Molecular dynamics simulations on the first two helices of Vpu from HIV-1

Biophysical Journal

Volumn 84, Issue 5, 2003, Pages 3276-3284

  Sramala, I ^a,c   Lemaitre, V ^a,b   Faraldo Gomez J D ^a   Vincent, S ^b   Watts, A ^a   Fischer, W B ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NESTLÉ RESEARCH CENTER   (Switzerland)

^c MAHIDOL UNIVERSITY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ARGININE; GLUTAMIC ACID; LYSINE; TYROSINE; VPU PROTEIN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CYTOPLASM; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDRATION; LIPID BILAYER; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN STABILITY; SIMULATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0037960370     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)70052-6     Document Type: Article

References (62)

1. Azpiazu, I., J. C. Gomez-Fernandez, and D. Chapman. 1993. Biophysical studies of the Pf1 coat protein in the filamentous phage, in detergent micelles, and in a membrane environment. Biochemistry. 32:10720-10726.
2. Barlow, D., and J. Thornton. 1988. Helix geometry in proteins. J. Mol. Biol. 201:601-619.
3. Berendsen, H. J. C., J. R. Grigera, and T. P. Straatsma. 1987. J. Phys. Chem. 91:6269-6271.
4. Boncheva, M., and H. Vogel. 1997. Formation of stable polypeptide monolayers at interfaces: controlling molecular conformation and orientation. Biophys. J. 73:1056-1072.
5. Bout, S., U. Schubert, and K. Strebel. 1995. The human immunodeficiency virus type 1 Vpu protein specifically binds to the cytoplasmic domain of CD4: implications for the mechanism of degradation. J. Virol. 69:1510-1520.
6. Branden, C., and J. Tooze. 1991. Introduction to Protein Structure. Garland, New York.
7. Brünger, A. T. 1992. X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. Yale University Press, New Haven.
8. Campbell, I. D., and A. K. Downing. 1998. NMR of modular proteins. Nat. Struct. Biol. Suppl:496-499.
9. Coadou, G., N. Evrard-Todeschi, J. Gharbi-Benarous, R. Benarous, and J.-P. Girault. 2001. Conformational analysis by NMR and molecular modelling of the 41-62 hydrophilic region of HIV-1 encoded virus protein U (Vpu). Effect of the phosphorylation on sites 52 and 56. C. R. Acad. Sci. Paris-Chemie/Chemistry. 4:751-758.
10. Cohen, E. A., E. F. Terwilliger, J. G. Sodroski, and W. A. Haseltine. 1988. Identification of a protein encoded by the vpu gene of HIV-1. Nature. 334:532-534.
11. Cordes, F., A. Kukol, L. R. Forrest, I. T. Arkin, M. S. P. Sansom, and W. B. Fischer.2001. The structure of the HIV-1 Vpu ion channel: modelling and simulation studies. Biochim. Biophys. Acta. 1512:291-298.
12. Cordes, F. S., A. Tustian, M. S. P. Sansom, A. Watts, and W. B. Fischer. 2002. Bundles consisting of extended transmembrane segments of Vpu from HIV-1: computer simulations and conductance measurements. Biochemistry. 41:7359-7365.
13. de Planque, M. R. R., J.-W. P. Boots, D. T. S. Rijkers, R. M. J. Liskamp, D. V. Greathouse, and J. A. Killian. 2002. The effect of hydrophobic mismatch between phosphatidylcholine bilayers and transmembrane a-helical peptides depend on the nature of interfacially exposed aromatic and charged residues. Biochemistry. 41:8396-8404.
14. Deisenhofer, J., O. Epp, K. Miki, R. Huber, and H. Michel. 1985. Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3A resolution. Nature. 318:618-624.
15. Deora, A., P. Spearman, and L. Ratner. 2000. The N-terminal matrix domain of HIV-1 Gag is sufficient but not necessary for viral protein U-mediated enhancement of particle release through a membrane-targeting mechanism. Virology. 269:305-312.
16. Doolittle, R. F. 1995. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64:287-314.
17. Ewart, G. D., T. Sutherland, P. W. Gage, and G. B. Cox. 1996. The Vpu protein of human immunodeficiency virus type 1 forms cation-selective ion channels. J. Virol. 70:7108-7115.
18. Faraldo-Gomez, J. D., G. R. Smith, and M. S. P. Sansom. 2002. Setting up and optimization of membrane protein simulations. Eur. Biophys. J. 31:217-227.
19. Federau T., U. Schubert, I. Floßdorf, P. Henklein, D. Schomburg, and V. Wray. 1996. Solution structure of the cytoplasmic domain of the human immunodeficiency virus type 1 encoded virus protein U (Vpu). Int. J. Peptide Protein Res. 47:297-310.
20. Fischer, W. B., L. R. Forrest, G. R. Smith, and M. S. P. Sansom. 2000. Transmembrane domains of viral ion channel proteins: a molecular dynamics simulation study. Biopolymers. 53:529-538.
21. Fischer, W. B., and M. S. P. Sansom. 2002. Viral ion channels: structure and function. Biochim. Biophys. Acta. 1561:27-45.
22. 13C-MAS NMR spectroscopy. Biochim. Biophys. Acta. 1463:151-161.
23. Grice, A. L., I. D. Kerr, and M. S. P. Sansom. 1997. Ion channels formed by HIV-Vpu: a modelling and simulation study. FEBS Lett. 405:299-304.
24. Hendsch, Z. S., and B. Tidor. 1994. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:211-226.
25. Henklein, P., R. Kinder, U. Schubert, and B. Bechinger. 2000. Membrane interactions and alignment of structures within the HIV-1 Vpu cytoplasmic domain: effect of phosphorylation of serines 52 and 56. FEBS Lett. 482:220-224.
26. 15N NMR resonances in detergent-solubilized M13 coat protein: a model for the coat protein dimer. Biochemistry. 31:5284-5297.
27. Horowitz, A., L. Serrano, B. Avron, M. Bycroft, and A. R. Fersht. 1990. Strength and co-operativity of contributions of salt bridges to protein stability. J. Mol. Biol. 216:1031-1044.
28. Kerr, I. D., R. Sankararamakrishnan, O. S. Smart, and M. S. P. Sansom. 1994. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophys. J. 67: 1501-1515.
29. Kukol, A., and I. T. Arkin. 1999. Vpu transmembrane peptide structure obtained by site-specific fourier transform infrared dichroism and global molecular dynamics searching. Biophys. J. 77:1594-1601.
30. Lopez, C. F., M. Montal, J. K. Blasie, M. L. Klein, and P. B. Moore. 2002. Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1. Biophys. J. 83:1259-1267.
31. Ma, C., F. M. Marassi, D. H. Jones, S. K. Straus, S. Bour, K. Strebel, U. Schubert, M. Oblatt-Montal, M. Montal, and S. J. Opella. 2002. Expression, purification, and activities of full-length and truncated versions of the integral membrane protein Vpu from HIV-1. Protein Sci. 11:546-557.
32. 15N-labeled helical membrane proteins in oriented lipid bilayers. J. Magn. Res. 144:156-161.
33. Marassi, F. M., C. Ma, H. Gratkowski, S. K. Straus, K. Strebel, M. Oblatt-Montal, M. Montal, and S. J. Opella. 1999. Correlation of the structural and functional domains in the membrane protein Vpu from HIV-1. Proc. Natl. Acad. Sci. USA. 96:14336-14341.
34. + salt bridges in short peptides of de novo design. Proc. Natl. Acad. Sci. USA. 84:8898-8902.
35. Mascioni, A., C. Karim, J. Zamoon, D. D. Thomas, and G. Veglia. 2002. Solid-state NMR and rigid body molecular dynamics to determine domain orientations of monomeric phospholamban. J. Am. Chem. Soc. 124:9392-9393.
36. Milik, M., and J. Skolnick. 1993. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins. 15:10-25.
37. Moore, P. B., Q. Zhong, T. Husslein, and M. L. Klein. 1998. Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle. FEBS Lett. 431:143-148.
38. Musafia, B., V. Buchner, and D. Arad. 1995. Complex salt bridges in proteins: statistical analysis of structure and function. J. Mol. Biol. 254:761-770.
39. Nambudripad, R., W. Stark, S. J. Opella, and L. Makowski. 1991. Membrane-mediated assembly of filamentous bacteriophage Pf1 coat protein. Science. 252:1305-1308.
40. Paul, M., S. Mazumder, N. Raja, and M. Abdul Jabbar. 1998. Mutational analysis of the human immunodeficiency virus type I Vpu transmembrane domain that promotes the enhanced release of virus-like particles from the plasma membrane of mammalian cells. J. Virol. 72:1270-1279.
41. Ridder, A. N. J. A., W. van de Hoef, J. Stam, A. Kuhn, B. de Kruijff, and J. A. Killian. 2002. Importance of hydrophobic matching for spontaneous insertion of a single-spanning membrane protein. Biochemistry. 41:4946-4952.
42. Roux, B., and T. B. Woolf. 1996. Molecular dynamics of Pfl coat protein in a phospholipid bilayer. In Biological Membranes, K. M. Metz, Jr. and B. Roux, editors. Birkhäuser, Boston. 555-587.
43. Sansom, M. S. P., I. H. Shrivastava, J. N. Bright, J. Tate, C. E. Capener, and P. C. Biggin. 2002. Potassium channels: structures, models, simulations. Biochim. Biophys. Acta. 1565:294-307.
44. Schubert, U., S. Bout, A. V. Ferrer-Montiel, M. Montal, F. Maldarelli, and K. Strebel. 1996a. The two biological activities of human immunodeficiency virus type I Vpu protein involve two separable structural domains. J. Virol. 70:809-819.
45. Schubert, U., A. V. Ferrer-Montiel, M. Oblatt-Montal, P. Henklein, K. Strebel, and M. Montal. 1996b. Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells. FEBS Lett. 398:12-18.
46. Shon, K.-J., Y. Kim, L. A. Colnago, and S. J. Opella. 1991. NMR studies of the structure and dynamics of membrane-bound bacteriophage Pf1 coat protein. Science. 252:1303-1305.
47. Shrivastava, I. H., and M. S. P. Sansom. 2000. Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys. J. 78:557-570.
48. Strebel, K., T. Klimkait, F. Maldarelli, and M. A. Martin. 1989. Molecular and biochemical analysis of human deficiency virus type 1 vpu protein. J. Virol. 63:3784-3791.
49. Strebel, K., T. Klimkait, and M. A. Martin. 1988. Novel gene of HIV-1, vpu, and its 16-kilodalton product. Science. 241:1221-1223.
50. Tiganos, E., J. Friborg, B. Allain, N. G. Daniel, X.-J. Yao, and E. A. Cohen. 1998. Structural and functional analyis of the membrane-spanning domain of the Human Immunodeficiency Virus Type 1 Vpu protein. Virology. 251:96-107.
51. Tobias, D. J., M. L. Klein, and S. J. Opella. 1993. Molecular dynamics simulation of Pfl coat protein. Biophys. J. 64:670-675.
52. Turner, R. J., and J. H. Weiner. 1993. Evaluation of transmembrane helix prediction methods using the recently defined NMR structures of the coat proteins from bacteriophages M13 and Pf1. Biochim. Biophys. Acta. 1202:161-168.
53. Ulmschneider, M., and M. S. P. Sansom. 2001. Amino acid distribution in integral membrane protein structures. Biochim. Biophys. Acta. 1512: 1-14.
54. 13C resonances in detergent-solubilized M13 coat protein via multinuclear multidimensional NMR: a model for the coat protein monomer. Biochemistry. 32:8322-8328.
55. van Gunsteren, W. F., and A. E. Mark. 1998. Validation of molecular dynamics simulation. J. Chem. Phys. 108:6109-6116.
56. Waldburger, C. D., J. F. Schildbach, and R. T. Sauer. 1995. Are buried salt bridges important for protein stability and conformational specifity? Nat. Struct. Biol. 2:122-128.
57. Willbold, D., S. Hoffmann, and P. Rösch. 1997. Secondary structure and tertiary fold of the human immunodeficiency virus protein U (Vpu) cytoplasmatic domain in solution. Eur. J. Biochem. 245:581-588.
58. Willey, R. L., F. Maldarelli, M. A. Martin, and K. Strebel. 1992. Human immunodeficiency virus type 1 Vpu protein induces rapid degradation of CD4. J. Virol. 66:7193-7200.
59. Wolkers, W. F., P. I. Haris, A. M. A. Pistorius, D. Chapman, and M. A. Hemminga. 1995. FT-IR spectroscopy of the major coat protein of MI3 and Pf1 in the phage and reconstituted into phospholipid systems. Biochemistry. 34:7825-7833.
60. 1H NMR-spectroscopy. Int. J. Pept. Protein Res. 45:35-43.
61. Wray, V., R. Kinder, T. Federau, P. Henklein, B. Bechinger, and U. Schubert. 1999. Solution structure and orientation of the transmembrane anchor domain of the HIV-1-encoded virus protein U by high resolution and solid-state NMR spectroscopy. Biochemistry. 38:5272-5282.
62. Zheng, S., J. Strzalka, C. Ma, S. J. Opella, B. M. Ocko, and J. K. Blasie. 2001. Structural studies of the HIV-1 accessory protein Vpu in Langmuir monolayers: synchroton x-ray reflectivity. Biophys. J. 80:1837-1850.