A method for the alignment of heterogeneous macromolecules from electron microscopy

Journal of Structural Biology

Volumn 166, Issue 1, 2009, Pages 67-78

  Shatsky, Maxim ^a,b   Hall, Richard J ^b   Brenner, Steven E ^a,b   Glaeser, Robert M ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

2D alignment; EM reconstruction; Heterogeneous data; Particle alignment

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA;

ARTICLE; ELECTRON MICROSCOPY; IMAGE ANALYSIS; MACROMOLECULE; PRIORITY JOURNAL; RIBOSOME; SIGNAL NOISE RATIO;

ALGORITHMS; CRYOELECTRON MICROSCOPY; DNA POLYMERASE I; EUKARYOTIC INITIATION FACTOR-3; FOURIER ANALYSIS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; RESEARCH DESIGN; RIBOSOME SUBUNITS, LARGE, BACTERIAL; RIBOSOMES; RNA, MESSENGER; RNA-BINDING PROTEINS;

EID: 60649101018     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.12.008     Document Type: Article

References (45)

1. Beese L.S., Friedman J.M., and Steitz T.A. Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. Biochemistry 32 (1993) 14095-14101
2. Borland L., and van Heel M. Classification of image data in conjugate representation spaces. J. Opt. Soc. Am. A7 (1990) 601
3. Brink J., Ludtke S.J., Kong Y., Wakil S.J., Ma J., and Chiu W. Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (Camb) 12 (2004) 185-191
4. Burgess S.A., Walker M.L., Thirumurugan K., Trinick J., and Knight P.J. Use of negative stain and single-particle image processing to explore dynamic properties of flexible macromolecules. J. Struct. Biol. 147 (2004) 247-258
5. Elad N., Clare D.K., Saibil H.R., and Orlova E.V. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J. Struct. Biol. 162 (2008) 108-120
6. Falke S., Tama F., Brooks III C.L., Gogol E.P., and Fisher M.T. The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J. Mol. Biol. 348 (2005) 219-230
7. Forsyth, D.A., Ponce, J., 2002. Computer vision: a modern approach prentice hall professional technical reference.
8. Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 303-319
9. Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 303-319
10. Frank J. Toward an understanding of the structural basis of translation. Genome Biol. 4 (2003) 237
11. Fu J., Gao H., and Frank J. Unsupervised classification of single particles by cluster tracking in multi-dimensional space. J. Struct. Biol. 157 (2007) 226-239
12. Gabashvili I.S., Agrawal R.K., Spahn C.M., Grassucci R.A., Svergun D.I., Frank J., and Penczek P. Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100 (2000) 537-549
13. Golas M.M., Sander B., Will C.L., Luhrmann R., and Stark H. Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Mol. Cell 17 (2005) 869-883
14. Grigorieff N. Resolution measurement in structures derived from single particles. Acta Crystallogr. D 56 (2000) 1270-1277
15. Hall R.J., Siridechadilok B., and Nogales E. Cross-correlation of common lines: a novel approach for single-particle reconstruction of a structure containing a flexible domain. J. Struct. Biol. 159 (2007) 474-482
16. Harauz G., and van Heel M. Exact filters for general geometry 3-dimensional reconstruction. Optik 73 (1986) 146-156
17. Joyeux L., and Penczek P.A. Efficiency of 2D alignment methods. Ultramicroscopy 92 (2002) 33-46
18. Leschziner, A., Nogales, E., in press. Visualizing flexibility at molecular resoluiton: analysis of heterogeneity in single-paticle electron microscopy reconstructions. Ann. Rev. Biophys. Biomol. Struct.
19. Maes, F., Collignon, A., Vandermeulen, D., Marchal, G., Suetens, P., 1996. Multi-modality image registration by maximization of mutual information. In: Proceedings of the 1996 Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA '96), pp. 14-22.
20. Matadeen R., Patwardhan A., Gowen B., Orlova E.V., Pape T., Cuff M., Mueller F., Brimacombe R., and van Heel M. The Escherichia coli large ribosomal subunit at 7.5 Å resolution. Struct. Fold Des. 7 (1999) 1575-1583
21. Olson C.F. Time and Space Efficient Pose Clustering (1993), University of California at Berkeley
22. Orlova E.V., Sherman M.B., Chiu W., Mowri H., Smith L.C., and Gotto Jr. A.M. Three-dimensional structure of low density lipoproteins by electron cryomicroscopy. Proc. Natl. Acad. Sci. USA 96 (1999) 8420-8425
23. Penczek P. Appendix: measures of resolution using Fourier shell correlation. J. Mol. Biol. 280 (1998) 115-116
24. Penczek P.A., Grassucci R.A., and 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
25. Penczek P.A., Zhu J., and Frank J. A common-lines based method for determining orientations for N > 3 particle projections simultaneously. Ultramicroscopy 63 (1996) 205-218
26. Penczek P.A., Frank J., and Spahn C.M. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 154 (2006) 184-194
27. Penczek P.A., Yang C., Frank J., and Spahn C.M. Estimation of variance in single-particle reconstruction using the bootstrap technique. J. Struct. Biol. 154 (2006) 168-183
28. Pluim J.P.W., Maintz J.B.A., and Viergever M.A. Mutual-information-based registration of medical images: a survey. Med. Imaging IEEE Trans. on 22 (2003) 986-1004
29. Radermacher M., Wagenknecht T., Verschoor A., and 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
30. Roseman A.M., Ranson N.A., Gowen B., Fuller S.D., and Saibil H.R. Structures of unliganded and ATP-bound states of the Escherichia coli chaperonin GroEL by cryoelectron microscopy. J. Struct. Biol. 135 (2001) 115-125
31. Saibil H.R., Horwich A.L., and Fenton W.A. Allostery and protein substrate conformational change during GroEL/GroES-mediated protein folding. Adv. Protein Chem. 59 (2001) 45-72
32. Scheres S.H., Gao H., Valle M., Herman G.T., Eggermont P.P., Frank J., and Carazo J.M. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods 4 (2007) 27-29
33. Siridechadilok B., Fraser C.S., Hall R.J., Doudna J.A., and Nogales E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310 (2005) 1513-1515
34. Staley J.P., and Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92 (1998) 315-326
35. Stockman G. Object recognition and localization via pose clustering. Comput. Vis. Graph. Image Process. 40 (1987) 361-387
36. Tagari M., Newman R., Chagoyen M., Carazo J.-M., and Henrick K. New electron microscopy database and deposition system. Trends Biochem. Sci. 27 (2002) 589
37. Telenczuk, B., Ledesma-Carbato, M.J., Velazquez-Muriel, J.A., Sorzano, C.O.S., Carazo, J.-M., Santos, A., 2006. Molecular image registration using mutual information and differential evolution optimization. In: 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, pp. 844-847.
38. Valle M., Sengupta J., Swami N.K., Grassucci R.A., Burkhardt N., Nierhaus K.H., Agrawal R.K., and Frank J. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21 (2002) 3557-3567
39. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 21 (1987) 111-123
40. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., and Patwardhan A. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys. 33 (2000) 307-369
41. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., and Patwardhan A. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys. 33 (2001) 307-369
42. Viola, P., Wells III, W.M., 1995. Alignment by maximization of mutual information. In: Wells III, W.M. (Ed.), Proceedings Fifth International Conference on Computer Vision, 1995, pp. 16-23.
43. White H.E., Saibil H.R., Ignatiou A., and Orlova E.V. Recognition and separation of single particles with size variation by statistical analysis of their images. J. Mol. Biol. 336 (2004) 453-460
44. Yang S., Yu X., VanLoock M.S., Jezewska M.J., Bujalowski W., and Egelman E.H. Flexibility of the rings: structural asymmetry in the DnaB hexameric helicase. J. Mol. Biol. 321 (2002) 839-849
45. Zhu Y.-M., and Cochoff S.M. Influence of implementation parameters on registration of MR and SPECT brain images by maximization of mutual information. J. Nucl. Med. 43 (2002) 160-166