The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry

Journal of Structural Biology

Volumn 171, Issue 2, 2010, Pages 216-222

  Sanz García, Eduardo ^a   Stewart, Aaron B ^a   Belnap, David M ^a  

^a Brigham Young University   (United States)

Author keywords

Asymmetric reconstruction; Cryo electron microscopy; Model validation; Single particle reconstruction; Starting model; Symmetry determination

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; ARTICLE; CONTROLLED STUDY; IMAGE ANALYSIS; IMAGE PROCESSING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; RANDOMIZATION; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS;

CRYOELECTRON MICROSCOPY; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MODELS, THEORETICAL;

EID: 77953691218     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.03.017     Document Type: Article

References (40)

1. Baker T.S., Cheng R.H. A model-based approach for determining orientations of biological macromolecules imaged by cryo-electron microscopy. J. Struct. Biol. 1996, 116:120-130.
2. Belnap D.M., Filman D.J., Trus B.L., Cheng N., Booy F.P., Conway J.F., Curry S., Hiremath C.N., Tsang S.K., Steven A.C., Hogle J.M. Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus. J. Virol. 2000, 74:1342-1354.
3. Bhella D., Goodfellow I.G., Roversi P., Pettigrew D., Chaudhry Y., Evans D.J., Lea S.M. The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). J. Biol. Chem. 2004, 279:8325-8332.
4. Bubeck D., Filman D.J., Cheng N., Steven A.C., Hogle J.M., Belnap D.M. The structure of the poliovirus 135S cell entry intermediate at 10-Angstrom resolution reveals the location of an externalized polypeptide that binds to membranes. J. Virol. 2005, 79:7745-7755.
5. Cantele F., Lanzavecchia S., Bellon P.L. The variance of icosahedral virus models is a key indicator in the structure determination: a model-free reconstruction of viruses, suitable for refractory particles. J. Struct. Biol. 2003, 141:84-92.
6. Castón 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. 1999, 125:209-215.
7. Conway J.F., Trus B.L., Booy F.P., Newcomb W.W., Brown J.C., Steven A.C. The effects of radiation damage on the structure of frozen hydrated HSV-1 capsids. J. Struct. Biol. 1993, 111:222-233.
8. Crowther R.A., Kiselev N.A., Böttcher B., Berriman J.A., Borisova G.P., Ose V., Pumpens P. Three-dimensional structure of hepatitis B virus core particles determined by electron cryomicroscopy. Cell 1994, 77:943-950.
9. Elmlund H., Lundqvist J., Al-Karadaghi S., Hansson M., Hebert H., Lindahl M. A new cryo-EM single-particle ab initio reconstruction method visualize secondary structure elements in an ATP-fueled AAA+ motor. J. Mol. Biol. 2008, 375:934-947.
10. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State 2006, Oxford University Press, New York.
11. Frank J., Verschoor A., Boublik M. Computer averaging of electron micrographs of 40S ribosomal subunits. Science 1981, 214:1353-1355.
12. Goddard T.D., Huang C.C., Ferrin T.E. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 2007, 157:281-287.
13. Harauz G., Ottensmeyer F.P. Direct three-dimensional reconstruction for macromolecular complexes from electron micrographs. Ultramicroscopy 1984, 12:309-319.
14. Harauz G., van Heel M. Direct 3D reconstruction from projections with initially unknown angles. Pattern Recognition in Practice II 1985, 279-288. Elsevier, North-Holland Publishing, Amsterdam. E.S. Gelsema, L.N. Kanal (Eds.).
15. Heymann J.B., Belnap D.M. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 2007, 157:3-18.
16. Leschziner A.E., Nogales E. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J. Struct. Biol. 2006, 153:284-299.
17. Liu X., Jiang W., Jakana J., Chiu W. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a multi-path simulated annealing optimization algorithm. J. Struct. Biol. 2007, 160:11-27.
18. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 1999, 128:82-97.
19. Ludtke S.J., Chen D.-H., Song J.-L., Chuang D.T., Chiu W. Seeing GroEL at 6Å resolution by single particle electron cryomicroscopy. Structure 2004, 12:1129-1136.
20. Ludtke S.J., Baker M.L., Chen D.-H., Song J.-L., Chuang D.T., Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 2008, 16:441-448.
21. Mullapudi S., Pullan L., Bishop O.T., Khalil H., Stoops J.K., Beckmann R., Kloetzel P.M., Kruger E., Penczek P.A. Rearrangement of the 16S precursor subunits is essential for the formation of the active 20S proteasome. Biophys. J. 2004, 87:4098-4105.
22. Ogura T., Sato C. A fully automatic 3D reconstruction method using simulated annealing enables accurate posterioric angular assignment of protein projections. J. Struct. Biol. 2006, 156:371-386.
23. 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 1994, 53:251-270.
24. R Development Core Team, 2009. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
25. 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. 1987, 146:113-136.
26. Rosenthal P.B., Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 2003, 333:721-745.
27. Saxton W.O., Baumeister W. The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 1982, 127:127-138.
28. Schatz M., Orlova E.V., Dube P., Jäger J., van Heel M. Structure of Lumbricus terrestris hemoglobin at 30Å resolution determined using angular reconstitution. J. Struct. Biol. 1995, 114:28-40.
29. Taylor K.A., Glaeser R.M. Retrospective on the early development of cryo-electron microscopy of macromolecules and a prospective on opportunities for the future. J. Struct. Biol. 2008, 163:214-223.
30. Thuman-Commike P.A., Chiu W. Improved common-line-based icosahedral particle image orientation estimation algorithms. Ultramicroscopy 1997, 68:231-255.
31. Unser M., Trus B.L., Frank J., Steven A.C. The spectral signal-to-noise ratio resolution criterion: computational efficiency and statistical precision. Ultramicroscopy 1989, 30:429-434.
32. Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., Frank J. Locking and unlocking of ribosomal motions. Cell 2003, 114:123-134.
33. Valle M., Zavialov A., Li W., Stagg S.M., Sengupta J., Nielsen R.C., Nissen P., Harvey S.C., Ehrenberg M., Frank J. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 2003, 10:899-906. 1074.
34. van Heel, M., 1984. Three-dimensional reconstruction from projections with unknown angular relationships. In: Csanády, Á. et al. (Eds.), Eighth European Congress on Electron Microscopy, vol. 2. Programme Committee of the Eighth European Congress on Electron Microscopy, Budapest, Hungary, pp. 1347-1348.
35. van Heel M. Similarity measures between images. Ultramicroscopy 1987, 21:95-99.
36. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 1987, 21:111-123.
37. Walz J., Tamura T., Tamura N., Grimm R., Baumeister W., Koster A.J. Tricorn protease exists as an icosahedral supermolecule in vivo. Mol. Cell 1997, 1:59-65.
38. Winkelmann D.A., Baker T.S., Rayment I. Three-dimensional structure of myosin subfragment-1 from electron microscopy of sectioned crystals. J. Cell Biol. 1991, 114:701-713.
39. Yan X., Dryden K.A., Tang J., Baker T.S. Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J. Struct. Biol. 2007, 157:211-225.
40. Zhang X., Settembre E., Xu C., Dormitzer P.R., Bellamy R., Harrison S.C., Grigorieff N. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl. Acad. Sci. USA 2008, 105:1867-1872.