Automated multi-model reconstruction from single-particle electron microscopy data

Journal of Structural Biology

Volumn 170, Issue 1, 2010, Pages 98-108

  Shatsky, Maxim ^a,b,c   Hall, Richard J ^c   Nogales, Eva ^b,c,d   Malik, Jitendra ^d   Brenner, Steven E ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Heterogeneous data; Heterogeneous reconstruction; Multi model reconstruction

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; ELONGATION FACTOR G; INITIATION FACTOR 3; RNA POLYMERASE II;

ANALYTIC METHOD; ARTICLE; AUTOMATION; CLUSTER ANALYSIS; COMPLEX FORMATION; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPY; IMAGE RECONSTRUCTION; INTERMETHOD COMPARISON; INTERNAL RIBOSOME ENTRY SITE; MACROMOLECULE; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE; SINGLE PARTICLE ELECTRON MICROSCOPY; STRUCTURAL EQUATION MODELING; STRUCTURE ANALYSIS;

ALGORITHMS; CHEMISTRY TECHNIQUES, ANALYTICAL; EUKARYOTIC INITIATION FACTOR-3; IMAGE PROCESSING, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; RIBOSOMES; RNA POLYMERASE II;

EID: 77950517750     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.01.007     Document Type: Article

References (33)

1. Beese L.S., Friedman J.M., Steitz T.A. Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. Biochemistry 1993, 32:14095-14101.
2. Borland L., van Heel M. Classification of image data in conjugate representation spaces. J. Opt. Soc. Am. A 1990, 7:601.
3. Brink J., Ludtke S.J., Kong Y., Wakil S.J., Ma J., Chiu W. Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure 2004, 12:185-191.
4. Burgess S.A., Walker M.L., Thirumurugan K., Trinick J., Knight P.J. Use of negative stain and single-particle image processing to explore dynamic properties of flexible macromolecules. J. Struct. Biol. 2004, 147:247-258.
5. Cheetham G.M.T., Jeruzalmi D., Steitz T.A. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 1999, 399:80-83.
6. Elad N., Clare D.K., Saibil H.R., Orlova E.V. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J. Struct. Biol. 2008, 162:108-120.
7. Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 2002, 31:303-319.
8. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State 2006, Oxford Press.
9. Fu J., Gao H., Frank J. Unsupervised classification of single particles by cluster tracking in multi-dimensional space. J. Struct. Biol. 2007, 157:226-239.
10. Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J. Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell 2003, 113:789-801.
11. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 33 a resolution. Science 2001, 292:1876-1882.
12. Hall R.J., Siridechadilok B., Nogales E. Cross-correlation of common lines: a novel approach for single-particle reconstruction of a structure containing a flexible domain. J. Struct. Biol. 2007, 159:474-482.
13. Herman G.T., Kalinowski M. Classification of heterogeneous electron microscopic projections into homogeneous subsets. Ultramicroscopy 2008, 108:327-338.
14. Kostek S.A., Grob P., De Carlo S., Lipscomb J.S., Garczarek F., Nogales E. Molecular architecture and conformational flexibility of human RNA polymerase II. Structure 2006, 14:1691-1700.
15. Leschziner A.E., Nogales E. Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions. Ann. Rev. Biophys. Biomol. Struct. 2007, 36:43-62.
16. Malik J., Belongie S., Leung T., Shi J. Contour and texture analysis for image segmentation. Int. J. Comput. Vis. 2001, 43:7-27.
17. Ng A.Y., Jordan M.I., Weiss Y. On spectral clustering: analysis and an algorithm. Adv. Neural Inform. Process. Syst. 2001, 14.
18. Orlova E.V., Sherman M.B., Chiu W., Mowri H., Smith L.C., Gotto A.M. Three-dimensional structure of low density lipoproteins by electron cryomicroscopy. Proc. Natl. Acad. Sci. 1999, 96:8420-8425.
19. Penczek P.A., Frank J., Spahn C.M.T. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 2006, 154:184-194.
20. Rawat U.B.S., Zavialov A.V., Sengupta J., Valle M., Grassucci R.A., Linde J., Vestergaard B., Ehrenberg M., Frank J. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 2003, 421:87-90.
21. Roseman A.M., Ranson N.A., Gowen B., Fuller S.D., Saibil H.R. Structures of unliganded and ATP-bound states of the Escherichia coli chaperonin GroEL by cryoelectron microscopy. J. Struct. Biol. 2001, 135:115-125.
22. Sali A., Glaeser R., Earnest T., Baumeister W. From words to literature in structural proteomics. Nature 2003, 422:216-225.
23. Scheres S.H.W., Gao H., Valle M., Herman G.T., Eggermont P.P.B., Frank J., Carazo J.-M. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nature Methods 2007, 4:27-29.
24. Shatsky M., Hall R.J., Brenner S.E., Glaeser R.M. A method for the alignment of heterogeneous macromolecules from electron microscopy. J. Struct. Biol. 2009, 166:67-78.
25. Shi J., Malik J. Normalized cuts and image segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 2000, 22(8):888-905.
26. Siridechadilok B., Fraser C.S., Hall R.J., Doudna J.A., Nogales E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 2005, 310:1513-1515.
27. Staley J.P., Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 1998, 92:315-326.
28. Tagari M., Newman R., Chagoyen M., Carazo J.-M., Henrick K. New electron microscopy database and deposition system. Trends Biochem. Sci. 2002, 27:589.
29. Tahirov T.H., Temiakov D., Anikin M., Patlan V., McAllister W.T., Vassylyev D.G., Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9Å resolution. Nature 2002, 420:43-50.
30. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 1987, 21:111-123.
31. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., Patwardhan A. Single-particle electron cryo-microscopy: towards atomic resolution. Quart. Rev. Biophys. 2001, 33:307-369.
32. White H.E., Saibil H.R., Ignatiou A., Orlova E.V. Recognition and separation of single particles with size variation by statistical analysis of their images. J. Mol. Biol. 2004, 336:453-460.
33. Yang S., Yu X., VanLoock M.S., Jezewska M.J., Bujalowski W., Egelman E.H. Flexibility of the rings: structural asymmetry in the DnaB hexameric helicase. J. Mol. Biol. 2002, 321:839-849.