doi:

DOI: 10.3724/SP.J.1260.2013.30159

Aata Biophysica Sinica (生物物理学报) 2013/29:12 PP.879-898

Electron Microscopy Reconstruction of Helical Assemblies


Abstract:
The cryo-electron microscopy reconstruction technique has been developed rapidly in recent years and becoming an important approach for structural studies of macromolecular complexes, and it includes three different methods, cryo-electron tomography, electron crystallography, and single particle analysis (SPA). Among them, the SPA technique is now becoming a powerful tool to determine near-atomic resolution structures of macromolecular complexes. However, for those biological macromolecular assemblies with helical symmetry, such as tobacco mosaic virus (TMV), microtubules, microfilament, human immunodeficiency virus 1 capsid protein and etc., it is not easy to obtain their three dimensional structures by using SPA because there are lots of math to deal with. In this paper, the authors described the helical reconstruction technique in details, including the basic mathematical description of helical assemblies, helical diffraction and its indexing, the relationship between Fourier transform of helical points array and that of real helical assemblies, and how to determine the helical parameters. Based on the above introduction, the authors reviewed two main helical reconstruction algorithms, the Fourier-Bessel reconstruction and the iterative helical real space reconstruction (IHRSR). At the end, they selected the helical assembly of Par-3 NTD (Par3 is a kind of protein related to cell polarity control and Par-3 NTD is its N-terminal domain) as an example to show a detailed helical reconstruction protocol using IHRSR algorithm.

Key words:Helical assemblies,Cryo-electron microscopy,Three dimensional reconstruction,Fourier-Bessel transform,Iterative helical real space reconstruction

ReleaseDate:2015-04-19 19:20:49



1. Sandblad L, Busch KE, Tittmann P, Gross H, Brunner D, Hoenger A. The Schizosaccharomyces pombe EB1 homolog Mal3p binds and stabilizes the microtubule lattice seam. Cell, 2006, 127(7): 1415~1424

2. des Georges A, Katsuki M, Drummond DR, Osei M, Cross RA, Amos LA. Mal3, the Schizosaccharomyces pombe homolog of EB1, changes the microtubule lattice. Nat Struct Mol Biol, 2008, 15(10): 1102~1108

3. McIntosh JR, Morphew MK, Grissom PM, Gilbert SP, Hoenger A. Lattice structure of cytoplasmic microtubules in a cultured mammalian cell. J Mol Biol, 2009, 394(2):177~182

4. Maurer SP, Fourniol FJ, Bohner G, Moores CA, Surrey T. EBs recognize a nucleotide-dependent structural cap at growing microtubule ends. Cell, 2012, 149(2): 371~382

5. Fujii T, Iwane AH, Yanagida T, Namba K. Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Nature, 2010, 467(7316): 724~728

6. Galkin VE, Orlova A, Schroder GF, Egelman EH. Structural polymorphism in F-actin. Nat Struct Mol Biol, 2010, 17(11):1318~1323

7. Murakami K, Yasunaga T, Noguchi TQ, Gomibuchi Y, Ngo KX, Uyeda TQ, Wakabayashi T. Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell, 2010, 143(2): 275~287

8. Woodhead JL, Zhao FQ, Craig R, Egelman EH, Alamo L, Padron R. Atomic model of a myosin filament in the relaxed state. Nature, 2005, 436(7054): 1195~1199

9. Alamo L, Wriggers W, Pinto A, Bartoli F, Salazar L, Zhao FQ, Craig R, Padron R. Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity. J Mol Biol, 2008, 384(4):780~797

10. Zhao FQ, Craig R, Woodhead JL. Head-head interaction characterizes the relaxed state of Limulus muscle myosin filaments. J Mol Biol, 2009, 385(2): 423~431

11. Liu J, Lin T, Botkin DJ, McCrum E, Winkler H, Norris SJ. Intact flagellar motor of Borrelia burgdorferi revealed by cryo-electron tomography: Evidence for stator ring curvature and rotor/C-ring assembly flexion. J Bacteriol, 2009, 19(16): 5026~5036

12. Mu XQ, 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, 2006, 103(26):9861~9866

13. Li YF, Poole S, Nishio K, Jang K, Rasulova F, McVeigh A, Savarino SJ, Xia D, Bullitt E. Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli. Proc Natl Acad Sci USA, 2009, 106(26): 10793~10798

14. LeBleu VS, Macdonald B, Kalluri R. Structure and function of basement membranes. Exp Biol Med (Maywood), 2007, 232(9): 1121~1129

15. Zhang P, Meng X, Zhao G. Tubular crystals and helical arrays: Structural determination of HIV-1 capsid assemblies using iterative helical real-space reconstruction. Methods Mol Biol, 2013, 955: 381~399

16. Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang R. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, 2013, 497(7451):643~646

17. Diaz R, Rice WJ, Stokes DL. Fourier-Bessel reconstruction of helical assemblies. Methods Enzymol, 2010, 482: 131~165

18. DeRosier DJ, Moore PB. Reconstruction of three-dimensional images from electron micrographs of structures with helical symmetry. J Mol Biol, 1970, 52(2): 355~369

19. DeRosier D, Stokes DL, Darst SA. Averaging data derived from images of helical structures with different symmetries. J Mol Biol, 1999, 289(1): 159~165

20. Cochran W, Crick FHC, Vand V. The strucuture of synthetic polypetides I. The transform of atoms on a helix. Acta Crystallogr, 1952, 5: 581~586

21. Klug A, Crick FHC, Wyckoff HW. Diffraction by helical structures. Acta Crystallogr, 1958, 11: 199~213

22. Amos LA, Klug A. Three-dimensional image reconstructions of the contractile tail of T4 bacteriophage. J Mol Biol, 1975, 99(1): 51~64

23. Moody MF. Biophysical electron microscopy: Basic concepts and modern techniques//HPWaV U. Image analysis of electron micrographs. Academic Press, 1990: 170~197, 208~222

24. Smith PR, Aebi U. Studies of the structure of the T4 bacteriophage tail sheath. I. The recovery of three-dimensional structural information from the extended sheath. J Mol Biol, 1976, 106(2): 243~271

25. Stewart M. Computer image processing of electron micrographs of biological structures with helical symmetry. J Electron Microsc Tech, 1988, 9(4): 325~358

26. Egelman EH. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy, 2000, 85(4): 225~234

27. Egelman EH. Single-particle reconstruction from EM images of helical filaments. Curr Opin Struct Biol, 2007, 17(5):556~561

28. Galkin VE, Orlova A, Egelman EH. Actin filaments as tension sensors. Curr Biol, 2012, 22(3): R96~101

29. Chen YJ, Zhang P, Egelman EH, Hinshaw JE. The stalk region of dynamin drives the constriction of dynamin tubes. Nat Struct Mol Biol, 2004, 11(6): 574~575

30. Wang YA, Yu X, Yip C, Strynadka NC, Egelman EH. Structural polymorphism in bacterial EspA filaments revealed by cryo-EM and an improved approach to helical reconstruction. Structure, 2006, 14(7): 1189~1196

31. Hawkes PW, Valdre U. Biophysical electron microscopy. London: Academic Press, 1990

32. Glaeser RM, Downing K, DeRosier D, Chiu W, Frank J. Electron crystallography of biological macromolecules. Oxford University Press, 2007

33. Kendall A, McDonald M, Stubbs G. Precise determination of the helical repeat of tobacco mosaic virus. Virology, 2007, 369(1): 226~227

34. Clare DK, Orlova EV. 4.6 Å Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4kx4k CCD camera. J Struct Biol, 2010, 171(3): 303~308

35. Baker TS, Caspar DL. Computer image modeling of pentamer packing in polyoma virus "hexamer" tubes. Ultramicroscopy, 1984, 13(1-2): 137~151

36. Murakami K, Yasunaga T, Noguchi TQP, Gomibuchi Y, Ngo KX, Uyeda TQP, Wakabayashi T. Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release. Cell, 2010, 143(2): 275~287

37. Lebedev NN. Speical functions and their applications. Dover, Mineola: NY, 1972

38. Robert M, Glaeser KD, David DeRosier, Wah Chiu, Joachim Frank. Electron crystallography of helical structures //Electron crystalllography of biological macro-molcules. Oxford University, 2007: 78~82, 304~342

39. 张凯, 张艳, 胡仲军, 季刚, 孙飞. 电子显微三维重构技术发展与前沿. 生物物理学报, 2010, 26(7): 533~559 Zhang K, Zhang Y, Hu ZJ, Ji G, Sun F. Development and frontier of electron microscopy 3D reconstruction. Acta Biophys Sin, 2010, 26(7): 533~559

40. DeRosier DJ, Klug A. Reconstruction of three dimensional structures from electron micrographs. Nature, 1968, 217:130~134

41. Toyoshima C. Structure determination of tubular crystals of membrane proteins. I. Indexing of diffraction patterns. Ultramicroscopy, 2000, 84(1-2): 1~14

42. Tsai CJ, Nussinov R. A unified convention for biological assemblies with helical symmetry. Acta Crystallogr D Biol Crystallogr, 2011, 67(Pt 8): 716~728

43. Ludtke SJ, Baldwin PR, Chiu W. EMAN: Semiautomated software for high-resolution single-particle reconstructions. J Struct Biol, 1999, 128(1): 82~97

44. Yonekura K, Toyoshima C, Maki-Yonekura S, Namba K. GUI programs for processing individual images in early stages of helical image reconstruction — For high-resolution structure analysis. J Struct Biol, 2003, 144(1-2): 184~194

45. Smith JM. Ximdisp — A visualization tool to aid structure determination from electron microscope images. J Struct Biol, 1999, 125(2-3): 223~228

46. Ward A, Moody MF, Sheehan B, Milligan RA, Carragher B. Windex: A toolset for indexing helices. J Struct Biol, 2003, 144(1-2): 172~183

47. Crowther RA, Henderson R, Smith JM. MRC image processing programs. J Struct Biol, 1996, 116(1): 9~16

48. Carragher B, Whittaker M, Milligan RA. Helical processing using PHOELIX. J Struct Biol, 1996, 116(1): 107~112

49. Owen CH, Morgan DG, DeRosier DJ. Image analysis of helical objects: The Brandeis helical package. J Struct Biol, 1996, 116(1): 167~175

50. Metlagel Z, Kikkawa YS, Kikkawa M. Ruby-Helix: An implementation of helical image processing based on object-oriented scripting language. J Struct Biol, 2007, 157(1): 95~105

51. Wang HW, Nogales E. An iterative Fourier-Bessel algorithm for reconstruction of helical structures with severe Bessel overlap. J Struct Biol, 2005, 149(1): 65~78

52. Ramey VH, Wang HW, Nogales E. Ab initio reconstruction of helical samples with heterogeneity, disorder and coexisting symmetries. J Struct Biol, 2009, 167(2): 97~105

53. Behrmann E, Tao G, Stokes DL, Egelman EH, Raunser S, Penczek PA. Real-space processing of helical filaments in SPARX. J Struct Biol, 2012, 177(2): 302~313

54. Meng X, Zhao G, Zhang P. Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction. J Vis Exp, 2011. DOI:10.3791/3041

55. Zhang Y, Wang W, Chen J, Zhang K, Gao F, Gao B, Zhang S, Dong M, Besenbacher F, Gong W, Zhang M, Sun F, Feng W. Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain. Structure, 2013, 21(6): 997~1006

56. 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, 1996, 116(1): 190~199

57. Chan KY, Gumbart J, McGreevy R, Watermeyer JM, Sewell BT, Schulten K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure, 2011, 19(9): 1211~1218

58. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem, 2005, 26(16): 1781~1802