Molecular dynamics simulations and conductance studies of the interaction of VP1 N-terminus from Polio virus and gp41 fusion peptide from HIV-1 with lipid membranes

Molecular Membrane Biology

Volumn 29, Issue 1, 2012, Pages 9-25

  Hong, Guo Sheng ^a   Chen, Chin Pei ^a   Lin, Meng Han ^a   Krüger, Jens ^a   Becker, Christian F W ^b   Fink, Rainer H A ^c   Fischer, Wolfgang B ^a  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Bilayer recordings; Computational modeling; Fusion peptide HIV 1; Protein lipid interaction; Viral entry; VP1 Polio virus

Indexed keywords

GLYCOPROTEIN GP 41; HYBRID PROTEIN; PROTEIN VP1;

AMINO TERMINAL SEQUENCE; ARTICLE; BIOLOGY; CELL MEMBRANE CONDUCTANCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; LIPID MEMBRANE; MOLECULAR DYNAMICS; NONHUMAN; POLIOMYELITIS VIRUS; PRIORITY JOURNAL; PROTEIN LIPID INTERACTION; VIRUS ENTRY;

CAPSID PROTEINS; HIV ENVELOPE PROTEIN GP41; HIV-1; HUMANS; MEMBRANE LIPIDS; MOLECULAR DYNAMICS SIMULATION; POLIOVIRUS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; VIRUS INTERNALIZATION;

HUMAN IMMUNODEFICIENCY VIRUS 1; MIRIDAE; POLIOVIRUS;

EID: 84863028656     PISSN: 09687688     EISSN: 14645203     Source Type: Journal    
DOI: 10.3109/09687688.2011.644589     Document Type: Article

References (49)

1. Bachar M, Becker OM. 2000. Protein-induced membrane disorder: A molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer. Biophys J 78:1359-1375. (Pubitemid 30141561)
2. Barz B, Wong TC, Kosztin I. 2008. Membrane curvature and surface area per lipid affect th conformation and oligomeric state of HIV-1 fusion peptide: A combined FTIR andMDsimulation study. Biochim Biophys Acta 1778:945-953.
3. Bechinger B. 1997. Structure and functions of channel-forming peptides: Maganins, cecropins, melittin and alamethicin. J Membr Biol 156:197-211. (Pubitemid 27208423)
4. Benz RW, Nanda H, Castro-Román F, White SH, Tobias DJ. 2006. Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations. Biophys J 91:3617-3629. (Pubitemid 44788305)
5. Bloch I, Quintana FJ, Gerber D, Cohen T, Cohen IR, Shai Y. 2007. T-cell inactivation and immunosupressive activity induced by HIV gp41 via novel interacting motif. FASEB J 21:393-401. (Pubitemid 46213487)
6. BodnerML,GabrysCM,StruppeJO,WelikyDP. 2008. 13C-13Cand 15N-13C correlation spectroscopy of membrane-associated and uniformly labeled human immunodeficiency virus and influenza fusion peptides: Amino acid-type assignments and evidence for multiple conformations. J Chem Phys 128: 052311-052319.
7. Brandenburg B, Lee LY, Lakadamyali M, Rust MJ, Zhuang X, Hogle JM. 2007. Imaging poliovirus entry in living cells. PLOS Biol 5:1543-1555. (Pubitemid 47105345)
8. Bubeck D, Filman DJ, Cheng N, Steven AC, Hogle JM, Belnap DM. 2005. The structure of the Poliovirus 135S cell entry intermediate at 10-Angstrom reslution reveals the location of an externalized polypeptide that binds to membranes. J Virol 79:7745-7755. (Pubitemid 40756808)
9. Camarero JA, Muir TW 2001. Native chemical ligation of polypeptides. Curr Protocols Prot Sci 18:14.11-14.21.
10. Castano S, Desbat B. 2005. Structure and orienation study of fusion peptide FP23 of gp41 from HIV-1 alone or inserted into various lipid membrane models (mono-, bi-and multibi-layers) by FTIR spectroscopies and Brewster angle microscopy. Biochim Biophys Acta Biomembr 1715:81-95. (Pubitemid 41219696)
11. Chang D-K, Cheng S-F, Chien W-J. 1997. The amino-terminal fusion domain peptide of human immunodeficiency virus type 1 gp41 inserts into the sodium dodecyl sulfate micelle primarily as a helix with a conserved glycine at the micelle-water interface. J Virol 71:6593-6602. (Pubitemid 27355317)
12. Chen CP, Kremer C, Henklein P, Schubert U, Fink RHA, Fischer WB. 2010. Modulating the activity of channels formed by a short segment of the Vpr protein from HIV-1. Eur Biophys J 39:1089-1095.
13. Chen H, Gu F, Huang Z. 2006. Improved Chou-Fasman method for protein secondary structure prediction. BMCBioinformatics 7(Suppl. 4):S14.
14. Chou PY, Fasman GD. 1974. Prediction of protein conformation. Biochemistry 13:222-245.
15. Chow M, Newman JF, Filman DJ, Hogle JM, Rowlands DJ, Brown F. 1987. Myristylation of picornavirus capsid protein VP4 and its structural significance. Nature 327:482-486. (Pubitemid 17085817)
16. Cook GA, Zhang H, Park SH, Wang Y, Opella SJ. 2011. Comparative NMR studies demonstrate profound differences between two viroporins: p7 of HCV and Vpu of HIV-1. Biochim Biophys Acta 1808:554-560.
17. Danthi P, Tosteson M, Li Q-H, Chow M. 2003. Genome delivery and ion channel properties are altered in Vp4 mutants of poliovirus. J Virol 77:5266-5274. (Pubitemid 36460940)
18. De Sena J, Mandel B. 1976. Studies on the in vitro uncoating of polio virus. I. Characterization of the modifying factor and the modifying reaction. Virology 70:470-483.
19. Earp LJ, Delos SE, Park HE, White JM. 2005. The many mechanisms of viral membrane fusion proteins. Curr Top Microbiol Immunol 285:25-66.
20. Fischer WB, Krüger J. 2009. Viral channel forming proteins. Int Rev Cell Mol Biol 275: 35-63.
21. Fricks CE, Hogle JM. 1990. Cell-induced conformational changes in poliovirus: Externalization of the amino terminus of VP1 is responsible for liposome binding. J Virol 64:1934-1945. (Pubitemid 20148434)
22. Grasnick D, Sternberg U, Strandberg E, Wadhwani P, Ulrich AS 2011. Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simualtions. Eur Biophys J 40:529-543.
23. Harrison SC. 2008. Viral membrane fusion. Nature Struc Mol Biol 15:690-697.
24. Hogle JM. 2002. Poliovirus cell entry: Common structural themes in viral cell entry pathways. Annu Rev Microbiol 56:677-702. (Pubitemid 35217471)
25. Jaroniec CP, Kaufman JD, Stahl SJ, Viard M, Blumenthal R, Wingfield PT, Bax A. 2005. Structure and dynamics of micelle-associated human immunodeficiency virus gp41 fusion domain. Biochemistry 44:16167-16180. (Pubitemid 41785815)
26. Kamath S, Wong TC. 2002. Membrane structure of the human immunodeficiencey virus gp41 fusion domain by molecular dynamics simulations. Biophys J 83:135-143. (Pubitemid 34694726)
27. Kielian M, Rey FA. 2006. Virus membrane-fusion proteins: More than one way to make a hairpin. Nature Rev Microbiol 4:67-76. (Pubitemid 43135288)
28. Kräusslich H-G, Hölscher C, Reuer Q, Harber J, Wimmer E. 1990. Myristoylation of the poliovirus polyprotein is required for proteolytic processing of the capsid and for viral infectivity. J Virol 64:2433-2436. (Pubitemid 20148498)
29. Krüger J, Fischer WB. 2008. Exploring the conformational space of Vpu from HIV-1: A versatile and adaptable protein. J Comp Chem 29:2416-2424.
30. Krüger J, Fischer WB. 2009. Assembly of viral membrane proteins. J Chem Theory Comput 5:2503-2513.
31. La Rocca P, Biggin PC, Tieleman DP, Sansom MSP. 1999. Simulation studies of the interaction of antimicrobial peptides and lipid bilayers. Biochim Biophys Acta 1462:185-200.
32. Li Y, Tamm LK. 2007. Structure and plasticity of the human immunodeficiency virus gp41 fusion domain in lipid micelles and bilayers. Biophys J 93:876-885. (Pubitemid 47219779)
33. MacCallum JL, Bennett WFD, Tieleman DP. 2008. Distribution of amino acids in a lipid bilayer from computer simualtions. Biophys J 94:3393-3404.
34. Martin I, Schaal H, Scheid A, 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. J Viol 70:298-304. (Pubitemid 126508798)
35. Patargias G, Zitzmann N, Dwek R, Fischer WB. 2006. Proteinprotein interactions: Modeling the hepatitis C virus ion channel p7. J Med Chem 49:648-655. (Pubitemid 43157494)
36. Polverini E, Coll EP, Tieleman DP, Harauz G. 2010. Conformational choreography of a molecular switch region in myelin basic protein-molecular dynamics shows induced folding and secondary structure type conversion upon threonyl phosphorylation in both aqueous and membrane-associated environments. Biochim Biophys Acta 1808:674-683.
37. Popot J-L, Engelman DM. 1990. Membrane protein folding and oligomerization: The two-stage model. Biochemistry 29:4031-4037. (Pubitemid 20145635)
38. Qiang W, Weliky DP. 2009. HIV fusion peptide and its cross-linked oligomers: Efficient synthesis, significance of the trimer in fusion activity, correlation of b strand conformation with membrane cholesterol, and proximity to lipid headgroups. Biochemistry 48:289-301.
39. Schmick SD, Weliky DP. 2010. Major antiparallel and minor parallel b sheet populations detected in the membrane-associated human immunodeficiency virus fusion peptide. Biochemistry 49:10623-10635.
40. Schnölzer M, Alewood P, Jones A, Alewood D, Kent SBH. 1992. In situ neutralization in Boc-chemistry solid phase peptide synthesis: Rapid, high yield assembly of difficult sequences. Int J Pept Protein Res 40:180-193.
41. Slepushkin VA, Melikyan GB, Sidorova MS, Chumakov VM, Andreev SM, Manulyan RA, Karamov EV. 1990. Interaction of human immunodeficiency virus (HIV-1) fusion peptides with artificial lipid membranes. Biochem Biophys Res Comm 172:952-957. (Pubitemid 20384516)
42. Tosteson M, Chow M. 1997. Characterization of the ion channels formed by poliovirus in planar lipid membranes. J Virol 71:507-511. (Pubitemid 26412320)
43. Tristram-Nagle S, Chan R, Kooijman E, Uppamoochikkal P, Qiang W, Weliky DP, Nagle JF. 2010. HIV fusion peptide penetrates, disorders and softens T-cell membrane mimics. J Mol Biol 402:139-153.
44. Ulmschneider MB, Doux JPF, Killian JA, Smith J, Ulmschneider JP 2010a. Mechanism and kinetics of peptide partitioning into membranes. J Am Chem Soc 132:3452-3460.
45. Ulmschneider MB, Smith JC, Ulmschneider JP 2010b. Peptide partitioning properties from directed insertion studies. Biophys J 98:L60-62.
46. Wang G. 2008. NMR of membrane-associated peptides and proteins. Curr Protein Pept Sci 9:50-69.
47. Wyatt R, Sodroski J. 1998. The HIV-1 envelope glycoproteins: Fusogens, antigens, and immunogens. Science 280:1884-1888. (Pubitemid 28299385)
48. Yang X, Kurteva S, Ren X, Lee S, Sodroski J. 2006. Subunit stoichiometry of human immunodeficiency virus type 1 envelope glycoprotein trimers during virus entry into host cells. J Virol 80:4388-4395.
49. Zheng Z, Yang R, Bodner ML, Weliky DP. 2006. Conformational flexibility and strand arrangements of the membrane-associated HIV fusion peptide trimer probed by solid-state NMR spectroscopy. Biochemistry 45:12960-12975. (Pubitemid 44763419)