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Modeling single-molecule translation.

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posted on 2019-10-16, 17:38 authored by Luis U. Aguilera, William Raymond, Zachary R. Fox, Michael May, Elliot Djokic, Tatsuya Morisaki, Timothy J. Stasevich, Brian Munsky

A) Translation is divided into three main processes: initiation, elongation, and termination. The ribosome footprint represents the physical space occluded by the ribosome, enforcing that no two ribosomes can occupy the same space and time. B) Kymographs represent ribosome movement as a function of time (y-axis) and position (x-axis). Each line represents a single ribosome trajectory. The average slope is proportional to the effective ribosome elongation rate. The plot to the right shows the relationship between ribosome movement and fluorescence intensity, and the plot below shows the ribosome loading at each codon position, calculated as the time-average of ribosome occupancy at the corresponding codon. C) Comparison of the average elongation time (top) and the mean (middle) or variance (bottom) of fluorescence intensity as calculated using the simplified model (Eqs 18 to 21), a linear moments-based model (Eqs 9 to 17), and a full stochastic model (Eqs 1 to 5). Gray area represents previously reported parameter values for ribosome initiation. Panels B and C correspond to simulations for the β-actin. Asterisks represent the specific parameter combination used for Table 1.

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