Pathway modeling of the mapk cascade
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Pathway Modeling of the MAPK cascade. Rishi Khan, Wenzhong Wang, Nate Woody. Goals. Model the MAPK Cascade pathway using Virtual Cell Create accesible geometry Input kinetic parameters Validate the Model Examine overall behavior of model Examine models sensitivity to key parameter changes

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Pathway modeling of the mapk cascade

Pathway Modeling of the MAPK cascade

Rishi Khan, Wenzhong Wang, Nate Woody


Goals
Goals

  • Model the MAPK Cascade pathway using Virtual Cell

    • Create accesible geometry

    • Input kinetic parameters

  • Validate the Model

    • Examine overall behavior of model

    • Examine models sensitivity to key parameter changes

  • Experiment

    • Change number of cascades

    • Examine unique parameter situations


Modeling the pathway

v1

v2

v3

v4

v5

MAPKK

MAPKKK

MAPK

MAPKKK-P

MAPKK-P

MAPK-P

v6

Modeling the Pathway

  • MAPK cascade using 6 species

  • 3 primary reactions

Membrane

Cytosol


Initial results
Initial results

Kholodenko BN

Eur J Biochem 2000 Mar;267(6):1583-8


Parameter importance
Parameter importance

  • Adjusting various parameters by 100x

  • Notice the strong effect of K3 on M2KP


Adjusting k3 and k4
Adjusting K3 and K4

  • Systematic adjustment of K3 and K4

  • All other parameters remain the same

  • High values approach linearity


Effects of cascading
Effects of Cascading

  • First order response of first cascade

  • Second order response of second cascade

  • MAPKP increases and decreases faster than MAPKKP


Evaluation of virtual cell

Advantages

No programming

False color plots

Only public resource

Disadvantages

Data VERY hard to export

Very little control over data display

Non-robust (math and interface)

Crashes often

Evaluation of Virtual Cell


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