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This article is part of the supplement: Selected articles from The 5th IEEE International Conference on Systems Biology (ISB 2011)

Open Access Research

Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example

Ru-Dong Li1 and Lei Liu12*

Author Affiliations

1 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

2 Shanghai Center for Bioinformatics Technology, Shanghai, China

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BMC Systems Biology 2012, 6(Suppl 1):S11  doi:10.1186/1752-0509-6-S1-S11

Published: 16 July 2012

Additional files

Additional file 1:

The metabolite-centric and enzyme-centric views of the E. coli central carbon metabolic network. The file is in the format of *.png, with figures included showing the metabolite-centric (Page 1) and enzyme-centric metabolic (Page 2) networks. In the metabolite-centric view, enzymes/reactions are abbreviated as symbols and denoted by rectangles; metabolites are also abbreviations; inhibitors/activators are drawn as circles beside the reactions. Synth1 is a lumped reaction for synthesizing chorismate and murine; Synth2 is lumped reaction for synthesizing isoleucine, alanine, ketoisovalerate, and diaminopimelate [5]. In the enzyme-centric view, enzymes are denoted by circles and arrows indicate interactions. For more detailed information, see the "Methods" section and Additional file 6.

Format: PNG Size: 48KB Download file

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Additional file 2:

Impacts on system states in the metabolite-centric view. The file is in the format of *.pdf, with each plot showing the impacts of enzymes deletions on the metabolite kinetics. The metabolite indexes, impact distances and state uation amplitudes form the 3 dimensions. Legends are the same as those in Figure 2.

Format: PDF Size: 714KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 3:

Impacts on system states in the enzyme-centric view. The file is in the format of *.pdf, with each plot showing the impacts of enzymes deletions on the kinetic fluxes. The reaction/enzyme indexes, impact distances and flux fluctuation amplitudes form the 3 dimensions. Legends are the same as those in Additional file 2.

Format: PDF Size: 732KB Download file

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Additional file 4:

The catalogue of the results of dynamical stability analysis. The file categorizes all enzymes that generate topologically equivalent system orbit structures, when deleted. Enzymes in the same category exert similar impacts on the qualitative dynamics of the system. The file is in the format of MS Word electronic table (*.doc).

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Additional file 5:

The flux-sum validations of critical and uncritical enzymes. The file is in the format of *.pdf, with each plot showing the flux-sums of the essential metabolites before and after the deletion of an enzyme. Deletions of all presented enzymes are shown. The metabolite symbols and flux-sum values form the lateral and vertical dimensions. Legends are the same as those in Figure 5.

Format: PDF Size: 219KB Download file

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Additional file 6:

Description of the modeling. The file is the supplementary text of the modeling. It is in the format of *.doc and includes detailed descriptions of metabolites, enzymes, kinetic rate equations and ODEs.

Format: DOC Size: 313KB Download file

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Additional file 7:

High resolution images of Figure 6A and 6B. The two files (in the format of *.png) are the high resolution versions of Figure 6A and 6B, respectively.

Format: PNG Size: 125KB Download file

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Additional file 8:

High resolution images of Figure 6A and 6B. The two files (in the format of *.png) are the high resolution versions of Figure 6A and 6B, respectively.

Format: PNG Size: 105KB Download file

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