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Article Evaluation
Page Title: Ribosome
Missing information:
In the section 'high resolution structure' X-ray crystallographic resolution of many ribosome structures have been mentioned and for the 50S prokaryotic ribosome structure characterised in 2000, the resolution is not mentioned, which is 2.4 and 3.3 angstroms, I believe it's important to have this information there as the Nobel prize was given for determining these structures.
Article Editing
P-site
The P-site (for peptidyl) is the second binding site for t-RNA in the ribosome. The other two sites are the A-site (aminoacyl), which is the first binding site in the ribosome, and the E-site (exit), which is the third and final binding site in the ribosome. The P-site during translation holds the t-RNA which is linked to the growing polypeptide chain. When a stop codon is reached ending translation, the peptidyl-tRNA bond of the t-RNA located in the P-site is cleaved releasing the newly synthesized protein.[1] During the translocation step of the elongation phase, the mRNA is advanced by one codon, coupled to movement of the tRNAs from the ribosomal A to P and P to E sites, catalyzed by elongation factor EF-G[2]
Overview
[edit]The ribosomal P-site plays a vital role in all phases of translation. Initiation involves recognition of the start codon (AUG) by initiator tRNA in the P-site, elongation phase involves passage of many elongator tRNAs through the P site, termination phase involves hydrolysis of the mature polypeptide from tRNA bound to the P-site, and ribosome recycling involves release of deacylated tRNA.
Binding a tRNA to the P-site in the presence of mRNA establishes codon-anticodon interaction and this interaction is important for small subunit ribosome (30S) contacts to the tRNA.[3]
Using Toeprinting assay, it has been shown that Protein Synthesis initiates from the A-site of the Ribosome in the cricket paralysis virus (CrPV). IGR-IRES (Intragenic regions-internal ribosome entry sites) can assemble 80S ribosomes from 40S and 60S ribosomal subunits in the absence of eIF2, Met-tRNAi, or GTP hydrolysis and without a coding triplet in the ribosomal P-site. Authors also showed IGR-IRES can direct translation of a protein whose N-terminal residue is not methionine.[4]
Classical two-state model[5] proposes that ribosome contains two binding sites for tRNA, P-site and A-site. The A-site binds to incoming to aminoacyl tRNA which has the anti-codon for the corresponding codon in the mRNA presented in the A-site. After peptide formation between the C-terminal carbonyl group of the growing polypeptide chain (attached to a P-site bound tRNA) and the amino group of the aminoacyl tRNA (A-site bound), the polypeptide chain is then attached to the tRNA in the A-site. The deacylated tRNA remains in the P-site and gets released once the peptidyl-tRNA is transferred to the P-site.
Using Chemical probing methods, a set of phylogenetically conserved bases in ribosomal RNA where the tRNA binds has been examined and suggested to be directly involved in the binding of tRNA to the ribosome.[6] Correlation of such site specific protected bases in rRNA and occupancy of the A, P and E sites has allowed diagnostic assays of these bases to study the location of tRNA in any given state of the translational cycle. Authors proposed a hybrid model where higher affinity of the deactivated tRNA and peptide tRNA for the E and P sites of the 50S subunit, thermodynamically favour the P/P to P/E and A/A to A/P transitions.
Structure
[edit]The complete three dimensional structure of the T. thermophilus 70S ribosome was determined using X-ray crystallography, containing mRNA and tRNAs bound to the P and E sites at 5.5 Å resolution and to the A site at 7 Å resolution. Authors found that all three tRNA binding sites (A, P, and E) of the ribosome contact all three tRNAs at universally conserved parts of their structures; this allows the ribosome to bind different tRNA species in precisely the same way. The translocation step of protein synthesis inescapably requires movements of 20 Å or more by the tRNAs, as they move from the A to P to E sites.[7]
tRNA Targeting Antibiotics
[edit]Oxazolidines (eg. linezolid) prevent the binding of the initiator tRNA at the P-site [8] Oxazolidines have been demonstrated to pleiotropically affect initiator-tRNA binding, EF-P (elongation factor P) stimulated synthesis of peptide bonds, and EF-G-mediated translocation of initiator-tRNA into the P-site.[9]
Macrolide, Lincosamide and Streptogramin class of antibiotics prevent peptide bond formation and/or the translocation of tRNA from the A-site to the P-site on the ribosome [10][11] that eventually leads to interference with the elongation step and thus the inhibition of protein translation.
References
[edit]- ^ Lodish, Harvey (2013). Molecular cell biology (Seventh ed.). New York: Worth Publ. pp. 141–143. ISBN 978-1429234139.
- ^ Rodnina MV, Savelsbergh A, Katunin VI, Wintermeyer W. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature. 1997 Jan 2;385(6611):37-41. PMID 8985244
- ^ Schäfer MA, Tastan AO, Patzke S, Blaha G, Spahn CM, Wilson DN, Nierhaus KH. Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit. J Biol Chem. 2002 May 24;277(21):19095-105. Epub 2002 Feb 26. PMID 11867615.
- ^ Wilson JE, Pestova TV, Hellen CU, Sarnow P. Initiation of protein synthesis from the A site of the ribosome. Cell. 2000 Aug 18;102(4):511-20. PMID 10966112.
- ^ WATSON JD. THE SYNTHESIS OF PROTEINS UPON RIBOSOMES. Bull Soc Chim Biol (Paris). 1964;46:1399-425. Review. PMID 14270536
- ^ Moazed D, Noller HF. Intermediate states in the movement of transfer RNA in the ribosome. Nature. 1989 Nov 9;342(6246):142-8. PMID 2682263.
- ^ Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science 2001 May 4 ;292(5518):883-96. PMID 11283358.
- ^ Chopra S, Reader J. tRNAs as Antibiotic Targets. Ibba M, ed. International Journal of Molecular Sciences. 2015;16(1):321-349. doi:10.3390/ijms16010321.
- ^ Aoki H., Ke L., Poppe S.M., Poel T.J., Weaver E.A., Gadwood R.C., Thomas R.C., Shinabarger D.L., Ganoza M.C. Oxazolidinone antibiotics target the P-site on Escherichia coli ribosomes. Antimicrob. Agents Chemother. 2002;46:1080–1085. doi: 10.1128/AAC.46.4.1080-1085.2002.
- ^ Johnston N.J., Mukhtar T.A., Wright G.D. Streptogramin antibiotics: Mode of action and resistance. Curr. Drug Targets. 2002;3:335–344. doi: 10.2174/1389450023347678.
- ^ Champney W.S., Tober C.L. Specific inhibition of 50s ribosomal subunit formation in Staphylococcus aureus cells by 16-membered macrolide, lincosamide, and streptogramin B antibiotics. Curr. Microbiol. 2000;41:126–135. doi: 10.1007/s002840010106