Progress curves for the purified Caulinobacter crescentus Weimberg pathway enzymes. Each reaction is followed up to completion and then the next enzyme in the pathway is added, i.e. XDH-XLA-XAD-KDXD and finally KGSADH

**SEEK ID:** https://fairdomhub.org/studies/584

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 10:12

**Last updated**: 6th Jan 2020 at 16:17

## 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 XLAC by Caulobacter crescentus XDH, measured in NMR.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis XDH

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis XLA

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis XAD

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis KDXD

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis KGSADH

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Snapshots: **Snapshot 1, Snapshot 2

Conversion of XYL to KG by sequential addition of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig2c/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis combined

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Snapshots: **Snapshot 1, Snapshot 2

Data files for the conversion of XYL to KG, via the sequential addition of 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:** Progress curves

**Assays:** Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 the progress curves 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:** Progress curves

**Assays:** Progress curve KGSADH

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 the progress curves 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:** Progress curves

**Assays:** Progress curve KDXD

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. 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 the progress curves 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:** Progress curves

**Assays:** Progress curve XAD

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Assays:** Progress curve XLA

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Assays:** Progress curve XDH

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Assays:** Progress curves combined

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.

**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:** Progress curves

**Assays:** Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined