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

**SEEK ID:** https://fairdomhub.org/studies/582

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**: 26th Mar 2019 at 14:01

**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

Kinetic characterisation and mathematical modelling of XDH.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**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

**Snapshots: **Snapshot 1

Kinetic characterisation and mathematical modelling of XLA.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**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

**Snapshots: **Snapshot 1

Kinetic characterisation and mathematical modelling of XAD.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**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

**Snapshots: **Snapshot 1

Kinetic characterisation and mathematical modelling of KDXD.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**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

**Snapshots: **Snapshot 1

Kinetic characterisation and mathematical modelling of KGSADH.

**Submitter**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**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

**Snapshots: **Snapshot 1

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.

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

**Assays:** KGSADH

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

**Assays:** 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

**Assays:** XLA

Model for the Caulobacter crescentus xylonate dehydratase, describing the initial rate kinetics for substrate dependence. 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 XAD 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

**Assays:** XAD

Model for the Caulobacter crescentus 2-keto-3-deoxy-D-xylonate dehydratase, 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 KDXD 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

**Assays:** KDXD