An agent-based model for mRNA export through the nuclear pore complex.
Bottom Line: On running the model, we observed that mRNA export is sensitive to the number and distribution of transport receptors coating the mRNA and that there is a rate-limiting step in the nuclear basket that is potentially associated with the mRNA reconfiguring itself to thread into the central channel.Of note, our results also suggest that using a single location-monitoring mRNA label may be insufficient to correctly capture the time regime of mRNA threading through the pore and subsequent transport.This has implications for future experimental design to study mRNA transport dynamics.
Affiliation: Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, Graduate Program in Chemical Biology, Berkeley, Berkeley, CA 94720.Show MeSH
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Mentions: In their simplest form, on-lattice ABMs consist of a mesh of “cells” that assemble the discretized space that agents occupy (Figure 9). The agents occupy these cells and are typically aware only of other agents within their “neighborhood” of cells, with the simplest neighborhood consisting of adjacent cells. Agents can be given the ability to move into adjacent cells and interact with other agents with some probability in conjunction with governing rules that define what movement and interactions are possible. On-lattice ABMs have been applied to biological systems involving diffusion, binding, and unbinding (Bonchev et al., 2010; Devillers et al., 2010; Dong et al., 2010).
Affiliation: Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, Graduate Program in Chemical Biology, Berkeley, Berkeley, CA 94720.