The Role of L1 Stalk–tRNA Interaction in the Ribosome Elongation Cycle

Trabuco, Leonardo G.; Schreiner, Eduard; Eargle, John M.; Cornish, Peter V.; Ha, Taekjip; Luthey‐Schulten, Zaida; Schulten, Klaus

doi:10.1016/j.jmb.2010.07.056

Cited by 103 publications

(125 citation statements)

References 68 publications

Supporting

Mentioning

123

Contrasting

Order By: Relevance

“…The complete atomic models of the E. coli ribosome with ERY bound (the ERY model) and without the compound (drug-free model) are based on X-ray crystal structures 3OFO/3OFR and 2AVY/2AW4, respectively (8,26). The systems were prepared as described (35). The final dimensions of both simulation systems were ∼280 × 340 × 340 Å (for details, see SI Experimental Procedures).…”

Section: Methodsmentioning

confidence: 99%

Macrolide antibiotics allosterically predispose the ribosome for translation arrest

Sothiselvam

Liu

Han

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

104

121

View full text Add to dashboard Cite

Translation arrest directed by nascent peptides and small cofactors controls expression of important bacterial and eukaryotic genes, including antibiotic resistance genes, activated by binding of macrolide drugs to the ribosome. Previous studies suggested that specific interactions between the nascent peptide and the antibiotic in the ribosomal exit tunnel play a central role in triggering ribosome stalling. However, here we show that macrolides arrest translation of the truncated ErmDL regulatory peptide when the nascent chain is only three amino acids and therefore is too short to be juxtaposed with the antibiotic. Biochemical probing and molecular dynamics simulations of erythromycin-bound ribosomes showed that the antibiotic in the tunnel allosterically alters the properties of the catalytic center, thereby predisposing the ribosome for halting translation of specific sequences. Our findings offer a new view on the role of small cofactors in the mechanism of translation arrest and reveal an allosteric link between the tunnel and the catalytic center of the ribosome.

show abstract

Section: Methodsmentioning

confidence: 99%

Macrolide antibiotics allosterically predispose the ribosome for translation arrest

Sothiselvam

Liu

Han

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

104

121

View full text Add to dashboard Cite

show abstract

“…The eCNEs 42 and 43 are part of the ribosomal protein L1 stalk whose conformational changes (Cornish et al 2009;Munro et al 2010;Budkevich et al 2011) play a role in the discharge of tRNA from the exit site (E site) of the ribosome (Korostelev et al 2008;Cornish et al 2009;Trabuco et al 2010), promoted by eEF3 in eukaryotes (Andersen et al 2006). Moreover, eCNE43 is a dsCNE that is uniquely conserved in Eukarya, suggesting its eukaryotic-specific functional role to evacuate tRNA from the ribosome.…”

Section: Domain-specific Cnes (Dscnes)mentioning

confidence: 99%

Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics

Doris

Smith

Beamesderfer

et al. 2015

RNA

View full text Add to dashboard Cite

Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance. For this, we developed a structurally aligned database, FLORA (full-length organismal rRNA alignment) to identify highly conserved nucleotide elements (CNEs) in 23S-28S rRNA from each phylogenetic domain (Eukarya, Bacteria, and Archaea). Universal CNEs (uCNEs) are conserved in sequence and structural position in all three domains. Those in regions known to be essential for translation validate our approach. Importantly, some uCNEs reside in areas of unknown function, thus identifying novel sequences of likely great importance. In contrast to uCNEs, domain-specific CNEs (dsCNEs) are conserved in just one phylogenetic domain. This is the first report of conserved sequence elements in rRNA that are domain-specific; they are largely a eukaryotic phenomenon. The locations of the eukaryotic dsCNEs within the structure of the ribosome suggest they may function in nascent polypeptide transit through the ribosome tunnel and in tRNA exit from the ribosome. Our findings provide insights and a resource for ribosome function studies.

show abstract

“…Further, in the SBM, the classical secondary structure is energetically favored over denatured configurations. In contrast, with some explicit-solvent models the native secondary structure is not always stable, even for sequences that are known to be stable experimentally (54,55). Thus, when using an explicit-solvent model, disrupted secondary structure can result, even though the secondary structure may be fully consistent with the EM density.…”

Section: Resultsmentioning

confidence: 97%

Excited states of ribosome translocation revealed through integrative molecular modeling

Whitford

Ahmed²,

Yu³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles). Here, we present a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements. To demonstrate the approach, we present a sequence of configurations that are suggested to be associated with transfer RNA (tRNA) movement through the ribosome (translocation). The models were constructed by combining information from X-ray crystallography, cryo-electron microscopy, and biochemical data. These models provide a structural framework for translocation that may be further investigated experimentally and theoretically to determine the precise energetic character of each configuration and the transition dynamics between them. free-energy landscape | modeling transient configurations | molecular machine | tRNA hybrid | translation S tructural biology techniques, including X-ray crystallography and cryo-electron microscopy (cryo-EM), have provided extraordinary insights into the details of the functional configurations of biomolecular machines, such as the ribosome (1-11). These successes have relied on the ability to isolate structurally homogeneous populations of the molecular complexes. Molecular systems undergo continual fluctuations (12). However, when the energetic minimum associated with a particular configuration is sufficiently deep, the structural fluctuations only lead to minor deviations from the average. The structural models provided by these approaches describe the average coordinates inside each basin, and occasionally the structural distribution within a basin may also be characterized (13-16). When the energy landscape contains multiple basins of comparable free energy, one must "trap" the system (5) in a particular configuration, which results in a modified energy landscape (17). This is often true for X-ray crystallographic models, because scattering patterns may only be obtained if the molecules in the crystal are of sufficiently similar configuration and orientation. In this respect, cryo-EM is more flexible because heterogeneities (i.e., molecules that are not trapped in the desired basin) may be computationally removed after data collection (8, 11). These sorting methods allow one to access information about less populated basins of attraction. The smaller number of images in these basins may result in limited resolution; however, several recent studies with ≈10 6 images have produced reconstructions of subpopulations with subnanometer resolution. In principle, it...

show abstract

The Role of L1 Stalk–tRNA Interaction in the Ribosome Elongation Cycle

Cited by 103 publications

References 68 publications

Macrolide antibiotics allosterically predispose the ribosome for translation arrest

Macrolide antibiotics allosterically predispose the ribosome for translation arrest

Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics

Excited states of ribosome translocation revealed through integrative molecular modeling

Contact Info

Product

Resources

About