Placement of the structural proteins in Sindbis virus

Journal of Virology

Volumn 76, Issue 22, 2002, Pages 11645-11658

  Zhang, Wei ^a   Mukhopadhyay, Suchetana ^a   Pletnev, Sergei V ^a   Baker, Timothy S ^a   Kuhn, Richard J ^a   Rossmann, Michael G ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; STRUCTURAL PROTEIN; VIRUS GLYCOPROTEIN; VIRUS PROTEIN;

ARTICLE; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; MEMBRANE FUSION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SINDBIS VIRUS; VIRUS ADSORPTION; VIRUS CELL INTERACTION; VIRUS MORPHOLOGY; VIRUS NUCLEOCAPSID;

EID: 0036827856     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.76.22.11645-11658.2002     Document Type: Article

References (64)

1. Ahn, A., M. R. Klimjack, P. K. Chatterjee, and M. Kielian. 1999. An epitope of the Semliki Forest virus fusion protein exposed during virus-membrane fusion. J. Virol. 73:10029-10039.
2. Baker, T. S., and R. H. Cheng. 1996. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J. Struct. Biol. 116:120-130.
3. Baker, T. S., N. H. Olson, and S. D. Fuller. 1999. Adding the third dimension to virus life cycles: Three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol. Mol. Biol. Rev. 63:862-922.
4. Barth, B. U., M. Suomalainen, P. Liljeström, and H. Garoff. 1992. Alphavirus assembly and entry: Role of the cytoplasmic tail of the E1 spike subunit. J. Virol. 66:7560-7564.
5. Bashton, M., and C. Chothia. 2002. The geometry of domain combination in proteins. J. Mol. Biol. 315:927-939.
6. Cancedda, R., L. Villa-Komaroff, H. F. Lodish, and M. Schlesinger. 1975. Initiation sites for translation of Sindbis virus 42S and 26S messenger RNAs. Cell 6:215-222.
7. Caspar, D. L. D., and A. Klug. 1962. Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27:1-24.
8. Cheng, R. H., R. J. Kuhn, N. H. Olson, M. G. Rossmann, H. K. Choi, T. J. Smith, and T. S. Baker. 1995. Nucleocapsid and glycoprotein organization in an enveloped virus. Cell 80:621-630.
9. Choi, H. K., L. Tong, W. Minor, P. Dumas, U. Boege, M. G. Rossmann, and G. Wengler. 1991. Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature (London) 354:37-43.
10. Crowther, R. A., D. J. DeRosier, and A. Klug. 1970. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc. R. Soc. London A317:319-340.
11. Edwards, J., E. Mann, and D. T. Brown. 1983. Conformational changes in Sindbis virus envelope proteins accompanying exposure to low pH. J. Virol. 45:1090-1097.
12. Ellenberger, T. E., C. J. Brandl, K. Struhl, and S. C. Harrison. 1992. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α helices: Crystal structure of the protein-DNA complex. Cell 71:1223-1237.
13. Ferlenghi, I., M. Clarke, T. Ruttan, S. L. Allison, J. Schalich, F. X. Heinz, S. C. Harrison, F. A. Rey, and S. D. Fuller. 2001. Molecular organization of a recombinant subviral particle from tick-borne encephalitis virus. Mol. Cell 7:593-602.
14. Forsell, K., L. Xing, T. Kozlovska, R. H. Cheng, and H. Garoff. 2000. Membrane proteins organize a symmetrical virus. EMBO J. 19:5081-5091.
15. Fuller, S. D., J. A. Berriman, S. J. Butcher, and B. E. Gowen. 1995. Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81:715-725.
16. Fuller, S. D., S. J. Butcher, R. H. Cheng, and T. S. Baker. 1996. Three-dimensional reconstruction of icosahedral particles - The uncommon line. J. Struct. Biol. 116:48-55.
17. Garoff, H., A. M. Frischauf, K. Simons, H. Lehrach, and H. Delius. 1980. Nucleotide sequence of cDNA coding for Semliki Forest virus membrane glycoproteins. Nature (London) 288:236-241.
18. Geigenmüller-Gnirke, U., H. Nitschko, and S. Schlesinger. 1993. Deletion analysis of the capsid protein of Sindbis virus: Identification of the RNA binding region. J. Virol. 67:1620-1626.
19. Gibbons, D. L., A. Ahn, P. K. Chatterjee, and M. Kielian. 2000. Formation and characterization of the trimeric form of the fusion protein of Semliki Forest virus. J. Virol. 74:7772-7780.
20. Hahn, C. S., and J. H. Strauss. 1990. Site-directed mutagenesis of the proposed catalytic amino acids of the Sindbis virus capsid protein autoprotease. J. Virol. 64:3069-3073.
21. Havelka, W. A., R. Henderson, and D. Oesterhelt. 1995. Three-dimensional structure of halorhodopsin at 7 Å resolution. J. Mol. Biol. 247:726-738.
22. Holm, L., and C. Sander. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138.
23. Kielian, M., M. R. Klimjack, S. Ghosh, and W. A. Duffus. 1996. Mechanisms of mutations inhibiting fusion and infection by Semliki Forest virus. J. Cell Biol. 134:863-872.
24. Kuhn, R. J., W. Zhang, M. G. Rossmann, S. V. Pletnev, J. Corver, E. Lenches, C. T. Jones, S. Mukhopadhyay, P. R. Chipman, E. G. Strauss, T. S. Baker, and J. H. Strauss. 2002. Structure of dengue virus: Implications for flavivirus organization, maturation, and fusion. Cell 108:717-725.
25. Lee, S., R. J. Kuhn, and M. G. Rossmann. 1998. Probing the potential glycoprotein binding site of Sindbis virus capsid protein with dioxane and model building. Proteins 33:311-317.
26. Lee, S., K. E. Owen, H. K. Choi, H. Lee, G. Lu, G. Wengler, D. T. Brown, M. G. Rossmann, and R. J. Kuhn. 1996. Identification of a protein binding site on the surface of the alphavirus nucleocapsid and its implication in virus assembly. Structure 4:531-541.
27. Lescar, J., A. Roussel, M. W. Wein, J. Navaza, S. D. Fuller, G. Wengler, G. Wengler, and F. A. Rey. 2001. The fusion glycoprotein shell of Semliki Forest virus: An icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 105:137-148.
28. Levy-Mintz, P., and M. Kielian. 1991. Mutagenesis of the putative fusion domain of the Semliki Forest virus spike protein. J. Virol. 65:4292-4300.
29. Luo, M., G. Vriend, G. Kamer, I. Minor, E. Arnold, M. G. Rossmann, U. Boege, D. G. Scraba, G. M. Duke, and A. C. Palmenberg. 1987. The atomic structure of Mengo virus at 3.0 Å resolution. Science 235:182-191.
30. Mancini, E. J., M. Clarke, B. Gowen, T. Rutten, and S. D. Fuller. 2000. Cryo-electron microscopy reveals the functional anatomy of an enveloped virus, Semliki Forest virus. Mol. Cell 5:255-266.
31. Matthews, B. W., and M. G. Rossmann. 1985. Comparison of protein structures. Methods Enzymol. 115:397-420.
32. Owen, K. E., and R. J. Kuhn. 1996. Identification of a region in the Sindbis virus nucleocapsid protein that is involved in specificity of RNA encapsidation. J Virol. 70:2757-2763.
33. Paredes, A. M., D. T. Brown, R. Rothnagel, W. Chiu, R. J. Schoepp, R. E. Johnston, and B. V. V. Prasad. 1993. Three-dimensional structure of a membrane-containing virus. Proc. Natl. Acad. Sci. USA 90:9095-9099.
34. Paredes, A. M., H. Heidner, P. Thuman-Commike, B. V. V. Prasad, R. E. Johnston, and W. Chiu. 1998. Structural localization of the E3 glycoprotein in attenuated Sindbis virus mutants. J. Virol. 72:1534-1541.
35. Perera, R., K. E. Owen, T. L. Tellinghuisen, A. E. Gorbalenya, and R. J. Kuhn. 2001. Alphavirus nucleocapsid protein contains a putative coiled coil α-helix important for core assembly. J. Virol. 75:1-10.
36. Phinney, B. S., K. Blackburn, and D. T. Brown. 2000. The surface conformation of Sindbis virus glycoproteins E1 and E2 at neutral and low pH, as determined by mass spectrometry-based mapping. J Virol. 74:5667-5678.
37. Pletnev, S. V., W. Zhang, S. Mukhopadhyay, B. R. Fisher, R. Hernandez, D. T. Brown, T. S. Baker, M. G. Rossmann, and R. J. Kuhn. 2001. Locations of carbohydrate sites on Sindbis virus glycoproteins show that E1 forms an icosahedral scaffold. Cell 105:127-136.
38. Rao, S. T., and M. G. Rossmann. 1973. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76:241-256.
39. Rey, F. A., F. X. Heinz, C. Mandl, C. Kunz, and S. C. Harrison. 1995. The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution. Nature (London) 375:291-298.
40. Rice, C. M., and J. H. Strauss. 1981. Synthesis, cleavage and sequence analysis of DNA complementary to the 26 S messenger RNA of Sindbis virus. J. Mol. Biol. 150:315-340.
41. Roseman, A. M. 2000. Docking structures of domains into maps from cryoelectron microscopy with local correlation. Acta Crystallogr. Sect. D 56:1332-1340.
42. Rossmann, M. G. 2000. Fitting atomic models into electron microscopy maps. Acta Crystallogr. Sect. D 56:1341-1349.
43. 5. J. Biol. Chem. 250:7525-7532.
44. Rossmann, M. G., E. Arnold, J. W. Erickson, E. A. Frankenberger, J. P. Griffith, H. J. Hecht, J. E. Johnson, G. Kamer, M. Luo, A. G. Mosser, R. R. Rueckert, B. Sherry, and G. Vriend. 1985. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature (London) 317:145-153.
45. Rossmann, M. G., R. Bernal, and S. V. Pletnev. 2002. Combining electron microscopic with X-ray crystallographic structures. J. Struct. Biol. 136:190-200.
46. Rossmann, M. G., and D. M. Blow. 1962. The detection of subunits within the crystallographic asymmetric unit. Acta Crystallogr. 15:24-31.
47. Rossmann, M. G., A. Liljas, C. I. Brändén, and L. J. Banaszak. 1975. Evolutionary and structural relationships among dehydrogenases, p. 61-102. In P. D. Boyer (ed.), The Enzymes, 3rd Ed., vol. XI. Academic Press, New York, N.Y.
48. Rossmann, M. G., D. Moras, and K. W. Olsen. 1974. Chemical and biological evolution of a nucleotide-binding protein. Nature (London) 250:194-199.
49. Schlesinger, M. J., and S. Schlesinger. 1986. Formation and assembly of alphavirus glycoproteins, p. 121-148. In S. Schlesinger and M. J. Schlesinger (ed.), The Togaviridae and Flaviviridae. Plenum Publishing Corp., New York, N.Y.
50. Skoging, U., M. Vihinen, L. Nilsson, and P. Liljeström. 1996. Aromatic interactions define the binding of the alphavirus spike to its nucleocapsid. Structure 4:519-529.
51. Smith, T. J., R. H. Cheng, N. H. Olson, P. Peterson, E. Chase, R. J. Kuhn, and T. S. Baker. 1995. Putative receptor binding sites on alphaviruses as visualized by cryoelectron microscopy. Proc. Natl. Acad. Sci. USA 92:10648-10652.
52. Strauss, J. H., and E. G. Strauss. 2001. Virus evolution: How does an enveloped virus make a regular structure? Cell 105:5-8.
53. Tellinghuisen, T. L., A. E. Hamburger, B. R. Fisher, R. Ostendorp, and R. J. Kuhn. 1999. In vitro assembly of alphavirus cores by using nucleocapsid protein expressed in Escherichia coli. J. Virol. 73:5309-5319.
54. Tellinghuisen, T. L., and R. J. Kuhn. 2000. Nucleic acid-dependent cross-linking of the nucleocapsid protein of Sindbis virus. J. Virol. 74:4302-4309.
55. Tellinghuisen, T. L., R. Perera, and R. J. Kuhn. 2001. In vitro assembly of Sindbis virus core-like particles from cross-linked dimers of truncated and mutant capsid proteins. J. Virol. 75:2810-2817.
56. Todd, A. E., C. A. Orengo, and J. M. Thornton. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:1113-1143.
57. Vénien-Bryan, C., and S. D. Fuller. 1994. The organization of the spike complex of Semliki Forest virus. J. Mol. Biol. 236:572-583.
58. Volkmann, N., K. J. Amann, S. Stoilova-McPhie, C. Egile, D. C. Winter, L. Hazelwood, J. E. Heuser, R. Li, T. D. Pollard, and D. Hanein. 2001. Structure of Arp2/3 complex in its activated state and in actin filament branch junctions. Science 293:2456-2459.
59. Wahlberg, J. M., R. Bron, J. Wilschut, and H. Garoff. 1992. Membrane fusion of Semliki Forest virus involves homotrimers of the fusion protein. J. Virol. 66:7309-7318.
60. Weiss, B., U. Geigenmüller-Gnirke, and S. Schlesinger. 1994. Interactions between Sindbis virus RNAs and a 68 amino acid derivative of the viral capsid protein further defines the capsid binding site. Nucleic Acids Res. 22:780-786.
61. Weiss, B., H. Nitschko, I. Ghattas, R. Wright, and S. Schlesinger. 1989. Evidence for specificity in the encapsidation of Sindbis virus RNAs. J. Virol. 63:5310-5318.
62. Wengler, G., G. Wengler, and F. A. Rey. 1999. The isolation of the ectodomain of the alphavirus E1 protein as a soluble hemagglutinin and its crystallization. Virology 257:472-482.
63. Wriggers, W., and P. Chacón. 2001. Modeling tricks and fitting techniques for multiresolution structures. Structure 9:779-788.
64. Wriggers, W., R. A. Milligan, and J. A. McCammon. 1999. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125:185-189.