Quick search Find article
Quick search
Find article

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

Ozge Kurkcuoglu1, Pemra Doruker1, Taner Z Sen2,3, Andrzej Kloczkowski4,5 and Robert L Jernigan1,4,1

Show affiliations


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.


PACS

87.14.G- Nucleic acids

87.14.E- Proteins

87.15.K- Molecular interactions; membrane-protein interactions

87.16.Tb Mitochondria and other organelles

87.15.N- Properties of solutions of macromolecules

87.15.La Mechanical properties

Subjects

Biological physics

Dates

Issue 4 (December 2008)

Received 25 July 2008, accepted for publication 21 October 2008

Published 24 November 2008

 
Image from The ribosome structure controls and directs mRNA entry, translocation and exit dynamics


View by subject




Export








Please login to access our web services, or create an account if you don't yet have one.

You must have cookies enabled in your web browser to be able to login.

Username
Password

Forgotten your password? Get a new one here.