The variance of icosahedral virus models is a key indicator in the structure determination: A model-free reconstruction of viruses, suitable for refractory particles

Journal of Structural Biology

Volumn 141, Issue 1, 2003, Pages 84-92

  Cantele, Francesca ^a   Lanzavecchia, Salvatore ^a   Bellon, Pier Luigi ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

Correspondence analysis; Model free reconstruction; Reconstruction of viruses; Refractory species; Variance of virus models; Viruses

Indexed keywords

ARTICLE; CLASSIFICATION; CORRESPONDENCE ANALYSIS; HEPATITIS B VIRUS; MODEL; POLIOMYELITIS VIRUS; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; VIRUS CAPSID; VIRUS MORPHOLOGY;

CAPSID; HEPATITIS B VIRUS; MICROSCOPY, ELECTRON; MODELS, STRUCTURAL; MODELS, THEORETICAL; POLIOVIRUS; VIRUSES;

HEPATITIS B VIRUS; POLIOVIRUS; SACCHAROMYCES CEREVISIAE VIRUS L-A (L1);

EID: 0037282736     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1047-8477(02)00577-4     Document Type: Article

References (43)

1. Baker T.S., Cheng R.H. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J. Struct. Biol. 116:1996;120-130.
2. Belnap D.M., McDermott B.M. Jr., Filman D.J., Cheng N., Trus B.L., Zuccola H.J., Racaniello V.R., Hogle J.M., Steven A.C. Three-dimensional structure of poliovirus receptor bound to poliovirus. Proc. Natl. Acad Sci. USA. 97:2000;73-78.
3. Benzecri J.P. Correspondence Analysis Handbook. 1992;Marcel Dekker, New York.
4. Böttcher B., Wynne S.A., Crowter R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 386:1997;88-91.
5. Caston J.R., Trus B.L., Booy F.P., Wickner R.B., Wall J.S., Steven A.C. Structure of L-A virus: a specialized compartment for the transcription and replication of double-stranded RNA. J. Cell. Biol. 138:1997;975-985.
6. Caston J.R., Belnap D.M., Steven A.C., Trus B.L. A strategy for determining the orientations of refractory particles for reconstruction from cryo-electron micrographs with particular reference to round, smooth-surfaced, icosahedral viruses. J. Struct. Biol. 125:1999;209-215.
7. Cheng R.H., Caston J.R., Wang G.J., Gu F., Smith T.J., Baker T.S., Bozarth R.F., Trus B.L., Cheng N., Wickner R.B., Steven A.C. Fungal virus capsids: cytoplasmic compartments for the replication of double-stranded RNA formed as icosahedral shells of asymmetric Gag dimers. J. Mol. Biol. 244:1994;255-258.
8. Cheng R.H., Reddy V., Olson N.H., Fisher A., Baker T.S., Johnson J.E. Functional implications of quasi-equivalence in a T=3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography. Structure. 2:1994;271-282.
9. Cheng R.H., Kuhn R.J., Olson N.H., Rossmann M.G., Choi H.-K., Smith T.J., Baker T.S. Three-dimensional structure of an enveloped alphavirus with T=4 icosahedral symmetry. Cell. 80:1995;621-630.
10. Conway J.F., Cheng N., Zlotnick A., Wingfield P.T., Stahl S.J., Steven A.C. Visualisation of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 386:1997;91-94.
11. Crowther R.A. Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos. Trans. R. Soc. London Ser. B. 261:1971;221-230.
12. Crowther R.A., Amos L.A. Three-dimensional image reconstruction of some small spherical viruses. Cold Spring Harbor Symp. Quant. Biol. 36:1972;489-494.
13. Crowther R.A., Amos L.A., Finch J.T., De Rosier D.J., Klug A. Three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Nature. 226:1970;421-425.
14. Crowther R.A., Kiselev N.A., Böttcher B., Berriman J.A., Borisova J.P., Ose V., Pumpens P. Three-dimensional structure of hepatitis B virus core particles determined by electron cryomicroscopy. Cell. 77:1994;943-950.
15. Dokland T., Murialdo H. Structural transitions during maturation of bacteriophage lambda capsids. J. Mol. Biol. 233:1993;682-694.
16. Frank J. Classification of macromolecular assemblies studied as "single particles." Rev. Biophys. 23:1990;281-329.
17. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies. first ed. 1996;Academic Press, San Diego.
18. Fuller S.D. The T=4 envelope of Sindbis virus is organized by interactions with a complementary T=3 capsid. Cell. 48:1987;923-934.
19. Fuller S.D., Berriman J.A., Butcher S.J., Gowen B.E. Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell. 81:1995;715-725.
20. Fuller S.D., Butcher S.J., Cheng R.H., Baker T.S. Three-dimensional reconstruction of icosahedral particles - The uncommon line. J. Struct. Biol. 116:1996;48-55.
21. Hagensee M., Olson N.H., Baker T.S., Galloway D. Three-dimensional structure of vaccinia virus-produced HPV-1 capsids. J. Virol. 68:1994;4503-4505.
22. Harauz G., Ottensmeyer F.P. Nucleosome reconstruction via phosphorus mapping. Science. 226:1984;936-940.
23. Harauz G., van Heel M. Direct 3D reconstruction from projections with initially unknown angles. Gelsema E.S., Kanal L.N. Pattern Recognition in Practice II. 1986;279-288 Elsevier, North-Holland.
24. Harauz G., van Heel M. Exact filters for general geometry three-dimensional reconstruction. Optik. 73:1986;146-156.
25. Hogle J.M., Chow M., Filman D.J. Three-dimensional structure of poliovirus at 2.9. Å resolution Science. 229:1985;1358-1365.
26. Ilag L.L., Olson N.H., Dokland T., Music C.L., Cheng R.H., Bowen Z., McKenna R., Rossmann M.G., Baker T.S., Incardona N.L. DNA packaging intermediates of bacteriophage. φ X174 Structure. 3:1995;353-363.
27. Johnson C.A., Weisenfeld N.I., Trus B.L., Conway J.F., Martino R.L., Steven A.C. Orientation determination in the 3D reconstruction of icosahedral viruses using a parallel computer. Proceedings, Supercomputing. 1994;550-559 IEEE Computer Society Press, Los Alamitos, CA.
28. Kenney J.M., Sjoberg M., Garoff H., Fuller S.D. Visualization of fusion activation in the Semliki Forest virus spike. Structure. 2:1994;823-832.
29. Lanzavecchia S., Cantele F., Radermacher M., Bellon P.L. Symmetry embedding in the reconstruction of macromolecular assemblies via the discrete Radon transform. J. Struct. Biol. 137:2002;259-272.
30. Lebart L., Morineau A., Tabard N. Technique de la description statistique. 1977;Dunod, Paris.
31. Penczek P., Radermacher M., Frank J. Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy. 40:1992;33-53.
32. Penczek P.A., Grassucci R.A., Frank J. The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy. 53:1994;251-270.
33. Provencher S.W., Vogel R.H. Three-dimensional reconstruction from electron micrographs of disordered specimens I. Method. Ultramicroscopy. 25:1988;209-222.
34. Radermacher M. Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms. Ultramicroscopy. 53:1994;121-136.
35. Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-dimensional reconstruction from a single exposure, random conical tilt series, applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146:1987;113-136.
36. Thuman-Commike P.A., Chiu W. Improved common line-based icosahedral particle image orientation estimation algorithms. Ultramicroscopy. 68:1997;231-255.
37. van Heel M. Similarity measures between images. Ultramicroscopy. 21:1987;95-100.
38. van Heel M. Classification of very large electron microscopial image data sets. Optik. 82:1989;114-126.
39. Venién-Bryan C., Fuller S.D. The organization of the spike complex of Semliki Forest virus. J. Mol. Biol. 236:1994;572-583.
40. Wikoff W.R., Wang G., Parrish C.R., Cheng R.H., Strassheim M.L., Baker T.S., Rossmann M.G. Structures of a neutralized virus: canine parvovirus complexed with neutralizing antibody fragments. Structure. 2:1994;595-607.
41. Yin Z., Zheng Y., Doerschuk P.C. An ab initio algorithm for low-resolution 3-D reconstructions from cryoelectron microscopy images. J. Struct. Biol. 133:2001;132-142.
42. Zhao X., Fox J., Olson N.H., Baker T.S., Young M.J. In vitro assembly of cowpea chlorotic mottle virus from coat protein expressed in E. coli and in vitro transcribed viral cDNA. Virology. 207:1995;486-494.
43. Zlotnick A., Cheng N., Conway J.F., Booy F.P., Steven A.C., Stahl S.J., Wingfield P.T. Dimorphism of hepatitis B virus capsids is strongly influenced by the C-terminus of the capsid protein. Biochemistry. 35:1996;7412-7421.