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Quantitative studies of ribosome conformational dynamics

Published online by Cambridge University Press:  12 December 2007

Christopher S. Fraser  and
Jennifer A. Doudna
Christopher S. Fraser
Affiliation:
Department of Molecular and Cell Biology & Department of Chemistry, Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
Jennifer A. Doudna*
Affiliation:
Department of Molecular and Cell Biology & Department of Chemistry, Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
*
*Author for correspondence: Dr J. A. Doudna, Department of Molecular and Cell Biology & Department of Chemistry, Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.Tel.: (510) 643-0225; Fax: (510) 643-0080; Email: [email protected]
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Abstract

The ribosome is a dynamic machine that undergoes many conformational rearrangements during the initiation of protein synthesis. Significant differences exist between the process of protein synthesis initiation in eubacteria and eukaryotes. In particular, the initiation of eukaryotic protein synthesis requires roughly an order of magnitude more initiation factors to promote efficient mRNA recruitment and ribosomal recognition of the start codon than are needed for eubacterial initiation. The mechanisms by which these initiation factors promote ribosome conformational changes during stages of initiation have been studied using cross-linking, footprinting, site-directed probing, cryo-electron microscopy, X-ray crystallography, fluorescence spectroscopy and single-molecule techniques. Here, we review how the results of these different approaches have begun to converge to yield a detailed molecular understanding of the dynamic motions that the eukaryotic ribosome cycles through during the initiation of protein synthesis.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 40 , Issue 2 , May 2007 , pp. 163 - 189
Copyright
Copyright © Cambridge University Press 2007

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References

7. References

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., Penczek, P., Grassucci, R. A., Li, Y., Leith, A., Nierhaus, K. H. & Frank, J. (1996). Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science 271, 1000–1002.CrossRefGoogle Scholar
Agrawal, R. K., Sharma, M. R., Kiel, M. C., Hirokawa, G., Booth, T. M., Spahn, C. M., Grassucci, R. A., Kaji, A. & Frank, J. (2004). Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications. Proceedings of the National Academy of Sciences USA 101, 8900–8905.CrossRefGoogle ScholarPubMed
Algire, M. A., Maag, D., Savio, P., Acker, M. G., Tarun, S. Z. Jr., Sachs, A. B., Asano, K., Nielsen, K. H., Olsen, D. S., Phan, L., Hinnebusch, A. G. & Lorsch, J. R. (2002). Development and characterization of a reconstituted yeast translation initiation system. RNA 8, 382–397.CrossRefGoogle ScholarPubMed
Allen, G. S. & Frank, J. (2007). Structural insights on the translation initiation complex: ghosts of a universal initiation complex. Molecular Microbiology 63, 941–950.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
Antoun, A., Pavlov, M. Y., Andersson, K., Tenson, T. & Ehrenberg, M. (2003). The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. EMBO Journal 22, 5593–5601.CrossRefGoogle ScholarPubMed
Antoun, A., Pavlov, M. Y., Tenson, T. & Ehrenberg, M. M. (2004). Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering. Biological Procedures Online 6, 35–54.CrossRefGoogle ScholarPubMed
Benne, R., Brown-Luedi, M. L. & Hershey, J. W. (1979). Protein synthesis initiation factors from rabbit reticulocytes: purification, characterization, and radiochemical labeling. Methods in Enzymology 60, 15–35.CrossRefGoogle ScholarPubMed
Benne, R. & Hershey, J. W. (1978). The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes. Journal of Biological Chemistry 253, 3078–3087.CrossRefGoogle ScholarPubMed
Berk, V., Zhang, W., Pai, R. D. & Cate, J. H. (2006). Structural basis for mRNA and tRNA positioning on the ribosome. Proceedings of the National Academy of Sciences USA 103, 15830–15834.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 & Molecular biology 11, 1008–1014.CrossRefGoogle ScholarPubMed
Blanchard, S. C., Kim, H. D., Gonzalez, R. L. Jr., 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
Boelens, R. & Gualerzi, C. O. (2002). Structure and function of bacterial initiation factors. Current Protein & Peptide science 3, 107–119.CrossRefGoogle ScholarPubMed
Bommer, U. A., Noll, F., Lutsch, G. & Bielka, H. (1980). Immunochemical detection of proteins in the small subunit of rat liver ribosomes involved in binding of the ternary initiation complex. FEBS Letters 111, 171–174.CrossRefGoogle ScholarPubMed
Carter, A. P., Clemons, W. M. Jr., Brodersen, D. E., Morgan-Warren, R. J., Hartsch, T., Wimberly, B. T. & Ramakrishnan, V. (2001). Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291, 498–501.CrossRefGoogle Scholar
Cate, J. H., Yusupov, M. M., Yusupova, G. Z., Earnest, T. N. & Noller, H. F. (1999). X-ray crystal structures of 70S ribosome functional complexes. Science 285, 2095–2104.CrossRefGoogle ScholarPubMed
Chapman, N. M. & Noller, H. F. (1977). Protection of specific sites in 16 S RNA from chemical modification by association of 30 S and 50 S ribosomes. Journal of Molecular Biology 109, 131–149.CrossRefGoogle ScholarPubMed
Chaudhuri, J., Chowdhury, D. & Maitra, U. (1999). Distinct functions of eukaryotic translation initiation factors eIF1A and eIF3 in the formation of the 40 S ribosomal preinitiation complex. Journal of Biological Chemistry 274, 17975–17980.CrossRefGoogle ScholarPubMed
Cheung, Y. N., Maag, D., Mitchell, S. F., Fekete, C. A., Algire, M. A., Takacs, J. E., Shirokikh, N., Pestova, T., Lorsch, J. R. & Hinnebusch, A. G. (2007). Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo. Genes & Development 21, 1217–1230.CrossRefGoogle ScholarPubMed
Cigan, A. M., Feng, L. & Donahue, T. F. (1988). tRNAi(met) functions in directing the scanning ribosome to the start site of translation. Science 242, 93–97.CrossRefGoogle Scholar
Culver, G. M. & Noller, H. F. (2000). Directed hydroxyl radical probing of RNA from iron(II) tethered to proteins in ribonucleoprotein complexes. Methods in Enzymology 318, 461–475.CrossRefGoogle ScholarPubMed
Ermolenko, D. N., Majumdar, Z. K., Hickerson, R. P., Spiegel, P. C., Clegg, R. M. & Noller, H. F. (2007). Observation of intersubunit movement of the ribosome in solution using FRET. Journal of Molecular Biology 370, 530–540.CrossRefGoogle ScholarPubMed
Fabbretti, A., Pon, C. L., Hennelly, S. P., Hill, W. E., Lodmell, J. S. & Gualerzi, C. O. (2007). The real-time path of translation factor IF3 onto and off the ribosome. Molecular Cell 25, 285–296.CrossRefGoogle ScholarPubMed
Fekete, C. A., Mitchell, S. F., Cherkasova, V. A., Applefield, D., Algire, M. A., Maag, D., Saini, A. K., Lorsch, J. R. & Hinnebusch, A. G. (2007). N- and C-terminal residues of eIF1A have opposing effects on the fidelity of start codon selection. EMBO Journal 26, 1602–1614.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., Zhu, J., Penczek, P., Li, Y., Srivastava, S., Verschoor, A., Radermacher, M., Grassucci, R., Lata, R. K. & Agrawal, R. K. (1995). A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376, 441–444.CrossRefGoogle Scholar
Fraser, C. S., Berry, K. E., Hershey, J. W. & Doudna, J. A. (2007). eIF3j is located in the decoding center of the human 40S ribosomal subunit. Molecular Cell 26, 811–819.CrossRefGoogle ScholarPubMed
Fraser, C. S. & Doudna, J. A. (2007). Structural and mechanistic insights into hepatitis C viral translation initiation. Nature Reviews 5, 29–38.Google ScholarPubMed
Fraser, C. S., Lee, J. Y., Mayeur, G. L., Bushell, M., Doudna, J. A. & Hershey, J. W. (2004). The j-subunit of human translation initiation factor eIF3 is required for the stable binding of eIF3 and its subcomplexes to 40 S ribosomal subunits in vitro. Journal of Biological Chemistry 279, 8946–8956.CrossRefGoogle ScholarPubMed
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 posttermination complex inferred from cryo-EM studies. Molecular Cell 18, 663–674.CrossRefGoogle ScholarPubMed
Gorisch, H., Goss, D. J. & Parkhurst, L. J. (1976). Kinetics of ribosome dissociation and subunit association studied in a light-scattering stopped-flow apparatus. Biochemistry 15, 5743–5753.CrossRefGoogle Scholar
Goss, D. J., Carberry, S. E., Dever, T. E., Merrick, W. C. & Rhoads, R. E. (1990a). A fluorescence study of the interaction of protein synthesis initiation factors 4A, 4E, and 4F with mRNA and oligonucleotide analogs. Biochimica et Biophysica Acta 1050, 163–166.CrossRefGoogle ScholarPubMed
Goss, D. J., Carberry, S. E., Dever, T. E., Merrick, W. C. & Rhoads, R. E. (1990b). Fluorescence study of the binding of m7GpppG and rabbit globin mRNA to protein synthesis initiation factors 4A, 4E, and 4F. Biochemistry 29, 5008–5012.CrossRefGoogle ScholarPubMed
Goss, D. J., Parkhurst, L. J. & Wahba, A. J. (1980). Kinetic studies of the rates and mechanism of assembly of the protein synthesis initiation complex. Biophysical Journal 32, 283–293.CrossRefGoogle ScholarPubMed
Goss, D. J., Parkhurst, L. J. & Wahba, A. J. (1982). Kinetic studies on the interaction of chain initiation factor 3 with 70 S Escherichia coli ribosomes and subunits. Journal of Biological Chemistry 257, 10119–10127.CrossRefGoogle ScholarPubMed
Goss, D. J., Rounds, D., Harrigan, T., Woodley, C. L. & Wahba, A. J. (1988). Effects of eucaryotic initiation factor 3 on eucaryotic ribosomal subunit equilibrium and kinetics. Biochemistry 27, 1489–1494.CrossRefGoogle ScholarPubMed
Goss, D. J. & Rounds, D. J. (1988). A kinetic light-scattering study of the binding of wheat germ protein synthesis initiation factor 3 to 40S ribosomal subunits and 80S ribosomes. Biochemistry 27, 3610–3613.CrossRefGoogle ScholarPubMed
Goss, D. J., Woodley, C. L. & Wahba, A. J. (1987). A fluorescence study of the binding of eucaryotic initiation factors to messenger RNA and messenger RNA analogues. Biochemistry 26, 1551–1556.CrossRefGoogle ScholarPubMed
Goumans, H., Thomas, A., Verhoeven, A., Voorma, H. O. & Benne, R. (1980). The role of eIF-4C in protein synthesis initiation complex formation. Biochimica et Biophysica Acta 608, 39–46.CrossRefGoogle ScholarPubMed
Green, R. & Noller, H. F. (1997). Ribosomes and translation. Annual Review of Biochemistry 66, 679–716.CrossRefGoogle ScholarPubMed
Greenleaf, W. J., Woodside, M. T. & Block, S. M. (2007). High-resolution, single-molecule measurements of biomolecular motion. Annual Review of Biophysics and Biomolecular Structure 36, 171–190.CrossRefGoogle ScholarPubMed
Gromadski, K. B. & Rodnina, M. V. (2004). Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Molecular Cell 13, 191–200.CrossRefGoogle ScholarPubMed
Grunberg-Manago, M., Dessen, P., Pantaloni, D., Godefroy-Colburn, T., Wolfe, A. D. & Dondon, J. (1975). Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes. Journal of Molecular Biology 94, 461–478.Google ScholarPubMed
Ha, T., Zhuang, X., Kim, H. D., Orr, J. W., Williamson, J. R. & Chu, S. (1999). Ligand-induced conformational changes observed in single RNA molecules. Proceedings of the National Academy of Sciences USA 96, 9077–9082.CrossRefGoogle ScholarPubMed
Hagenbuchle, O., Santer, M., Steitz, J. A. & Mans, R. J. (1978). Conservation of the primary structure at the 3′ end of 18S rRNA from eucaryotic cells. Cell 13, 551–563.CrossRefGoogle ScholarPubMed
Han, H. & Dervan, P. B. (1994). Visualization of RNA tertiary structure by RNA-EDTA.Fe(II) autocleavage: analysis of tRNA(Phe) with uridine-EDTA.Fe(II) at position 47. Proceedings of the National Academy of Sciences USA 91, 4955–4959.CrossRefGoogle Scholar
Hayes, J. J., Kam, L. & Tullius, T. D. (1990). Footprinting protein-DNA complexes with gamma-rays. Methods in Enzymology 186, 545–549.CrossRefGoogle ScholarPubMed
Hennelly, S. P., Antoun, A., Ehrenberg, M., Gualerzi, C. O., Knight, W., Lodmell, J. S. & Hill, W. E. (2005). A time-resolved investigation of ribosomal subunit association. Journal of Molecular Biology 346, 1243–1258.CrossRefGoogle ScholarPubMed
Herr, W., Chapman, N. M. & Noller, H. F. (1979). Mechanism of ribosomal subunit association: discrimination of specific sites in 16 S RNA essential for association activity. Journal of Molecular Biology 130, 433–449.CrossRefGoogle ScholarPubMed
Hinnebusch, A. G. (2006). eIF3: a versatile scaffold for translation initiation complexes. Trends in Biochemical Sciences 31, 553–562.CrossRefGoogle ScholarPubMed
Hinnebusch, A. G., Dever, T. E. & Asano, K. (2007). Mechanism of translation initiation in the yeast Saccharomyces cerevisiae. In Translational Control in Biology and Medicine (ed. Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.), pp. 225–268. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Holmberg, L., Melander, Y. & Nygard, O. (1994). Probing the conformational changes in 5·8S, 18S and 28S rRNA upon association of derived subunits into complete 80S ribosomes. Nucleic Acids Research 22, 2776–2783.CrossRefGoogle ScholarPubMed
Holmberg, L. & Nygard, O. (1997). Mapping of nuclease-sensitive sites in native reticulocyte ribosomes – an analysis of the accessibility of ribosomal RNA to enzymatic cleavage. European Journal of Biochemistry/FEBS 247, 160–168.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
Hui, D. J., Terenzi, F., Merrick, W. C. & Sen, G. C. (2005). Mouse p56 blocks a distinct function of eukaryotic initiation factor 3 in translation initiation. Journal of Biological Chemistry 280, 3433–3440.CrossRefGoogle ScholarPubMed
Jackson, R. J. (2005). Alternative mechanisms of initiating translation of mammalian mRNAs. Biochemical Society Transactions 33, 1231–1241.CrossRefGoogle ScholarPubMed
Jackson, R. J. & Hunt, T. (1983). Preparation and use of nuclease-treated rabbit reticulocyte lysates for the translation of eukaryotic messenger RNA. Methods in Enzymology 96, 50–74.CrossRefGoogle ScholarPubMed
Jia, Y., Sytnik, A., Li, L., Vladimirov, S., Cooperman, B. S. & Hochstrasser, R. M. (1997). Nonexponential kinetics of a single tRNAPhe molecule under physiological conditions. Proceedings of the National Academy of Sciences USA 94, 7932–7936.CrossRefGoogle ScholarPubMed
Joseph, S. & Noller, H. F. (2000). Directed hydroxyl radical probing using iron(II) tethered to RNA. Methods in Enzymology 318, 175–190.CrossRefGoogle ScholarPubMed
Joseph, S., Weiser, B. & Noller, H. F. (1997). Mapping the inside of the ribosome with an RNA helical ruler. Science 278, 1093–1098.CrossRefGoogle ScholarPubMed
Kaminishi, T., Wilson, D. N., Takemoto, C., Harms, J. M., Kawazoe, M., Schluenzen, F., Hanawa-Suetsugu, K., Shirouzu, M., Fucini, P. & Yokoyama, S. (2007). A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction. Structure 15, 289–297.CrossRefGoogle ScholarPubMed
Kapp, L. D. & Lorsch, J. R. (2004). The molecular mechanics of eukaryotic translation. Annual Review of Biochemistry 73, 657–704.CrossRefGoogle ScholarPubMed
King, P. A., Jamison, E., Strahs, D., Anderson, V. E. & Brenowitz, M. (1993). ‘Footprinting’ proteins on DNA with peroxonitrous acid. Nucleic Acids Research 21, 2473–2478.CrossRefGoogle ScholarPubMed
Klaholz, B. P., Pape, T., Zavialov, A. V., Myasnikov, A. G., Orlova, E. V., Vestergaard, B., Ehrenberg, M. & Van Heel, M. (2003). Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421, 90–94.CrossRefGoogle ScholarPubMed
Knapp, G. (1989). Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods in Enzymology 180, 192–212.CrossRefGoogle ScholarPubMed
Kolupaeva, V. G., Unbehaun, A., Lomakin, I. B., Hellen, C. U. & Pestova, T. V. (2005). Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. RNA 11, 470–486.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
Kozak, M. (1986). Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44, 283–292.CrossRefGoogle ScholarPubMed
Kozak, M. (1987). An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Research 15, 8125–8148.CrossRefGoogle Scholar
Kozak, M. (1989a). Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems. Molecular and Cellular Biology 9, 5073–5080.Google ScholarPubMed
Kozak, M. (1989b). The scanning model for translation: an update. Journal of Cell Biology 108, 229–241.CrossRefGoogle ScholarPubMed
Kozak, M. (1990). Evaluation of the fidelity of initiation of translation in reticulocyte lysates from commercial sources. Nucleic Acids Research 18, 2828.CrossRefGoogle ScholarPubMed
Kozak, M. (2005). Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361, 13–37.CrossRefGoogle ScholarPubMed
Lake, J. A., Pendergast, M., Kahan, L. & Nomura, M. (1974). Localization of Escherichia coli ribosomal proteins S4 and S14 by electron microscopy of antibody-labeled subunits. Proceedings of the National Academy of Sciences USA 71, 4688–4692.CrossRefGoogle ScholarPubMed
Lomakin, I. B., Kolupaeva, V. G., Marintchev, A., Wagner, G. & Pestova, T. V. (2003). Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes & Development 17, 2786–2797.CrossRefGoogle ScholarPubMed
Lomakin, I. B., Shirokikh, N. E., Yusupov, M. M., Hellen, C. U. & Pestova, T. V. (2006). The fidelity of translation initiation: reciprocal activities of eIF1, IF3 and YciH. EMBO Journal 25, 196–210.CrossRefGoogle ScholarPubMed
Lorsch, J. R. & Herschlag, D. (1999). Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro. EMBO Journal 18, 6705–6717.CrossRefGoogle ScholarPubMed
Lutsch, G., Benndorf, R., Westermann, P., Bommer, U. A. & Bielka, H. (1986). Structure and location of initiation factor eIF-3 within native small ribosomal subunits from eukaryotes. European Journal of Cell Biology 40, 257–265.Google ScholarPubMed
Lutsch, G., Noll, F., Theise, H., Enzmann, G. & Bielka, H. (1979). Localization of proteins S1, S2, S16 and S23 on the surface of small subunits of rat liver ribosomes by immune electron microscopy. Molecular & General Genetics 176, 281–291.CrossRefGoogle ScholarPubMed
Maag, D., Fekete, C. A., Gryczynski, Z. & Lorsch, J. R. (2005). A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon. Molecular Cell 17, 265–275.CrossRefGoogle ScholarPubMed
Maag, D. & Lorsch, J. R. (2003). Communication between eukaryotic translation initiation factors 1 and 1A on the yeast small ribosomal subunit. Journal of Molecular Biology 330, 917–924.CrossRefGoogle ScholarPubMed
Majumdar, R., Bandyopadhyay, A. & Maitra, U. (2003). Mammalian translation initiation factor eIF1 functions with eIF1A and eIF3 in the formation of a stable 40 S preinitiation complex. Journal of Biological Chemistry 278, 6580–6587.CrossRefGoogle ScholarPubMed
Marcotrigiano, J., Gingras, A. C., Sonenberg, N. & Burley, S. K. (1997). Cocrystal structure of the messenger RNA 5′ cap-binding protein (eIF4E) bound to 7-methyl-GDP. Cell 89, 951–961.CrossRefGoogle ScholarPubMed
Marintchev, A. & Wagner, G. (2004). Translation initiation: structures, mechanisms and evolution. Quarterly Reviews of Biophysics 37, 197–284.CrossRefGoogle ScholarPubMed
Marsden, S., Nardelli, M., Linder, P. & McCarthy, J. E. (2006). Unwinding single RNA molecules using helicases involved in eukaryotic translation initiation. Journal of Molecular Biology 361, 327–335.CrossRefGoogle ScholarPubMed
Masutani, M., Sonenberg, N., Yokoyama, S. & Imataka, H. (2007). Reconstitution reveals the functional core of mammalian eIF3. EMBO Journal 26, 3373–3383.CrossRefGoogle ScholarPubMed
McCutcheon, J. P., Agrawal, R. K., Philips, S. M., Grassucci, R. A., Gerchman, S. E., Clemons, W. M. Jr., Ramakrishnan, V. & Frank, J. (1999). Location of translational initiation factor IF3 on the small ribosomal subunit. Proceedings of the National Academy of Sciences USA 96, 4301–4306.CrossRefGoogle ScholarPubMed
Melander, Y., Holmberg, L. & Nygard, O. (1997). Structure of 18 S ribosomal RNA in native 40 S ribosomal subunits. Journal of Biological Chemistry 272, 3254–3258.CrossRefGoogle ScholarPubMed
Merrick, W. C. (1979). Assays for eukaryotic protein synthesis. Methods in Enzymology 60, 108–123.CrossRefGoogle ScholarPubMed
Merrick, W. C. (2004). Cap-dependent and cap-independent translation in eukaryotic systems. Gene 332, 1–11.CrossRefGoogle ScholarPubMed
Merryman, C., Moazed, D., Daubresse, G. & Noller, H. F. (1999a). Nucleotides in 23S rRNA protected by the association of 30S and 50S ribosomal subunits. Journal of Molecular Biology 285, 107–113.CrossRefGoogle ScholarPubMed
Merryman, C., Moazed, D., McWhirter, J. & Noller, H. F. (1999b). Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits. Journal of Molecular Biology 285, 97–105.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. & Noller, H. F. (1989a). Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57, 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
Moazed, D. & Noller, H. F. (1990). Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. Journal of Molecular Biology 211, 135–145.CrossRefGoogle Scholar
Moazed, D., Samaha, R. R., Gualerzi, C. & Noller, H. F. (1995). Specific protection of 16 S rRNA by translational initiation factors. Journal of Molecular Biology 248, 207–210.CrossRefGoogle ScholarPubMed
Moazed, D., Stern, S. & Noller, H. F. (1986). Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. Journal of Molecular Biology 187, 399–416.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.CrossRefGoogle ScholarPubMed
Myong, S., Stevens, B. C. & Ha, T. (2006). Bridging conformational dynamics and function using single-molecule spectroscopy. Structure 14, 633–643.CrossRefGoogle ScholarPubMed
Nguyenle, T., Laurberg, M., Brenowitz, M. & Noller, H. F. (2006). Following the dynamics of changes in solvent accessibility of 16 S and 23 S rRNA during ribosomal subunit association using synchrotron-generated hydroxyl radicals. Journal of Molecular Biology 359, 1235–1248.CrossRefGoogle ScholarPubMed
Nielsen, K. H., Valasek, L., Sykes, C., Jivotovskaya, A. & Hinnebusch, A. G. (2006). Interaction of the RNP1 motif in PRT1 with HCR1 promotes 40S binding of eukaryotic initiation factor 3 in yeast. Molecular and Cellular Biology 26, 2984–2998.CrossRefGoogle ScholarPubMed
Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930.CrossRefGoogle ScholarPubMed
Noller, H. F. (2007). Structure and function of the bacterial ribosome and some implications for translational regulation. In Translational Control in Biology and Medicine (ed. Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.), pp. 41–58. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Nygard, O. & Westermann, P. (1982). Specific interaction of one subunit of eukaryotic initiation factor eIF-3 with 18S ribosomal RNA within the binary complex, eIF-3 small ribosomal subunit, as shown by cross-linking experiments. Nucleic Acids Research 10, 1327–1334.CrossRefGoogle ScholarPubMed
Olsen, D. S., Savner, E. M., Mathew, A., Zhang, F., Krishnamoorthy, T., Phan, L. & Hinnebusch, A. G. (2003). Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo. EMBO Journal 22, 193–204.CrossRefGoogle ScholarPubMed
Palade, G. E. (1955). A small particulate component of the cytoplasm. Journal of Biophysical and Biochemical Cytology 1, 59–68.CrossRefGoogle ScholarPubMed
Pan, D., Kirillov, S. V. & Cooperman, B. S. (2007). Kinetically competent intermediates in the translocation step of protein synthesis. Molecular Cell 25, 519–529.CrossRefGoogle ScholarPubMed
Passmore, L. A., Schmeing, T. M., Maag, D., Applefield, D. J., Acker, M. G., Algire, M. A., Lorsch, J. R. & Ramakrishnan, V. (2007). The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Molecular Cell 26, 41–50.CrossRefGoogle ScholarPubMed
Pelham, H. R. & Jackson, R. J. (1976). An efficient mRNA-dependent translation system from reticulocyte lysates. European Journal of Biochemistry/FEBS 67, 247–256.CrossRefGoogle ScholarPubMed
Peske, F., Rodnina, M. V. & Wintermeyer, W. (2005). Sequence of steps in ribosome recycling as defined by kinetic analysis. Molecular Cell 18, 403–412.CrossRefGoogle ScholarPubMed
Pestova, T. V., Borukhov, S. I. & Hellen, C. U. (1998a). Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons. Nature 394, 854–859.CrossRefGoogle ScholarPubMed
Pestova, T. V., Lomakin, I. B., Lee, J. H., Choi, S. K., Dever, T. E. & Hellen, C. U. (2000). The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403, 332–335.CrossRefGoogle ScholarPubMed
Pestova, T. V., Lorsch, J. R. & Hellen, C. U. T. (2007). The mechanism of translation initiation in eukaryotes. In Translational Control in Biology and Medicine (ed. Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.), pp. 87–128. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Pestova, T. V., Shatsky, I. N., Fletcher, S. P., Jackson, R. J. & Hellen, C. U. (1998b). A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes & Development 12, 67–83.CrossRefGoogle Scholar
Peterson, D. T., Merrick, W. C. & Safer, B. (1979). Binding and release of radiolabeled eukaryotic initiation factors 2 and 3 during 80 S initiation complex formation. Journal of Biological Chemistry 254, 2509–2516.CrossRefGoogle ScholarPubMed
Pisarev, A. V., Kolupaeva, V. G., Pisareva, V. P., Merrick, W. C., Hellen, C. U. & Pestova, T. V. (2006). Specific functional interactions of nucleotides at key −3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex. Genes & Development 20, 624–636.CrossRefGoogle ScholarPubMed
Pisarev, A. V., Shirokikh, N. E. & Hellen, C. U. (2005). Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites. Comptes Rendus Biologies 328, 589–605.CrossRefGoogle ScholarPubMed
Pogozelski, W. K., McNeese, T. J. & Tullius, T. D. (1995). What species is responsible for strand scission in the reaction of [FeIIEDTA]2- and H202 with DNA? Journal of American Chemical Society 117, 6428–6433.CrossRefGoogle Scholar
Proud, C. G. (2006). Regulation of protein synthesis by insulin. Biochemical Society Transactions 34, 213–216.CrossRefGoogle ScholarPubMed
Rana, T. M. & Meares, C. F. (1991). Transfer of oxygen from an artificial protease to peptide carbon during proteolysis. Proceedings of the National Academy of Sciences USA 88, 10578–10582.CrossRefGoogle ScholarPubMed
Rawat, U. B., Zavialov, A. V., Sengupta, J., Valle, M., Grassucci, R. A., Linde, J., Vestergaard, B., Ehrenberg, M. & Frank, J. (2003). A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421, 87–90.CrossRefGoogle ScholarPubMed
Rodnina, M. V. & Wintermeyer, W. (2001). Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annual Review of Biochemistry 70, 415–435.CrossRefGoogle ScholarPubMed
Schluenzen, F., Takemoto, C., Wilson, D. N., Kaminishi, T., Harms, J. M., Hanawa-Suetsugu, K., Szaflarski, W., Kawazoe, M., Shirouzu, M., Nierhaus, K. H., Yokoyama, S. & Fucini, P. (2006). The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nature Structural & Molecular Biology 13, 871–878.CrossRefGoogle ScholarPubMed
Schreier, M. H., Erni, B. & Staehelin, T. (1977). Initiation of mammalian protein synthesis. I. Purification and characterization of seven initiation factors. Journal of Molecular Biology 116, 727–753.CrossRefGoogle ScholarPubMed
Schreier, M. H. & Staehelin, T. (1973). Translation of rabbit hemoglobin messenger RNA in vitro with purified and partially purified components from brain or liver of different species. Proceedings of the National Academy of Sciences USA 70, 462–465.CrossRefGoogle ScholarPubMed
Schuwirth, B. S., Day, J. M., Hau, C. W., Janssen, G. R., Dahlberg, A. E., Cate, J. H. & Vila-Sanjurjo, A. (2006). Structural analysis of kasugamycin inhibition of translation. Nature Structural & Molecular Biology 13, 879–886.CrossRefGoogle ScholarPubMed
Sclavi, B., Woodson, S., Sullivan, M., Chance, M. R. & Brenowitz, M. (1997). Time-resolved synchrotron X-ray ‘footprinting’, a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. Journal of Molecular Biology 266, 144–159.CrossRefGoogle Scholar
Selmer, M., Dunham, C. M., Murphy, F. V. T., 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.CrossRefGoogle ScholarPubMed
Sharp, J. S., Becker, J. M. & Hettich, R. L. (2004). Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry. Analytical Chemistry 76, 672–683.CrossRefGoogle ScholarPubMed
Shenvi, C. L., Dong, K. C., Friedman, E. M., Hanson, J. A. & Cate, J. H. (2005). Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations – implications for the study of ribosome dynamics. RNA 11, 1898–1908.CrossRefGoogle Scholar
Shine, J. & Dalgarno, L. (1974). The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proceedings of the National Academy of Sciences USA 71, 1342–1346.CrossRefGoogle Scholar
Sonenberg, N., Morgan, M. A., Merrick, W. C. & Shatkin, A. J. (1978). A polypeptide in eukaryotic initiation factors that crosslinks specifically to the 5′-terminal cap in mRNA. Proceedings of the National Academy of Sciences USA 75, 4843–4847.CrossRefGoogle Scholar
Spahn, C. M., Beckmann, R., Eswar, N., Penczek, P. A., Sali, A., Blobel, G. & Frank, J. (2001a). Structure of the 80S ribosome from Saccharomyces cerevisiae – tRNA-ribosome and subunit-subunit interactions. Cell 107, 373–386.CrossRefGoogle ScholarPubMed
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
Spahn, C. M., Kieft, J. S., Grassucci, R. A., Penczek, P. A., Zhou, K., Doudna, J. A. & Frank, J. (2001b). Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science 291, 1959–1962.CrossRefGoogle Scholar
Srivastava, S., Verschoor, A. & Frank, J. (1992). Eukaryotic initiation factor 3 does not prevent association through physical blockage of the ribosomal subunit-subunit interface. Journal of Molecular Biology 226, 301–304.CrossRefGoogle Scholar
Staehelin, T., Erni, B. & Schreier, M. H. (1979). Purification and characterization of seven initiation factors for mammalian protein synthesis. Methods in Enzymology 60, 136–165.CrossRefGoogle ScholarPubMed
Stahl, J., Bohm, H., Pozdnjakov, V. A. & Girshovich, A. S. (1979). Photoaffinity labeling of rat liver ribosomes by phenylalanine-tRNA N-acylated by 2-nitro-4-azidobenzoic acid. FEBS Letters 102, 273–276.CrossRefGoogle ScholarPubMed
Stahl, J., Bohm, H. & Voderberg, M. (1981). Affinity labeling of ribosomes from the livers of different vertebrates by 2-nitro-4-azidobenzoyl-phe-tRNA. Acta Biologica et Medica Germanica 40, 1101–1104.Google ScholarPubMed
Stark, H., Rodnina, M. V., Rinke-Appel, J., Brimacombe, R., Wintermeyer, W. & Van Heel, M. (1997). Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389, 403–406.CrossRefGoogle ScholarPubMed
Steitz, J. A. & Jakes, K. (1975). How ribosomes select initiator regions in mRNA: base pair formation between the 3′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proceedings of the National Academy of Sciences USA 72, 4734–4738.CrossRefGoogle ScholarPubMed
Stern, S., Moazed, D. & Noller, H. F. (1988). Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods in Enzymology 164, 481–489.CrossRefGoogle ScholarPubMed
Studer, S. M., Feinberg, J. S. & Joseph, S. (2003). Rapid kinetic analysis of EF-G-dependent mRNA translocation in the ribosome. Journal of Molecular Biology 327, 369–381.CrossRefGoogle ScholarPubMed
Subramanian, A. R. & Davis, B. D. (1970). Activity of initiation factor F3 in dissociating Escherichia coli ribosomes. Nature 228, 1273–1275.CrossRefGoogle ScholarPubMed
Sytnik, A., Vladimirov, S., Jia, Y., Li, L., Cooperman, B. S. & Hochstrasser, R. M. (1999). Peptidyl transferase center activity observed in single ribosomes. Journal of Molecular Biology 285, 49–54.CrossRefGoogle ScholarPubMed
Taylor, D. J., Frank, J. & Kinzy, T. G. (2007). Structure and function of the eukaryotic ribosome and elongation factors. In Translational Control in Biology and Medicine (ed. Mathews, M. B., Sonenberg, N. & Hershey, J. W. B.), pp. 59–85. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Tenson, T. & Mankin, A. (2006). Antibiotics and the ribosome. Molecular Microbiology 59, 1664–1677.CrossRefGoogle ScholarPubMed
Tinoco, I. Jr., Li, P. T. & Bustamante, C. (2006). Determination of thermodynamics and kinetics of RNA reactions by force. Quarterly Reviews of Biophysics 39, 325–360.CrossRefGoogle ScholarPubMed
Tischendorf, G. W., Zeichhardt, H. & Stoffler, G. (1975). Architecture of the Escherichia coli ribosome as determined by immune electron microscopy. Proceedings of the National Academy of Sciences USA 72, 4820–4824.CrossRefGoogle ScholarPubMed
Trachsel, H., Erni, B., Schreier, M. H. & Staehelin, T. (1977). Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors. Journal of Molecular Biology 116, 755–767.CrossRefGoogle ScholarPubMed
Tullius, T. D. & Dombroski, B. A. (1985). Iron(II) EDTA used to measure the helical twist along any DNA molecule. Science 230, 679–681.CrossRefGoogle ScholarPubMed
Uemura, S., Dorywalska, M., Lee, T. H., Kim, H. D., Puglisi, J. D. & Chu, S. (2007). Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Nature 446, 454–457.CrossRefGoogle ScholarPubMed
Unbehaun, A., Borukhov, S. I., Hellen, C. U. & Pestova, T. V. (2004). Release of initiation factors from 48S complexes during ribosomal subunit joining and the link between establishment of codon-anticodon base-pairing and hydrolysis of eIF2-bound GTP. Genes & Development 18, 3078–3093.CrossRefGoogle ScholarPubMed
Unbehaun, A., Marintchev, A., Lomakin, I. B., Didenko, T., Wagner, G., Hellen, C. U. & Pestova, T. V. (2007). Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. EMBO Journal 26, 3109–3123.CrossRefGoogle ScholarPubMed
Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M. & Frank, J. (2003). Locking and unlocking of ribosomal motions. Cell 114, 123–134.CrossRefGoogle ScholarPubMed
Verschoor, A., Zhang, N. Y., Wagenknecht, T., Obrig, T., Radermacher, M. & Frank, J. (1989). Three-dimensional reconstruction of mammalian 40 S ribosomal subunit. Journal of Molecular Biology 209, 115–126.CrossRefGoogle ScholarPubMed
Wang, J. F. & Cech, T. R. (1992). Tertiary structure around the guanosine-binding site of the Tetrahymena ribozyme. Science 256, 526–529.CrossRefGoogle ScholarPubMed
Weiel, J. & Hershey, J. W. (1981). Fluorescence polarization studies of the interaction of Escherichia coli protein synthesis initiation factor 3 with 30S ribosomal subunits. Biochemistry 20, 5859–5865.CrossRefGoogle ScholarPubMed
Weixlbaumer, A., Petry, S., Dunham, C. M., Selmer, M., Kelley, A. C. & Ramakrishnan, V. (2007). Crystal structure of the ribosome recycling factor bound to the ribosome. Nature Structural & Molecular Biology 14, 733–737.CrossRefGoogle ScholarPubMed
Westermann, P., Heumann, W., Bommer, U. A., Bielka, H., Nygard, O. & Hultin, T. (1979). Crosslinking of initiation factor eIF-2 to proteins of the small subunit of rat liver ribosomes. FEBS Letters 97, 101–104.CrossRefGoogle ScholarPubMed
Westermann, P. & Nygard, O. (1984). Cross-linking of mRNA to initiation factor eIF-3, 24 kDa cap binding protein and ribosomal proteins S1, S3/3a, S6 and S11 within the 48S pre-initiation complex. Nucleic Acids Research 12, 8887–8897.CrossRefGoogle ScholarPubMed
Westermann, P., Nygard, O. & Bielka, H. (1980). The alpha and gamma subunits of initiation factor eIF-2 can be cross-linked to 18S ribosomal RNA within the quaternary initiation complex, eIF-2.Met-tRNAf.GDPCP.small ribosomal subunit. Nucleic Acids Research 8, 3065–3071.CrossRefGoogle ScholarPubMed
Westermann, P., Nygard, O. & Bielka, H. (1981). Cross-linking of Met-tRNAf to eIF-2 beta and to the ribosomal proteins S3a and S6 within the eukaryotic inhibition complex, eIF-2.GMPPCP.Met-tRNAf.small ribosomal subunit. Nucleic Acids Research 9, 2387–2396.CrossRefGoogle Scholar
Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. & Noller, H. F. (2001). Crystal structure of the ribosome at 5·5 A resolution. Science 292, 883–896.CrossRefGoogle ScholarPubMed
Yusupova, G., Jenner, L., Rees, B., Moras, D. & Yusupov, M. (2006). Structural basis for messenger RNA movement on the ribosome. Nature 444, 391–394.CrossRefGoogle ScholarPubMed
Zhuang, X. (2005). Single-molecule RNA science. Annual Review of Biophysics and Biomolecular Structure 34, 399–414.CrossRefGoogle ScholarPubMed
Zucker, F. H. & Hershey, J. W. (1986). Binding of Escherichia coli protein synthesis initiation factor IF1 to 30S ribosomal subunits measured by fluorescence polarization. Biochemistry 25, 3682–3690.CrossRefGoogle ScholarPubMed