A multiresolution approach to orientation assignment in 3D electron microscopy of single particles

Journal of Structural Biology

Volumn 146, Issue 3, 2004, Pages 381-392

  Sorzano, C O S ^a,b,c   Jonic S ^b   El Bez, C ^d   Carazo, J M ^c   De Carlo, S ^e   Thevenaz P ^b   Unser, M ^b  

^a UNIVERSIDAD SAN PABLO CEU   (Spain)

^b EPFL   (Switzerland)

^c CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^d UNIVERSITY OF LAUSANNE   (Switzerland)

^e INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; ELECTRON MICROSCOPY; IMAGE PROCESSING; MACROMOLECULE; MATHEMATICAL ANALYSIS; NOISE; PARTICULATE MATTER; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; VELOCITY;

ALGORITHMS; BACTERIORHODOPSINS; COMPUTER SIMULATION; GROEL PROTEIN; IMAGING, THREE-DIMENSIONAL; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; PARTICLE SIZE;

EID: 1942489352     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.01.006     Document Type: Article

References (37)

1. Aldroubi A., Unser M. Wavelets in Medicine and Biology. 1996;CRC Press, Boca Raton.
2. Basu S., Bresler Y. Feasibility of tomography with unknown view angles. IEEE Trans. Image Process. 9:2000;1107-1122.
3. Basu S., Bresler Y. Uniqueness of tomography with unknown view angles. IEEE Trans. Image Process. 9:2000;1094-1106.
4. Berman H., Westbrook J., Feng Z., Gilliland G., Bhat T., Weissig H., Shindyalov I., Bourne P. The protein data bank. Nucleic Acids Res. 28:2000;235-242.
5. Boutselakis H., Dimitropoulos D., Fillon J., Golovin A., Henrick K., Hussain A., Ionides J., John M., Keller P.A., Krissinel E., McNeil P., Naim A., Newman R., Oldfield T., Pineda J., Rachedi A., Copeland J., Sitnov A., Sobhany S., Suarez-Uruena A., Swaminathan J., Tagari M., Tate J., Tromm S., Velankar S., Vranken W. E-MSD: The european bioinformatics institute macromolecular structure database. Nucleic Acids Res. 31:2003;458-462.
6. Braig K., Otwinowski Z., Hegde R., Boisvert D.C., Joachimiak A., Horwich A.L., Sigler P.B. The crystal structure of the bacterial chaperonin GroEL at 2.8. Å Nature. 371:1994;578-586.
7. Braig K., Adams P.D., Brunger A.T. Conformational variability in the refined structure of the chaperonin GroEL at 2.8. Å resolution Nat. Struct. Biol. 2:1995;1083-1094.
8. Dengler J. A multi-resolution approach to the 3d reconstruction from an electron microscope tilt series solving the alignment problem without gold particles. Ultramicroscopy. 30:1989;337-348.
9. Desco M., Herández J.A., Santos A., Brammer M. Multiresolution analysis in fMRI: sensitivity and specificity in the detection of brain activation. Hum. Brain Mapp. 14:2001;16-27.
10. De Carlo S., El-Bez C., Alvarez-Rúa C., Borge J., Dubochet J. Cryo-negative staining reduces electron-beam sensitivity of vitrified biological particles. J. Struct. Biol. 138:2002;216-226.
11. Frank J. Three Dimensional Electron Microscopy of Macromolecular Assemblies. 1996;Academic Press, San Diego, CA.
12. Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 2002;303-319.
13. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116:1996;190-199.
14. Gelfand M.S., Goncharov A.B. Spatial rotational alignment of identical particles given their projections: theory and practice. Transl. Math. Monogr. 81:1990;97-122.
15. Goncharov A.B. Three-dimensional reconstruction of arbitrarily arranged identical particles given their projections. Transl. Math. Monogr. 81:1990;67-95.
16. Henderson R., Baldwin J.M., Downing K., Lepault J., Zemlin F. Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5. Å resolution Ultramicroscopy. 19:1986;147-178.
17. Jonić, S., Thévenaz, P., Unser, M., 2003. Multiresolution-based registration of a volume to a set of its projections. In: Proceedings of the SPIE Symposium on Medical Imaging, vol. 5032. San Diego, pp. 1049-1052
18. Kuhlbrandt W., Williams K. Analysis of macromolecular structure and dynamics by electron cryo-microscopy. Curr. Opin. Struct. Biol. 3:1999;537-543.
19. Lauren P.D., Nandhakumar N. Estimating the viewing parameters of random, noisy projections of asymmetric objects for tomographic reconstruction. IEEE Trans. Pattern Anal. Mach. Intell. 19:1997;417-430.
20. Marabini R., Masegosa I.M., Martín M.C.S., Marco S., Fernández J.J., de la Fraga L.G., Vaquerizo C., Carazo J.M. Xmipp: an image processing package for electron microscopy. J. Struct. Biol. 116:1996;237-240.
21. Marabini R., Herman G.T., Carazo J.M. 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy. 72:1998;53-65.
22. Penczek P.A., Grasucci 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.
23. Press W., Teukolsky S., Vetterling W., Flannery B. Numerical Recipes in C. second ed. 1992;Cambridge University Press, Cambridge.
24. Provencher S.W., Vogel R.H. Three-dimensional reconstruction from electron micrographs of disordered specimens. I. Method. Ultramicroscopy. 25:1988;209-222.
25. Radermacher M. Three-dimensional reconstruction from random projections-orientational alignment via Radon transforms. Ultramicroscopy. 53:1994;121-136.
26. Rux J.J., Burnett R.M. Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon. Mol. Ther. 1:2000;18-30.
27. Saad, A., Chiu, W., 2000. Hierarchical wavelets projection matching for orientation determination of low contrast electron cryomicroscopic images of icosahedral virus particles. In: Proceedings of the IEEE ICASSP'00, vol. 4. pp. 2270-2273
28. Salzman D.B. A method of general moments for orienting 2D projections of unknown 3D objects. Comput. Vis. Graph. Image Process. 50:1990;129-156.
29. Simoncelli E.P., Freeman W.T., Adelson E.H., Heeger D.J. Shiftable multiscale transforms. IEEE Trans. Inform. Theory. 38:1992;587-607.
30. Thévenaz P., Ruttiman U.E., Unser M. A pyramid approach to subpixel registration based on intensity. IEEE Trans. Image Process. 7:1998;27-41.
31. Unger V.M. Electron cryomicroscopy methods. Curr. Opin. Struct. Biol. 11:2001;548-554.
32. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy. 21:1987;111-124.
33. van Heel M., Gowen B., Matadeen R. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys. 33:2000;307-369.
34. Vardeman S.B. Statistics for Engineering Problem Solving. 1994;Academic Press, Boston.
35. Velázquez-Muriel J.A., Sorzano C.O.S., Fernández J.J., Carazo J.M. A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjusting. Ultramicroscopy. 96:2003;17-35.
36. Vogel R.H., Provencher S.W. Three-dimensional reconstruction from electron micrographs of disordered specimens. II. Implementation and results. Ultramicroscopy. 25:1988;223-240.
37. β3 in complex with an Arg-Gly-Asp ligand Science. 296:2002;151-155.