BIOPHYSICAL THEORY AND MODELING |
A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates
Hermioni D Zouridis 1 and Vassily Hatzimanikatis 1*
1 Northwestern University
* To whom correspondence should be addressed. E-mail: vassily{at}northwestern.edu.
Submitted on June 28, 2006
Revised on August 28, 2006
Accepted on 29 August 2006
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Abstract |
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The genetic information in DNA is transcribed to mRNA and then translated to proteins, which form the building blocks of life. Translation, or protein synthesis, is hence a central cellular process. We have developed a gene sequence specific mechanistic model for the translation machinery which accounts for all the elementary steps of the translation mechanism. We performed a sensitivity analysis in order to determine the effects of kinetic parameters and concentrations of the translational components on protein synthesis rate. Utilizing our mathematical framework and sensitivity analysis, we investigated the translational kinetic properties of a single mRNA species in E. coli. We propose that translation rate at a given polysome size depends on the complex interplay between ribosomal occupancy of elongation phase intermediate states and ribosome distributions with respect to codon position along the length of the mRNA, and this interplay leads to polysome self-organization that drives translation rate to maximum levels.
Key Words:
complex systems, kinetics, protein expression, protein synthesis, ribosomes, system behavior
