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. 2011 Dec;5(3-4):139-50.
doi: 10.1007/s11693-011-9088-1. Epub 2011 Oct 19.

A systems view of the protein expression process

Sucheta Gokhale  1 , Dimpal Nyayanit, Chetan Gadgil
Affiliations

A systems view of the protein expression process

Sucheta Gokhale et al. Syst Synth Biol. 2011 Dec.

Abstract

Many biological processes are regulated by changing the concentration and activity of proteins. The presence of a protein at a given subcellular location at a given time with a certain conformation is the result of an apparently sequential process. The rate of protein formation is influenced by chromatin state, and the rates of transcription, translation, and degradation. There is an exquisite control system where each stage of the process is controlled both by seemingly unregulated proteins as well as through feedbacks mediated by RNA and protein products. Here we review the biological facts and mathematical models for each stage of the protein production process. We conclude that advances in experimental techniques leading to a detailed description of the process have not been matched by mathematical models that represent the details of the process and facilitate analysis. Such an exercise is the first step towards development of a framework for a systems biology analysis of the protein production process.

Electronic supplementary material: The online version of this article (doi:10.1007/s11693-011-9088-1) contains supplementary material, which is available to authorized users.

Keywords: Mathematical model; Regulatory network; Transcription; Translation.

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Figures

Fig. 1
Fig. 1
Sub processes in protein production: A chromatin remodelling and histone modification, B transcription and RNA processing, C RNA degradation, D translation, E protein degradation
Fig. 2
Fig. 2
Some models for the protein production process organised in terms of breadth and level of detail included. The intensity of the bar qualitatively indicates the relative level of details included in the model
See this image and copyright information in PMC

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