dorsal/arxiv
View SchemaTowards a model for protein production rates
| Authors | J. J. Dong, B. Schmittmann, R. K. P. Zia |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0602024 |
| URL | https://arxiv.org/abs/q-bio/0602024 |
| DOI | 10.1007/s10955-006-9134-7 |
| Journal | Journal of Statistical Physics, Volume 128, Numbers 1-2 / July, 2007 |
Abstract
In the process of translation, ribosomes read the genetic code on an mRNA and assemble the corresponding polypeptide chain. The ribosomes perform discrete directed motion which is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. Using Monte Carlo simulations and a simple mean-field theory, we discuss the effect of one or two ``bottlenecks'' (i.e., slow codons) on the production rate of the final protein. Confirming and extending previous work by Chou and Lakatos, we find that the location and spacing of the slow codons can affect the production rate quite dramatically. In particular, we observe a novel ``edge'' effect, i.e., an interaction of a single slow codon with the system boundary. We focus in detail on ribosome density profiles and provide a simple explanation for the length scale which controls the range of these interactions.
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"abstract": "In the process of translation, ribosomes read the genetic code on an mRNA and\nassemble the corresponding polypeptide chain. The ribosomes perform discrete\ndirected motion which is well modeled by a totally asymmetric simple exclusion\nprocess (TASEP) with open boundaries. Using Monte Carlo simulations and a\nsimple mean-field theory, we discuss the effect of one or two ``bottlenecks\u0027\u0027\n(i.e., slow codons) on the production rate of the final protein. Confirming and\nextending previous work by Chou and Lakatos, we find that the location and\nspacing of the slow codons can affect the production rate quite dramatically.\nIn particular, we observe a novel ``edge\u0027\u0027 effect, i.e., an interaction of a\nsingle slow codon with the system boundary. We focus in detail on ribosome\ndensity profiles and provide a simple explanation for the length scale which\ncontrols the range of these interactions.",
"arxiv_id": "q-bio/0602024",
"authors": [
"J. J. Dong",
"B. Schmittmann",
"R. K. P. Zia"
],
"categories": [
"q-bio.BM",
"cond-mat.stat-mech",
"physics.bio-ph"
],
"doi": "10.1007/s10955-006-9134-7",
"journal_ref": "Journal of Statistical Physics, Volume 128, Numbers 1-2 / July,\n 2007",
"title": "Towards a model for protein production rates",
"url": "https://arxiv.org/abs/q-bio/0602024"
},
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