Modeling Experimental Image Formation for Likelihood-Based Classification of Electron Microscopy Data

Structure

Volumn 15, Issue 10, 2007, Pages 1167-1177

  Scheres, Sjors H W ^a   Núñez Ramírez, Rafael ^a   Gómez Llorente, Yacob ^a   San Martín, Carmen ^a   Eggermont, Paul P B ^b   Carazo, José María ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF DELAWARE   (United States)

Author keywords

PROTEINS

Indexed keywords

ARCHAEAL PROTEIN; HELICASE; VIRUS T ANTIGEN;

ALGORITHM; ARTICLE; DATA ANALYSIS; ELECTRON MICROSCOPY; ESCHERICHIA COLI; FOURIER ANALYSIS; IMAGE ANALYSIS; IMAGING SYSTEM; MATHEMATICAL MODEL; METHANOBACTERIUM THERMOAUTOTROPHICUM; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RIBOSOME; SIGNAL NOISE RATIO; SIMIAN VIRUS 40; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANTIGENS, POLYOMAVIRUS TRANSFORMING; ARCHAEAL PROTEINS; CRYOELECTRON MICROSCOPY; DNA HELICASES; ESCHERICHIA COLI; IMAGING, THREE-DIMENSIONAL; LIKELIHOOD FUNCTIONS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; RIBOSOMES;

ARCHAEA; SIMIAN VIRUS 40;

EID: 35148891312     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.09.003     Document Type: Article

References (40)

1. Adams P.D., Pannu N.S., Read R.J., and Brunger A.T. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA 94 (1997) 5018-5023
2. Carazo J.M., Rivera F.F., Zapata E.L., Radermacher M., and Frank J. Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles. J. Microsc. 157 (1990) 187-203
3. Dang T.X., Hotze E.M., Rouiller I., Tweten R.K., and Wilson-Kubalek E.M. Prepore to pore transition of a cholesterol-dependent cytolysin visualized by electron microscopy. J. Struct. Biol. 150 (2005) 100-108
4. DeLucia A.L., Deb S., Partin K., and Tegtmeyer P. Functional interactions of the simian virus 40 core origin of replication with flanking regulatory sequences. J. Virol. 57 (1986) 138-144
5. Dempster A.P., Laird N.M., and Rubin D.B. Maximum-likelihood from incomplete data via the EM algorithm. J. Roy. Statist. Soc. Ser. B. Methodological 39 (1977) 1-38
6. 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
7. Doerschuk P.C., and Johnson J.E. Ab initio reconstruction and experimental design for cryo electron microscopy. IEEE Trans. Inf. Theory 46 (2000) 1714-1729
8. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies (2006), Oxford University Press, New York
9. Gómez-Llorente Y., Fletcher R.J., Chen X.S., Carazo J.M., and San Martín C. Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum. J. Biol. Chem. 280 (2005) 40909-40915
10. Grigorieff N. FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol. 157 (2007) 117-125
11. Gubellini F., Francia F., Busselez J., Venturoli G., and Levy D. Functional and structural analysis of the photosynthetic apparatus of Rhodobacter veldkampii. Biochemistry 45 (2006) 10512-10520
12. Lehmann E.L., and Casella G. Theory of Point Estimation. Second Edition (1998), Springer-Verlag, New York
13. Leschziner A.E., and Nogales E. Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions. Annu. Rev. Biophys. Biomol. Struct. 36 (2007) 43-62
14. Llorca O. Introduction to 3D reconstruction of macromolecules using single particle electron microscopy. Acta Pharmacol. Sin. 26 (2005) 1153-1164
15. Marabini R., Herman G.T., and Carazo J.M. 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy 72 (1998) 53-65
16. Martín-Benito J., Gómez-Reino J., Stirling P.C., Lundin V.F., Gómez-Puertas P., Boskovic J., Chacón P., Fernández J.J., Berenguer J., Leroux M.R., and Valpuesta J.M. Divergent substrate-binding mechanisms reveal an evolutionary specialization of eukaryotic prefoldin compared to its archaeal counterpart. Structure 15 (2007) 101-110
17. Mindell J.A., and Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142 (2003) 334-347
18. Pascual A., Bárcena M., Merelo J.J., and Carazo J.M. Mapping and fuzzy classification of macromolecular images using self-organizing neural networks. Ultramicroscopy 84 (2000) 85-99
19. Pascual-Montano A., Donate L.E., Valle M., Bárcena M., Pascual-Marquí R.D., and Carazo J.M. A novel neural network technique for analysis and classification of EM single-particle images. J. Struct. Biol. 133 (2001) 233-245
20. Penczek P., Zhu J., Schroeder R., and Frank J. Three dimensional reconstruction with contrast transfer compensation from defocus series. Scanning Microsc. 11 (1997) 147-154
21. Provencher S.W., and Vogel R.H. Three-dimensional reconstruction from electron micrographs of disordered specimens. I. Method. Ultramicroscopy 25 (1988) 209-221
22. Read R.J. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1373-1382
23. Scheres S.H.W., Valle M., and Carazo J.M. Fast maximum-likelihood refinement of electron microscopy images. Bioinformatics 21 Suppl 2 (2005) ii243-ii244
24. Scheres S.H.W., Valle M., Núñez R., Sorzano C.O.S., Marabini R., Herman G.T., and Carazo J.M. Maximum-likelihood multi-reference refinement for electron microscopy images. J. Mol. Biol. 348 (2005) 139-149
25. Scheres S.H.W., 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
26. Schleiff E., Soll J., Kuchler M., Kuhlbrandt W., and Harrer R. Characterization of the translocon of the outer envelope of chloroplasts. J. Cell Biol. 160 (2003) 541-551
27. Sigworth F.J. A maximum-likelihood approach to single-particle image refinement. J. Struct. Biol. 122 (1998) 328-339
28. Simanis V., and Lane D.P. An immunoaffinity purification procedure for SV40 large T antigen. Virology 144 (1985) 88-100
29. Sorzano C.O.S., Jonic S., El-Bez C., Carazo J.M., De Carlo S., Thevenaz P., and Unser M. A multiresolution approach to orientation assignment in 3D electron microscopy of single particles. J. Struct. Biol. 146 (2004) 381-392
30. Sorzano C.O.S., Marabini R., Velázquez-Muriel J., Bilbao-Castro J.R., Scheres S.H.W., Carazo J.M., and Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 148 (2004) 194-204
31. Stewart A., and Grigorieff N. Noise bias in the refinement of structures derived from single particles. Ultramicroscopy 102 (2004) 67-84
32. Stirling P.C., Cuellar J., Alfaro G.A., El Khadali F., Beh C.T., Valpuesta J.M., Melki R., and Leroux M.R. PhLP3 modulates CCT-mediated actin and tubulin folding via ternary complexes with substrates. J. Biol. Chem. 281 (2006) 7012-7021
33. Tan P.N., Steinbach M., and Kumar V. Introduction to Data Mining (2006), Addison-Wesley, Reading, MA
34. Terwilliger T.C. Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 965-972
35. Trussel H.J. A priori knowledge in algebraic reconstruction methods. In: Huang T.S. (Ed). Image Reconstruction in Incomplete Observations (1984), Jai Press, London 276-279
36. Unser M., Trus B.L., and Steven A.C. A new resolution criterion based on spectral signal-to-noise ratios. Ultramicroscopy 23 (1987) 39-51
37. Unser M., Sorzano C.O.S., Thevenaz P., Jonic S., El-Bez C., De Carlo S., Conway J.F., and Trus B.L. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J. Struct. Biol. 149 (2005) 243-255
38. Valle M., Chen X.S., Donate L.E., Fanning E., and Carazo J.M. Structural basis for the cooperative assembly of large T antigen on the origin of replication. J. Mol. Biol. 357 (2006) 1295-1305
39. Yin Z., Zheng Y., Doerschuk P.C., Natarajan P., and Johnson J.E. A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction. J. Struct. Biol. 144 (2003) 24-50
40. Young T.Y., and Fu K.-S. Handbook of Pattern Recognition and Image Processing (1986), Academic Press, San Diego