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29 March 2024
 
  » arxiv » cond-mat/0310682

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Clustered bottlenecks in mRNA translation and protein synthesis
Tom Chou ; Greg Lakatos ;
Date 29 Oct 2003
Subject Statistical Mechanics; Soft Condensed Matter; Subcellular Processes | cond-mat.stat-mech cond-mat.soft q-bio.SC
AbstractWe construct an algorithm that generates large, band-diagonal transition matrices for a totally asymmetric exclusion process (TASEP) with local hopping rate inhomogeneities. The matrices are diagonalized numerically to find steady-state currents of TASEPs with local variations in hopping rate. The results are then used to investigate clustering of slow codons along mRNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size, beyond $approx 3-4$, does not significantly reduce ribosome current. Our results are verified by extensive Monte-Carlo simulations and provide a biologically-motivated explanation for the experimentally-observed clustering of low-usage codons.
Source arXiv, cond-mat/0310682
Other source [GID 148453] pmid15600884
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