membrane-bound HIV-1 fusion peptide formed from soluble monomers Biophysical Journal 87 2004 1951 1963
17. W. Qiang, and D.P. Weliky HIV fusion peptide and its cross-linked oligomers: efficient syntheses, significance of the trimer in fusion activity, correlation of [beta] strand conformation with membrane cholesterol, and proximity to lipid headgroups Biochemistry 48 2009 289 301
18. Y. Li, and L.K. Tamm Structure and plasticity of the human immunodeficiency virus gp41 fusion domain in lipid micelles and bilayers Biophysical Journal 93 2007 876 885
19. D. Grasnick, U. Sternberg, E. Strandberg, P. Wadhwani, and A. Ulrich Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations European Biophysics Journal 40 2011 529 543
20. S. Afonin, U.H.N. Dürr, R.W. Glaser, and A.S. Ulrich 'Boomerang'-like insertion of a fusogenic peptide in a lipid membrane revealed by solid-state 19F NMR Magnetic Resonance in Chemistry 42 2004 195 203
21. Z. Zheng, R. Yang, M.L. Bodner, and D.P. Weliky Conformational flexibility and strand arrangements of the membrane-associated HIV fusion peptide trimer probed by solid-state NMR spectroscopy Biochemistry 45 2006 12960 12975
22. P. Wadhwani, J. Reichert, J. Bürck, and A. Ulrich Antimicrobial and cell-penetrating peptides induce lipid vesicle fusion by folding and aggregation European Biophysics Journal 41 2012 177 187
23. P. Lagüe, B. Roux, and R.W. Pastor Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids Journal of Molecular Biology 354 2005 1129 1141
24. A. Panahi, and M. Feig Conformational sampling of influenza fusion peptide in membrane bilayers as a function of termini and protonation states The Journal of Physical Chemistry. B 114 2009 1407 1416
25. J. Li, P. Das, and R. Zhou Single mutation effects on conformational change and membrane deformation of influenza hemagglutinin fusion peptides The Journal of Physical Chemistry. B 114 2010 8799 8806
26. Q. Huang, C.L. Chen, and A. Herrmann Bilayer conformation of fusion peptide of influenza virus hamgglutinin: a molecular dynamics study Biophysical Journal 87 2004 14 22
27. V.K. Gangupomu, and C.F. Abrams All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics Biophysical Journal 99 2010 3438 3444
28. D. Bechor, and N. Ben-Tal Implicit solvent model studies of the interactions of the influenza hemagglutinin fusion peptide with lipid bilayers Biophysical Journal 80 2001 643 655
29. P.E. Volynsky, A.A. Polyansky, N.A. Simakov, A.S. Arseniev, and R.G. Efremov Effect of lipid composition on the "membrane response" induced by a fusion peptide Biochemistry 44 2005 14626 14637
30. R.G. Efremov, D.E. Nolde, P.E. Volynsky, A.A. Chernyavsky, P.V. Dubovskii, and A.S. Arseniev Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin FEBS Letters 462 1999 205 210
31. T.C. Wong Membrane structure of the human immunodeficiency virus gp41 fusion peptide by molecular dynamics simulation: II. The glycine mutants Biochimica et Biophysica Acta, Biomembranes 1609 2003 45 54
32. S. Kamath, and T.C. Wong Membrane structure of the human immunodeficiency virus gp41 fusion domain by molecular dynamics simulation Biophysical Journal 83 2002 135 143
33. M.W. Maddox, and M.L. Longo Conformational partitioning of the fusion peptide of HIV-1 gp41 and its structural analogs in bilayer membranes Biophysical Journal 83 2002 3088 3096
34. C. Gray, S.A. Tatulian, S.A. Wharton, and L.K. Tamm Effect of the N-terminal glycine on the secondary structure, orientation, and interaction of the influenza hemagglutinin fusion peptide with lipid bilayers Biophysical Journal 70 1996 2275 2286
35. J.L. Nieva, S. Nir, A. Muga, F.M. Goni, and J. Wilschut Interaction of the HIV-1 fusion peptide with phospholipid vesicles: different structural requirements for fusion and leakage Biochemistry 33 1994 3201 3209
36. T. Matsumoto Membrane destabilizing activity of influenza virus hemagglutinin-based synthetic peptide: implications of critical glycine residue in fusion peptide Biophysical Chemistry 79 1999 153 162
37. E.I. Pecheur, I. Martin, A. Bienvene, J.M. Ruysschaert, and D. Hoekstra Protein-induced fusion can be modulated by target membrane lipids through a structural switch at the level of the fusion peptide The Journal of Biological Chemistry 275 2000 3936 3942
38. C. Curtain, F. Separovic, K. Nielsen, D. Craik, Y. Zhong, and A. Kirkpatrick The interactions of the N-terminal fusogenic peptide of HIV-1 gp41 with neutral phospholipids European Biophysics Journal 28 1999 427 436
39. R.M. Epand, and R.F. Epand Relationship between the infectivity of influenza virus and the ability of its fusion peptide to perturb bilayers Biochemical and Biophysical Research Communications 202 1994 1420 1425
40. X. Han, D.A. Steinhauer, S.A. Wharton, and L.K. Tamm Interaction of mutant influenza virus hemagglutinin fusion peptides with lipid bilayers: probing the role of hydrophobic residue size in the central region of the fusion peptide Biochemistry 38 1999 15052 15059
41. B.R. Brooks, C.L. Brooks, A.D. Mackerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, and M. Karplus CHARMM: the biomolecular simulation program Journal of Computational Chemistry 30 2009 1545 1614
42. T.B. Woolf, and B. Roux Molecular dynamics simulation of the gramicidin a channel in a phospholipid bilayer Proceedings of the National Academy of Sciences of the United States of America 91 1994 11631 11635
43. T.B. Woolf, and B. Roux Molecular dynamics simulation of the gramicidin a channel in a phospholipid bilayer PROT: Struct Funct Genomics 24 1996 92 114
44. S. Berneche, M. Nina, and B. Roux Molecular dynamics of melittin in a dimyristoyl phosphatidylcholine bilayer membrane Biophysical Journal 75 1998 1603 1618
45. S. Berneche, and B. Roux Molecular dynamics of the KcsA K + channel in a bilayer membrane Biophysical Journal 78 2000 2900 2917
46. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water The Journal of Chemical Physics 79 1983 926 935
47. E. Lindahl, B. Hess, and D. van der Spoel A package for molecular simulation and trajectory analysis Journal of Molecular Modeling 7 2001 306 317
48. I. Chandrasekhar, M. Kastenholz, R.D. Lins, C. Oostenbrink, L.D. Schuler, D.P. Tieleman, and W.F. van Gunsteren A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field European Biophysics Journal 32 2003 67 77
49. H.J.C. Berendsen, J.R. Grigera, and T.P. Straatsma The missing term in effective pair potentials The Journal of Physical Chemistry 91 1987 6269 6271
50. W.F. van Gunsteren, and H.J.C. Berendsen Gromos-87 Manual 1987
51. S. Miyamoto, and P.A. Kollman SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models Journal of Computational Chemistry 13 1992 952 962
52. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
53. J.F. Nagle, and S. Tristram-Nagle Lipid bilayer structure Current Opinion in Structural Biology 10 2000 474 480
54. H.I. Petrache, S.W. Dodd, and M.F. Brown Area per lipid and acyl length distributions in fluid phosphatidylcholines determined by 2H NMR spectroscopy Biophysical Journal 79 2000 3172 3192
55. D.P. Tieleman, L.R. Forrest, M.S.P. Sansom, and H.J.C. Berendsen Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations Biochemistry 37 1998 17554 17561