Submitted to: Physical Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2008
Publication Date: 11/24/2008
Citation: Kurkcuoglu, O., Doruker, P., Sen, T.Z., Kloczkowski, A., Jernigan, R.L. 2008. The Ribosome Shape Directs mRNA Translocation through Entrance and Exit Dynamics. Physical Biology. 5(4):40005.
Interpretive Summary: Protein synthesis plays an essential role in all biological systems. It requires the ribosomal machinery that continuously synthesizes proteins in the cell with high fidelity. But how does ribosome perform this complex processing? In this paper, we analyze the structural motions of a ribosome in order to elucidate the dynamics of the protein synthesis process. Our work identifies some of the most critical parts of this complicated machinery. This information will be useful to biologists and biochemists who study protein synthesis. Better understanding of protein synthesis has a broad range of benefits, from facilitating the development of antibiotics to improvement of crops.
Technical Abstract: The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs (transfer ribonucleic acids) and mRNA (messenger ribonucleic acid); here the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP (guanosine triphosphate) hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11, and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3’ end forming the Shine-Dalgarno complex at the initiation step; the 3’ end may act as a ‘hook’ to reel in the mRNA to facilitate its exit.