Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Details Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

2010-08-02

arxiv.org/abs/1008.0298v3

Physical Biology, 8 (2011) 026005

Physics

Biological Physics

This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Lt

Scientific paper

10.1088/1478-3975/8/2/026005

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.

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