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Two-thirds of the ribosome consist of ribosomal RNA (rRNA) ..

In order to understand GTP hydrolysis in EF-Tu, we studied theribosome-induced EF-Tu conformational changes that trigger GTPhydrolysis on the factor as revealed by cryo-electron microscopy(cryo-EM) studies. We applied MDFF to obtain an atomic model of a 6.7-Åcryo-EM map of the pre-accommodated 70S ribosome bound to thePhe-tRNAPhe:EF-Tu:GDP ternary complex stalled by the antibiotickirromycin (kir), showed in Fig. 3.

Dense spherical bodies in the nucleus that are the synthesis site for ribosomal RNA

The structure and function of the ribosome are fascinatinglycomplex. Two-thirds of the ribosome consist of ribosomal RNA (rRNA),while over 50 ribosomal proteins make up the rest. The geneticinformation is delivered to the ribosome by a messenger RNA(mRNA). Transfer RNAs (tRNAs) are adapter molecules, each equipped withan anticodon to match the codons in the mRNA, and charged with an aminoacid that corresponds to the anticodon as dictated by the geneticcode. The ribosome contains three tRNA-binding sites: A, P, and E (seeelongation cycle box, or watch a ). In addition to mRNA and tRNAs, the ribosomeinteracts with protein factors such as the elongation factors Tu (EF-Tu)and G (EF-G), that are important players in the so-called elongationcycle. The elongation cycle results in the addition of an amino acid tothe nascent peptide chain, and consists of three main steps. In thedecoding step, a ternary complex comprised of an aminoacyl-tRNA(aa-tRNA), EF-Tu, and GTP binds to the ribosome,leading to the recognition of the codon by the anticodon. The followingstep is the peptidyl transfer. Here the peptide chain bound to theP-site tRNA is covalently linked to the amino acid bound to the A-sitetRNA. In the translocation step, the position of the mRNA/tRNA complexshifts by one codon, accompanied by a ratchet-like motion of theribosomal subunits.

Ribosomal RNA Synthesis and Processing in a ..

Due to great advances in the structural resolution of the ribosome, animpressive feat given its large size, the system is considered one ofthe hottest focal areas in molecular cell biology today. During theprocess of translation, the ribosome undergoes several conformationalchanges and binds to different factors that catalyze specificreactions. As detailed below, techniques to determine structure of theribosome can only image snapshots of the ribosome, often at medium tolow resolution. Atomic details of the interactions between the factorsand the ribosome, along with a dynamic description of the conformationalchanges of the ribosome itself, are crucial to understanding itsfunction.

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.

The Roles of RNA in the Synthesis of Protein

The translation of genetic information into proteins is essential forlife. At the core of this process lies the ribosome, a quintessentiallarge (2.5-4.5 MDa) molecular machine responsible for translatinggenetic material into functional proteins. In a growing cell, ribosomescomprise up to half of the net dry weight. Because of its fundamental rolein the cell, 50% of all efforts to develop antibiotics target bacterialribosomes, taking advantage of the structural differences between bacterialand human ribosomes.

After the accommodation of the tRNA brought by EF-Tu and successful peptidyl transfer, the ribosome is able to spontaneously undergo an intersubunit rotation (Fig. 1 (i) to (ii)). In this state the tRNAs assume a hybrid occupation relative to the ribosome: while the anticodon is still located in the original site on the small subunit, the other end of the tRNA is shifted to the next binding site on the large subunit generating so called A/P and P/E hybrid states. The P/E tRNA engages in interactions with the L1 stalk, a very dynamic part of the ribosome. These interactions are thought to stabilize the hybrid state. Interestingly, based on FRET experiments it seems that the initiator tRNA interacts weaker with the L1 stalk.

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composed of protein and RIBOSOMAL RNA

Using MDFF and equilibrium MD we addressed the nature of the interactions between the L1 stalk and a tRNA in the hybrid P/E state. In particular, we compared the behavior of the initiator tRNAfMet versus the elongator tRNAPhe. Not only do the two tRNAs assume different conformations within the ribosome (Fig. 10), they interact differently with the L1 stalk. While for both tRNAs a peculiar stacking with the ribosomal RNA of the L1 stalk is observed, it is less pronounced for the initiator tRNA compared to an elongator tRNA (Fig. 10). Interestingly, the behavior of the tRNAs is strongly impacted by their respective modification patterns.

Molecules of ribosomal RNA are produced in the nucleolus

During the spontaneous intersubunit rotation, or the so-called ratcheting, of the ribosome, tRNAs inside the ribosome adopt two different conformations, the classical (A/A and P/P) state and the hybrid (A/P and P/E) state. Together with the motion of L1 stalk, these conformations are collectively termed as two distinct states, namely "macrostate I" (unratcheted ribosome, classical tRNAs and open L1 stalk) and "macrostate II" (ratcheted ribosome, hybrid tRNAs and a closed L1 stalk), as shown in Fig 11A. The transition from "macrostate I" to "macrostate II" is essential for translocating the tRNAs inside the ribosome such that the site for tRNA bearing the next amino acid can be vacated. The existence of intermediate states in between these two conformations is of great debate due to lack of structural data.

Cellular site of Escherichia coli ribosomal RNA synthesis.

Application of MDFF to cryo-EM data of the ribosome revealed two previously unseen intermediate states (Fig 11B). The identification of these new intermediate states help elucidating the pathway of transition, in particular the formation of hybrid tRNAs inside the ribosome. Our results also support the idea that the ribosome is employing a Brownian mechanism to progress through the distinct states during the translocation of mRNA-tRNAs.

Cellular site of Escherichia coli ribosomal RNA synthesis

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.

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