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Chemotaxis: Another go

Chemotaxis: Another go. Chrisantha Fernando Systems Biology Centre Birmingham University. Now add Chemoattractant. CheA. CheB. CheB-P. CheY-P. CheY. Motor. TUMBLE. RUN. = Active Tar. = Inactive Tar. = Methyl group. R. R m. CheA-P. Tumbling via CheY. R m. R. S. CheA. CheAP.

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Chemotaxis: Another go

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  1. Chemotaxis: Another go Chrisantha Fernando Systems Biology Centre Birmingham University

  2. Now add Chemoattractant CheA CheB CheB-P CheY-P CheY Motor TUMBLE RUN = Active Tar = Inactive Tar = Methyl group

  3. R Rm CheA-P Tumbling via CheY

  4. Rm R S CheA CheAP CheB CheBP

  5. Rm R S CheA CheAP CheB CheBP Use MM kinetics to describe each of the enzyme reactions i.e.

  6. Rm R S CheA CheAP CheB CheBP

  7. Initial values Parameters Methylation and De-methylation is ‘Saturated’ [R] Rate of reaction per unit CheBP concentration

  8. [Rm] = Methylated Receptor [CheA-P] ≈ tumbling frequency [CheB-P] 0.0001 [S] 0.001 0.01 0.1

  9. [Rm] = Methylated Receptor The limit of perfect adaptation occurs when new Rm can no longer be produced 0.001 0.01 0.1 1.0

  10. Non-saturated methylation and demethylation No-perfect adaptation. 0.0001 [S] 0.001 0.01 0.1

  11. The First (wrong) Model Available at… http://www.pdn.cam.ac.uk/groups/comp-cell/Publications.html

  12. Moving on… • We can go through points that were confusing again… • It is important you understand the principles of how to model these systems.. • Mass action kinetics • MM kinetics • Inhibition (competitive and non-competitive) • Saturation of enzymes

  13. Stochastic Modeling • So far we have been doing deterministic modeling. • Stochastic models consider individual molecules, undergoing discrete reaction events. • These models diverge when particle numbers are low. • By the end of this course you will be able to model both using ODEs and stochastic modeling, all the circuits I’ve talked about previously, and more. For now, familiarize yourself with bionetS.

  14. BioNetS Easy to use

  15. Here is a paper written using the tool…

  16. Lets start with some simple chemical networks…

  17. R RCheZ Rm CheZ Example of a Saturated Enzyme (CheZ) acting to methylate R

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