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Brownian dynamics study of the association between the 70S ribosome and elongation factor G
Author(s) -
Długosz Maciej,
Huber Gary A.,
McCammon J. Andrew,
Trylska Joanna
Publication year - 2011
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21619
Subject(s) - ribosome , chemistry , transfer rna , ribosomal rna , elongation factor , brownian dynamics , messenger rna , internal ribosome entry site , biophysics , translation (biology) , ribosomal protein , ribosomal binding site , rna , biochemistry , physics , brownian motion , biology , gene , quantum mechanics
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.