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- 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

**SEEK ID:** https://fairdomhub.org/projects/138

**Public web page:**
Not specified

**Organisms:**
Caulobacter

**FAIRDOM PALs:**
No PALs for this Project

**Project created:**
12th Mar 2019

## Related items

- People (3)
- Institutions (2)
- Investigations (1)
- Studies (4)
- Assays (19)
- Data files (13+1)
- Models (22+1)
- Publications (1)

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

**Institutions:** University Duisburg-Essen

**Projects:** SulfoSys, SulfoSys - Biotec, HOTSOLUTE, Computational pathway design for biotechnological applications, ScyCode

**Institutions:** University Duisburg-Essen, Universitity Duisburg-Essen

**Roles:** Project Coordinator, Vice Coordinator

**Expertise:** Carbohydrate Metabolism of Archaea, Reconstruction of metabolic pathways, Regulation of carbohydrate metabolism, Archaeal physiology, Hyperthermophiles, Thermoacidohiles, Biotechnology

**Tools:** Biochemistry, Molecular Biology, Microbiology, Physiology, Systems Biology

Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.

Archaea possess many novel enzymes and pathways and our aim is

...

**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

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

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

...

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**Investigation:** Caulobacter crescentus Weimberg pathway

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

Initial rate kinetics for the purified Caulinobacter crescentus Weimberg pathway enzymes, including substrate dependence, and product inhibition.

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

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

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

Cell free extract - pathway analysis for Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, and Mn2+ on Xylose to aKG conversion is studied.

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, without Mn2+ added, but with NAD recycling, metabolites measured enzymatically.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig4d/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE analysis (shen2), CFE no Mn, with NADrec

**SOPs:** No SOPs

**Data files:** CFE no-Mn but with NADrec data

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, but no NAD recycling, metabolites measured enzymatically.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig4c/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE Mn noNADrec, CFE analysis (shen2)

**SOPs:** No SOPs

**Data files:** CFE Mn no-NADrec data

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, and with NAD recycling, metabolites measured enzymatically.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig4b/simulate

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE Mn NADrec, CFE analysis (shen2)

**SOPs:** No SOPs

**Data files:** CFE Mn NADrec data

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

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Snapshots: **Snapshot 1, Snapshot 2

**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

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE steady state analysis (shen3)

**SOPs:** No SOPs

**Data files:** No Data files

Kinetic characterisation and mathematical modelling of XDH.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** XDH model

**SOPs:** No SOPs

**Data files:** XDH-initial rate kinetics data

Kinetic characterisation and mathematical modelling of XLA.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** XLA model

**SOPs:** No SOPs

**Data files:** XLA-initial rate kinetics data

Kinetic characterisation and mathematical modelling of XAD.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** XAD model

**SOPs:** No SOPs

**Data files:** XAD-initial rate kinetics data

Kinetic characterisation and mathematical modelling of KDXD.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** KDXD model

**SOPs:** No SOPs

**Data files:** KDXD-initial rate kinetics data

Kinetic characterisation and mathematical modelling of KGSADH.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** KGSADH model

**SOPs:** No SOPs

**Data files:** KGSADH-initial rate kinetics data

Conversion of Xyl to XLAC by Caulobacter crescentus XDH, measured in NMR.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**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

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

Initial rate kinetics for the α-ketoglutarate semialdehyde dehydrogenase of Caulobacter crescentus, α-ketoglutarate semialdehyde and NAD saturation, and α-ketoglutarate, NADH and 2-keto-3-deoxy-D-xylonate inhibition.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Initial rate kinetics

**Assays:** KGSADH

Initial rate kinetics for the 2-keto-3-deoxy-D-xylonate dehydrates of Caulobacter crescentus, 2-keto-3-deoxy-D-xylonate saturation and inhibitor titrations.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

Initial rate kinetics for the xylonate dehydratase of Caulobacter crescentus, xylonate saturation.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

Initial rate kinetics for the xylonolactonase reaction of Caulobacter crescentus, xylonolactone saturation for the enzyme catalysed reaction, and for the non-enzymatic reaction.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

Initial rate kinetics for xylose dehydrogenase of Caulobacter crescentus, saturation with xylose and NAD, and inhibition by NADH and xylonolactone.

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, in Caulobacter crescentus cell free extract, with NAD recycling, and additional Mn2+ (0.15 mM) added.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, without NAD recycling, but with additional Mn2+ (0.15 mM) added.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, but without additional Mn2+ added.

**Creators: **Jacky Snoep, Lu Shen

**Submitter**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

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 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

**Modelling analyses:** 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

**Modelling analyses:** 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

**Modelling analyses:** 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

**Modelling analyses:** 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

**Modelling analyses:** 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

**Modelling analyses:** Progress curves combined

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. 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 cell free extract with added Mn, but no NAD rec, 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:** Cell free extract

**Modelling analyses:** Cell free extract, with Mn, no NAD recycling

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

**Modelling analyses:** One pot cascade 12

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. 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 cell free extract with no added Mn, but with NAD rec, 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:** Cell free extract

**Modelling analyses:** Cell free extract, without added Mn, with NAD r...

Steady state model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

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

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Caulobacter

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

**Modelling analyses:** Steady state cell free extract, with Mn and NAD...

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

**Modelling analyses:** 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

**Modelling analyses:** 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

**Modelling analyses:** 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

**Modelling analyses:** One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. 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 cell free extract with added Mn and NAD rec 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:** Cell free extract

**Modelling analyses:** Cell free extract, with Mn and NAD recycling

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts

**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:** Cell free extract

**Modelling analyses:** Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD r...

Model for the Caulobacter crescentus Î±-ketoglutarate semialdehyde dehydrogenase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KGSADH 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:** Initial rate kinetics

**Modelling analyses:** KGSADH

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

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

Model for the Caulobacter crescentus xylose dehydrogenase, describing the initial rate kinetics including substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XDH kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XDH 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:** Initial rate kinetics

**Modelling analyses:** XDH

Model for the Caulobacter crescentus xylonolactonase, describing the initial rate kinetics and substrate dependence. If the Mathematica notebook is downloaded and the data file for the XLA kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XLA 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:** Initial rate kinetics

**Modelling analyses:** XLA

**Abstract** (Expand)

**Authors: **Lu Shen, Martha Kohlhaas, Junichi Enoki, Roland Meier, Bernhard Schönenberger, Roland Wohlgemuth, Robert Kourist, Felix Niemeyer, David van Niekerk, Christopher Bräsen, Jochen Niemeyer, Jacky Snoep, Bettina Siebers

**Date Published**: 1st Dec 2020

**Publication Type**: Not specified

**DOI: **10.1038/s41467-020-14830-y

**Citation**: Nat Commun 11(1) : 82