Abstract
Protein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF-G) that facilitates the translocation of transfer RNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF-G/ribosome diffusional encounter and EF-G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF-G/70S ribosome system. We estimated the EF-G association rate constants at 150 and 300 mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF-G/ribosome association paths and found that positioning of the L11 protein of the large ribosomal subunit is likely crucial for EF-G entry to its binding site. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 616–627, 2011.
Highlights
The ribosome, protein synthesis machinery, is a ribonucleoprotein complex composed of two subunits that in bacteria are named 30S and 50S based on their sedimentation coefficients
Association Pathways Initially, 1,000,000 Brownian dynamics (BD) trajectories of elongation factor G (EF-G) diffusing in the electrostatic field of the 70S ribosome were generated
That according to our recent molecular dynamics (MD) study,[39] the EF-G protein is flexible in solution and even though the conformational changes observed in the simulations were not as pronounced as seen in the post-translational complex[5] (Figure 1B), they were still considerable
Summary
The ribosome, protein synthesis machinery, is a ribonucleoprotein complex composed of two subunits that in bacteria are named 30S and 50S based on their sedimentation coefficients. These two subunits, which consist of three RNA chains and over 50 proteins, interact through a network of intersubunit bridges to form the 70S active %2.5 MDa ribosome. Peptide bond synthesis takes place between the aminoacyl and peptidyl termini of the A- and P-site tRNAs. After the reaction, tRNAs translocate to their new positions (P and E) with the advance of mRNA by a distance of one codon to preserve the reading frame. The peptide elongation cycle is repeated and cognate-tRNAs bind to the A-site until a stop-codon on the mRNA is recognized
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
