Brownian dynamics study of the association between the 70S ribosome and elongation factor G

• Published in: Biopolymers 2011-09, Vol.95 (9), p.616-627
• Main Authors: Długosz, Maciej, Huber, Gary A., McCammon, J. Andrew, Trylska, Joanna
• Format: Article
• Language: English
• Subjects: 70S ribosome; Bacteria; Binding Sites; Biopolymers; Brownian dynamics; Codon; Computer Simulation; Dynamic tests; Dynamical systems; Dynamics; Elongation; Escherichia coli - metabolism; Ions; Kinetics; Models, Statistical; Molecular Conformation; Molecular Dynamics Simulation; Peptide Elongation Factor G - chemistry; Proteins; Ribosomes - chemistry; RNA, Messenger - metabolism; RNA, Transfer - chemistry; Static Electricity; Thermus thermophilus - metabolism; translation
• ISSN: 0006-3525; 1097-0282; 1097-0282
• DOI: 10.1002/bip.21619

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.