Hostname: page-component-5cf477f64f-tgq86 Total loading time: 0 Render date: 2025-04-07T09:56:02.947Z Has data issue: false hasContentIssue false
  • English
  • Français

Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu

Published online by Cambridge University Press:  22 December 2009

Xabier Agirrezabala  and
Joachim Frank
Xabier Agirrezabala
Affiliation:
The Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Joachim Frank*
Affiliation:
The Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA Department of Biological Sciences, Columbia University, New York, NY, USA
*
*Author for correspondence: Dr. J. Frank, The Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, P&S BB 2-221, 650 West 168th Street, New York, NY 10032, USA. Email: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

The ribosome is a complex macromolecular machine that translates the message encoded in the messenger RNA and synthesizes polypeptides by linking the individual amino acids carried by the cognate transfer RNAs (tRNAs). The protein elongation cycle, during which the tRNAs traverse the ribosome in a coordinated manner along a path of more than 100 Å, is facilitated by large-scale rearrangements of the ribosome. These rearrangements go hand in hand with conformational changes of tRNA as well as elongation factors EF-Tu and EF-G – GTPases that catalyze tRNA delivery and translocation, respectively. This review focuses on the structural data related to the dynamics of the ribosomal machinery, which are the basis, in conjunction with existing biochemical, kinetic, and fluorescence resonance energy transfer data, of our knowledge of the decoding and translocation steps of protein elongation.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 42 , Issue 3 , August 2009 , pp. 159 - 200
Copyright
Copyright © Cambridge University Press 2009

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abel, K. M., Yoder, M. D., Hilgenfeld, R. & Jurnak, F. (1996). An α to β conformational switch in EF-Tu. Structure 4, 1153–1159.CrossRefGoogle ScholarPubMed
Aevarsson, A., Brazhnikov, E., Garber, M., Zheltonosava, J., Chirgadze, Y., Al-karadaghi, S., Svensson, L. A. & Liljas, A. (1994). Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO Journal 13, 3669–3677.CrossRefGoogle ScholarPubMed
Agirrezabala, X., Lei, J., Brunelle, J. L., Ortiz-Meoz, R. F., Green, R. & Frank, J. (2008). Visualization of the hybrid state of binding promoted by spontaneous ratcheting of the ribosome. Molecular Cell 32, 190–197.CrossRefGoogle ScholarPubMed
Agrawal, R. K., Penczek, P., Grassucci, R. A. & Frank, J. (1998). Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proceedings of the National Academy of Sciences USA 95, 6134–6138.CrossRefGoogle ScholarPubMed
Agrawal, R. K., Heagle, A. B., Penczek, P., Grassucci, R. & Frank, J. (1999). EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nature Structural Biology 6, 643–647.Google Scholar
Ali, I. K., Lancaster, L., Feinberg, J., Joseph, S. & Noller, H. F. (2006). Deletion of a central ribosomal intersubunit RNA bridge. Molecular Cell 23, 865–874.CrossRefGoogle ScholarPubMed
Al-Karadaghi, S., Aevarsson, A., Garber, M., Zheltonova, J. & Liljas, A. (1996). The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange. Structure 4, 555–565.CrossRefGoogle ScholarPubMed
Allen, G. S., Zavialov, A., Gursky, R., Ehrenberg, M. & Frank, J. (2005). The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 121, 703–712.CrossRefGoogle ScholarPubMed
Almlof, M., Ander, M. & Aqvist, J. (2007). Energetics of codon–anticodon recognition on the small ribosomal subunit. Biochemistry 46, 200–209.CrossRefGoogle ScholarPubMed
Bashan, A., Agmon, I., Zarivach, R., Schluenzen, F., Harms, J., Berisio, R., Bartels, H., Franceschi, F., Auerbach, T., Hansen, H. A., Kossoy, E., Kessler, M. & Yonath, A. (2003). Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression. Molecular Cell 11, 91–102.CrossRefGoogle ScholarPubMed
Belitsina, N. V., Glukhova, M. A. & Spirin, A. S. (1975). Translocation in ribosomes by attachment-detachment of elongation factor G without GTP cleavage: evidence from a column-bound ribosome system. FEBS Letters 54, 35–38.Google Scholar
Belitsina, N. V., Tnalina, G. Z. & Spirin, A. S. (1981). Template-free ribosomal synthesis of polylysine from lysyl-tRNA. FEBS Letters 131, 289–292.CrossRefGoogle ScholarPubMed
Berchtold, H., Reshetnikova, L., Reiser, C. O., Schirmer, N. K., Sprinzl, M. & Hilgenfeld, R. (1993). Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature 365, 126–132.CrossRefGoogle ScholarPubMed
Beringer, M. & Rodnina, M. V. (2007). The ribosomal peptidyl transferase. Molecular Cell 26, 311–321.CrossRefGoogle ScholarPubMed
Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S. & Puglisi, J. D. (2004a). tRNA selection and kinetic proofreading in translation. Nature Structural and Molecular Biology 11, 1008–1014.CrossRefGoogle ScholarPubMed
Blanchard, S. C., Kim, H. D., Gonzalez, R. L., Puglisi, J. D. & Chu, S. (2004b). tRNA dynamics on the ribosome during translation. Proceedings of the National Academy of Sciences USA 101, 12893–12898.CrossRefGoogle ScholarPubMed
Bouadloun, F., Donner, D. & Kurland, C. G. (1983). Codon-specific missense errors in vivo. EMBO Journal 2, 1351–1356.CrossRefGoogle ScholarPubMed
Bourne, H. R., Sanders, D. A. & Mc Cormick, F. (1991). The GTPase superfamily: conserved structure and molecular mechanism. Nature 349, 117–127.CrossRefGoogle ScholarPubMed
Bowman, C. M., Dahlberg, J. E., Ikemura, T., Konisky, J. & Nomura, M. (1971). Specific inactivation of 16S ribosomal RNA induced by colicin E3 in vivo. Proceedings of the National Academy of Sciences USA 68, 964–968.CrossRefGoogle ScholarPubMed
Bretscher, M. S. (1968). Translocation in protein synthesis: a hybrid structure model. Nature 218, 675–677.CrossRefGoogle ScholarPubMed
Cochella, L. & Green, R. (2005). An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308, 1178–1180.CrossRefGoogle ScholarPubMed
Cochella, L., Brunelle, J. L. & Green, R. (2007). Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the. Nature Structural and Molecular Biology 14, 30–36.Google Scholar
Connell, S. R., Takemoto, C., Wilson, D. N., Wang, H., Muryama, K., Terada, T., Shirouzu, M., Rost, M., Schuler, M., Giesebrecht, J., Dabrowski, M., Mielke, T., Fucini, P., Yokoyama, S. & Spahn, C. M. (2007). Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Molecular Cell 25, 751–764.CrossRefGoogle ScholarPubMed
Cool, R. H. & Parmeggiani, A. (1991). Substitution of histidine-84 and the GTPase mechanism of elongation factor Tu. Biochemistry 30, 362–366.CrossRefGoogle ScholarPubMed
Cornish, P. V., Ermolenko, D. N., Noller, H. F. & Ha, T. (2008). Spontaneous intersubunit rotation in single ribosomes. Molecular Cell 30, 578–588.CrossRefGoogle ScholarPubMed
Cornish, P. V., Ermolenko, D. N., Staple, D. W., Hoang, L., Hickerson, R. P., Noller, H. F. & Ha, T. (2009). Following movement of the L1 stalk between three functional states in single ribosomes. Proceedings of the National Academy of Sciences USA 106, 2571–2576.CrossRefGoogle ScholarPubMed
Cromie, M. J., Shi, Y., Latifi, T. & Groisman, E. A. (2006). An RNA sensor for intracellular Mg2+. Cell 125, 71–84.CrossRefGoogle Scholar
Czworkowski, J., Wang, J., Steitz, T. A. & Moore, P. B. (1994). The crystal structure of elongation factor G complexed with GDP, at 2·7 Å resolution. EMBO Journal 13, 3661–3668.CrossRefGoogle ScholarPubMed
Daviter, T., Wieden, H. J. & Rodnina, M. V. (2003). Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome. Journal of Molecular Biology 332, 689–699.CrossRefGoogle ScholarPubMed
Dell, V. A. , V. A., Miller, D. L. & Jonhson, A. E. (1990). Effects of nucleotide- and aurodox-induced changes in elongation factor Tu conformation upon its interactions with aminoacyl transfer RNA. A fluorescence study. Biochemistry 29, 1757–1763.CrossRefGoogle ScholarPubMed
Diaconu, M., Kothe, U., Schlunzen, F., Fischer, N., Harms, J. M., Tonevitsky, A. G., Stark, H., Rodnina, M. V. & Wahl, M. C. (2005). Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell 121, 991–1004.CrossRefGoogle ScholarPubMed
Dorner, S., Brunelle, J. L., Sharma, D. & Green, R. (2006). The hybrid state of tRNA binding is an authentic translation elongation intermediate. Nature Structural and Molecular Biology 13, 234–241.CrossRefGoogle ScholarPubMed
Ermolenko, D. N., Majumdar, Z. K., Hickerson, R. P., Spiegel, P. C., Clegg, R. M. & Noller, H. F. (2007a). Observation of intersubunit movement of the ribosome in solution using FRET. Journal of Molecular Biology 370, 530–540.CrossRefGoogle ScholarPubMed
Ermolenko, D. N., Spiegel, P. C., Majumdar, Z. K., Hickerson, R. P., Clegg, R. M. & Noller, H. F. (2007b). The antibiotic viomycin traps the ribosome in an intermediate state of translocation. Nature Structural and Molecular Biology 14, 493–497.CrossRefGoogle Scholar
Fei, J., Kosuri, P., Mac Dougall, D. D. & Gonzalez, R. L. (2008). Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Molecular Cell 30, 348–359.Google Scholar
Feinberg, J. S. & Joseph, S. (2001). Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proceedings of the National Academy of Sciences USA 98, 11120–11125.CrossRefGoogle ScholarPubMed
Fourmy, D., Recht, M. I., Blanchard, S. C. & Puglisi, J. D. (1996). Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274, 1367–1371.CrossRefGoogle ScholarPubMed
Frank, J. & Agrawal, R. K. (2000). A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406, 318–322.CrossRefGoogle ScholarPubMed
Frank, J., Sengupta, J., Gao, H., Li, W., Valle, M., Zavialov, A. & Ehrenberg, M. (2005). The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Letters 579, 959–962.Google Scholar
Frank, J., Gao, H., Sengupta, J., Gao, N. & Taylor, D. J. (2007). The process of mRNA–tRNA translocation. Proceedings of the National Academy of Sciences USA 104, 19671–19678.Google Scholar
Fredrick, K. & Noller, H. F. (2003). Catalysis of ribosomal translocation by sparsomycin. Science 300, 1159–1162.Google Scholar
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T. & Turner, D. H. (1986). Improved free-energy parameters for predictions of RNA duplex stability. Proceedings of the National Academy of Sciences of Sciences of the United States of America 83, 9373–9377.Google ScholarPubMed
Gao, H., Sengupta, J., Valle, M., Korostelev, A., Eswar, N., Stagg, S. M., Van Roey, P., Agrawal, R. K., Harvey, S. C., Sali, A., Chapman, M. S. & Frank, J. (2003). Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell 113, 789–801.Google Scholar
Gao, N., Zavialov, A. V., Li, W., Sengupta, J., Valle, M., Gursky, R. P., Ehrenberg, M. & Frank, J. (2005). Mechanism for the disassembly of the post-termination complex inferred from cryo-EM studies. Molecular Cell 18, 663–674.Google Scholar
Gao, H., Zhou, Z., Rawat, U., Huang, C., Bouakaz, L., Wang, C., Cheng, Z., Liu, Y., Zavialov, A., Gursky, R., Sanyal, S., Ehrenberg, M., Frank, J. & Song, H. (2007). RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129, 929–941.CrossRefGoogle ScholarPubMed
Gao, H., Lebarron, J. & Frank, J. (2009). Ribosomal dynamics: intrinsic instability of a molecular machine. In Non-Protein Coding RNAs (eds. Walter, N. G., Woodson, S. A. & Batey, R. T.), pp 303–316. Berlin: Springer-Verlag.CrossRefGoogle Scholar
Gavrilova, L. P. & Spirin, A. S. (1971). Stimulation of “non-enzymic” translocation in ribosomes by p-chloromercuribenzoate. FEBS Letters 17, 324–326.CrossRefGoogle ScholarPubMed
Gomez-Lorenzo, M. G., Spahn, C. M., Agrawal, R. K., Grassucci, R. A., Penczek, P., Chakraburtty, K., Ballesta, J. P., Lavandera, J. L., Garcia-Bustos, J. F. & Frank, J. (2000). Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17·5 Å resolution. EMBO Journal 19, 2710–2718.CrossRefGoogle ScholarPubMed
Gonzalez, R. L., Chu, S. & Puglisi, J. D. (2007). Thiostrepton inhibition of tRNA delivery to the ribosome. RNA 13, 2091–2097.Google Scholar
Gromadski, K. B. & Rodnina, M. V. (2004). Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Molecular Cell 13, 191–200.Google Scholar
Gromadski, K. B., Daviter, T. & Rodnina, M. V. (2006). A uniform response to mismatches in codon–anticodon complexes ensures ribosomal fidelity. Molecular Cell 21, 369–377.CrossRefGoogle ScholarPubMed
Hansen, J. L., Ippolito, J. A., Ban, N., Nissen, P., Moore, P. B. & Steitz, T. A. (2002). The structures of four macrolide antibiotics bound to the large ribosomal subunit. Molecular Cell 10, 117–128.CrossRefGoogle Scholar
Hansson, S., Singh, R., Gudkov, A. T., Liljas, A. & Logan, D. T. (2005). Crystal structure of a mutant elongation factor G trapped with a GTP analogue. FEBS Letters 579 4492–4497.CrossRefGoogle ScholarPubMed
Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F. & Yonath, A. (2001). High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679–688.CrossRefGoogle ScholarPubMed
Hausner, T. P., Atmadja, J. & Nierhaus, K. H. (1987). Evidence that the G2661 region of 23S rRNA is located at the ribosomal binding sites of both elongation factors. Biochimie 69, 911–923.CrossRefGoogle ScholarPubMed
Helgstrand, M., Mandava, C. S., Mulder, F. A., Liljas, A., Sanyal, S. & Akke, M. (2007). The ribosomal stalk binds to translation factors IF2, EF-Tu, EF-G and RF3 via a conserved region of the L12 C-terminal domain. Journal of Molecular Biology 365, 468–479.CrossRefGoogle Scholar
Hilgenfeld, R. (1995). Regulatory GTPases. Current Opinion in Structural Biology 5, 810–817.CrossRefGoogle ScholarPubMed
Hopfield, J. J. (1974). Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proceedings of the National Academy of Sciences USA 71, 4135–4139.CrossRefGoogle ScholarPubMed
Horan, L. H. & Noller, H. F. (2007). Intersubunit movement is required for ribosomal translocation. Proceedings of the National Academy of Sciences USA 104, 4881–4885.CrossRefGoogle ScholarPubMed
Inoue-Yokosawa, N., Ishikawa, C. & Kaziro, Y. (1974). The role of guanosine triphosphate in translocation reaction catalyzed by elongation factor G. Journal of Biological Chemistry 249, 4321–4323.Google Scholar
Johansson, M., Lovmar, M. & Ehrenberg, M. (2008). Rate and accuracy of bacterial protein synthesis revisited. Current Opinion in Microbiology 11, 141–147.Google Scholar
Jorgensen, R., Ortiz, P. A., Carr-Schmid, A., Nissen, P., Kinzy, T. G. & Andersen, G. R. (2003). Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase. Nature Structural Biology 10, 379–385.CrossRefGoogle ScholarPubMed
Jorgensen, R., Yates, S. P., Teal, D. J., Nilsson, J., Prentice, G. A., Merrill, A. R. & Andersen, G. R. (2004). Crystal structure of ADP-ribosylated ribosomal translocase from Saccharomyces cerevisiae. Journal of Biological Chemistry 279, 45919–45925.CrossRefGoogle ScholarPubMed
Jorgensen, R., Merrill, A. R., Yates, S. P., Marquez, V. E., Schawan, A. L., Boesen, T. & Andersen, G. R. (2005). Exotoxin A–eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature 436, 979–984.CrossRefGoogle ScholarPubMed
Joseph, S. & Noller, H. F. (1998). EF-G-catalyzed translocation of anticodon stem-loop analogs of transfer RNA in the ribosome. EMBO Journal 17, 3478–3483.Google Scholar
Julian, P., Konevega, A. L., Scheres, S. H., Lazaro, M., Gil, D., Wintemeyer, W., Rodnina, M. V. & Valle, M. (2008). Structure of ratcheted ribosomes with tRNAs in hybrid states. Proceedings of the National Academy of Sciences USA 104, 4881–4885.Google Scholar
Kaziro, Y. (1978). The role of guanosine 5′-triphosphate in polypeptide chain elongation. Biochimica et Biophysica Acta 505, 95–127.CrossRefGoogle ScholarPubMed
Kim, D. F. & Green, R. (1999). Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Molecular Cell 4, 859–864.Google Scholar
Kim, H. D., Puglisi, J. D. & Chu, S. (2007). Fluctuations of transfer RNAs between classical and hybrid states. Biophysical Journal 93, 3575–3582.CrossRefGoogle ScholarPubMed
Kjeldgaard, M., Nissen, P., Thirup, S. & Nyborg, J. (1993). The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure 1, 35–50.Google Scholar
Klaholz, B. P., Myasnikov, A. G. & Van Heel, M. (2004). Visualization of release factor 3 on the ribosome during termination of protein synthesis. Nature 427, 862–865.CrossRefGoogle ScholarPubMed
Knudsen, C. R. & Clark, B. F. (1995). Site-directed mutagenesis of Arg58 and Asp86 of elongation factor Tu from Escherichia coli: effects on the GTPase reaction and aminoacyl-tRNA binding. Protein Engineering 8, 1267–1273.CrossRefGoogle ScholarPubMed
Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. (2006). Crystal structure of a 70S ribosome–tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065–1077.CrossRefGoogle ScholarPubMed
Korostelev, A., Ermolenko, D. N. & Noller, H. F. (2008). Structural dynamics of the ribosome. Current Opinion in Chemical Biology 12, 674–683.Google Scholar
La Cour, T. F., Nyborg, J., Thirup, S. & Clark, B. F. (1985). Structural details of the binding of guanosine diphosphate to elongation factor Tu from E. coli as studied by X-ray crystallography. EMBO Journal 4, 2385–2388.CrossRefGoogle Scholar
Laurberg, M., Asahara, H., Korostelev, A., Zhu, J., Trakhanov, S. & Noller, H. F. (2008). Structural basis for translation termination on the 70S ribosome. Nature 454, 852–857.CrossRefGoogle ScholarPubMed
Lebarron, J., Mitra, K. & Frank, J. (2007). Displaying 3D data on RNA secondary structures: ColoRNA. Journal of Structural Biology 157, 262–270.CrossRefGoogle ScholarPubMed
Lebarron, J., Grassucci, R. A., Shaikh, T. R., Baxter, W. T., Sengupta, J. & Frank, J. (2008). Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. Journal of Structural Biology 164, 24–32.CrossRefGoogle Scholar
Lee, T. H., Blanchard, S. C., Kim, H. D., Puglisi, J. D. & Chu, S. (2007). The role of fluctuations in tRNA selection by the ribosome. Proceedings of the National Academy of Sciences USA 104, 13661–13665.CrossRefGoogle ScholarPubMed
Li, W., Agirrezabala, X., Lei, J., Bouakaz, L., Brunelle, J. L., Ortiz-Meoz, R. F., Green, R., Sanyal, S., Ehrenberg, M. & Frank, J. (2008). Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. EMBO Journal 27, 3322–3331.CrossRefGoogle ScholarPubMed
Liljas, A. (2004). Structural Aspects of Protein Synthesis. Hackensack, NJ: World Scientific Publishing.Google Scholar
Lill, R., Robertson, J. M. & Wintermeyer, W. (1989). Binding of the 3′ terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation. EMBO Journal 8, 3933–3938.CrossRefGoogle ScholarPubMed
Maguire, B. A., Beniaminov, A. D., Ramu, H., Mankin, A. S. & Zimmermann, R. A. (2005). A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome. Molecular Cell 20, 427–435.CrossRefGoogle ScholarPubMed
Marshall, R. A., Dorywalska, M. & Puglisi, J. D. (2008). Irreversible chemical steps control intersubunit dynamics during translation. Proceedings of the National Academy of Sciences USA 105, 15364–15369.Google Scholar
Meroueh, M. & Chow, C. S. (1999). Thermodynamics of RNA hairpins containing single internal mismatches. Nucleic Acids Research 27, 1118–1125.CrossRefGoogle ScholarPubMed
Moazed, D. & Noller, H. F. (1986). Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47, 985–994.CrossRefGoogle ScholarPubMed
Moazed, D., Robertson, J. M. & Noller, H. F. (1988). Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. Nature 180, 362–364.CrossRefGoogle Scholar
Moazed, D. & Noller, H. F. (1989a). Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 4, 585–597.CrossRefGoogle Scholar
Moazed, D. & Noller, H. F. (1989b). Intermediate states in the movement of transfer RNA in the ribosome. Nature 342, 142–148.CrossRefGoogle ScholarPubMed
Munro, J. B., Altman, R. B., O'connor, N. & Blanchard, S. C. (2007). Identification of two distinct hybrid state intermediates on the ribosome. Molecular Cell 25, 505–517.Google Scholar
Ninio, J. (1975). Kinetic amplification of enzyme discrimination. Biochimie 57, 587–595.Google Scholar
Ninio, J. (2006). Multiple stages in codon–anticodon recognition: double-trigger mechanisms and geometric constraints. Biochimie 88, 963–992.CrossRefGoogle ScholarPubMed
Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B. F. & Nyborg, J. (1995). Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu and a GTP analog. Science 270, 1464–1472.CrossRefGoogle Scholar
Nissen, P., Thirup, S., Kjeldgaard, M. & Nyborg, J. (1999). The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in the tRNA. Structure 15, 143–156.CrossRefGoogle Scholar
Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000a). The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930.CrossRefGoogle ScholarPubMed
Nissen, P., Kjeldgaard, M. & Nyborg, J. (2000b). Macromolecular mimicry. EMBO Journal 19, 489–495.Google Scholar
Noller, H. F. & Chaires, J. B. (1972). Functional modification of 16S ribosomal RNA by kethoxal. Proceedings of the National Academy of Sciences USA 69, 3113–3118.Google Scholar
Noller, H. F., Hoffarth, V. & Zimniak, L. (1992). Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416–1419.Google Scholar
Noller, H. F., Yusupov, M. M., Yusupova, G. Z., Baucom, A. & Cate, J. H. D. (2002). Translocation of tRNA during protein synthesis. FEBS Letters 514, 11–16.Google Scholar
Noller, H. F. (2006). Biochemical characterization of the ribosomal decoding site. Biochimie 88, 935–941.Google Scholar
Ogle, J. M., Brodersen, D. E., Jr.Clemons, W. M., Tarry, M. J., Carter, A. P. & Ramakrishnan, V. (2001). Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902.Google Scholar
Ogle, J. M., Murphy, F. V. IV, Tarry, M. J. & Ramakrishnan, V. (2002). Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111, 721–732.CrossRefGoogle ScholarPubMed
Ogle, J. M. & Ramakrishnan, V. (2005). Structural insights into translational fidelity. Annual Reviews in Biochemistry 74, 129–177.Google Scholar
Pan, D., Kirillov, S. V., Zhang, C. M., Hou, Y. M. & Cooperman, B. S. (2006). Rapid ribosomal translocation depends on the conserved 18–55 base pair in the P-site transfer RNA. Nature Structural and Molecular Biology 13, 354–359.Google Scholar
Pan, D., Kirillov, S. V. & Cooperman, B. S. (2007). Kinetically competent intermediates in the translocation step of protein synthesis. Molecular Cell 25, 519–529.Google Scholar
Pape, T., Wintermeyer, W. & Rodnina, M. V. (1998). Complete kinetic mechanism of elongation factor Tu-dependant binding of aminoacyl-tRNA to the A site of E. coli ribosome. EMBO Journal 17, 7490–7497.CrossRefGoogle Scholar
Pape, T., Wintermeyer, W. & Rodnina, M. V. (1999). Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO Journal 18, 3800–3807.Google Scholar
Parmeggiani, A. & Nissen, P. (2006). Elongation factor Tu-targeted antibiotics: four structures, two mechanisms of action. FEBS Letters 580, 4576–4581.CrossRefGoogle ScholarPubMed
Peske, F., Matasovva, N. B., Savelbergh, A., Rodnina, M. V. & Wintermeyer, W. (2000). Conformationally restricted elongation factor G retains GTPase activity but is inactive in translocation on the ribosome. Molecular Cell 6, 501–505.Google Scholar
Pestka, S. (1968). Studies on the formation of trensfer ribonucleic acid-ribosome complexes. V. On the function of a soluble transfer factor in protein synthesis. Proceedings of the National Academy of Sciences USA 61, 726–733.CrossRefGoogle ScholarPubMed
Pestka, S. (1969). Studies on the formation of transfer ribonucleic acid–ribosome complexes. VI. Oligopeptide synthesis and translocation on ribosomes in the presence and absence of soluble transfer factors. Journal of Biological Chemistry 244, 1533–1539.Google Scholar
Piepenburg, O., Pape, T., Pleiss, J. A., Wintermeyer, W., Uhlenbeck, O. C. & Rodnina, M. V. (2000). Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome. Biochemistry 39, 1734–1738.Google Scholar
Polekhina, G, Thirup, S., Kjeldgaard, M., Nissen, P., Lippmann, C. & Nyborg, J. (1996). Helix unwinding in the effector region of elongation factor EF-Tu-GDP. Structure 4, 1141–1151.Google Scholar
Rheinberger, H. J. & Nierhaus, K. H. (1986). Allosteric interactions between the ribosomal transfer RNA-binding sites A and E. Journal of Biological Chemistry 261, 9133–9139.Google Scholar
Rodnina, M. V., Fricke, R. & Wintermeyer, W. (1994). Transient conformational states of aminoacyl-tRNA during ribosome binding catalyzed by elongation factor Tu. Biochemistry 33, 12267–12275.CrossRefGoogle ScholarPubMed
Rodnina, M. V., Fricke, R., Kuhn, L. & Wintermeyer, W. (1995). Codon-dependent conformational change of elongation factor Tu preceding GTP hydrolysis on the ribosome. EMBO Journal 14, 2613–2619.Google Scholar
Rodnina, M. V., Pape, T., Fricke, R., Kuhn, L. & Wintermeyer, W. (1996). Initial binding of the elongation factor Tu.GTP.aminoacyl–tRNA complex preceding codon recognition on the ribosome. Journal of Biological Chemistry 27, 646–652.Google Scholar
Rodnina, M. V., Savelsbergh, A., Katutin, V. I. & Wintermeyer, W. (1997). Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385, 37–41.Google Scholar
Rodnina, M. V. & Wintermeyer, W. (2001). Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanism. Annual Reviews in Biochemistry 70, 415–435.Google Scholar
Ruusala, T., Ehrenberg, M. & Kurland, C. G. (1982). Is there proofreading during polypeptide synthesis? EMBO Journal 1, 741–745.CrossRefGoogle ScholarPubMed
Samaha, R. R., Green, R. & Noller, H. F. (1995). A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377, 309–314.Google Scholar
Savelsbergh, A., Matassova, N. B., Rodnina, M. V. & Wintermeyer, W. (2000). Role of domains 4 and 5 in elongation factor G functions on the ribosome. Journal of Molecular Biology 300, 951–961.Google Scholar
Savelsbergh, A., Katutin, V. I., Mohr, D., Peske, F., Rodnina, M. V. & Wintermeyer, W. (2003). Role of domains 4 and 5 in elongation factor G functions on the ribosome. Molecular Cell 11, 1517–1523.Google Scholar
Scarano, G., Krab, I. M., Bocchini, V. & Parmeggiani, A. (1995). Relevance of histidine-84 in the elongation factor Tu GTPase activity and in poly(Phe) synthesis: its substitution by glutamine and alanine. FEBS Letters 365, 214–218.Google Scholar
Schmeing, T. M., Seila, A. C., Hansen, J. L., Freeborn, B., Soukup, J. K., Scaringe, S. A., Strobel, S. A., Moore, P. B. & Steitz, T. A. (2002). A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nature Structural Biology 9, 225–230.Google Scholar
Schmeing, T. M., Huang, K. S., Kitchen, D. E., Strobel, S. A. & Steitz, T. A. (2005a). Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA n the peptidyl transferase reaction. Molecular Cell 20, 437–448.CrossRefGoogle Scholar
Schmeing, T. M., Huang, K. S., Strobel, S. A. & Steitz, T. A. (2005b). An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438, 520–524.Google Scholar
Schuette, J. C., Murphy, F. V. IV, 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. (2009). GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO Journal 28, 755–765.CrossRefGoogle ScholarPubMed
Schultz, D. W. & Yarus, M. (1994a). tRNA structure and ribosomal function. I. tRNA nucleotide 27–43 mutations enhance first position wobble. Journal of Molecular Biology 235, 1381–1394.Google Scholar
Schultz, D. W. & Yarus, M. (1994b). tRNA structure and ribosomal function. II. Interaction between anticodon helix and other tRNA mutations. Journal of Molecular Biology 235, 1395–1405.CrossRefGoogle ScholarPubMed
Schuwirth, B. S., Borovinskaya, M. A., Hau, C. W., Zhang, W., Vila-Sanjuro, A., Holton, J. M. & Cate, J. H. D. (2005). Structures of the bacterial ribosome at 3·5 Å resolution. Science 310, 827–834.CrossRefGoogle ScholarPubMed
Selmer, M., Dunham, C. M., Murphy, F. V. IV, Weixlbaumer, A., Petry, S., Kelley, A. C., Weir, J. R. & Ramakrishnan, V. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942.Google Scholar
Semenkov, Y. P., Shapkina, T., Makhono, V. & Kirillov, S. (1992). Puromycin reaction for the A site-bound peptidyl-tRNA. FEBS Letters 296, 207–210.CrossRefGoogle ScholarPubMed
Semenkov, Y. P., Rodnina, M. V. & Wintermeyer, W. (2000). Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome. Nature Structural Biology 7, 1027–1031.Google ScholarPubMed
Senior, B. W. & Holland, I. B. (1971). Effect of colicin E3 upon the 30S ribosomal subunit of Escherichia coli. Proceedings of the National Academy of Sciences USA 69, 959–964.CrossRefGoogle Scholar
Sharma, D., Southworth, D. R. & Green, R. (2004). EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding. RNA 10, 102–113.CrossRefGoogle ScholarPubMed
Sharma, D., Cukras, A. R., Rogers, E. J., Southworth, D. R. & Green, R. (2007). Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome. Journal of Molecular Biology 374, 1065–1076.Google Scholar
Simonovic, M. & Steitz, T. A. (2008). Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit. Proceedings of the National Academy of Sciences USA 105, 500–505.CrossRefGoogle ScholarPubMed
Smith, D. & Yarus, M. (1989a). Transfer RNA structure and coding specificity. I. Evidence that a D-arm mutation reduces tRNA dissociation form the ribosome. Journal of Molecular Biology 206, 489–501.Google Scholar
Smith, D. & Yarus, M. (1989b). Transfer RNA structure and coding specificity. II. A D-arm tertiary interaction that restricts coding range. Journal of Molecular Biology 206, 503–511.CrossRefGoogle Scholar
Song, H., Parsons, M. R., Rowsell, S., Leonard, G. & Phillips, S. E. (1999). Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2·05 Å resolution. Journal of Molecular Biology 285, 1245–1256.Google Scholar
Spahn, C. M., Gomez-Lorenzo, M. G., Grassucci, R. A., Jorgensen, R., Andersen, G. R., Beckmann, R., Penczek, P. A., Ballesta, J. P. & Frank, J. (2004). Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO Journal 23, 1008–1019.CrossRefGoogle ScholarPubMed
Spiegel, P. C., Ermolenko, D. N. & Noller, H. F. (2007). Elongation factor G stabilized the hybrid-state conformation of the 70S ribosome. RNA 13, 1473–1482.CrossRefGoogle ScholarPubMed
Spirin, A. S. (1968). How does the ribosome work? A hypothesis based on the two subunit construction of the ribosome. Currents in Modern Biology 2, 115–127.Google Scholar
Spirin, A. S. (2009). The ribosome as a conveying thermal ratchet machine. Journal of Biological Chemistry 284, 21103–21119.Google Scholar
Stark, H., Rodnina, M. V., Widen, H. J., Van Heel, M. & Wintermeyer, (2000). Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100, 301–309.Google Scholar
Stark, H., Rodnina, M. V., Widen, H. J., Zemlin, F., Wintermeyer, W. & Van Heel, M. (2002). Ribosome interaction of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nature Structural Biology 9, 849–854.Google Scholar
Steitz, T. A. (2008). A structural understanding of the dynamic ribosome machine. Nature Reviews Molecular Cell Biology 9, 242–253.CrossRefGoogle ScholarPubMed
Sugimoto, N., Kierzek, R., Freier, S. M. & Turner, D. H. (1986). Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry 25, 5755–5759.CrossRefGoogle ScholarPubMed
Tama, F., Valle, M., Frank, J. & Brooks, C. L. III (2003). Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proceedings of the National Academy of Sciences USA 100, 9319–9323.Google Scholar
Taylor, D. J., Nilsson, J., Merrill, A. R., Andersen, G. R., Nissen, P. & Frank, J. (2007). Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO Journal 26, 2421–2431.CrossRefGoogle ScholarPubMed
Thompson, R. C. & Stone, P. J. (1979). Proofreading of the codon–anticodon interaction on ribosomes. Proceedings of the National Academy of Sciences USA 74, 198–202.Google Scholar
Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. (2008). Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673–683.Google Scholar
Valle, M., Sengupta, J., Swami, N. K., Grassucci, R. A., Burkhardt, N., Nierhaus, K. H., Agrawal, R. K. & Frank, J. (2002). Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO Journal 21, 3557–3567.Google Scholar
Valle, M., Zavialov, A., Li, W., Stagg, S. M., Sengupta, J., Nielsen, R. C., Nissen, P., Harvey, S. C., Ehrenberg, M. & Frank, J. (2003a). Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nature Structural Biology 10, 899–906.CrossRefGoogle ScholarPubMed
Valle, M., Zavialov, A. V., Sengupta, J., Rawat, U., Ehrenberg, M. & Frank, J. (2003b). Locking and unlocking of ribosomal motions. Cell 114, 123–134.CrossRefGoogle ScholarPubMed
Van Loock, M. S., Agrawal, R. K., Gabashvili, I. S., Qi, L., Frank, J. & Harvey, S. C. (2000). Movement of the decoding region of the 16S ribosomal RNA accompanies tRNA translocation. Journal of Molecular Biology 304, 507–515.Google Scholar
Vetter, I. R. & Wittinghofer, A. (2001). The guanine nucleotide-binding switch in three dimensions. Science 294, 1299–1304.Google Scholar
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. (2009a). Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proceedings of the National Academy of Sciences USA 106, 1063–1068.Google Scholar
Villa, E., Li, W. & Frank, J. (2009b). tRNA entry into the ribosome during the decoding process. In preparation.Google Scholar
Virumae, K., Saarma, U., Horowitz, J. & Remme, J. (2002). Functional importance of the 3′-terminal adenosine of tRNA in ribosomal translation. Journal of Biological Chemistry 277, 24128–24134.CrossRefGoogle ScholarPubMed
Vogeley, L., Palm, G. J., Mesters, J. R. & Hilgenfeld, R. (2001). Conformational change of elongation factor Tu (EF-Tu) induced by antibiotic binding. Crystal structure of the complex between EF-Tu.GDP and aurodox. Journal of Biological Chemistry 276, 17149–17155.CrossRefGoogle ScholarPubMed
Voorhees, R. M., Weixlbaumer, A., Loakes, D., Kelley, A. C. & Ramakrishnan, V. (2009). Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nature Structural and Molecular Biology 16, 528–533.Google Scholar
Walker, S. E., Shoji, S., Pan, D., Cooperman, B. S. & Fredrick, K. (2008). Role of hybrid tRNA-binding states in ribosomal translocation. Proceedings of the National Academy of Sciences USA 105, 9192–9197.Google Scholar
Wang, Y., Rader, A. J., Bahar, I. & Jernigan, R. L. (2004). Global ribosome motions revealed with elastic network model. Journal of Structural Biology 147, 302–314.Google Scholar
Weixlbaumer, A., Jin, H., Neubauer, C., Voorhees, R. M., Petry, S., Kelley, A. C. & Ramakrishnan, V. (2008). Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322, 953–956.CrossRefGoogle ScholarPubMed
Wilden, B., Savelsbergh, A., Rodnina, M. V. & Wintermeyer, W. (2006). Role and timing of GTP binding and hydrolysis during EF-G-dependant tRNA translocation on the ribosome. Proceedings of the National Academy of Sciences USA 103, 13670–13675.CrossRefGoogle ScholarPubMed
Wohlgemuth, I., Beringer, M. & Rodnina, M. V. (2006). Rapid peptide bond formation on isolate 50S ribosomal subunits. EMBO Reports 7, 699–703.Google Scholar
Wriggers, W., Agrawal, R. K., Drew, D. L., Mccammon, A. & Frank, J. (2000). Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures. Biophysical Journal 79, 1670–1678.Google Scholar
Yarus, M., Valle, M. & Frank, J. (2003). A twisted tRNA intermediate sets the threshold for decoding. RNA 9, 364–365.CrossRefGoogle ScholarPubMed
Yoshizawa, S., Fourmy, D. & Puglisi, J. D. (1999). Recognition of the codon–anticodon helix by ribosomal RNA. Science 285, 1722–1725.CrossRefGoogle ScholarPubMed
Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D. & Noller, H. F. (2001). Crystal structure of the ribosome at 5·5 Å resolution. Science 292, 883–896.CrossRefGoogle ScholarPubMed
Yusupova, G. Z., Yusupov, M. M., Cate, J. H. D. & Noller, H. F. (2001). The path of messenger RNA through the ribosome. Cell 106, 233–241.Google Scholar
Zaher, H. S. & Green, R. (2009). Fidelity at the molecular level: lessons from protein synthesis. Cell 136, 746–762.CrossRefGoogle ScholarPubMed
Zavialov, A. V. & Ehrenberg, M. (2003). Peptidyl-tRNA regulates the GTPase activity of translation factors. Cell 114, 113–122.Google Scholar
Zeidler, W., Egle, C., Ribeiro, S., Wagner, A., Katunin, V., Kreutzer, R., Rodnina, M., Wintermeyer, W. & Sprinzl, M. (1995). Site-directed mutagenesis of Thermus thermophilus elongation factor Tu. Replacement of His85, Asp81, and Arg300. European Journal of Biochemistry 229, 596–604.Google Scholar