Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT
1 Department of Systems Biology & Bioinformatics, Institute of Computer Science, University of Rostock, 18051, Rostock, Germany
2 Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
3 Institute of Structural and Molecular Biology, School of Biological Sciences, Edinburgh University, Edinburgh, EH9 3JR, UK
4 Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600, South Africa
BMC Systems Biology 2013, 7:3 doi:10.1186/1752-0509-7-3Published: 15 January 2013
Additional file 1:
Figure S1. Akbar et al. (2001)  (Figure 5A) studied beta-galactosidase expression for stressosomes composed only of RsbRC and RsbRD, of both of them (RsbRC+RsbRD) as well as a stressosome with all RsbR proteins (A+B+C+D). Although stressosome activation in the experiments (left) took place by transition to the stationary phase. RsbRC and RsbRD have been shown to be sensitive towards energy stress in B. subtilis (Martinez et al., 2010) . The simplest way to reproduce the results of Akbar et al. (2001) , is to increase the phosphorylation parameter of RsbS, kphs. The open circles represent the wildtype with all kphs are RsbD stressosomes (Akbar et al. (2001)  left), reproduced in the simulation with an increase of kphs to 0.75 (filled circles, right). Akbar et al. (2001)  measured the highest background and stimulated response for a stressosome composed completely of RsbRC (filled squares, left). In the simulation a further increase in the response could be generated by an additional increase in kphs to 0.9 (tilled square, right). The experiments show that RsbRC and RsbRD are sensitive to energy stress but mixture with RsbRA and RsbRB lowers the overall stressosome sensitivity. In the simulation this is represented by a reduction of the RsbS phosphorylation rate.
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Additional file 2:
The Additional file 2 contains the matlab files for reproduction of the results. To use it unpack all files into one directory. The main file is called liebal_stressosome-model_12_workflow-matlab.m. it is written using cell-mode. The cells can be evaluated sequentially by setting the cursor in a cell and evaluating it, eg. by Ctrl+Enter. Please contact firstname.lastname@example.org for any questions.
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