The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers

Journal of Structural Biology

Volumn 157, Issue 1, 2007, Pages 83-94

  Egelman, Edward H ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Electron microscopy; Helical reconstruction; Polymers

Indexed keywords

POLYMER;

ALGORITHM; ARTICLE; ELECTRON MICROSCOPY; FOURIER ANALYSIS; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE RECONSTRUCTION; MACROMOLECULE; MICROSCOPE IMAGE; PRIORITY JOURNAL;

ACTINS; ALGORITHMS; CALCIUM-BINDING PROTEINS; COMPUTATIONAL BIOLOGY; DYNAMINS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROFILAMENT PROTEINS; MICROFILAMENTS; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; POLYMERS; PROTEIN STRUCTURE, QUATERNARY;

FILAMENTOUS BACTERIOPHAGE;

EID: 33845305513     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.05.015     Document Type: Article

References (57)

1. Bluemke D.A., Carragher B., and Josephs R. The reconstruction of helical particles with variable pitch. Ultramicroscopy 26 (1988) 255-270
2. Burgess S., Walker M., Knight P.J., Sparrow J., Schmitz S., Offer G., Bullard B., Leonard K., Holt J., and Trinick J. Structural studies of arthrin: monoubiquitinated actin. J. Mol. Biol. 341 (2004) 1161-1173
3. Chen Y.J., Yu X., Kasiviswanathan R., Shin J.H., Kelman Z., and Egelman E.H. Structural polymorphism of Methanothermobacter thermautotrophicus MCM. J. Mol. Biol. 346 (2005) 389-394
4. Chen Y.J., Zhang P., Egelman E.H., and Hinshaw J.E. The stalk region of dynamin drives the constriction of dynamin tubes. Nat. Struct. Mol. Biol. 11 (2004) 574-575
5. Cherepanova O., Orlova A., Galkin V.E., van D.V., Furst D.O., Jin J.P., and Egelman E.H. Xin-repeats and Nebulin-like repeats bind to F-actin in a similar manner. J. Mol. Biol. 356 (2006) 714-723
6. Cohen-Krausz S., and Trachtenberg S. The structure of the archeabacterial flagellar filament of the extreme halophile Halobacterium salinarum R1M1 and its relation to eubacterial flagellar filaments and type IV pili. J. Mol. Biol. 321 (2002) 383-395
7. Cordes F.S., Komoriya K., Larquet E., Yang S., Egelman E.H., Blocker A., and Lea S.M. Helical structure of the needle of the type III secretion system of Shigella flexneri. J. Biol. Chem. 278 (2003) 17103-17107
8. Craig, L., Volkmann, N., Arvai, A.S., Pique, M.E., Yeager, M., Egelman, E.H., Tainer, J.A., 2006. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus functions in pathogenicity. Mol. Cell. in press.
9. Crowther R.A., Padron R., and Craig R. Arrangement of the heads of myosin in relaxed thick filaments from tarantula muscle. J. Mol. Biol. 184 (1985) 429-439
10. Dang T.X., Farah S.J., Gast A., Robertson C., Carragher B., Egelman E., and Wilson-Kubalek E.M. Helical crystallization on lipid nanotubes: streptavidin as a model protein. J. Struct. Biol. 150 (2005) 90-99
11. DeRosier D.J., and Klug A. Reconstruction of three-dimensional structures from electron micrographs. Nature 217 (1968) 130-134
12. Egelman E.H. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85 (2000) 225-234
13. Egelman E.H. An algorithm for straightening images of curved filamentous structures. Ultramicroscopy 19 (1986) 367-373
14. Egelman E.H., and DeRosier D.J. The Fourier transform of actin and other helical systems with cumulative random angular disorder. Acta Crystallogr. A38 (1982) 796-799
15. Egelman E.H., Francis N., and DeRosier D.J. F-actin is a helix with a random variable twist. Nature 298 (1982) 131-135
16. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., and Leith A. SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116 (1996) 190-199
17. Galkin V.E., Esashi F., Yu X., Yang S., West S.C., and Egelman E.H. BRCA2 BRC motifs bind RAD51-DNA filaments. Proc. Natl. Acad. Sci. USA 102 (2005) 8537-8542
18. Galkin V.E., Orlova A., Fattoum A., Walsh M.P., and Egelman E.H. The CH-domain of calponin does not determine the modes of calponin binding to F-actin. J. Mol. Biol. 359 (2006) 478-485
19. Galkin V.E., Orlova A., Koleske A.J., and Egelman E.H. The Arg non-receptor tyrosine kinase modifies F-actin structure. J. Mol. Biol. 346 (2005) 565-575
20. Galkin V.E., Orlova A., Lukoyanova N., VanLoock M.S., Haag P., Bullard B., and Egelman E.H. The location of ubiquitin in Lethocerus arthrin. J. Mol. Biol. 325 (2003) 623-628
21. Galkin V.E., Orlova A., Lukoyanova N., Wriggers W., and Egelman E.H. Actin depolymerizing factor stabilizes an existing state of F-actin and can change the tilt of F-actin subunits. J. Cell Biol. 153 (2001) 75-86
22. Galkin V.E., Orlova A., VanLoock M.S., and Egelman E.H. Do the utrophin tandem calponin homology domains bind F-actin in a compact or extended conformation?. J. Mol. Biol. 331 (2003) 967-972
23. Galkin V.E., Orlova A., VanLoock M.S., Rybakova I.N., Ervasti J.M., and Egelman E.H. The utrophin actin-binding domain binds F-actin in two different modes: implications for the spectrin superfamily of proteins. J. Cell Biol. 157 (2002) 243-251
24. Galkin V.E., Orlova A., VanLoock M.S., Shvetsov A., Reisler E., and Egelman E.H. ADF/cofilin use an intrinsic mode of F-actin instability to disrupt actin filaments. J. Cell Biol. 163 (2003) 1057-1066
25. Galkin V.E., Orlova A., VanLoock M.S., Zhou D., Galan J.E., and Egelman E.H. The bacterial protein SipA polymerizes G-actin and mimics muscle nebulin. Nat. Struct. Biol. 9 (2002) 518-521
26. Galkin V.E., VanLoock M.S., Orlova A., and Egelman E.H. A new internal mode in F-actin helps explain the remarkable evolutionary conservation of actin's sequence and structure. Cur. Biol. 12 (2002) 570-575
27. Gonen T., Cheng Y., Sliz P., Hiroaki Y., Fujiyoshi Y., Harrison S.C., and Walz T. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438 (2005) 633-638
28. Haruta N., Yu X., Yang S., Egelman E.H., and Cox M.M. A DNA pairing-enhanced conformation of bacterial RecA proteins. J. Biol. Chem. 278 (2003) 52710-52723
29. Klug A., Crick F.H.C., and Wyckoff H.W. Diffraction by helical structures. Acta Crystallogr. 11 (1958) 199-213
30. Kudryashov D.S., Galkin V.E., Orlova A., Phan M., Egelman E.H., and Reisler E. Cofilin cross-bridges adjacent actin protomers and replaces part of the longitudinal F-actin interface. J. Mol. Biol. (2006)
31. Lilic M., Galkin V.E., Orlova A., VanLoock M.S., Egelman E.H., and Stebbins C.E. Salmonella SipA polymerizes actin by stapling filaments with nonglobular protein arms. Science 301 (2003) 1918-1921
32. Lukoyanova N., VanLoock M.S., Orlova A., Galkin V.E., Wang K., and Egelman E.H. Each actin subunit has three nebulin-binding sites: implications for steric blocking. Cur. Biol. 12 (2002) 383-388
33. Miyazawa A., Fujiyoshi Y., Stowell M., and Unwin N. Nicotinic acetylcholine receptor at 4.6 Å resolution: transverse tunnels in the channel wall. J. Mol. Biol. 288 (1999) 765-786
34. Miyazawa A., Fujiyoshi Y., and Unwin N. Structure and gating mechanism of the acetylcholine receptor pore. Nature 424 (2003) 949-955
35. Mu X.Q., Egelman E.H., and Bullitt E. Structure and function of Hib pili from Haemophilus influenzae type b. J. Bacteriol. 184 (2002) 4868-4874
36. Mu X.Q., and Bullitt E. Structure and assembly of P-pili: a protruding hinge region used for assembly of a bacterial adhesion filament. Proc. Natl. Acad. Sci. USA 103 (2006) 9861-9866
37. Orlova A., Galkin V.E., VanLoock M.S., Kim E., Shvetsov A., Reisler E., and Egelman E.H. Probing the structure of F-actin: cross-links constrain atomic models and modify actin dynamics. J. Mol. Biol. 312 (2001) 95-106
38. Orlova A., Shvetsov A., Galkin V.E., Kudryashov D.S., Rubenstein P.A., Egelman E.H., and Reisler E. Actin-destabilizing factors disrupt filaments by means of a time reversal of polymerization. Proc. Natl. Acad. Sci. USA 101 (2004) 17664-17668
39. Paul D., Patwardhan A., Squire J.M., and Morris E.P. Single particle analysis of filamentous and highly elongated macromolecular assemblies. J. Struct. Biol. 148 (2004) 236-250
40. Shaikh T.R., Hegerl R., and Frank J. An approach to examining model dependence in EM reconstructions using cross-validation. J. Struct. Biol. 142 (2003) 301-310
41. Sosa H., Hoenger A., and Milligan R.A. Three different approaches for calculating the three-dimensional structure of microtubules decorated with kinesin motor domains. J. Struct. Biol. 118 (1997) 149-158
42. Stewart M., and Kensler R.W. Arrangement of myosin heads in relaxed thick filaments from frog skeletal muscle. J. Mol. Biol. 192 (1986) 831-851
43. Toyoshima C. Structure determination of tubular crystals of membrane proteins. I. Indexing of diffraction patterns 3. Ultramicroscopy 84 (2000) 1-14
44. Trachtenberg S., Galkin V.E., and Egelman E.H. Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism. J. Mol. Biol. 346 (2005) 665-676
45. VanLoock M.S., Yu X., Yang S., Lai A.L., Low C., Campbell M.J., and Egelman E.H. ATP-mediated conformational changes in the RecA filament. Structure (Camb.) 11 (2003) 187-196
46. VanLoock M.S., Yu X., Yang S., Galkin V.E., Huang H., Rajan S.S., Anderson W.F., Stohl E.A., Seifert H.S., and Egelman E.H. Complexes of RecA with LexA and RecX differentiate between active and inactive RecA nucleoprotein filaments. J. Mol. Biol. 333 (2003) 345-354
47. Wall J.S., and Hainfeld J.F. Mass mapping with the scanning transmission electron microscope. Annu. Rev. Biophys. Biophys. Chem. 15 (1986) 355-376
48. Wang H.W., and Nogales E. An iterative Fourier-Bessel algorithm for reconstruction of helical structures with severe Bessel overlap. J. Struct. Biol. 149 (2005) 65-78
49. Ward A., Moody M.F., Sheehan B., Milligan R.A., and Carragher B. Windex: a toolset for indexing helices 1. J. Struct. Biol. 144 (2003) 172-183
50. Woodhead J.L., Zhao F.Q., Craig R., Egelman E.H., Alamo L., and Padron R. Atomic model of a myosin filament in the relaxed state. Nature 436 (2005) 1195-1199
51. Yang S., VanLoock M.S., Yu X., and Egelman E.H. Comparison of bacteriophage T4 UvsX and human Rad51 filaments suggests that RecA-like polymers may have evolved independently. J. Mol. Biol. 312 (2001) 999-1009
52. Yang S., Yu X., Galkin V.E., and Egelman E.H. Issues of resolution and polymorphism in single-particle reconstruction. J. Struct. Biol. 144 (2003) 162-171
53. Yang S., Yu X., Seitz E.M., Kowalczykowski S.C., and Egelman E.H. Archaeal RadA protein binds DNA as both helical filaments and octameric rings. J. Mol. Biol. 314 (2001) 1077-1085
54. Yonekura K., Maki-Yonekura S., and Namba K. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424 (2003) 643-650
55. Yonekura K., Stokes D.L., Sasabe H., and Toyoshima C. The ATP-binding site of Ca(2+)-ATPase revealed by electron image analysis. Biophys. J. 72 (1997) 997-1005
56. Yu X., Jacobs S.A., West S.C., Ogawa T., and Egelman E.H. Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA. Proc. Natl. Acad. Sci. USA 98 (2001) 8419-8424
57. Zhang P., and Hinshaw J.E. Three-dimensional reconstruction of dynamin in the constricted state. Nat. Cell Biol. 3 (2001) 922-926