Multiparticle Cryo-EM of Ribosomes

Methods in Enzymology

Volumn 483, Issue C, 2010, Pages 161-177

  Loerke, Justus ^a   Giesebrecht, Jan ^a   Spahn, Christian M T ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MOCIMYCIN; RIBOSOME PROTEIN;

AMINO ACID SEQUENCE; BOOK; COMPUTER MODEL; CRYOELECTRON MICROSCOPY; FEASIBILITY STUDY; IMAGE PROCESSING; IMAGE RECONSTRUCTION; MACROMOLECULE; MICROSCOPY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; RIBOSOME; STRUCTURE ANALYSIS; THERMODYNAMICS;

EID: 77957255312     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)83008-3     Document Type: Chapter

References (41)

1. Alberts B. The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 1998, 92:291-294.
2. Allen G.S., Zavialov A., Gursky R., Ehrenberg M., Frank J. The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 2005, 121:703-712.
3. Chen J.Z., Grigorieff N. SIGNATURE: A single-particle selection system for molecular electron microscopy. J. Struct. Biol. 2007, 157:168-173.
4. Connell S.R., Takemoto C., Wilson D.N., Wang H., Murayama K., Terada T., Shirouzu M., Rost M., Schüler M., Giesebrecht J., Dabrowski M., Mielke T., et al. Structure basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol. Cell 2007, 25:751-764.
5. Connell S.R., Topf M., Qin Y., Wilson D.N., Mielke T., Fucini P., Nierhaus K.N., Spahn C.M.T. A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation. Nat. Struct. Mol. Biol. 2008, 15:910-915.
6. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies 2006, Oxford University Press, New York.
7. Frank J. Single-particle reconstruction of biological macromolecules in electron microscopy-30 years. Q. Rev. Biophys. 2009, 42:139-158.
8. Frank J., Spahn C.M.T. The ribosome and the mechanism of protein synthesis. Rep. Prog. Phys. 2006, 69:1383-1417.
9. Frank J., Penczek P.A., Grassucci R.A., Srivastava S. Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: The distribution of ribosomal RNA. J. Cell Biol. 1991, 115:597-605.
10. Frank J., Radermacher M., Penczek P.A., 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, 116:190-199.
11. Frank J., Penczek P.A., Agrawal R.K., Grassucci R.A., Heagle A.B. Three-dimensional cryoelectron microscopy of ribosomes. Methods Enzymol. 2000, 317:276-291.
12. Gabashvili I.S., Agrawal R.K., Spahn C.M.T., Grassucci R.A., Svergun D.I., Frank J., Penczek P.A. Solution structure of the E. coli 70S ribosome at 11.5Å resolution. Cell 2000, 100:537-549.
13. Gao H., Valle M., Ehrenberg M., Frank J. Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. J. Struct. Biol. 2004, 147:283-290.
14. Halic M., Becker T., Pool M.R., Spahn C.M.T., Grassucci R.A., Frank J., Beckmann R. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 2004, 427:806-814.
15. Hellen C.U.T., Sarnow P. Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev. 2001, 15:1593-1612.
16. Likas A., Vlassis N., Verbeek J.J. The global K-means clustering algorithm. Pattern Recognit. 2003, 36:451-461.
17. Mindell J.A., Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 2003, 142:334-347.
18. Munro J.B., Sanbonmatsu K.Y., Spahn C.M.T., Blanchard S.C. Navigating the ribosome's metastable energy landscape. Trends Biochem. Sci. 2009, 34:390-400.
19. Orzechowski M., Tama F. Flexible fitting of high-resolution X-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations. Biophys. J. 2008, 95:5692-5705.
20. Penczek P.A., Grassucci 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 1994, 53:251-270.
21. Penczek P.A., Frank J., Spahn C.M.T. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 2006, 154:184-194.
22. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera-A visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
23. Pfingsten J.S., Costantino D., Kieft J.S. Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science 2006, 314:1450-1454.
24. Ratje A.H., Loerke J., Mikolajka A., Brünner M., Hildebrand P.W., Starosta A., Doenhoefer A., Connell S.R., Fucini P., Mielke T., Whitford P.C., Onuchic J.N., et al. 2010, Submitted.
25. Saad A., Ludtke S.J., Jakana J., Rixon F.J., Tsuruta H., Chiu W. Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 2001, 133:32-42.
26. Scheres S.H.W., Gao H., Valle M., Herman G.T., Eggermont P.P.B., Frank J., Carazo J.-M. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods 2007, 4:27-29.
27. Schmeing T.M., Ramakrishnan V. What recent ribosome structures have revealed about the mechanism of translation. Nature 2009, 461:1234-1242.
28. Schuette J.-C., Murphy F.V., Kelley A.C., Weir J.R., Giesebrecht J., Connell S.R., Loerke J., Mielke T., Zhang W., Penczek P.A., Ramakrishnan V., Spahn C.M.T. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J. 2009, 28:755-765.
29. Schüler M., Connell S.R., Lescoute A., Giesebrecht J., Dabrowski M., Schroeer B., Mielke T., Penczek P.A., Westhof E., Spahn C.M.T. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat. Struct. Mol. Biol. 2006, 13:1092-1096.
30. Seidelt B., Innis C.A., Wilson D.N., Gartmann M., Armache J.-P., Villa E., Trabuco L.G., Becker T., Mielke T., Schulten K., Steitz T.A., Beckmann R. Structural insight into nascent polypeptide chain-mediated translational stalling. Science 2009, 326:1412-1415.
31. Selmer M., Dunham C., Murphy F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 2006, 313:1935-1942.
32. Spahn C.M.T., Penczek P.A. Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM. Curr. Opin. Struct. Biol. 2009, 19:623-631.
33. Stark H., Rodnina M.V., Rinke-Appel J., Brimacombe R., Wintermeyer W., van Heel M. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 1997, 389:403-406.
34. Trabuco L.G., Villa E., Mitra K., Frank J., Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 2008, 16:673-683.
35. Valle M., Sengupta J., Swami N.K., Grassucci R.A., Burkhardt N., Nierhaus K.N., Agrawal R., Frank J. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 2001, 21:3557-3567.
36. Valle M., Zavialov A., Snegupta J., Ehrenberg M., Frank J. Locking and unlocking of ribosomal motions. Cell 2003, 114:123-134.
37. Villa E., Sengupta J., Trabuco L.G., LeBarron J., Baxter W.T., Shaikh T.R., Grassucci R.A., Nissen P., Ehrenberg M., Schulten K., Frank J. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc. Natl. Acad. Sci. USA 2009, 106:1063-1068.
38. Wade R.H. A brief look at imaging and contrast transfer. Ultramicroscopy 1992, 46:145-156.
39. Wade R.H., Frank J. Electron microscopic transfer functions for partially coherent axial illumination and chromatic defocus spread. Optik 1977, 49:81-92.
40. Whitford P.C., Noel J.K., Gosavi S., Schug A., Sanbonmatsu K.Y., Onuchic J.N. An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Proteins 2009, 75:430-441.
41. Wriggers W., Milligan R.A., McCammon J.A. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 1999, 125:185-195.