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BIOMD0000000026 - Markevich2004_MAPK_orderedElementary

 

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Reference Publication
Publication ID: 14744999
Markevich NI, Hoek JB, Kholodenko BN.
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades.
J. Cell Biol. 2004 Feb; 164(3): 353-359
Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, PA 19107, USA.  [more]
Model
Original Model: BIOMD0000000026.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6618379269
Submission Date: 13 Sep 2005 13:33:21 UTC
Last Modification Date: 15 May 2012 21:41:59 UTC
Creation Date: 23 May 2005 12:47:22 UTC
Encoders:  Nicolas Le Novère
   Rainer Machne
set #1
bqbiol:occursIn Taxonomy Xenopus laevis
set #2
bqbiol:isVersionOf Gene Ontology MAPK cascade
Notes

The model corresponds to the schemas 1 and 2 of Markevich et al 2004, as described in the figure 1 and the supplementary table S1. Phosphorylations and dephosphorylations follow distributive ordered kinetics. The phosphorylations are modeled with three elementary reactions:
E+S<=>ES->E+P
The dephosphorylations are modeled with five elementary reactions:
E+S<=>ES->EP<=>E+P

Model
Publication ID: 14744999 Submission Date: 13 Sep 2005 13:33:21 UTC Last Modification Date: 15 May 2012 21:41:59 UTC Creation Date: 23 May 2005 12:47:22 UTC
Mathematical expressions
Reactions
binding MAPK and PP-MAPKK phosphorylation of MAPK binding PP-MAPKK and P-MAPK phosphorylation of P-MAPK
binding MKP and PP-MAPK dephosphorylation of PP-MAPK dissociation of MKP from P-MAPK binding MKP and P-MAPK
dephosphorylation of P-MAPK dissociation of MKP from MAPK    
Physical entities
Compartments Species
uVol M Mp Mpp
MAPKK MKP M_MAPKK
Mp_MAPKK Mpp_MKP Mp_MKP
Mp_MKP* M_MKP  
Global parameters
k1 k_1 k2 k3
k_3 k4 h1 h_1
h2 h3 h_3 h4
h_4 h5 h6 h_6
Reactions (10)
 
 binding MAPK and PP-MAPKK [M] + [MAPKK] ↔ [M_MAPKK];  
 
 phosphorylation of MAPK [M_MAPKK] → [Mp] + [MAPKK];  
 
 binding PP-MAPKK and P-MAPK [Mp] + [MAPKK] ↔ [Mp_MAPKK];  
 
 phosphorylation of P-MAPK [Mp_MAPKK] → [Mpp] + [MAPKK];  
 
 binding MKP and PP-MAPK [Mpp] + [MKP] ↔ [Mpp_MKP];  
 
 dephosphorylation of PP-MAPK [Mpp_MKP] → [Mp_MKP];  
 
 dissociation of MKP from P-MAPK [Mp_MKP] ↔ [Mp] + [MKP];  
 
 binding MKP and P-MAPK [Mp] + [MKP] ↔ [Mp_MKP*];  
 
 dephosphorylation of P-MAPK [Mp_MKP*] → [M_MKP];  
 
 dissociation of MKP from MAPK [M_MKP] ↔ [M] + [MKP];  
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 M
Compartment: uVol
Initial amount: 500.0
 
 Mp
Compartment: uVol
Initial amount: 0.0
 
 Mpp
Compartment: uVol
Initial amount: 0.0
 
 MAPKK
Compartment: uVol
Initial amount: 50.0
 
 MKP
Compartment: uVol
Initial amount: 100.0
 
 M_MAPKK
Compartment: uVol
Initial amount: 0.0
 
 Mp_MAPKK
Compartment: uVol
Initial amount: 0.0
 
 Mpp_MKP
Compartment: uVol
Initial amount: 0.0
 
 Mp_MKP
Compartment: uVol
Initial amount: 0.0
 
 Mp_MKP*
Compartment: uVol
Initial amount: 0.0
 
 M_MKP
Compartment: uVol
Initial amount: 0.0
 
Global Parameters (16)
 
   k1
Value: 0.02
Constant
 
   k_1
Value: 1.0
Constant
 
   k2
Value: 0.01
Constant
 
   k3
Value: 0.032
Constant
 
   k_3
Value: 1.0
Constant
 
   k4
Value: 15.0
Constant
 
   h1
Value: 0.045
Constant
 
   h_1
Value: 1.0
Constant
 
   h2
Value: 0.092
Constant
 
   h3
Value: 1.0
Constant
 
   h_3
Value: 0.01
Constant
 
   h4
Value: 0.01
Constant
 
   h_4
Value: 1.0
Constant
 
   h5
Value: 0.5
Constant
 
   h6
Value: 0.086
Constant
 
   h_6
Value: 0.0011
Constant
 
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