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

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.

SUBMITTER: Dlugosz M

PROVIDER: S-EPMC3125448 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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

Długosz Maciej M Huber Gary A GA McCammon J Andrew JA Trylska Joanna J

Biopolymers 20110310 9

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 b ...[more]

PMID: 21394717

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