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Ribosomal protein L15 as a probe of 50S ribosomal subunit structure.

Development of directedhydroxyl radical probing methods allowed us to position ribosomalproteins, translation factors and tRNAs in three dimensions relativeto structural features of rRNA.

The 23 S rRNA environment of ribosomal protein L9 in the 50 S ribosomal subunit.

This can happen by gain-of-function mutations inproto-oncogenes or loss-of-function mutations in tumor suppressor genes.

Specific protection of 16S rRNA by translational initiation factors.

Identification of an RNA-protein bridge spanning the ribosomal subunit interface.

Althoughuntranslated, this region may influence the mRNA secondary structure andstability, efficacy of translation initiation, or binding of sequence-specificmRNA-binding proteins (a review by ).

Many of the identifiedcis-acting elements for translational regulation occur within the 3' UTR, andsome occur with regularity within certain protein function classes (a review by).

Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA.

Mapping the ribosomal RNA neighborhood of protein L11 by directed hydroxyl radical probing.

In vitro reconstitution of 30S ribosomal subunits using complete set of recombinant proteins, in RNA-Ligand Interactions, Part B: Molecular Biology Methods, , (eds.

Directed hydroxyl Radical Probing of RNA from Iron (II) tethered to Proteins in ribonucleoprotein complexes, Part B: Molecular biology Methods, , (eds.

Nucleotides in 23S rRNA protected by association of 30S and 50S ribosomal subunits.
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Interaction of proteins S16, S17 and S20 with 16S ribosomal RNA.

In summary, our MD simulations show that the macrolide ERY may triggerantibiotic effects to the bacterial ribosome through allosterically altering the ribosome structures, rather than through interplay with the nascent protein aspreviously suggested. This finding unveils a principally new view of the antibiotic action ofmacrolides to the bacterial ribosomes.

Protection of ribosomal RNA from kethoxal in polyribosomes.

Much of what is known about SecM stalling comes from biochemicalexperiments, in which every amino acid in SecM's sequence has beenmutated and the resulting effects measured. These experiments revealedfew residues as critical, although one stands out in every species asinvariable: arginine 163 (R163, see Fig. 13 below). However, untilrecently, little was known about the precise mechanisms at work. Acryo-EM map of a SecM-stalled ribosome revealed a shifted linkage in thePTC between the P-site tRNA and the SecM peptide. Although the shift wasonly 0.2 nm, it was hypothesized to be sufficient to inhibit peptide-bondformation, preventing synthesis of the remainder of SecM.

Alteration of 5S RNA conformation by ribosomal proteins L18 and L25.

Similar to TnaC described above, the peptide SecM exists solely to stallthe ribosome synthesizing it. But unlike TnaC, which also requires thepresence of high levels of trytophan, SecM has an intrinsic stallingcapability. Stalling of the ribosome synthesizing SecM provides time fora downstream RNA helix on the same mRNA strand to unwind. Unwinding ofthis helix then allows for a new ribosome to bind and synthesize anew protein, SecA, a bacterial ATP-driven translocase that aids the passage ofnascent proteins across membranes in conjunction with SecY (see also ). When sufficient levels of SecA have been reached,SecA interacts with the SecM-stalled ribosome to pull on SecM, freeingit and allowing translation to resume (illustrated schematically inFig. 13). SecM, which serves no otherpurpose than to stall the ribosome, is released into the cell anddegraded.

Ribosomal proteins of Escherichia coli.

The structural basis for TnaC-mediated translational stalling wasaddressed by obtaining a 5.8-Å cryo-EM map of the ribosome stalled byTnaC and high concentrations of tryptophan (Fig. 8). The cryo-EM datashows that the nascent chain adopts a distinct conformation in the exittunnel. We applied MDFF to obtain an atomic model of the entire ribosomeand the stalling nascent chain (Fig. 8F). The model allowed us to mapthe contacts between TnaC and the exit tunnel, as well as proposepossible communication pathways that would lead to inactivation of thecatalytic center of the ribosome (the so-called peptidyltransferasecenter, or PTC). One of the main findings was that two criticalribosomal residues at the PTC adopt conformations that are incompatiblewith cohabitation by release factors, which catalyze termination ofprotein synthesis.

This permits identification of the protein binding regions of theDNA.

Certain nascent peptide chains are able to regulate ribosome functionwhile they are still being synthesized, i.e., when they are still insidethe ribosomal exit tunnel. One of the classical examples is TnaC, aleader peptide of the tryptophanase operon in . At highconcentrations of tryptophan, TnaC stalls the ribosome, inhibitingtermination of its synthesis. Through an intricate gene regulatorymechanism, stalling ultimately leads to the expression of genesresponsible for degrading tryptophan.

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