Models

Mechanistical model of the catalytic cycle of Trypanothione Synthetase

An ODE model of the gene regulation network governing sporulation initiation in Bacillus subtilis to be run in Matlab.

The network incorporates four sporulation-related signals: nutrient supply, DNA damage, the products of the competence genes and the bacterial population size.

Run execute_bacillus_sporulation_initiation.m to simulate the model. This file also contains the signal-related parameters which can be altered to investigate the effect of competing signals.

Some results for this model ...

Here, we use hyperbolic tangents to fit experimental data of AB fermentation in C. acetobutylicum in continous culture at steady state for different external pHs. The estimated parameters are used to define acidogenic and solventogenic phase. Furthermore, an transition phase is identified which cannot be assigned to acidogenesis or solventogenesis.

Several plots compare the fits to the experimental data.

This function estimates the parameters of growth functions of the acid-forming and solvent-forming population observed in 'forward'-shift experiments of phosphate-limited continuous cultures of C. acetobutylicum. The parameters are used in the 'Two-Populations'-Model of the pH-induced metabolic shift.

It assumed that the found behaviour of the optical density during these experiments results from a phenotypic switch caused by the changing pH level.

3D structure prediction of LDH enzymes from four LAB by comparative modeling against x-ray structure of LDH from B. stearothermophilis (template, PDB ID: 1LDN). The computation was performed with a protocol that uses "automodel.very_fast" settings of Modeller program (http://salilab.org/modeller/).

Comparison of electrostatic potentials within the allosteric binding sites of LDH enzymes to estimate the binding affinity of the FBP molecule is performed with the PIPSA program. The program uses the structure of enzymes in the PDB format and computed electrostatic potentials in the GRD format.

Computation is performed for the modeled 3D structures of LDH enzymes (in PDB format) with the UHBD program, for pH 6 and pH 7.

Binding energies of phosphate ions to the allosteric and catalytic sites were estimated with a program GRID (http://www.moldiscovery.com/soft_grid.php). The calculations were performed for the modeled LDH structures from four LABs, at pH 6 and 7, in presence and absence of the FBP molecule. The phosphate ion was presented as a probe.

In order to estimate whether Pi has an activatory or an inhibitory effect on the enzymes, the computed probe binding energies (from GRID results, Part 4) were compared with those for the LDH from L. plantarum whose activity is known to be unaffected by Pi.

The binding energies of the Pi probe in the allosteric binding site (AS) and the COO probe in the catalytic binding site (CS) of LDH from L. plantarum were defined as E¬AS,threshold and ECS,threshold, respectively. For the other LDH enzymes, ...

The zip file contains two executable Matlab functions.

File named 'fnct_gen_tfcompmod.m' generates a Simbiology model based on the following interactions: R + X <-> RX -> R + X + Px R + Y <-> RY -> R + Y + Py R + Z <-> RZ -> R + Z + Pz Y + Pz -> Pz Px -> Py -> Pz ->

We assume much higher reaction speeds of sigma factor RNApol binding/unbinding compared to protein expression. Protein expression can therefore be represented by Michaelis-Menten like kinetic ...

The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.

The model is described ...

Structural models of the LAB PYKs of L. lactis, L. plantarum, S. pyogenes and E. faecalis including the "best" docking solutions of potential allosteric ligands. The structures were derived by homology modeling based on the template of E. coli and B. stearothermophilus. PYK models and ligands are provided as .pdb files and can be displayed by using the program PyMOL, for instance.

Model of reconstituted gluconeogenesis system in S. solfataricus based on the individual kinetic models for PGK, GAPDH, TPI, FBPAase.

Exponential decay model of gluconeogenic intermediates

Mathematical model for TPI kinetics, GAP and DHAP saturation, and inhibition with 3PG and PEP.

Mathematical model for GAPDH kinetics, BPG, NADPH, NADP, GAP and Pi saturation.

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

Mathematical model for PGK kinetics, ADP, ATP, 3PG and BPG saturation.

SBML models without activity of the glycolytic enzymes in the cytosol:

Glycolysis_noActivityInCytosol_1a.xml Model 1a Glycolysis_noActivityInCytosol_1b.xml Model 1b Glycolysis_noActivityInCytosol_2.xml Model 2 Glycolysis_noActivityInCytosol_3.xml Model 3 Glycolysis_noActivityInCytosol_4.xml Model 4 Glycolysis_noActivityInCytosol_5.xml Model 5 Glycolysis_noActivityInCytosol_6.xml Model 6

SBML models with activity of the glycolytic enzymes in the cytosol:

Glycolysis_withActivityInCytosol_1a.xm Model ...

This ordinary-differential equation model is a spatially lumped model showing the behaviour of oxygen in the three compartments medium, membrane and cytoplasm and its impact on FNR inactivation, hereby showing the effects of different oxygen concentrations, diffusion coefficients and reaction rates. The model was created with the Matlab SimBiology toolbox.

This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.

Code for joint probabilistic inference of transcription factor behaviour and gene-transcription factor as well as metabolite-transcription factor interaction based on genome and metabolite data.

The model presents the response of E.coli to different levels of oxygen supply, in which the oxidases, Cyo and Cyd, and their regulators, FNR and ArcBA systems, are included. The initial file 0.xml and supporting documents are for the model with FNR only. Four 0.xml files provided are at AAU level 31, 85, 115 and 217 respectively. The ArcBA system can be activated by revising the number of agents, ArcB, ArcA dimer, ArcA monomer, ArcA tetramer and ArcA octamer, in the initial file. The model needs ...

only lacZ synthesis reduced by inhibitor in BSA115

The model file represents the expression of beta-gal from a sigB dependent promoter after sigb production was stimulated by IPTG. The model is based on an assumption that a hypothetical protein degrates the sigb factor.

This is a JWS model of the successful model for data representation. It realises regulation by a hypothetical sigB dependent protein that degrades beta-Gal.

The model represents a hypothetical situation in which an anti-sigmafactor reduces sigB efficacy.

The zip folder contains files that allow simulation of stressosome dynamics. The models are based on a cellular automaton approach. Each protein of RsbR and RsbS is located in the crystal structure of the stressosome. The proteins can be phosphorylated or not and these states determine the future of neighbouring proteins. To simulate the model open the file 'liebal_stressosome-model_12_workflow-matlab.m' in Matlab. It is written in the cell-model, put the cursor into a cell that you wish to ...

Bayesian model for inference of the activity of transcription factors from targets' mRNA levels. A standalone C sharp package (runs on linux and mac under MONO).

This model assumes a phenotypic switch between an acid- and solvent-forming population caused by the changing pH levels. The two phenotypes differ in their transcriptomic, proteomic, and ,thus, their metabolomic profile. Because the growth rates of these phenotypes depends on the extracellular pH, the initiation of the pH-shift results in a significant decline of the acidogenic population. Simultaneously, the solvent-forming population rises and establishes an new steady state.

The model is build ...