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PLoS One. 2012;7(1):e29377. doi: 10.1371/journal.pone.0029377. Epub 2012 Jan 3.

A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome.

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1
Chemical and Systems Biology, Stanford University, Stanford, California, United States of America. rbrandman@gmail.com

Abstract

The ribosome is a large macromolecular machine, and correlated motion between residues is necessary for coordinating function across multiple protein and RNA chains. We ran two all-atom, explicit solvent molecular dynamics simulations of the bacterial ribosome and calculated correlated motion between residue pairs by using mutual information. Because of the short timescales of our simulation (ns), we expect that dynamics are largely local fluctuations around the crystal structure. We hypothesize that residues that show coupled dynamics are functionally related, even on longer timescales. We validate our model by showing that crystallographic B-factors correlate well with the entropy calculated as part of our mutual information calculations. We reveal that A-site residues move relatively independently from P-site residues, effectively insulating A-site functions from P-site functions during translation.

PMID:
22235290
PMCID:
PMC3250440
DOI:
10.1371/journal.pone.0029377
[Indexed for MEDLINE]
Free PMC Article
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