# Models

**118**Models visible to you, out of a total of

**194**

The fitted function describes the pH-drop during 'forward'-shift experiments and the increase of the pH during 'reverse'-shift experiments. The estimated parameters are used to compute the changing pH level in the models of the pH.induced metabolic shift in continuous cultures under phosphate limitation of C. acetobutylicum. Furthermore, the parameters can be applied to join different independent experiments into a single data set.

To fit the changing pH level, an exponential function and a

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**Creator: **Thomas Millat

**Contributor**: Thomas Millat

**Model type**: Not specified

**Model format**: Matlab package

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/).

**Creator: **Anna Feldman-Salit

**Contributor**: Anna Feldman-Salit

**Model type**: Not specified

**Model format**: Not specified

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

**Creator: **Anna Feldman-Salit

**Contributor**: Anna Feldman-Salit

**Model type**: Not specified

**Model format**: Not specified

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.

**Creator: **Anna Feldman-Salit

**Contributor**: Anna Feldman-Salit

**Model type**: Not specified

**Model format**: Not specified

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.

**Creator: **Anna Feldman-Salit

**Contributor**: Anna Feldman-Salit

**Model type**: Not specified

**Model format**: Not specified

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,

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**Creator: **Anna Feldman-Salit

**Contributor**: Anna Feldman-Salit

**Model type**: Algebraic equations

**Model format**: Not specified

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

**Creator: **Samantha Nolan

**Contributor**: David Knies

**Model type**: Partial differential equations (PDE)

**Model format**: Mathematica

Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

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

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

Mathematica notebook for the parameterisation of the PGM rate equation based on SEEK linked experimental data.

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

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.

**Creator: **Thomas Millat

**Contributor**: Thomas Millat

**Model type**: Not specified

**Model format**: Matlab package

Mathematica notebook for the parameterisation of the PK rate equation based on the experimental SEEK data set

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.

**Creators: **Jennifer Levering, Mark Musters

**Contributor**: Jennifer Levering

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

The kinetic model includes sugar uptake, degradation of glucose into pyruvate and the fermentation of pyruvate.

**Creator: **Jennifer Levering

**Contributor**: Jennifer Levering

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

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.

**Creators: **Nadine Veith, Anna Feldman-Salit, Stefan Henrich, Rebecca Wade

**Contributor**: Nadine Veith

**Model type**: Not specified

**Model format**: Not specified

Mathematica notebook for the pyruvate transport rate equation, based on literature data.

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica