Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
Myoppase_actMyoppase |
Myoppase inactivation by ROCK
Cytoplasm
|
HMMIrreversible | Myoppase_actMyoppase |
|
|
reaction rate (J): ((Vmax * Myoppase_act) / (Km + Myoppase_act))[uM.s-1]
Km (1/2 max) (Km): 0.1[uM] max reaction rate (Vmax): (kcat * ROCK_act)[uM.s-1] user defined (kcat): 2.357[s-1] |
|
cofilin_actCofilin_p |
Cofilin inactivation by LIMK
Cytoplasm
|
GeneralKinetics | cofilin_actCofilin_p |
|
|
reaction rate (J): (kcat * LIMK_P * cofilin_act / (Km + cofilin_act))[uM.s-1]
user defined (kcat): 0.1[s-1] |
|
PP1_actPP1 |
PP1 inactivation by CaMKII
Cytoplasm
|
HMMIrreversible | PP1_actPP1 |
|
|
reaction rate (J): ((Vmax * PP1_act) / (Km + PP1_act))[uM.s-1]
Km (1/2 max) (Km): 4.97[uM] max reaction rate (Vmax): (kcat * CaMKIIp)[uM.s-1] user defined (kcat): 0.07166[s-1] |
|
Ca+CaMCa_CaM |
calcium binding calmodulin
Cytoplasm
|
GeneralKinetics | Ca+CaMCa_CaM |
|
|
reaction rate (J): ((kf * (n * (Ca ^ 3.0)) * CaM) - (kr * Ca_CaM))[uM.s-1]
user defined (kr): 1.0[tbd] user defined (kf): 7.75[tbd] user defined (n): 1.0[tbd] |
|
Calcineurin_actCalcineurin |
calcinuerin inactivation
Cytoplasm
|
HMMIrreversible | Calcineurin_actCalcineurin |
|
|
reaction rate (J): ((Vmax * Calcineurin_act) / (Km + Calcineurin_act))[uM.s-1]
Km (1/2 max) (Km): 127.0[uM] max reaction rate (Vmax): (0.34 * CaMKIIp)[uM.s-1] |
|
Cofilin_pcofilin_act |
Cofilin activation through SSH1 dephosphorylation
Cytoplasm
|
HMMIrreversible | Cofilin_pcofilin_act |
|
|
reaction rate (J): ((Vmax * Cofilin_p) / (Km + Cofilin_p))[uM.s-1]
Km (1/2 max) (Km): 4.0[uM] max reaction rate (Vmax): (kcat * SSH1_act)[uM.s-1] user defined (kcat): 0.34[s-1] |
|
RhoGTPRhoGDP |
RhoGTP hydrolysis
Cytoplasm
|
HMMIrreversible | RhoGTPRhoGDP |
|
|
reaction rate (J): ((Vmax * RhoGTP) / (Km + RhoGTP))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (0.1 * RhoGAP_act)[uM.s-1] |
|
SSH1SSH1_act |
SSH1 dephosphorylation by CaN
Cytoplasm
|
HMMIrreversible | SSH1SSH1_act |
|
|
reaction rate (J): ((Vmax * SSH1) / (Km + SSH1))[uM.s-1]
Km (1/2 max) (Km): 4.97[uM] max reaction rate (Vmax): (0.34 * Calcineurin_act)[uM.s-1] |
|
cdc42GTP+WASPWASP_act |
cdc42 activates WASP
Cytoplasm
|
MassAction | cdc42GTP+WASPWASP_act |
|
|
reaction rate (J): (((Kf * cdc42GTP) * WASP) - (Kr * WASP_act))[uM.s-1]
forward rate constant (Kf): 0.02[s-1.uM-1] reverse rate constant (Kr): 0.001[s-1] |
|
cdc42GTPcdc42GDP |
cdc42 hydrolysis
Cytoplasm
|
HMMIrreversible | cdc42GTPcdc42GDP |
|
|
reaction rate (J): ((Vmax * cdc42GTP) / (Km + cdc42GTP))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * RhoGAP_act)[uM.s-1] user defined (kcat): 0.1[s-1] |
|
LIMKLIMK_P |
LIMK activation by ROCK
Cytoplasm
|
HMMIrreversible | LIMKLIMK_P |
|
|
reaction rate (J): ((Vmax * LIMK) / (Km + LIMK))[uM.s-1]
Km (1/2 max) (Km): 0.3[uM] max reaction rate (Vmax): (kcat * ROCK_act)[uM.s-1] user defined (kcat): 0.9[s-1] |
|
MLCMLC_p |
MLC Phosphorylation by ROCK
Cytoplasm
|
HMMIrreversible | MLCMLC_p |
|
|
reaction rate (J): ((Vmax * MLC) / (Km + MLC))[uM.s-1]
Km (1/2 max) (Km): 2.47[uM] max reaction rate (Vmax): (kcat * ROCK_act)[uM.s-1] user defined (kcat): 1.8[s-1] |
|
cdc42GEF_actCdc42GEF |
Cdc42 GEF inactivation
Cytoplasm
|
HMMIrreversible | cdc42GEF_actCdc42GEF |
|
|
reaction rate (J): ((Vmax * cdc42GEF_act) / (Km + cdc42GEF_act))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * PP1_act)[uM.s-1] user defined (kcat): 0.01[s-1] |
|
arp23_actarp23 |
Arp23 inactivation
Cytoplasm
|
GeneralKinetics | arp23_actarp23 |
|
|
reaction rate (J): (k * arp23_act)[uM.s-1]
user defined (k): 0.1[s-1] |
|
B |
Barbed ends
Cytoplasm
|
GeneralKinetics | B |
|
|
reaction rate (J): ((kappa * (f_sev + f_nuc)) - (k_cap * B))[uM.s-1]
user defined (f_sev): (C0 * k_sev * ((cofilin_act / C0) ^ n1) * l * F_actin)[tbd] user defined (kappa): 106.0[tbd] user defined (n1): 4.0[1] |
|
RhoGEFRhoGEF_act |
RhoGEF activation by CaMKII
Cytoplasm
|
HMMIrreversible | RhoGEFRhoGEF_act |
|
|
reaction rate (J): ((Vmax * RhoGEF) / (Km + RhoGEF))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * CaMKIIp)[uM.s-1] user defined (kcat): 0.1[s-1] |
|
Il1_actIl1 |
Il1 inactivation
Cytoplasm
|
HMMIrreversible | Il1_actIl1 |
|
|
reaction rate (J): ((Vmax * Il1_act) / (Km + Il1_act))[uM.s-1]
Km (1/2 max) (Km): 127.0[uM] max reaction rate (Vmax): (kcat * CaMKIIp)[uM.s-1] user defined (kcat): 0.0688[s-1] |
|
Il1Il1_act |
Il1 activation by CaN
Cytoplasm
|
HMMIrreversible | Il1Il1_act |
|
|
reaction rate (J): ((Vmax * Il1) / (Km + Il1))[uM.s-1]
Km (1/2 max) (Km): 4.97[uM] max reaction rate (Vmax): (0.034 * Calcineurin_act)[uM.s-1] |
|
arp23+WASP_actarp23_act |
Arp23 activation
Cytoplasm
|
MassAction | arp23+WASP_actarp23_act |
|
|
reaction rate (J): (((Kf * arp23) * WASP_act) - (Kr * arp23_act))[uM.s-1]
forward rate constant (Kf): 0.02[s-1.uM-1] reverse rate constant (Kr): 0.01[s-1] |
|
F_actinG_actin |
severing
Cytoplasm
|
GeneralKinetics | F_actinG_actin |
|
|
reaction rate (J): ((C0 * k_sev * ((cofilin_act / C0) ^ 4.0) * l * F_actin) + (k_deg * F_actin) + (k_age * F_actin))[uM.s-1]
user defined (k_deg): 0.1[tbd] user defined (k_age): 0.001[tbd] |
|
CaMKIICaMKIIp |
CaMKII activation by CaM
Cytoplasm
|
GeneralKinetics | CaMKIICaMKIIp |
|
|
reaction rate (J): ((kcat3 * (Ca_CaM ^ 4.0) * CaMKII / ((Km ^ 4.0) + (Ca_CaM ^ 4.0))) + (CaMKII * kcat * CaMKIIp / (Km1 + CaMKII)))[uM.s-1]
user defined (kcat): 1.0[s-1] user defined (kcat3): 120.0[tbd] user defined (Km1): 10.0[uM] user defined (Km): 4.0[uM] |
|
PP1PP1_act |
PP1 activation by IL1
Cytoplasm
|
GeneralKinetics | PP1PP1_act |
|
|
reaction rate (J): ((kcat1 * Il1_act * PP1 / (Km1 + PP1)) + (kcat2 * PP1_act * PP1 / (Km2 + PP1)))[uM.s-1]
user defined (Km2): 10.0[uM] user defined (kcat1): 50.0[s-1] user defined (kcat2): 2.0[s-1] user defined (Km1): 80.0[uM] |
|
cdc42GDPcdc42GTP |
cdc42 activation
Cytoplasm
|
HMMIrreversible | cdc42GDPcdc42GTP |
|
|
reaction rate (J): ((Vmax * cdc42GDP) / (Km + cdc42GDP))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * cdc42GEF_act)[uM.s-1] user defined (kcat): 0.75[s-1] |
|
Bp |
pushing barbed ends
Cytoplasm
|
GeneralKinetics | Bp |
|
|
reaction rate (J): (((V0 - Vmb) * B) - (k_cap * Bp))[uM.s-1]
|
|
CaMKII+G_actinCaMKII_G_actin |
CaMKII sequestration of G-actin
Cytoplasm
|
MassAction | CaMKII+G_actinCaMKII_G_actin |
|
|
reaction rate (J): (((Kf * CaMKII) * G_actin) - (Kr * CaMKII_G_actin))[uM.s-1]
forward rate constant (Kf): 1.0[s-1.uM-1] reverse rate constant (Kr): 4.0[s-1] |
|
Ng+CaMCaM_Ng |
Calmodulin binding neurogranin
Cytoplasm
|
MassAction | Ng+CaMCaM_Ng |
|
|
reaction rate (J): (((Kf * Ng) * CaM) - (Kr * CaM_Ng))[uM.s-1]
forward rate constant (Kf): 5.0[s-1.uM-1] reverse rate constant (Kr): 1.0[s-1] |
|
R |
Radius
Cytoplasm
|
GeneralKinetics | R |
|
|
reaction rate (J): (Vmb - (k_shrink * MLC_p * R))[uM.s-1]
|
|
RhoGAP_actRhoGAP |
RhoGAP inactivation by PP1
Cytoplasm
|
HMMIrreversible | RhoGAP_actRhoGAP |
|
|
reaction rate (J): ((Vmax * RhoGAP_act) / (Km + RhoGAP_act))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (0.1 * PP1_act)[uM.s-1] |
|
RhoGDPRhoGTP |
RhoGTP activation by RhoGEF
Cytoplasm
|
HMMIrreversible | RhoGDPRhoGTP |
|
|
reaction rate (J): ((Vmax * RhoGDP) / (Km + RhoGDP))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * RhoGEF_act)[uM.s-1] user defined (kcat): 0.5[s-1] |
|
MyoppaseMyoppase_act |
Myoppase activation by autodephosphorylation
Cytoplasm
|
HMMIrreversible | MyoppaseMyoppase_act |
|
|
reaction rate (J): ((Vmax * Myoppase) / (Km + Myoppase))[uM.s-1]
Km (1/2 max) (Km): 16.0[uM] max reaction rate (Vmax): (kcat * Myoppase_act)[uM.s-1] user defined (kcat): 3.0[s-1] |
|
RhoGEF_actRhoGEF |
Rho GEF inactivation
Cytoplasm
|
HMMIrreversible | RhoGEF_actRhoGEF |
|
|
reaction rate (J): ((Vmax * RhoGEF_act) / (Km + RhoGEF_act))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (0.1 * PP1_act)[uM.s-1] |
|
CalcineurinCalcineurin_act |
Calcineurin activation by CaM
Cytoplasm
|
GeneralKinetics | CalcineurinCalcineurin_act |
|
|
reaction rate (J): (k * (Ca_CaM ^ 4.0) * Calcineurin / ((Km ^ 4.0) + (Ca_CaM ^ 4.0)))[uM.s-1]
user defined (k): 127.0[s-1] user defined (Km): 0.34[uM] |
|
LIMK_PLIMK |
LIMK inactivation by ROCK
Cytoplasm
|
HMMIrreversible | LIMK_PLIMK |
|
|
reaction rate (J): ((Vmax * LIMK_P) / (Km + LIMK_P))[uM.s-1]
Km (1/2 max) (Km): 4.0[uM] max reaction rate (Vmax): (0.34 * SSH1_act)[uM.s-1] |
|
MLC_pMLC |
MLC dephosphorylation
Cytoplasm
|
HMMIrreversible | MLC_pMLC |
|
|
reaction rate (J): ((Vmax * MLC_p) / (Km + MLC_p))[uM.s-1]
Km (1/2 max) (Km): 16.0[uM] max reaction rate (Vmax): (kcat * Myoppase_act)[uM.s-1] user defined (kcat): 1.0[s-1] |
|
CaMKIIpCaMKII |
CaMKII inactivation
Cytoplasm
|
HMMIrreversible | CaMKIIpCaMKII |
|
|
reaction rate (J): ((Vmax * CaMKIIp) / (Km + CaMKIIp))[uM.s-1]
Km (1/2 max) (Km): 3.0[uM] max reaction rate (Vmax): (kcat * PP1_act)[uM.s-1] user defined (kcat): 15.0[s-1] |
|
ROCK+RhoGTPROCK_act |
ROCK activation by Rho
Cytoplasm
|
MassAction | ROCK+RhoGTPROCK_act |
|
|
reaction rate (J): (((Kf * ROCK) * RhoGTP) - (Kr * ROCK_act))[uM.s-1]
forward rate constant (Kf): 0.04[s-1.uM-1] reverse rate constant (Kr): 0.001[s-1] |
|
Cdc42GEFcdc42GEF_act |
cdc42 GEF activation
Cytoplasm
|
HMMIrreversible | Cdc42GEFcdc42GEF_act |
|
|
reaction rate (J): ((Vmax * Cdc42GEF) / (Km + Cdc42GEF))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * CaMKIIp)[uM.s-1] user defined (kcat): 0.01[s-1] |
|
MyoppaseMyoppase_act |
myosin phosphatase activation basal
Cytoplasm
|
MassAction | MyoppaseMyoppase_act |
|
|
reaction rate (J): ((Kf * Myoppase) - (Kr * Myoppase_act))[uM.s-1]
forward rate constant (Kf): 0.01[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
MLCMLC_p |
MLC phosphorylation basal
Cytoplasm
|
MassAction | MLCMLC_p |
|
|
reaction rate (J): ((Kf * MLC) - (Kr * MLC_p))[uM.s-1]
forward rate constant (Kf): 0.01[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
ROCK_act |
ROCK inactivation 1
Cytoplasm
|
MassAction | ROCK_act |
|
|
reaction rate (J): (Kf * ROCK_act)[uM.s-1]
forward rate constant (Kf): 0.1[s-1] reverse rate constant (Kr): 0.0[uM.s-1] |
|
RhoGAPRhoGAP_act |
RhoGAP activation by CaMKII
Cytoplasm
|
HMMIrreversible | RhoGAPRhoGAP_act |
|
|
reaction rate (J): ((Vmax * RhoGAP) / (Km + RhoGAP))[uM.s-1]
Km (1/2 max) (Km): 1.0[uM] max reaction rate (Vmax): (kcat * CaMKIIp)[uM.s-1] user defined (kcat): 0.01[s-1] |
|
CaMKII+F_actinCaMKII_F_actin |
CaMKII sequestration of F-actin
Cytoplasm
|
MassAction | CaMKII+F_actinCaMKII_F_actin |
|
|
reaction rate (J): (((Kf * CaMKII) * F_actin) - (Kr * CaMKII_F_actin))[uM.s-1]
forward rate constant (Kf): 1.0[s-1.uM-1] reverse rate constant (Kr): 4.0[s-1] |
|
SSH1_actSSH1 |
SSH1 phosphorylation by CaMKIIp
Cytoplasm
|
HMMIrreversible | SSH1_actSSH1 |
|
|
reaction rate (J): ((Vmax * SSH1_act) / (Km + SSH1_act))[uM.s-1]
Km (1/2 max) (Km): 127.0[uM] max reaction rate (Vmax): (0.34 * CaMKIIp)[uM.s-1] |
|
F_actin+arp23_act+G_actinF_actin |
Actin growth
Cytoplasm
|
GeneralKinetics | F_actin+arp23_act+G_actinF_actin |
|
|
reaction rate (J): f_nuc[uM.s-1]
|
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
c0 |
Compartment
(+) (-)
|
|
|
Cytoplasm |
Compartment
(+) (-)
|
|
|
plasma membrane |
Membrane
N/A
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
F_actin | Cytoplasm | |
|
|
|
CaMKII_F_actin | Cytoplasm | |
|
|
|
Il1_act | Cytoplasm | |
|
|
|
Myoppase | Cytoplasm | |
|
|
|
Myoppase_act | Cytoplasm | |
|
|
|
ROCK | Cytoplasm | |
|
|
|
Il1 | Cytoplasm | |
|
|
|
RhoGTP | Cytoplasm | |
|
|
|
ROCK_act | Cytoplasm | |
|
|
|
LIMK | Cytoplasm | |
|
|
|
LIMK_P | Cytoplasm | |
|
|
|
RhoGAP_act | Cytoplasm | |
|
|
|
RhoGDP | Cytoplasm | |
|
|
|
RhoGEF | Cytoplasm | |
|
|
|
RhoGEF_act | Cytoplasm | |
|
|
|
RhoGAP | Cytoplasm | |
|
|
|
Ng | Cytoplasm | |
|
|
|
CaM_Ng | Cytoplasm | |
|
|
|
SSH1_act | Cytoplasm | |
|
|
|
cdc42GTP | Cytoplasm | |
|
|
|
WASP | Cytoplasm | |
|
|
|
PP1 | Cytoplasm | |
|
|
|
PP1_act | Cytoplasm | |
|
|
|
MLC | Cytoplasm | |
|
|
|
MLC_p | Cytoplasm | |
|
|
|
arp23 | Cytoplasm | |
|
|
|
WASP_act | Cytoplasm | |
|
|
|
B | Cytoplasm | |
|
|
|
R | Cytoplasm | |
|
|
|
cdc42GDP | Cytoplasm | |
|
|
|
Ca_CaM | Cytoplasm | |
|
|
|
Bp | Cytoplasm | |
|
|
|
CaM | Cytoplasm | |
|
|
|
arp23_act | Cytoplasm | |
|
|
|
SSH1 | Cytoplasm | |
|
|
|
Ca | Cytoplasm | |
|
|
|
CaMKII | Cytoplasm | |
|
|
|
CaMKIIp | Cytoplasm | |
|
|
|
G_actin | Cytoplasm | |
|
|
|
CaMKII_G_actin | Cytoplasm | |
|
|
|
Calcineurin_act | Cytoplasm | |
|
|
|
Cdc42GEF | Cytoplasm | |
|
|
|
cdc42GEF_act | Cytoplasm | |
|
|
|
Cofilin_p | Cytoplasm | |
|
|
|
Calcineurin | Cytoplasm | |
|
|
|
cofilin_act | Cytoplasm | |
|
|
Name | Text Annotations | BioNetGen Definition |
---|
Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
Application0 | Deterministic (ODE) Compartmental |
Application - Application0
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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F_actin | 0.0 [uM] | 0.0
[um2/s] CaMKII_F_actin |
10.0
[uM]
|
0.0
[um2/s] | Il1_act |
0.0
[uM]
|
0.0
[um2/s] | Myoppase |
1.0
[uM]
|
0.0
[um2/s] | Myoppase_act |
0.1
[uM]
|
0.0
[um2/s] | ROCK |
1.0
[uM]
|
0.0
[um2/s] | Il1 |
1.8
[uM]
|
0.0
[um2/s] | RhoGTP |
0.0
[uM]
|
0.0
[um2/s] | ROCK_act |
0.0
[uM]
|
0.0
[um2/s] | LIMK |
2.0
[uM]
|
0.0
[um2/s] | LIMK_P |
0.0
[uM]
|
0.0
[um2/s] | RhoGAP_act |
0.0
[uM]
|
0.0
[um2/s] | RhoGDP |
1.0
[uM]
|
0.0
[um2/s] | RhoGEF |
0.1
[uM]
|
0.0
[um2/s] | RhoGEF_act |
0.0
[uM]
|
0.0
[um2/s] | RhoGAP |
0.1
[uM]
|
0.0
[um2/s] | Ng |
20.0
[uM]
|
0.0
[um2/s] | CaM_Ng |
0.0
[uM]
|
0.0
[um2/s] | SSH1_act |
0.0
[uM]
|
0.0
[um2/s] | cdc42GTP |
0.0
[uM]
|
0.0
[um2/s] | WASP |
1.0
[uM]
|
0.0
[um2/s] | PP1 |
0.36
[uM]
|
0.0
[um2/s] | PP1_act |
0.0
[uM]
|
0.0
[um2/s] | MLC |
1.0
[uM]
|
0.0
[um2/s] | MLC_p |
0.0
[uM]
|
0.0
[um2/s] | arp23 |
1.0
[uM]
|
0.0
[um2/s] | WASP_act |
0.0
[uM]
|
0.0
[um2/s] | B |
30.0
[uM]
|
0.0
[um2/s] | R |
0.0
[uM]
|
0.0
[um2/s] | cdc42GDP |
1.0
[uM]
|
0.0
[um2/s] | Ca_CaM |
0.0
[uM]
|
0.0
[um2/s] | Bp |
1.0
[uM]
|
0.0
[um2/s] | CaM |
10.0
[uM]
|
0.0
[um2/s] | arp23_act |
0.0
[uM]
|
0.0
[um2/s] | SSH1 |
2.0
[uM]
|
0.0
[um2/s] | Ca |
((12.0 * (t > 1.0)) && (t < 5.0))
[uM]
|
0.0
[um2/s] | CaMKII |
0.0
[uM]
|
0.0
[um2/s] | CaMKIIp |
0.0
[uM]
|
0.0
[um2/s] | G_actin |
0.0
[uM]
|
0.0
[um2/s] | CaMKII_G_actin |
10.0
[uM]
|
0.0
[um2/s] | Calcineurin_act |
0.0
[uM]
|
0.0
[um2/s] | Cdc42GEF |
0.1
[uM]
|
0.0
[um2/s] | cdc42GEF_act |
0.0
[uM]
|
0.0
[um2/s] | Cofilin_p |
2.0
[uM]
|
0.0
[um2/s] | Calcineurin |
1.0
[uM]
|
0.0
[um2/s] | cofilin_act |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
Myoppase inactivation by ROCK | included |
Cofilin inactivation by LIMK | included |
PP1 inactivation by CaMKII | included |
calcium binding calmodulin | included |
calcinuerin inactivation | included |
Cofilin activation through SSH1 dephosphorylation | included |
RhoGTP hydrolysis | included |
SSH1 dephosphorylation by CaN | included |
cdc42 activates WASP | included |
cdc42 hydrolysis | included |
LIMK activation by ROCK | included |
MLC Phosphorylation by ROCK | included |
Cdc42 GEF inactivation | included |
Arp23 inactivation | included |
Barbed ends | included |
RhoGEF activation by CaMKII | included |
Il1 inactivation | included |
Il1 activation by CaN | included |
Arp23 activation | included |
severing | included |
CaMKII activation by CaM | included |
PP1 activation by IL1 | included |
cdc42 activation | included |
pushing barbed ends | included |
CaMKII sequestration of G-actin | included |
Calmodulin binding neurogranin | included |
Radius | included |
RhoGAP inactivation by PP1 | included |
RhoGTP activation by RhoGEF | included |
Myoppase activation by autodephosphorylation | included |
Rho GEF inactivation | included |
Calcineurin activation by CaM | included |
LIMK inactivation by ROCK | included |
MLC dephosphorylation | included |
CaMKII inactivation | included |
ROCK activation by Rho | included |
cdc42 GEF activation | included |
myosin phosphatase activation basal | included |
MLC phosphorylation basal | included |
ROCK inactivation 1 | included |
RhoGAP activation by CaMKII | included |
CaMKII sequestration of F-actin | included |
SSH1 phosphorylation by CaMKIIp | included |
Actin growth | included |
Name | End Time | Output Options |
---|---|---|
basic simulation | 300.0 [s] |
OutputTimeStep 1.0 |
Arp23 variation | 300.0 [s] |
OutputTimeStep 1.0 |
Nuc-Sev phase | 300.0 [s] |
OutputTimeStep 1.0 |
cofilin variation | 300.0 [s] |
OutputTimeStep 1.0 |
CaM variation | 300.0 [s] |
OutputTimeStep 1.0 |
Ng variation | 300.0 [s] |
OutputTimeStep 1.0 |
PP1 variation | 300.0 [s] |
OutputTimeStep 1.0 |
CaN variation | 300.0 [s] |
OutputTimeStep 1.0 |
Rho GTP level | 300.0 [s] |
OutputTimeStep 1.0 |
sensitivity kage | 240.0 [s] |
OutputTimeStep 1.0 |
sensitivity with cofilin | 240.0 [s] |
OutputTimeStep 1.0 |
sensitivity with Arp2/3 | 240.0 [s] |
OutputTimeStep 1.0 |
CaN sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
CaMKII-f-actin | 240.0 [s] |
OutputTimeStep 1.0 |
CaMKII-G-actin sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
cdc42GTP sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
Cdc42 GEF sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
I1 sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
LIMK sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
MLC sensitivity | 240.0 [s] |
OutputTimeStep 1.0 |
Myoppase active sens | 240.0 [s] |
OutputTimeStep 1.0 |
Myoppase sens | 240.0 [s] |
OutputTimeStep 1.0 |
Ng sens | 240.0 [s] |
OutputTimeStep 1.0 |
phi sens | 240.0 [s] |
OutputTimeStep 1.0 |
PP1 sens | 240.0 [s] |
OutputTimeStep 1.0 |
Rho GAP sens | 240.0 [s] |
OutputTimeStep 1.0 |
Rho GEF sens | 240.0 [s] |
OutputTimeStep 1.0 |
Rho GDP sens | 240.0 [s] |
OutputTimeStep 1.0 |
ROCK sens | 240.0 [s] |
OutputTimeStep 1.0 |
SSH1 sens | 240.0 [s] |
OutputTimeStep 1.0 |
VO sens | 240.0 [s] |
OutputTimeStep 1.0 |
w sens | 240.0 [s] |
OutputTimeStep 1.0 |
WASP sens | 240.0 [s] |
OutputTimeStep 1.0 |
k-arp23 inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
k-calcineurin-activation-by-cam | 240.0 [s] |
OutputTimeStep 1.0 |
kcap | 240.0 [s] |
OutputTimeStep 1.0 |
kdeg | 240.0 [s] |
OutputTimeStep 1.0 |
knuc | 240.0 [s] |
OutputTimeStep 1.0 |
ksev | 240.0 [s] |
OutputTimeStep 1.0 |
kshrink | 240.0 [s] |
OutputTimeStep 1.0 |
KAPPA | 240.0 [s] |
OutputTimeStep 1.0 |
kcat1 | 240.0 [s] |
OutputTimeStep 1.0 |
kcat2 | 240.0 [s] |
OutputTimeStep 1.0 |
kcat 3 | 240.0 [s] |
OutputTimeStep 1.0 |
Kcat CaMKII activation by CAM | 240.0 [s] |
OutputTimeStep 1.0 |
kcat camkii inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
kcat cd42 acticaion | 240.0 [s] |
OutputTimeStep 1.0 |
kcat cdc42 gef activation | 240.0 [s] |
OutputTimeStep 1.0 |
kcat cdc42 gef inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
kcat cdc42 hydrolysis | 240.0 [s] |
OutputTimeStep 1.0 |
kcat cofilin activation through ssh1 | 240.0 [s] |
OutputTimeStep 1.0 |
kcat cofilin inactivation through LIMK | 240.0 [s] |
OutputTimeStep 1.0 |
kcat i1 inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
kcat limk rock | 240.0 [s] |
OutputTimeStep 1.0 |
kcat mlc rock | 240.0 [s] |
OutputTimeStep 1.0 |
kcat myoppase dephos | 240.0 [s] |
OutputTimeStep 1.0 |
kcat myoppase rock1 | 240.0 [s] |
OutputTimeStep 1.0 |
kcat myoppase rock | 240.0 [s] |
OutputTimeStep 1.0 |
kcat pp1 by camkii | 240.0 [s] |
OutputTimeStep 1.0 |
kcat rhogap camkii | 240.0 [s] |
OutputTimeStep 1.0 |
kcat rho gef camkii | 240.0 [s] |
OutputTimeStep 1.0 |
kcat Rho gtp by Rho gef | 240.0 [s] |
OutputTimeStep 1.0 |
kf | 240.0 [s] |
OutputTimeStep 1.0 |
kf arp23 activation | 240.0 [s] |
OutputTimeStep 1.0 |
kf CaM NG | 240.0 [s] |
OutputTimeStep 1.0 |
camkii f-actin | 240.0 [s] |
OutputTimeStep 1.0 |
camkii g-actin | 240.0 [s] |
OutputTimeStep 1.0 |
kf cdc42 wasp | 240.0 [s] |
OutputTimeStep 1.0 |
kf MLC phosphorylation | 240.0 [s] |
OutputTimeStep 1.0 |
kf myoppase basal | 240.0 [s] |
OutputTimeStep 1.0 |
kf rock act by rho | 240.0 [s] |
OutputTimeStep 1.0 |
kf rock inact | 240.0 [s] |
OutputTimeStep 1.0 |
Km | 240.0 [s] |
OutputTimeStep 1.0 |
km1 camkii activation by cam | 240.0 [s] |
OutputTimeStep 1.0 |
km1 PP1 activation by i1 | 240.0 [s] |
OutputTimeStep 1.0 |
km2 | 240.0 [s] |
OutputTimeStep 1.0 |
km can cam | 240.0 [s] |
OutputTimeStep 1.0 |
CaN inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
CaMKii activation by CaM | 240.0 [s] |
OutputTimeStep 1.0 |
Km CaMKII inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
km cdc42 activation | 240.0 [s] |
OutputTimeStep 1.0 |
km cdc42 gef activation | 240.0 [s] |
OutputTimeStep 1.0 |
km cdc42 gef | 240.0 [s] |
OutputTimeStep 1.0 |
km cdc42 hydrolysis | 240.0 [s] |
OutputTimeStep 1.0 |
km cofilin actiation ssh1 | 240.0 [s] |
OutputTimeStep 1.0 |
km i1 activation by CaN | 240.0 [s] |
OutputTimeStep 1.0 |
Km i1 inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
km limk activation by rock | 240.0 [s] |
OutputTimeStep 1.0 |
km limk inactivation by rock | 240.0 [s] |
OutputTimeStep 1.0 |
km mlc dephosphorylation | 240.0 [s] |
OutputTimeStep 1.0 |
km myoppase activation dephos | 240.0 [s] |
OutputTimeStep 1.0 |
km myoppase inactivation rock | 240.0 [s] |
OutputTimeStep 1.0 |
km pp1 inct by camkii | 240.0 [s] |
OutputTimeStep 1.0 |
km rho gef inactivation | 240.0 [s] |
OutputTimeStep 1.0 |
km rhogap camkii | 240.0 [s] |
OutputTimeStep 1.0 |
km rho gap pp1 | 240.0 [s] |
OutputTimeStep 1.0 |
km rhogef camkii | 240.0 [s] |
OutputTimeStep 1.0 |
km rhogtp by rhogef | 240.0 [s] |
OutputTimeStep 1.0 |
km rhogtp hhydrolysis | 240.0 [s] |
OutputTimeStep 1.0 |
km ssh1 dephos | 240.0 [s] |
OutputTimeStep 1.0 |
km ssh1 phos camkii | 240.0 [s] |
OutputTimeStep 1.0 |
kr | 240.0 [s] |
OutputTimeStep 1.0 |
kr arp activation | 240.0 [s] |
OutputTimeStep 1.0 |
kr CaM binding NG | 240.0 [s] |
OutputTimeStep 1.0 |
kr caMkii binding f-actin | 240.0 [s] |
OutputTimeStep 1.0 |
kr camkii g-actin | 240.0 [s] |
OutputTimeStep 1.0 |
kr cdc42 wasp | 240.0 [s] |
OutputTimeStep 1.0 |
kr MLCp basal | 240.0 [s] |
OutputTimeStep 1.0 |
kr myosin ppase basal | 240.0 [s] |
OutputTimeStep 1.0 |
kr rock by rho | 240.0 [s] |
OutputTimeStep 1.0 |
kr rock inacivation | 240.0 [s] |
OutputTimeStep 1.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | plasma membrane |
Global Parameters
Name | Expression |
---|---|
k_sev | 0.01[tbd] |
|
|
C0 | 0.5[tbd] |
|
|
l | 0.255[tbd] |
|
|
k_nuc | 60.0[tbd] |
|
|
Km | 2.0[uM] |
|
|
V0 | 0.07[tbd] |
|
|
w | 25.0[tbd] |
|
|
phi | 10.0[tbd] |
|
|
k_cap | 0.04[s-1] |
|
|
k_shrink | 0.01[uM-1.s-1] |
|
|
Vmb | (V0 * Bp / (Bp + (phi * exp((w / Bp)))))[s-1] |
|
|
f_nuc | (k_nuc * arp23_act * l * F_actin * G_actin / (Km + arp23_act))[tbd] |
|
|