Single particle analysis of filamentous and highly elongated macromolecular assemblies

Journal of Structural Biology

Volumn 148, Issue 2, 2004, Pages 236-250

  Paul, Danielle ^a   Patwardhan, Ardan ^a   Squire, John M ^a   Morris, Edward P ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

3D reconstruction; Actin; Electron microscopy; Filamentous macromolecular complexes; Single particle analysis; Thin filament; Tropomyosin; Troponin

Indexed keywords

TROPOMYOSIN; TROPONIN;

ARTICLE; ELECTRON MICROSCOPE; ELECTRON MICROSCOPY; MACROMOLECULE; MYOFILAMENT; PRIORITY JOURNAL; THIN FILAMENT; THREE DIMENSIONAL IMAGING;

ANIMALS; CALCIUM; CRYSTALLOGRAPHY, X-RAY; FOURIER ANALYSIS; GOLDFISH; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; MICROFILAMENTS; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; MODELS, STATISTICAL; MUSCLES; PROTEIN CONFORMATION; SOFTWARE; TROPOMYOSIN; TROPONIN; X-RAY DIFFRACTION;

EID: 5144229056     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.05.004     Document Type: Article

References (52)

1. AL-Khayat, H.A., Morris, E.P., Powell A.S., Kensler, R.W., Squire, J.M., 2004. 3D structure of vertebrate (fish) muscle myosin filaments by single particle analysis. Manscript in preparation
2. Al-Khayat H.A., Yagi N., Squire J.M. Structural changes in actin-tropomyosin during muscle regulation: computer modelling of low-angle X-ray diffraction data. J. Mol. Biol. 252:1995;611-632
3. Boekema E.J., Berden J.A., van Heel M.G. Structure of mitochondrial F1-ATPase studied by electron microscopy and image processing. Biochim. Biophys. Acta. 851:1986;353-360
4. Boettcher C., Stark H., van Heel M. Stacked bilayer helices: a new structural organisation of amphiphilic molecules. Ultramicroscopy. 62:1996;133-139
5. CCP4., 1994. The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763
6. Crowther R.A., De Rosier D.J., Klug A. The reconstruction of a three-dimensional structure from its projections and its application to electron microscopy. Proc. R. Soc. Lond. A Biol. Sci. 317:1970;319-340
7. Deans S.R. The Radon Transform and Some of its Applications. 1983;Wiley, New York
8. DeRosier D.J., Klug A. Reconstruction of three-dimensional structures from electron micrographs. Nature. 217:1968;130-134
9. DeRosier D.J., Moore P.B. Reconstruction of three-dimensional images from electron micrographs of structures with helical symmetry. J. Mol. Biol. 52:1970;335-369
10. Eakins F., Al-Khayat H.A., Kensler R.W., Morris E.P., Squire J.M. 3D structure of fish muscle myosin filaments. J. Struct. Biol. 137:2002;154-163
11. Ebashi S., Endo M., Ohtsuki I. Control of muscle contraction. Q. Rev. Biophys. 2:1969;351-384
12. Ebashi S. Calcium ions and muscle contraction. Nature. 240:1972;217-218
13. Egelman E.H. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy. 85:2000;225-234
14. Egelman E.H., DeRosier D.J. Image analysis shows that variations in actin crossover spacings are random, not compensatory. Biophys. J. 63:1992;1299-1305
15. Egelman E.H., Francis N., DeRosier D.J. F-actin is a helix with a random variable twist. Nature. 298:1982;131-135
16. Flicker P.F., Phillips G.N., Cohen C. Troponin and its interactions with tropomyosin - an electron-microscope study. J. Mol. Biol. 162:1982;495-501
17. Frank J. Cryo-electron microscopy as an investigative tool: the ribosome as an example. Bioessays. 23:2001;725-732
18. 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;189-190
19. Goncharov A.B., Gefland M.S. Determination of mutual orientation of identical particles from their projections by the moments method. Ultramicroscopy. 25:1988;317-328
20. Harauz G., van Heel M. Exact filters for general geometry three-dimensional reconstruction. Optik. 73:1986;146-156
21. Holmes K.C., Angert I., Kull F.J., Jahn W., Schroder R.R. Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide. Nature. 425:2003;423-427
22. Jimenez J.L., Guijarro J.I., Orlova E., Zurdo J., Dobson C.M., Sunde M., Saibil H.R. Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. EMBO J. 18:1999;815-821
23. Kabsch W., Mannherz H.G., Suck D., Pai E.F., Holmes K.C. Atomic-structure of the actin - DNase-I complex. Nature. 347:1990;37-44
24. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128:1999;82-97
25. Lukoyanova N., Van Loock M.S., Orlova A., Galkin V.E., Wang K., Egelman E.H. Each actin subunit has three nebulin binding sites: implications for steric blocking. Curr. Biol. 12:2002;383-388
26. Metoz F., Arnal I., Wade R.H. Tomography without tilt: three-dimensional imaging of microtubule/motor complexes. J. Struct. Biol. 118:1997;159-168
27. 2+-induced switching of troponin and tropomyosin on actin filaments as revealed by electron cryo-microscopy. J. Mol. Biol. 308:2001;241-261
28. Ohtsuki I. Localization of troponin in thin filament and tropomyosin paracrystal. J. Biochem. 75:1974;753-765
29. Patwardhan, A., Paul, D., Al-Khayat, H.A., Morris, E.P., 2004. A measure for the angle between projections based on the extent of correlation between corresponding central sections. J. Mol. Biol., submitted
30. Peters, C., Steffen, W., Kuznetsov, S., Hodgkinson, J., 2003. The dynactin complex: the keys to molecular motors? The Proceedings of the Royal Microscopical Society 38 Pt 3, 221-222
31. Radermacher M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J Electron Microsc. Tech. 9:1988;359-394
32. Radermacher M. Weighted back-projection methods. Frank J. Electron Tomography. first ed.:1992;91-115 Plenum, New York
33. Radermacher M. Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms. Ultramicroscopy. 53:1994;121-136
34. Radon J. Uber die Bestimmung von Funktionen durch ihre Integralwerte langs gewisser Manningfaltigkeiten. Beritchte uber die Verhandlungen der Koniglich Sachsischen Gesellschaft der Wissenschaften zu Leipzig. Math. Phys. Klasse. 69:1917;262-277
35. Ramachandran G.N., Lakshminarayanan A.V. Three-dimensional reconstruction from radiographs and electron micrographs: application of convolutions instead of Fourier transforms. Proc. Natl. Acad. Sci. USA. 68:1971;2236-2240
36. Rayment I., Holden H.M., Whittaker M., Yohn C.B., Lorenz M., Holmes K.C., Milligan R.A. Structure of the actin-myosin complex and its implications for muscle contraction. Science. 261:1993;58-65
37. Schatz M., van Heel M. Invariant classification of molecular views in electron micrographs. Ultramicroscopy. 32:1990;255-264
38. Schroder R.R., Manstein D.J., Jahn W., Holden H., Rayment I., Holmes K.C., Spudich J.A. Three-dimensional atomic model of F-actin decorated with dictyostelium myosin S1. Nature. 364:1993;171-174
39. Serysheva I.I., Orlova E.V., Chiu W., Sherman M.B., Hamilton S.L., van Heel M. Electron cryomicroscopy and angular reconstitution used to visualize the skeletal muscle calcium release channel. Nat. Struct. Biol. 2:1995;18-24
40. Sosa H., Milligan R.A. Three-dimensional structure of ncd-decorated microtubules obtained by a back-projection method. J. Mol. Biol. 260:1996;743-755
41. Squire J.M., Morris E.P. A new look at thin filament regulation in vertebrate skeletal muscle. FASEB J. 12:1998;761-771
42. Stokes D.L., DeRosier D.J. The variable twist of actin and its modulation by actin binding proteins. J. Cell. Biol. 104:1987;1005-1017
43. van Heel M. Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy. 13(1-2):1984;165-183
44. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy. 21:1987;111-123
45. van Heel M. Classification of very large electron microscopical image datasets. Optik. 82:1989;114-126
46. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., et al. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys. 33:2000;307-369
47. van Heel M., Harauz G., Orlova E.V., Schmidt R., Schatz M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116:1996;17-24
48. van Heel M., Stoffler-Meilicke M. Characteristic views of E. coli and B. stearothermophilus 30S ribosomal subunits in the electron microscope. EMBO J. 4:1985;2389-2395
49. Wade R.H., Horowitz R., Milligan R.A. Towards understanding the structure and interactions of microtubules and motor proteins. Proteins. 23:1995;502-509
50. 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. 336:2004;453-460
51. Yonekura K., Maki S., Morgan D.G., De Rosier D.J., Vonderviszt F., Imanda K., Namba K. The bacterial flagellar cap as the rotary promoter of flagellin self-assembly. Science. 290:2000;2148-2152
52. Yonekura K., Maki-Yonekura S., Namba K. Structure analysis of the flagellar cap-filament complex by electron cryomicroscopy and single-particle image analysis. J. Struct. Biol. 133:2001;246-253