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Ribosome dynamics: Progress in the characterization of mRNA-tRNA translocation by cryo-electron microscopy

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Ribosomes

Abstract

The ribosome is a highly complex molecular machine performing protein synthesis in all forms of life with an amazing degree of accuracy. Knowledge of its atomic structure, the result of pioneering work now honored by the award of the Nobel Prize, has prepared us for the next stage of inquiry, with the focus on the dynamics of the system. Key to understanding the mechanism of protein synthesis is provided by experimental data informing us about the ribosome’s conformational changes and dynamic interactions with its functional ligands, mRNA, tRNA, EF-G and EF-Tu during the elongation cycle.

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References

  • Agirrezabala X, Lei J, Brunelle JL, Ortiz-Meoz RF, Green R, and Frank J (2008) Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol Cell 32: 190–197

    Article  PubMed  CAS  Google Scholar 

  • Agirrezabala X, Frank J (2009) Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu. Quart Rev Biophys 42: 159–200

    Article  CAS  Google Scholar 

  • Agrawal RK, Penczek P, Grassucci RA, Frank J (1998) Visualization of elongation factor G on the Escherichia coli 70S ribosome: The mechanism of translocation. Proc Natl Acad Sci USA. 95: 6134–6138

    Article  PubMed  CAS  Google Scholar 

  • Agrawal RK, Heagle AB, Penczek P, Grassucci RA, Frank J (1999) EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome, Nat Struct Biol 6: 643–647

    Article  PubMed  CAS  Google Scholar 

  • Blanchard SC, Kim HD, Gonzalez Jr RL, Puglisi JD, Chu S (2004) tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA 101: 12 893–12 898

    CAS  Google Scholar 

  • Bokov K, Steinberg SV (2009) A hierarchical model for evolution of 23S ribosomal RNA. Nature 457: 977–980

    Article  PubMed  CAS  Google Scholar 

  • Bretscher MS (1968) Translocation in protein synthesis: a hybrid structure model. Nature 218: 675–677

    Article  PubMed  CAS  Google Scholar 

  • Cornish PV, Ermolenko D.N, Noller HF, Ha T (2008) Spontaneous intersubunit rotation in single ribosomes. Mol Cell 30: 578–588

    Article  PubMed  CAS  Google Scholar 

  • Ermolenko DN, Majumdar ZK, Hickerson RP, Spiegel PC, Clegg RM, Noller HF (2007) Observation of intersubunit movement of the ribosome in solution using FRET J Mol Biol 370: 530–540

    Article  PubMed  CAS  Google Scholar 

  • Fei J, Kosuri P, MacDougall DD, Ruben L Gonzalez RL (2008) Coupling of Ribosomal L1 Stalk and tRNA Dynamics during Translation Elongation. Mol Cell 30: 348–359

    Article  PubMed  CAS  Google Scholar 

  • Fei,J, Bronson JE, Hofman JM, Srinivas RL, Wiggins CH, Gonzalez RL Jr. (2009) Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci USA 106: 15 702–15 707

    Article  Google Scholar 

  • Fischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H (2010) Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature 466: 329–333

    Article  PubMed  CAS  Google Scholar 

  • Frank J, Agrawal RK (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406: 318–322

    Article  PubMed  CAS  Google Scholar 

  • Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK (1995) A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376: 441–444

    Article  PubMed  CAS  Google Scholar 

  • Fu J, Kennedy D, Munro JB, Lei J, Blanchard SC, Frank J (2009) The P-site tRNA reaches the P/E position through intermediate positions. (Abstract) J. Biomol. Struct. Dyn. 26: 794–795

    Google Scholar 

  • Fu J, Munro JB, Blanchard SC, Frank J (2011) Cryo-EM structures of the ribosome complex in intermediate states during tRNA translocation. Proc Natl Acad Sci USA (in press)

    Google Scholar 

  • Gabashvili IS, Agrawal RK, Spahn CM, Grassucci RA, Svergun DI, Frank J, Penczek P (2000) Solution structure of the E. coli 70S ribosome at 11.5Å resolution. Cell 100: 537–549

    Article  PubMed  CAS  Google Scholar 

  • Garai A, Chowdhury D, Ramakrishnan TV (2009) Stochastic kinetics of ribosomes: single motor properties and collective behavior. Phys Rev E 80: 011 908

    Article  CAS  Google Scholar 

  • Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM et al. (2003) Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell 113: 789–801

    Article  PubMed  CAS  Google Scholar 

  • Gao H, LeBarron J, Frank J (2009a) Ribosomal dynamics: intrinsic instability of a molecular machine. In: Walter NG, Woodson SA, Batey RT (eds) Non-protein coding RNAs. Springer Berlin pp 303–316

    Chapter  Google Scholar 

  • Gao Y-G, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V (2009b) The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326: 694–699

    Article  PubMed  CAS  Google Scholar 

  • Gromadski KB, Daviter T, Rodnina MV (2006) A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity. Mol Cell 21: 369–377

    Article  PubMed  CAS  Google Scholar 

  • Harms J, Tocilj A, Levin I, Agmon I, Holger Stark3, Ingo Kölln1, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A (2000) Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Structure 7: 931–941

    Article  Google Scholar 

  • Julián P, Konevega AL, Scheres SH W, Lázaro M, Gil D, Wintermeyer W, Rodnina MV, Valle M (2008) Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc Natl Acad Sci USA 105: 16924–16927

    Article  PubMed  Google Scholar 

  • Kim HD, Puglisi J, Chu S (2007) Fluctuations of transfer RNAs between classical and hybrid states. Biophys. J. 93: 3575–3582

    Article  PubMed  CAS  Google Scholar 

  • Li W, Sengupta J, Rath BK, Frank J (2006) Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations. RNA 12: 1240–1253

    Article  PubMed  CAS  Google Scholar 

  • Liao H, Frank J (2010) Classification by bootstrapping in single particle methods. Proc IEEE Int Symp on Biomedical Imaging: from nano to macro. IEEE Int Symp Biomedica (in press)

    Google Scholar 

  • Malhotra A, Penczek P, Agrawal RK, Gabashvili IS, Grassucci RA, Junemann R, Burkhardt N, Nierhaus KH, Frank J (1998) Escherichia coli 70 S ribosome at 15Å resolution by cryo-electron microscopy: localization of fMet-tRNAfMet and fitting of L1 protein. J. Mol. Biol. 280: 103–116

    Article  PubMed  CAS  Google Scholar 

  • Moazed D, Noller HF (1989) Intermediate states in the movement of transfer RNA in the ribosome. Nature 342: 142–148

    Article  PubMed  CAS  Google Scholar 

  • Moran SJ, Flanagan IV, JF, Namy O, Stuart DI, Brierley I, Gilbert RJ C (2008) The mechanics of translocation: a molecular “Spring-and-Ratchet” system. Structure 16: 664–672

    Article  PubMed  CAS  Google Scholar 

  • Munro J. B, Altman RB, O’Connor N, Blanchard SC (2007) Identification of two distinct hybrid state intermediates on the ribosome. Mol Cell 25: 505–517

    Article  PubMed  CAS  Google Scholar 

  • Munro JB, Sanbonmatsu KY, Spahn CM, Blanchard SC (2009) Navigating the ribosome’s metastable energy landscape. Trends Biochem. Sci. 34: 390–400

    Article  PubMed  CAS  Google Scholar 

  • Munro JB, Altman RB, Tung C-S, Cate JH D, Sanbonmatsu KY, Blanchard SC (2010b) Spontaneous formation of the unlocked state of the ribosome is a multistep process. Proc Natl Acad USA 107: 709–714

    Article  Google Scholar 

  • Munro JB, Altman RB, Tung C-S, Sanbonmatsu KY, Blanchard SC (2009a) A fast dynamic mode of the EF-G-bound ribosome. EMBO J. 29: 770–781

    Article  PubMed  CAS  Google Scholar 

  • Penczek PA, Frank J, Spahn CM T (2006) A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J Struct Biol 154: 184–194

    Article  PubMed  CAS  Google Scholar 

  • Polacek N, Patzke S, Nierhaus KH, Barta A (2000) Periodic conformational changes in rRNA: monitoring the dynamics of translating ribosomes. Mol Cell 6: 159–171

    PubMed  CAS  Google Scholar 

  • Reblova K, Razga F, Li W, Gao H, Frank J, Sponer J (2010) Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucl Acid Res 38: 1325–1340

    Article  CAS  Google Scholar 

  • Sanbonmatsu KY, Joseph S, Tung CS (2005) Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci USA 102: 15 854–15 859

    Article  CAS  Google Scholar 

  • Savelsbergh A, Katunin VI, Mohr D, Peske F, Rodnina M. V, Wintermeyer W (2003) An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol Cell 11: 1517–1523

    Article  PubMed  CAS  Google Scholar 

  • Scheres SH, Gao H, Valle M, Herman GT, Eggermont PP, Frank J, Carazo JM (2007) Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat Methods 4: 27–29

    Article  PubMed  CAS  Google Scholar 

  • Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (2005) Structures of the bacterial ribosome at 3.5 Å resolution. Science 310: 827–834

    Article  PubMed  CAS  Google Scholar 

  • Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache J-P, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, Beckmann R (2010) Structural insight into nascent polypeptide chain—mediated translational stalling. Science 326: 1412–1415

    Article  CAS  Google Scholar 

  • Spirin AS (1969) A model of the functioning ribosome: locking and unlocking of the ribosome subparticles, Cold Spring Harbor Symp. Quant Biol 34: 197–207

    Article  PubMed  CAS  Google Scholar 

  • Spirin AS, Baranov VI, Polubesov GS, Serdyuk IN, May RP (1987) Translocation makes the ribosome less compact. J Mol Biol 194: 119–126

    Article  PubMed  CAS  Google Scholar 

  • Spirin AS (2009) The ribosome as a conveying thermal ratchet machine. J Biol Chem 284: 21 103–21 119

    Article  CAS  Google Scholar 

  • Spahn CMT and Penczek PA (2009) Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM. Cur Opin Struct Biol 19: 623–631

    Article  CAS  Google Scholar 

  • Stark H, Mueller F, Orlova EV, Schatz M, Dube P, Erdemir T, Zemlin F, Brimacombe R, van Heel M (1995) The 70S Escherichia coli ribosome at 23Å resolution: fitting the ribosomal RNA. Structure 3: 815–821

    Article  PubMed  CAS  Google Scholar 

  • Stark H, Rodnina MV, Wieden HJ, van Heel M, Wintermeyer W (2000) Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100: 301–309

    Article  PubMed  CAS  Google Scholar 

  • Tama F, Valle M, Frank J, Brooks CL, 3rd (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci USA 100: 9319–9323

    Article  PubMed  CAS  Google Scholar 

  • Tama F, Miyashita O, Brooks CL (2004) Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol 147: 315–326

    Article  PubMed  CAS  Google Scholar 

  • Taylor DJ, Nilsson J, Merrill AR, Andersen GR, Nissen P, Frank J (2007) Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J. 26: 2421–2431

    Article  PubMed  CAS  Google Scholar 

  • Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J (2003) Locking and unlocking of ribosomal motions. Cell 114: 123–134

    Article  PubMed  CAS  Google Scholar 

  • Wimberly BT, Brodersen DE, Clemons Jr WM, Morgan-Warren RJ, Carter A. P, Vonrhein C et al. (2000) Structure of the 30S ribosomal subunit. Nature 407: 327–339

    Article  PubMed  CAS  Google Scholar 

  • Yusupov M, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF (2001), Crystal structure of the ribosome at 5.5 Å resolution. Science 292: 883–896

    Article  PubMed  CAS  Google Scholar 

  • Zhang W, Kimmel M, Spahn CM, Penczek PA (2008) Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis. Structure 16: 1770–1776

    Article  PubMed  CAS  Google Scholar 

  • Zhang W, Dunkle JA, Cate JH D (2009) Structures of the ribosome in intermediate states of ratcheting. Science 325: 1014–1017

    Article  PubMed  CAS  Google Scholar 

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Authors
  1. Joachim Frank
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Editors and Affiliations

  1. Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany

    Marina V. Rodnina  & Wolfgang Wintermeyer  & 

  2. Howard Hughes Medical Institute Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

    Rachel Green

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Frank, J. (2011). Ribosome dynamics: Progress in the characterization of mRNA-tRNA translocation by cryo-electron microscopy. In: Rodnina, M.V., Wintermeyer, W., Green, R. (eds) Ribosomes. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0215-2_25

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