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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.
SEEK ID: https://fairdomhub.org/studies/586
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 14:50
Last updated: 6th Jan 2020 at 16:17
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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
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
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
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
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
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
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
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
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
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
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
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
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
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
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
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
