Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Genetics, Development and Cell Biology, Baker Center for Bioinformatics and Biological Statistics

Document Type


Publication Version

Accepted Manuscript

Publication Date


Journal or Book Title

Physical Biology





First Page





The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; 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 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.


This is a manuscript of an article published as Kurkcuoglu, Ozge, Pemra Doruker, Taner Z. Sen, Andrzej Kloczkowski, and Robert L. Jernigan. "The ribosome structure controls and directs mRNA entry, translocation and exit dynamics." Physical biology 5, no. 4 (2008): 046005. doi: 10.1088/1478-3975/5/4/046005. Posted with permission.

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IOP Publishing Ltd



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Published Version