User:R Lo87/High resolution ribosome structure

High resolution ribosome structure
The overall mechanism of the ribosome translation has been known. The translation can be divided into four key pathways. The process of protein synthesis begins with the initiation step, where the small ribosome subunits attached to the mRNA translation initiation site, which is always the AUG start codon. Next the tRNA, which is carrying an amino acid, by an initiation factor binds to the start codon with its anticodon and occupies the P- site of the now joining large subunit. A second tRNA is brought into the ribosome by the elongation factor. If the anticodon of the tRNA pairs with the next codon of the mRNA, the tRNA occupies the A site on the large subunit. The amino acid from the first tRNA will be transferred to the second tRNA on the A site and the P site is now occupied by an uncharged tRNA molecule. The ribosome will now moves along the mRNA by one codon, this movement shifts the growing polypeptide chain to the P position and the uncharged tRNA to the E site and exit, resulting in an empty A site, where a new charged tRNA can enter and pair. This process known as elongation will continue until it reached the stop codon, where a release factor enters the A site so the translation will be terminating. At that point the action of a termination factor releases, the newly synthesized peptide chain will exit from the P site. Exactly after the release, the ribosome disassembles into its separate subunits, ready for next translation to begin.

It was in the past decades the full structure determination of the ribosome was firstly to display on Thermus thermophilius (T. thermophilius ). The structure determination of T. thermophilius 70S ribosome with 5.5 Å resolution was obtained with x-ray crystallography when the ribosome was in function with tRNA and mRNA in the A and P site and the P and E site respectively. The same technique was used to determine the Escherichia coli (E.coli) ribosome structure by creating crystals that contained two unique copies of the 70S ribosome. The E.coli crystals diffracted to beyond 3.5 Å resolution. At this resolution the RNA backbone was visible and nearly all of the ribosomal RNA (rRNA) was visible in the electron density. The two ribosomes in crystal structures showed different conformations which is a result of rigid body motions. This result show that the small subunit swiveled as a rigid body around the neck region in the E site direction. Comparison of this data with the T. thermophilius 5.5 Å resolution data revealed the total rotation. This rotation was later on defined to a ratchet-like rotational motion and has a central role in coordinating the conformational changes of ribosome during protein synthesis. The Cryoelectron microscopy provides information to demonstrate the precise mechanism involved in the ratchet-like-rotation, the peptide-bond formation, the elongation factor G (EF-G) and subsequent GTP hydrolysis induce the movement of the ratchet-like rotation, suggesting that the chemical energy of GTP hydrolysis is used to perform mechanical work on the ribosome The binding of EF-G induces large-scale conformational changes in the ribosome which cause a ratchet-like subunit rearrangement (RSR) and presumably correspond to the translocation at the P/E hybrid site.

The path from A to P (called the pretranslocation state) site is kind of unobstructed while in the path from P to E (posttranslocation state) the 16S form a stable ridge on the small subunit and separates the anticodon stem-loop of P-site tRNA from the E site. The space gap that appears during this stage is big enough to allow the tRNA movement to enter the P/E hybrid state but prevent the RNA helix from the A site. The decoding mechanism of the A-site is driven by how A1492 and A1493 interact with the minor groove of the codon-anticodon base pair and form a three sequence-independent hydrogen bond, two of the bonds was similar and the third one was specific which made the case of only a correct Watson-Crick interaction will take place, cause the hydrogen bond have an optimal geometry and thus serve the highest bond energy.