One pot cascade - pathway analysis for the purified Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, removal of XLA, and optimisation on Xylose to aKG is studied.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate

**SEEK ID:** https://fairdomhub.org/studies/585

Caulobacter crescentus Weimberg pathway

**Projects:** Computational pathway design for biotechnological applications

**Study position: **

**Projects:** Computational pathway design for biotechnological applications

**Experimentalists:**
Lu Shen (experiments), Jacky Snoep (model)

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**Created**: 29th Mar 2019 at 14:38

**Last updated**: 30th Jan 2020 at 09:52

## Related items

**Projects:** PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, Project Coordination, WP 3: Drug release kinetics study

**Institutions:** Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, University of Manchester - Department of Computer Science, Stellenbosch University

The currently used mathematical models for medical treatment at the individual or population level are largely phenomenological and have limited quantitative predictive power. It is usually not possible to predict the effect of an intervention in a specific process or to predict the effect of a pharmaceutical drug since the step or enzyme on which the intervention/drug works is not explicit in the model.

Taking HIV pathogenesis as an example, the immune system response, vaccine exposure, and drug ...

**Projects:** Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications

The goal of the project is to establish a new biotechnological platform for the production of hydroxy-amino acids, since the current production of these important building blocks is very expensive. Enzyme engineering, systems biotechnology and metabolic engineering will be used in a synthetic biology approach.

**Programme**: SARCHI: Mechanistic modelling of health and epidemiology

**Public web page**: Not specified

**Organisms:** Caulobacter

The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model ...

**Submitter**: Jacky Snoep

**Studies:** Cell free extract, Initial rate kinetics, One pot cascade, Progress curves

**Assays:** Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD recycling, KDXD, KGSADH, One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16, Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined, Steady state cell free extract, with Mn and NAD recycling, XAD, XDH, XLA

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One-Pot-Cascade 10

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 10 data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, omitting XLA, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One pot cascade 12

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 12 data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, with NAD recycling, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One-Pot-Cascade 13

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 13 data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, using old enzymes with optimal protein distribution, with NAD recycling, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One pot cascade 16

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 16 data

**Snapshots: **Snapshot 1, Snapshot 2

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway, using old enzymes: XDH, XLA, XAD, KDXD, KGSADH, with NAD recycling, and optimal protein distribution.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 16

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes, XDH, XLA, XAD, KDXD, KGSADH.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 10

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes, omitting XLA: XDH, XAD, KDXD, KGSADH.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 12

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes: XDH, XLA, XAD, KDXD, KGSADH, with NAD recycling.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 13

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 12 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 12

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with NAD recycling. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 13 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 13

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 10 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 10

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, using old enzymes, with optimal protein distribution. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 16 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 16

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

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

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16