- Open Access
From DNA to proteins via the ribosome: Structural insights into the workings of the translation machinery
© Henry Stewart Publications 2010
- Received: 13 April 2010
- Accepted: 13 April 2010
- Published: 13 April 2010
Understanding protein synthesis in bacteria and humans is important for understanding the origin of many human diseases and devising treatments for them. Over the past decade, the field of structural biology has made significant advances in the visualisation of the molecular machinery involved in protein synthesis. It is now possible to discern, at least in outline, the way that interlocking ribosomal components and factors adapt their conformations throughout this process. The determination of structures in various functional contexts, along with the application of kinetic and fluorescent resonance energy transfer approaches to the problem, has given researchers the frame of reference for what remains as the greatest challenge: the complete dynamic portrait of protein synthesis in the cell.
- protein synthesis
The translation of the genetic code is one of the most crucial (and energy-costly) processes of life. This task is performed by ribosomes -- large ribonucleoprotein assemblies that read the message encoded in the messenger RNA (mRNA) and synthesise proteins by sequential polymerisation of amino acids carried by transfer RNAs (tRNAs), in the form of aminoacyl-tRNAs (aa-tRNAs). The functional complexity of the protein translation process is reflected by the structural complexity of the ribosome, as it is composed of more than 50 different proteins and several RNA components, even in the simplest organisms. The recent award of the Nobel Prize to three X-ray crystallographers, Venki Ramakrishnan, Tom Steitz and Ada Yonath, amounts to a recognition not only of outstanding individual scientific achievements, but also of the pre-eminent role of this molecular machinery in all forms of life. The architectural sophistication and functional virtuosity of the ribosome are astounding, especially considering that it is one of the most ancient macromolecules, having evidently emerged at the very earliest stages of evolution.
The structure of the ribosome is defined by the architecture and arrangement of its distinctly sized subunits, large and small, whose association is mediated by several inter-subunit bridges. In eubacteria and archaea, the small and large subunits are referred to by their sedimentation values as 30S and 50S, respectively, while their eukaryotic counterparts are designated 40S and 60S. Due to the unique topology of the two subunits, their association results in the formation of a ~100-Å long cavity open on both sides, the inter-subunit space. The tRNAs employ this cavity to traverse the entire ribosome as they pass the different primary binding sites (termed A for amino-acyl, P for peptidyl and E for exit). The cyclic protein elongation process, encompassing decoding, peptide bond transfer and translocation, relies on universally conserved mechanisms. Indeed, the functional centres of the ribosome (ie decoding and peptidyl-transferase centres) are located centrally, with highly conserved tertiary structure and disposition.
In contrast to elongation, the processes of initiation, termination and recycling diverge much more among the different kingdoms, and are in general significantly more complex in eukaryotes compared with their bacterial counterparts. This is especially true for initiation. While eubacteria accomplish this task with the aid of three factors (initiation factor [IF]1, IF2 and IF3), initiation in eukaryotes is an intricate, highly regulated process in which more than ten different factors, some of which are multi-subunit complexes, are required . This high degree of complexity is also reflected in the biogenesis of the subunits, a process that requires the assistance of hundreds of accessory proteins and small nucleolar ribosomal RNAs (rRNA) in eukaryotic systems. In addition, the process is highly compartmentalised: the first steps occur in the nucleolus, and the pre-ribosomes are then exported to the nucleoplasm and, finally, to the cytoplasm. By contrast, self-assembly seems to be an intrinsic property of bacterial ribosomes .
Since the discovery of the ribosome in the mid-1950s, extensive research has been carried out on ribosomal structure and morphogenesis, as well as on the mechanism of its action and regulation. Yet, despite the wide-scale efforts and widespread interest, our knowledge of the mechanisms governing protein synthesis by the ribosome has remained incomplete. Progress toward an understanding of the mechanism of translation in bacteria is of great importance in fighting debilitating pathogenic diseases, as it has the potential to provide clues for the synthesis and application of semi-synthetic (ie derived for natural sources) or totally synthetic antibiotics against drug-resistant pathogenic strains . Several human disorders linked to disruptions of the protein translation process, including those caused by mutations in specific mRNAs, tRNAs or the ribosome itself, have been described throughout these studies. Among the mutations that affect human ribosomal components is Diamond-Blackfan anaemia, which is caused by alterations in ribosomal protein S19. Human bone marrow failure syndromes related to mutations of genes that encode additional ribosomal proteins also include Shwachman-Diamond disease, cartilage-hair hypoplasia, dyskeratosis congenita and the Treacher-Collins and 5q- syndromes [11, 12].
During the past decade, several structural studies have described the ribosome's architecture with increasing precision and resolution. X-ray crystallography has been enormously successful as an approach to solve the structure of certain ribosomal complexes, but this technique runs into limitations when it comes to the analysis of the inherently dynamic behaviour of the ribosome, as many transient structures are very difficult to trap and crystallise. By contrast, the results coming from cryo-electron microscopy (cryo-EM) data, albeit originally at lower resolution, are highly informative in functional terms when obtained from ribosomes captured in the process of performing their work. When interpreted with the aid of existing X-ray structures, these data provide very accurate three-dimensional (3D) information on each of the elements implicated in the course of the reaction, as well as on the way they are dynamically coupled. Thus cryo-EM studies, in conjunction with other biophysical techniques such as fluorescence stopped-flow and quench-flow analysis or single-molecule fluorescent resonance energy transfer (sm-FRET), have helped to shape our present understanding of two highly complex dynamic processes during the elongation cycle -- decoding and mRNA-tRNA translocation.
The current drawback of this approach, which might be gradually overcome with time, is that the spatial resolution of the resulting reconstructions is limited, with the best resolution for asymmetric molecules in the range of 5-7 Å[14–16]. Higher resolutions, coming close to the atomic level, have only been achieved for molecules with high symmetry, where symmetry averaging could be applied . In many cases, however, the atomic structures of most of the players in the molecular binding interactions of a complex are known from X-ray crystallography, or have at least become inferable from related X-ray structures by homology modelling based on sequence comparisons. When all the individual components of a macromolecular complex are known to atomic resolution, the lower-resolution map of the complex will then allow the components to be placed and their atomic interactions to be inferred. Thus, fully to exploit the potential of cryo-EM, it is necessary to fit and dock the X-ray coordinates into the lower-resolution cryo-EM maps. Recent examples for atomic models obtained by such "hybrid" methods are the E. coli and yeast ribosomes .
All aspects of translation involve dynamic events. The whole translation apparatus must be viewed as a machinery that is dynamically assembled (during initiation), that engages functional ligands in a cyclic way (during elongation) and that is dynamically disassembled (during termination and recycling). In fact, it is now recognised that the ribosome is a Brownian motor whose main source of energy comes from the thermal environment [19, 20]. sm-FRET has given us a sense of the ribosome as a molecule in constant motion, fluctuating between different states [21–23] that represent local minima of a complex free-energy landscape. Conformations observable in ensemble averages provided by cryo-EM or X-ray crystallography reflect molecules trapped in those energy minima. The more sharply we can distinguish single-particle projections by classification, the better we will be able to map the entire landscape, toward an understanding of how the ribosome works.
Subsequent research by bulk  and sm-FRET  revealed that the binding of a factor is not required for the pre-translocational ribosome to switch its conformation - under suitable conditions (low Mg2+ concentration), this transition occurs spontaneously, apparently as a result of thermal Brownian motions. Indeed, recently, cryo-EM studies have provided the first structural evidence for the occurrence of spontaneous ratcheting,[37, 38] in agreement with the findings of independent FRET studies [39–42]. These studies highlight the fact that the rearrangement is in fact inherent to the ribosome's labile architecture: the subunits are coupled such that relative rotation requires little expenditure of energy, which is readily supplied by thermal agitation in the surrounding substrate.
Following up with a closer look at the structures, the cryo-EM maps [37, 38] also brought the first visual evidence for an important event of the translocation process (first inferred from footprinting studies by Moazed and Noller), the formation of the hybrid state of tRNA binding, a state that precedes the complete translocation of the tRNA-mRNA moiety. In this configuration, the acceptor ends of the tRNAs interact with the P and E sites of the large subunit, while the anticodon stem loops (ASLs) of the tRNAs still reside in the A and P sites of the small subunit, respectively. It is noteworthy that earlier cryo-EM work had already visualised the hybrid P/E configuration, but exclusively in EF-G-bound ribosomes with a single deacylated tRNA . It is now understood, on the basis of the new cryo-EM work, that the new configuration is predisposed by a rearrangement of proteins S13, L1 and L5 and helices 68, 69 and 38 of 23S rRNA -elements that alter their relative location concurrently with the spontaneous ratchet motion (Figure 4B,C). In a newly completed study, X-ray crystallography of pre-translocational complexes has produced structures of ribosomes in an intermediate state of ratcheting . These structural intermediates, albeit obtained using ASL tRNA mimics instead of complete tRNA molecules, are shedding light on the way that the tRNAs acquire the hybrid configuration in atomic detail.
In the cryo-EM studies, the ratcheting of the small subunit is observed to be coupled with the movement of another very dynamic component of the translation machinery, the L1 stalk. This structural element of the large subunit is seen in two different positions, open and closed relative to the body of the large subunit (Figure 4A right). Like a gate-keeper, the L1 stalk is located at the end of the tRNA's pathway. In its closed position (which coincides with the ratcheted position of the small subunit ), the L1 stalk is displaced toward the inter-subunit space, in essence blocking the exit as it makes contact with the P/E hybrid tRNA. Recent sm-FRET experiments have identified three positions of the L1 stalk . These conformations, open, half-closed and closed, are coupled to the tRNA configuration. New studies suggest the existence of an allosteric collaboration between the L1 stalk and EF-G during tRNA translocation and, possibly, during the release of the E-site tRNA from the ribosome .
Other relevant illustrative examples of dynamic features essential for tRNA translocation are the bending movement of helix 44 (see Figure 4A, left), causing a displacement of its vertex (where the decoding centre is located) toward the P site by ~8 Å, as well as the small subunit's head rotation (or 'swivelling') with respect to the body. The rotation, which proceeds toward the E site, parallels the trajectory of the tRNAs through the ribosome. This rearrangement accounts for the remaining distance of 10-12 Å that separates the A and P sites after the afore-mentioned bending of helix 44. Observed first in cryo-EM reconstructions of eEF2-bound 80S ribosomes,[49, 50] the relevance of such a movement for the completion of mRNA-tRNA translocation has been reiterated based on the observation of different head orientations in crystal structures of vacant ribosomes .
Of fundamental importance in all translational activity is the recruitment of translational factors by the ribosome. Some of these factors perform their catalysis in a GTP-dependent manner (IF2, EF-Tu and EF-G, and RF3 in eubacteria). Several lines of research show that the recruitment and GTP-hydrolysis activity of all these factors is facilitated by the so-called L7/L12 stalk (see Figure 4A, right), a very flexible structural component located at the side opposite of the L1 stalk [52, 53]. This stalk, formed by protein L10 and multiple copies of L7/12 (with the exact number depending on the organism), protrudes laterally from the ribosome and changes its conformation in the course of elongation. Due to its mobility and highly dynamic nature, the electron density corresponding to the stalk is not generally seen in the structures of either isolated 50S subunits or complete 70S ribosomal structures; however, cryo-EM studies, combined with atomic coordinates of its individual components, have helped to delineate its structure and suggested a mechanism of action .
Of particular interest are the dynamic events of decoding, crucial for the high-fidelity synthesis of proteins. The structural basis of mRNA decoding by the ribosome was elucidated by X-ray crystallography of 30S subunits bound with a tRNA fragment in the presence of an antibiotic . These data show that nucleotides G530, and A1492 and A1493 from helix 44 of 16S rRNA monitor the correctness of the Watson-Crick geometry of the helix formed by the base pairing of codon and anticodon. When the correct (ie corresponding to cognate pairing) geometry is recognised, these bases form firm contacts with the minor groove of the helix. An ensuing global change of head and shoulder domains, referred to as domain closure, is the most prominent signature of a cognate match .
One of the most fascinating problems in translation is the nature of the conformational signal reporting on the successful cognate match at the decoding centre and travelling to the active region of EF-Tu. It is still an open question if the signal is transmitted through the tRNA itself, through a contact between the 30S subunit and EF-Tu, or by a combination of these pathways (see Li et al., Ogle and Ramakrishnan,, Cochella and Green , and Schmeing et al. for further insights).
Peptide bond formation
For completeness, the structural basis of peptide bond formation should briefly be mentioned. Little is known from cryo-EM data due to resolution limitations; however, X-ray crystallography studies have characterised the structure of the peptidyltransferase centre in great detail, highlighting the structural basis for its catalytic mechanism. According to the present view, the rapid ribosome-induced peptidyl-transfer reaction (~107-fold enhancement ) is facilitated by local conformational changes in the cavity where the peptidyl moiety is positioned upon binding of the A-site substrate [63, 64]. This model invokes an induced-fit mechanism involving nucleotides 2553, 2585 and 2506 (Escherichia coli numbering), in charge of aligning the reactive substrates -- that is, the a-amino group of the incoming amino acid and the terminal carboxyl group of the P-site tRNA (for more details, see Simonovic and Steitz  and references therein).
The field of ribosome research has undergone astonishing progress in recent years, due to our increasingly acute insights into the structural basis of the translational machinery. Advances in both X-ray crystallography and cryo-EM of the ribosome have provided extensive information on the structure and dynamics of ribosomal subunits and functional ligands, their changing binding constellations and mechanism of action. A revolution of sorts has taken place in the understanding of ribosomal interaction with its ligands, paralleling the change in the understanding of enzyme kinetics elsewhere. It is now recognised that in the thermal environment, the structures of both host and ligand molecules are in constant flux, and that the final conformation of the host in which we find the ligand bound already pre-exists within the whole range of its dynamically changing conformations. Most strikingly, as discussed above, both cryo-EM and sm-FRET show evidence that, after peptidyl transfer, the ribosome constantly fluctuates between two major conformations, and that one of these is stabilised by the binding of EF-G, an event that triggers GTP hydrolysis and renders translocation irreversible. Other examples are the spontaneous fluctuations of the L1 stalk between (at least) three functional states, probably coupled to the binding and movement of tRNAs along the inter-subunit cavity, or the changes in the decoding centre and the ternary complex triggered upon cognate codon-anticodon match.
Compared with what is known for bacteria, the eukaryotic ribosome is still a largely uncharted territory. Due to the absence of crystals suitable for X-ray crystallography, despite many efforts of several laboratories, the only structural information has come from density maps from cryo-EM [3, 4, 49, 50, 66–69]. On this basis, some atomic models have been built that depict the interesting evolutionary development of peripheral, nonconserved regions [3, 4, 70]. As far as the mechanism of translation during the elongation cycle is concerned, there is evidence for yeast that mRNA-tRNA translocation is facilitated by the same large-scale structural reorganisation and EF-binding mechanism as in bacteria [49, 50, 71]. Considering that the most ambitious goal is the understanding of regulation and control of the human ribosome, particularly the various dysfunctions of these mechanisms in human disease, a very long and tedious path of discovery is still ahead.
We thank Lila Iino-Rubenstein for assistance with the preparation of the illustrations. This work was supported by HHMI and NIH grants R01 GM55440 and R37 GM29169 (to J.F.). X.A is a recipient of a 'Ramon y Cajal' fellowship from the Spanish Government.
- Acker MG, Lorsch JR: 'Mechanism of ribosomal joining during eukaryotic translation initiation'. Biochem Soc Trans. 2008, 36: 653-657. 10.1042/BST0360653.View ArticlePubMedGoogle Scholar
- Dinman JD: 'The eukaryotic ribosome: Current status and challenges'. J Biol Chem. 2008, 284: 11761-11765.View ArticlePubMedGoogle Scholar
- Spahn CM, Beckmann R, Eswar N, et al: 'Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions'. Cell. 2001, 107: 373-386. 10.1016/S0092-8674(01)00539-6.View ArticlePubMedGoogle Scholar
- Taylor DJ, Devkota B, Huang AD, et al: 'Comprehensive molecular structure of the eukaryotic ribosome'. Structure. 2009, 17: 1591-1604. 10.1016/j.str.2009.09.015.PubMed CentralView ArticlePubMedGoogle Scholar
- Musters W, Boon CA, van der Sande H, et al: 'Functional analysis of transcribed spacers of yeast ribosomal DNA'. EMBO J. 1990, 9: 3989-3996.PubMed CentralPubMedGoogle Scholar
- Sweeney RL, Chen L, Yao MC: 'An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence'. Mol Cell Biol. 1994, 14: 4203-4215.PubMed CentralView ArticlePubMedGoogle Scholar
- Ferreira-Cerca SG, Poll G, Gleizes PE, et al: 'Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function'. Mol Cell. 2005, 20: 263-275. 10.1016/j.molcel.2005.09.005.View ArticlePubMedGoogle Scholar
- Sengupta J, Nilsson J, Gursky R, et al: 'Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM'. Nat Struct Mol Biol. 2004, 11: 957-962. 10.1038/nsmb822.View ArticlePubMedGoogle Scholar
- Nilsson J, Sengupta J, Frank J, et al: 'Regulation of eukaryotic translation by the RACK1 protein: a platform for signalling molecules on the ribosome'. EMBO Rep. 2004, 5: 1137-1141. 10.1038/sj.embor.7400291.PubMed CentralView ArticlePubMedGoogle Scholar
- Tenson T, Mankin A: 'Antibiotics and the ribosome'. Mol Microbiol. 2006, 59: 1664-1677. 10.1111/j.1365-2958.2006.05063.x.View ArticlePubMedGoogle Scholar
- Scheper GC, van der Knaap MS, Proud CG: 'Translation matters: Protein synthesis defects in inherited disease'. Nat Rev Genet. 2007, 8: 711-723. 10.1038/nrg2142.View ArticlePubMedGoogle Scholar
- Narla A, Ebert BL: 'Ribosomopathies: Human disorders of ribosome dysfunction'. Blood. 2010Google Scholar
- Schmeing TM, Ramakrishnan V: 'What recent ribosome structures have revealed about the mechanism of translation'. Nature. 2009, 461: 1234-1242. 10.1038/nature08403.View ArticlePubMedGoogle Scholar
- LeBarron J, Grassucci RA, Shaikh TR, et al: 'Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome'. J Struct Biol. 2008, 164: 24-32. 10.1016/j.jsb.2008.05.007.PubMed CentralView ArticlePubMedGoogle Scholar
- Schuette JC, Murphy FV, Kelley AC, et al: 'GTPase activation of elongation factor EF-Tu by the ribosome during decoding'. EMBO J. 2009, 28: 755-765. 10.1038/emboj.2009.26.PubMed CentralView ArticlePubMedGoogle Scholar
- Seidelt B, Innis CA, Wilson DN, et al: 'Structural insight into nascent polypeptide chain-mediated translational stalling'. Science. 2009, 326: 1412-1415. 10.1126/science.1177662.PubMed CentralView ArticlePubMedGoogle Scholar
- Yu X, Yin L, Zhou ZH: '3.88Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy'. Nature. 2008, 453: 415-419. 10.1038/nature06893.PubMed CentralView ArticlePubMedGoogle Scholar
- Trabuco LG, Villa E, Mitra K, et al: 'Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics'. Structure. 2008, 16: 673-683. 10.1016/j.str.2008.03.005.PubMed CentralView ArticlePubMedGoogle Scholar
- Spirin AS: 'The ribosome as a conveying thermal ratchet machine'. J Biol Chem. 2009, 284: 21103-21119. 10.1074/jbc.X109.001552.PubMed CentralView ArticlePubMedGoogle Scholar
- Frank J, Gonzalez RL: 'Structure and dynamics of a processive Brownian motor: The translating ribosome'. Ann Rev Biochem. 2010Google Scholar
- Marshall RA, Aitken CE, Dorywalska M, et al: 'Translation at the single-molecule level'. Annu Rev Biochem. 2008, 77: 177-203. 10.1146/annurev.biochem.77.070606.101431.View ArticlePubMedGoogle Scholar
- Munro JB, Vaiana A, Sanbonmatsu KY, et al: 'A new view of protein synthesis: Mapping the free energy landscape of the ribosome using single-molecule FRET'. Biopolymers. 2008, 89: 565-577. 10.1002/bip.20961.PubMed CentralView ArticlePubMedGoogle Scholar
- Munro JB, Sanbonmatsu KY, Spahn CM, et al: 'Navigating the ribosome's metastable energy landscape'. Trends Biochem Sci. 2009, 34: 390-400. 10.1016/j.tibs.2009.04.004.PubMed CentralView ArticlePubMedGoogle Scholar
- Frank J, Agrawal RG: 'A ratchet-like inter-subunit reorganization of the ribosome during translocation'. Nature. 2000, 406: 318-322. 10.1038/35018597.View ArticlePubMedGoogle Scholar
- Spirin AS: 'How does the ribosome work? A hypothesis based on the two subunit construction of the ribosome'. Curr Mod Biol. 1968, 2: 115-127.PubMedGoogle Scholar
- Horan LH, Noller HF: 'Intersubunit movement is required for ribosomal translocation'. Proc Natl Acad Sci USA. 2007, 104: 4881-4885. 10.1073/pnas.0700762104.PubMed CentralView ArticlePubMedGoogle Scholar
- Allen GS, Zavialov A, Gursky R, et al: 'The cryo-EM structure of a translation initiation complex from Escherichia coli'. Cell. 2005, 121: 703-712. 10.1016/j.cell.2005.03.023.View ArticlePubMedGoogle Scholar
- Klaholz BP, Myasnikov AG, Van Heel M: 'Visualization of release factor 3 on the ribosome during termination of protein synthesis'. Nature. 2004, 427: 862-865. 10.1038/nature02332.View ArticlePubMedGoogle Scholar
- Gao H, Zhou Z, Rawat U, et al: 'RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors'. Cell. 2007, 129: 929-941. 10.1016/j.cell.2007.03.050.View ArticlePubMedGoogle Scholar
- Gao N, Zavialov AV, Li W, et al: 'Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies'. Mol Cell. 2005, 18: 663-674. 10.1016/j.molcel.2005.05.005.View ArticlePubMedGoogle Scholar
- Frank J, Gao H, Sengupta J, et al: 'The process of mRNA-tRNA translocation'. Proc Natl Acad Sci USA. 2007, 104: 19671-19678. 10.1073/pnas.0708517104.PubMed CentralView ArticlePubMedGoogle Scholar
- Agirrezabala X, Frank J: 'Elongation in translation as a dynamic interaction between the ribosome, tRNA, and elongation factors EF-G and EF-Tu'. Q Rev Biophys. 2009, 3: 159-200.View ArticleGoogle Scholar
- Valle M, Zavialov A, Li W, et al: 'Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy'. Nat Struct Biol. 2003, 10: 899-906. 10.1038/nsb1003.View ArticlePubMedGoogle Scholar
- Li W, Agirrezabala X, Lei J, et al: 'Recognition of aminoacyl-tRNA: A common molecular mechanism revealed by cryo-EM'. EMBO J. 2008, 27: 3322-3331. 10.1038/emboj.2008.243.PubMed CentralView ArticlePubMedGoogle Scholar
- Ermolenko DN, Majumdar ZK, Hickerson RP, et al: 'Observation of intersubunit movement of the ribosome in solution using FRET'. J Mol Biol. 2007, 370: 530-540. 10.1016/j.jmb.2007.04.042.View ArticlePubMedGoogle Scholar
- Kim HD, Puglisi JD, Chu S: 'Fluctuations of transfer RNAs between classical and hybrid states'. Biophys J. 2007, 93: 3575-3582. 10.1529/biophysj.107.109884.PubMed CentralView ArticlePubMedGoogle Scholar
- Agirrezabala X, Lei J, Brunelle JL, et al: 'Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome'. Mol Cell. 2008, 32: 190-197. 10.1016/j.molcel.2008.10.001.PubMed CentralView ArticlePubMedGoogle Scholar
- Julian P, Konevega SH, Scheres SH, et al: 'Structure of ratcheted ribosomes with tRNAs in hybrid states'. Proc Natl Acad Sci USA. 2008, 105: 16924-16927. 10.1073/pnas.0809587105.PubMed CentralView ArticlePubMedGoogle Scholar
- Munro JB, Altman RB, O'Connor N, et al: 'Identification of two distinct hybrid state intermediates on the ribosome'. Mol Cell. 2007, 25: 505-517. 10.1016/j.molcel.2007.01.022.PubMed CentralView ArticlePubMedGoogle Scholar
- Fei J, Kosuri P, MacDougall DD, et al: 'Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation'. Mol Cell. 2008, 30: 348-359. 10.1016/j.molcel.2008.03.012.View ArticlePubMedGoogle Scholar
- Cornish PV, Ermolenko DN, Noller HF, et al: 'Spontaneous intersubunit rotation in single ribosomes'. Mol Cell. 2008, 30: 578-588. 10.1016/j.molcel.2008.05.004.PubMed CentralView ArticlePubMedGoogle Scholar
- Marshall RA, Dorywalska M, Puglisi JD: 'Irreversible chemical steps control intersubunit dynamics during translation'. Proc Natl Acad Sci USA. 2008, 105: 15364-15369. 10.1073/pnas.0805299105.PubMed CentralView ArticlePubMedGoogle Scholar
- Moazed D, Noller HF: 'Intermediate states in the movement of transfer RNA in the ribosome'. Nature. 1989, 342: 142-148. 10.1038/342142a0.View ArticlePubMedGoogle Scholar
- Valle M, Zavialov A, Sengupta J, et al: 'Locking and unlocking of ribosomal motions'. Cell. 2003, 114: 123-134. 10.1016/S0092-8674(03)00476-8.View ArticlePubMedGoogle Scholar
- Zhang W, Dunkle JA, Cate JH: 'Structures of the ribosome in intermediate states of ratcheting'. Science. 2009, 325: 1014-1017. 10.1126/science.1175275.PubMed CentralView ArticlePubMedGoogle Scholar
- Cornish PV, Ermolenko DN, Staple DW, et al: 'Following movement of the L1 stalk between three functional states in single ribo-somes'. Proc Natl Acad Sci USA. 2009, 106: 2571-2576. 10.1073/pnas.0813180106.PubMed CentralView ArticlePubMedGoogle Scholar
- Sternberg SH, Fei J, Prywes N, et al: 'Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling'. Nat Struct Mol Biol. 2009, 16: 861-868. 10.1038/nsmb.1622.View ArticlePubMedGoogle Scholar
- Van Loock MS, Agrawal RK, Gabashvili IS, et al: 'Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation'. J Mol Biol. 2000, 304: 507-515. 10.1006/jmbi.2000.4213.View ArticleGoogle Scholar
- Spahn CM, Gomez-Lorenzo MG, Grassucci RA, et al: 'Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation'. EMBO J. 2004, 23: 1008-1019. 10.1038/sj.emboj.7600102.PubMed CentralView ArticlePubMedGoogle Scholar
- Taylor DJ, Nilsson J, Merrill AR, et al: 'Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation'. EMBO J. 2007, 26: 2421-2431. 10.1038/sj.emboj.7601677.PubMed CentralView ArticlePubMedGoogle Scholar
- Schuwirth BS, Borovinskaya MA, Hau CW, et al: 'Structures of the bacterial ribosome at 3.5 A resolution'. Science. 2005, 310: 827-834. 10.1126/science.1117230.View ArticlePubMedGoogle Scholar
- Mohr DW, Wintermeyer W, Rodnina MV: 'GTPase activation of elongation factors Tu and G on the ribosome'. Biochemistry. 2002, 41: 12520-12528. 10.1021/bi026301y.View ArticlePubMedGoogle Scholar
- Helgstrand M, Mandava CS, Mulder FA, et al: 'The ribosomal stalk binds to translation factors IF2, EF-Tu EF-G and RF3 via a conserved region of the L12 C-terminal domain'. J Mol Biol. 2007, 365: 468-479. 10.1016/j.jmb.2006.10.025.View ArticlePubMedGoogle Scholar
- Diaconu M, Kothe U, Schlunzen F, et al: 'Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation'. Cell. 2005, 121: 991-1004. 10.1016/j.cell.2005.04.015.View ArticlePubMedGoogle Scholar
- Ogle JM, Brodersen DE, Clemons WM, et al: 'Recognition of cognate transfer RNA by the 30S ribosomal subunit'. Science. 2001, 292: 897-902. 10.1126/science.1060612.View ArticlePubMedGoogle Scholar
- Ogle JM, Murphy FV, Tarry MJ, et al: 'Selection of tRNA by the ribosome requires a transition from an open to a closed form'. Cell. 2002, 111: 721-732. 10.1016/S0092-8674(02)01086-3.View ArticlePubMedGoogle Scholar
- Villa E, Sengupta J, Trabuco LG, et al: 'Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis'. Proc Natl Acad Sci USA. 2009, 106: 1063-1068. 10.1073/pnas.0811370106.PubMed CentralView ArticlePubMedGoogle Scholar
- Schuette JC, Murphy FV, Kelley AC, et al: 'GTPase activation of elongation factor EF-Tu by the ribosome during decoding'. EMBO J. 2009, 28: 755-765. 10.1038/emboj.2009.26.PubMed CentralView ArticlePubMedGoogle Scholar
- Ogle JM, Ramakrishnan V: 'Structural insights into translational fidelity'. Annu Rev Biochem. 2005, 74: 129-177. 10.1146/annurev.biochem.74.061903.155440.View ArticlePubMedGoogle Scholar
- Cochella L, Green R: 'An active role for tRNA in decoding beyond codon:anticodon pairing'. Science. 2005, 308: 1178-1180. 10.1126/science.1111408.PubMed CentralView ArticlePubMedGoogle Scholar
- Schmeing TM, Voorhees RM, Kelley AC, et al: 'The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA'. Science. 2009, 326: 688-694. 10.1126/science.1179700.PubMed CentralView ArticlePubMedGoogle Scholar
- Beringer M, Rodnina M: 'The ribosome peptidyl transferase'. Mol Cell. 2007, 26: 311-321. 10.1016/j.molcel.2007.03.015.View ArticlePubMedGoogle Scholar
- Schmeing TM, Huang KS, Strobel SA, et al: 'An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA'. Nature. 2005, 438: 520-524. 10.1038/nature04152.View ArticlePubMedGoogle Scholar
- Vorhees RM, Weixlbaumer A, Loakes D, et al: 'Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome'. Nat Struct Mol Biol. 2009, 16: 528-533. 10.1038/nsmb.1577.View ArticleGoogle Scholar
- Simonovic M, Steitz TA: 'A structural view on the mechanism of the ribosome-catalyzed peptide bond formation'. Biochim Biophys Acta. 2009, 1789: 612-623. 10.1016/j.bbagrm.2009.06.006.PubMed CentralView ArticlePubMedGoogle Scholar
- Beckmann R, Spahn CM, Eswar N, et al: 'Architecture of the protein-conducting channel associated with the translating 80S ribosome'. Cell. 2001, 107: 361-372. 10.1016/S0092-8674(01)00541-4.View ArticlePubMedGoogle Scholar
- Morgan DG, Menetret JF, Neuhof A, et al: 'Structure of the mammalian ribosome-channel complex at 17A resolution'. J Mol Biol. 2002, 324: 871-886. 10.1016/S0022-2836(02)01111-7.View ArticlePubMedGoogle Scholar
- Spahn CM, Jan E, Mulder A, et al: 'Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: The IRES functions as an RNA-based translation factor'. Cell. 2004, 118: 465-475. 10.1016/j.cell.2004.08.001.View ArticlePubMedGoogle Scholar
- Halic M, Gartmann M, Schlenker O, et al: 'Signal recognition particle receptor exposes the ribosomal translocon binding site'. Science. 2006, 312: 745-747. 10.1126/science.1124864.View ArticlePubMedGoogle Scholar
- Chandramouli PM, Topf M, Menetret JF, et al: 'Structure of the mammalian 80S ribosome at 8.7 A resolution'. Structure. 2008, 16: 535-548. 10.1016/j.str.2008.01.007.PubMed CentralView ArticlePubMedGoogle Scholar
- Sengupta J, Nilsson J, Gursky R, et al: 'Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy'. J Mol Biol. 2008, 382: 179-187. 10.1016/j.jmb.2008.07.004.PubMed CentralView ArticlePubMedGoogle Scholar