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)
Export PNG

Views: 595
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