Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Myoppase inactivation by ROCK Universal ID's
Myoppase inactivation by ROCK Text Annotations
Cofilin inactivation by LIMK Universal ID's
Cofilin inactivation by LIMK Text Annotations
PP1 inactivation by CaMKII Universal ID's
PP1 inactivation by CaMKII Text Annotations
calcium binding calmodulin Universal ID's
calcium binding calmodulin Text Annotations
calcinuerin inactivation Universal ID's
calcinuerin inactivation Text Annotations
Cofilin activation through SSH1 dephosphorylation Universal ID's
Cofilin activation through SSH1 dephosphorylation Text Annotations
RhoGTP hydrolysis Universal ID's
RhoGTP hydrolysis Text Annotations
SSH1 dephosphorylation by CaN Universal ID's
SSH1 dephosphorylation by CaN Text Annotations
cdc42 activates WASP Universal ID's
cdc42 activates WASP Text Annotations
cdc42 hydrolysis Universal ID's
cdc42 hydrolysis Text Annotations
LIMK activation by ROCK Universal ID's
LIMK activation by ROCK Text Annotations
MLC Phosphorylation by ROCK Universal ID's
MLC Phosphorylation by ROCK Text Annotations
Cdc42 GEF inactivation Universal ID's
Cdc42 GEF inactivation Text Annotations
Arp23 inactivation Universal ID's
Arp23 inactivation Text Annotations
Barbed ends Universal ID's
Barbed ends Text Annotations
RhoGEF activation by CaMKII Universal ID's
RhoGEF activation by CaMKII Text Annotations
Il1 inactivation Universal ID's
Il1 inactivation Text Annotations
Il1 activation by CaN Universal ID's
Il1 activation by CaN Text Annotations
Arp23 activation Universal ID's
Arp23 activation Text Annotations
severing Universal ID's
severing Text Annotations
CaMKII activation by CaM Universal ID's
CaMKII activation by CaM Text Annotations
PP1 activation by IL1 Universal ID's
PP1 activation by IL1 Text Annotations
cdc42 activation Universal ID's
cdc42 activation Text Annotations
CaMKII sequestration of G-actin Universal ID's
CaMKII sequestration of G-actin Text Annotations
Calmodulin binding neurogranin Universal ID's
Calmodulin binding neurogranin Text Annotations
Radius Universal ID's
Radius Text Annotations
RhoGAP inactivation by PP1 Universal ID's
RhoGAP inactivation by PP1 Text Annotations
RhoGTP activation by RhoGEF Universal ID's
RhoGTP activation by RhoGEF Text Annotations
Myoppase activation by autodephosphorylation Universal ID's
Myoppase activation by autodephosphorylation Text Annotations
Rho GEF inactivation Universal ID's
Rho GEF inactivation Text Annotations
Calcineurin activation by CaM Universal ID's
Calcineurin activation by CaM Text Annotations
LIMK inactivation by ROCK Universal ID's
LIMK inactivation by ROCK Text Annotations
MLC dephosphorylation Universal ID's
MLC dephosphorylation Text Annotations
CaMKII inactivation Universal ID's
CaMKII inactivation Text Annotations
ROCK activation by Rho Universal ID's
ROCK activation by Rho Text Annotations
cdc42 GEF activation Universal ID's
cdc42 GEF activation Text Annotations
myosin phosphatase activation basal Universal ID's
myosin phosphatase activation basal Text Annotations
MLC phosphorylation basal Universal ID's
MLC phosphorylation basal Text Annotations
ROCK inactivation 1 Universal ID's
ROCK inactivation 1 Text Annotations
RhoGAP activation by CaMKII Universal ID's
RhoGAP activation by CaMKII Text Annotations
CaMKII sequestration of F-actin Universal ID's
CaMKII sequestration of F-actin Text Annotations
SSH1 phosphorylation by CaMKIIp Universal ID's
SSH1 phosphorylation by CaMKIIp Text Annotations
Actin growth Universal ID's
Actin growth Text Annotations
Expressions for Myoppase inactivation by ROCK
reaction rate
J
((Vmax * Myoppase_act) / (Km + Myoppase_act)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
0.1 [uM]
max reaction rate
Vmax
(kcat * ROCK_act) [uM.s-1]
local
kcat
2.357 [s-1]
Expressions for Cofilin inactivation by LIMK
reaction rate
J
(kcat * LIMK_P * cofilin_act / (Km + cofilin_act)) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
local
kcat
0.1 [s-1]
Expressions for PP1 inactivation by CaMKII
reaction rate
J
((Vmax * PP1_act) / (Km + PP1_act)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
4.97 [uM]
max reaction rate
Vmax
(kcat * CaMKIIp) [uM.s-1]
local
kcat
0.07166 [s-1]
Expressions for calcium binding calmodulin
reaction rate
J
((kf * (n * (Ca ^ 3.0)) * CaM) - (kr * Ca_CaM)) [uM.s-1]
local
kr
1.0 [tbd]
local
kf
7.75 [tbd]
local
n
1.0 [tbd]
Expressions for calcinuerin inactivation
reaction rate
J
((Vmax * Calcineurin_act) / (Km + Calcineurin_act)) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
Km (1/2 max)
Km
127.0 [uM]
max reaction rate
Vmax
(0.34 * CaMKIIp) [uM.s-1]
Expressions for Cofilin activation through SSH1 dephosphorylation
reaction rate
J
((Vmax * Cofilin_p) / (Km + Cofilin_p)) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
Km (1/2 max)
Km
4.0 [uM]
max reaction rate
Vmax
(kcat * SSH1_act) [uM.s-1]
local
kcat
0.34 [s-1]
Expressions for RhoGTP hydrolysis
reaction rate
J
((Vmax * RhoGTP) / (Km + RhoGTP)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(0.1 * RhoGAP_act) [uM.s-1]
Expressions for SSH1 dephosphorylation by CaN
reaction rate
J
((Vmax * SSH1) / (Km + SSH1)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
4.97 [uM]
max reaction rate
Vmax
(0.34 * Calcineurin_act) [uM.s-1]
global
l
0.255 [tbd]
Expressions for cdc42 activates WASP
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]
Expressions for cdc42 hydrolysis
reaction rate
J
((Vmax * cdc42GTP) / (Km + cdc42GTP)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * RhoGAP_act) [uM.s-1]
local
kcat
0.1 [s-1]
Expressions for LIMK activation by ROCK
reaction rate
J
((Vmax * LIMK) / (Km + LIMK)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
0.3 [uM]
max reaction rate
Vmax
(kcat * ROCK_act) [uM.s-1]
local
kcat
0.9 [s-1]
Expressions for MLC Phosphorylation by ROCK
reaction rate
J
((Vmax * MLC) / (Km + MLC)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
2.47 [uM]
max reaction rate
Vmax
(kcat * ROCK_act) [uM.s-1]
local
kcat
1.8 [s-1]
Expressions for Cdc42 GEF inactivation
reaction rate
J
((Vmax * cdc42GEF_act) / (Km + cdc42GEF_act)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * PP1_act) [uM.s-1]
local
kcat
0.01 [s-1]
Expressions for Arp23 inactivation
reaction rate
J
(k * arp23_act) [uM.s-1]
local
k
0.1 [s-1]
Expressions for Barbed ends
reaction rate
J
((kappa * (f_sev + f_nuc)) - (k_cap * B)) [uM.s-1]
global
k_cap
0.04 [s-1]
global
f_nuc
(k_nuc * arp23_act * l * F_actin * G_actin / (Km + arp23_act)) [tbd]
local
f_sev
(C0 * k_sev * ((cofilin_act / C0) ^ n1) * l * F_actin) [tbd]
global
k_sev
0.01 [tbd]
global
C0
0.5 [tbd]
global
l
0.255 [tbd]
local
kappa
106.0 [tbd]
local
n1
4.0 [1]
Expressions for RhoGEF activation by CaMKII
reaction rate
J
((Vmax * RhoGEF) / (Km + RhoGEF)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * CaMKIIp) [uM.s-1]
local
kcat
0.1 [s-1]
Expressions for Il1 inactivation
reaction rate
J
((Vmax * Il1_act) / (Km + Il1_act)) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
Km (1/2 max)
Km
127.0 [uM]
max reaction rate
Vmax
(kcat * CaMKIIp) [uM.s-1]
local
kcat
0.0688 [s-1]
Expressions for Il1 activation by CaN
reaction rate
J
((Vmax * Il1) / (Km + Il1)) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
Km (1/2 max)
Km
4.97 [uM]
max reaction rate
Vmax
(0.034 * Calcineurin_act) [uM.s-1]
global
l
0.255 [tbd]
Expressions for Arp23 activation
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]
Expressions for severing
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]
global
k_sev
0.01 [tbd]
global
C0
0.5 [tbd]
global
l
0.255 [tbd]
local
k_deg
0.1 [tbd]
local
k_age
0.001 [tbd]
Expressions for CaMKII activation by CaM
reaction rate
J
((kcat3 * (Ca_CaM ^ 4.0) * CaMKII / ((Km ^ 4.0) + (Ca_CaM ^ 4.0))) + (CaMKII * kcat * CaMKIIp / (Km1 + CaMKII))) [uM.s-1]
global
Km
2.0 [uM]
local
kcat
1.0 [s-1]
local
kcat3
120.0 [tbd]
local
Km1
10.0 [uM]
local
Km
4.0 [uM]
Expressions for PP1 activation by IL1
reaction rate
J
((kcat1 * Il1_act * PP1 / (Km1 + PP1)) + (kcat2 * PP1_act * PP1 / (Km2 + PP1))) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
local
Km2
10.0 [uM]
local
kcat1
50.0 [s-1]
local
kcat2
2.0 [s-1]
local
Km1
80.0 [uM]
Expressions for cdc42 activation
reaction rate
J
((Vmax * cdc42GDP) / (Km + cdc42GDP)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * cdc42GEF_act) [uM.s-1]
local
kcat
0.75 [s-1]
Expressions for pushing barbed ends
reaction rate
J
(((V0 - Vmb) * B) - (k_cap * Bp)) [uM.s-1]
global
V0
0.07 [tbd]
global
k_cap
0.04 [s-1]
global
Vmb
(V0 * Bp / (Bp + (phi * exp((w / Bp))))) [s-1]
Expressions for CaMKII sequestration of 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]
Expressions for Calmodulin binding neurogranin
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]
Expressions for Radius
reaction rate
J
(Vmb - (k_shrink * MLC_p * R)) [uM.s-1]
global
k_shrink
0.01 [uM-1.s-1]
global
Vmb
(V0 * Bp / (Bp + (phi * exp((w / Bp))))) [s-1]
Expressions for RhoGAP inactivation by PP1
reaction rate
J
((Vmax * RhoGAP_act) / (Km + RhoGAP_act)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(0.1 * PP1_act) [uM.s-1]
Expressions for RhoGTP activation by RhoGEF
reaction rate
J
((Vmax * RhoGDP) / (Km + RhoGDP)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * RhoGEF_act) [uM.s-1]
local
kcat
0.5 [s-1]
Expressions for Myoppase activation by autodephosphorylation
reaction rate
J
((Vmax * Myoppase) / (Km + Myoppase)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
16.0 [uM]
max reaction rate
Vmax
(kcat * Myoppase_act) [uM.s-1]
local
kcat
3.0 [s-1]
Expressions for Rho GEF inactivation
reaction rate
J
((Vmax * RhoGEF_act) / (Km + RhoGEF_act)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(0.1 * PP1_act) [uM.s-1]
Expressions for Calcineurin activation by CaM
reaction rate
J
(k * (Ca_CaM ^ 4.0) * Calcineurin / ((Km ^ 4.0) + (Ca_CaM ^ 4.0))) [uM.s-1]
global
l
0.255 [tbd]
global
Km
2.0 [uM]
local
k
127.0 [s-1]
local
Km
0.34 [uM]
Expressions for LIMK inactivation by ROCK
reaction rate
J
((Vmax * LIMK_P) / (Km + LIMK_P)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
4.0 [uM]
max reaction rate
Vmax
(0.34 * SSH1_act) [uM.s-1]
Expressions for MLC dephosphorylation
reaction rate
J
((Vmax * MLC_p) / (Km + MLC_p)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
16.0 [uM]
max reaction rate
Vmax
(kcat * Myoppase_act) [uM.s-1]
local
kcat
1.0 [s-1]
Expressions for CaMKII inactivation
reaction rate
J
((Vmax * CaMKIIp) / (Km + CaMKIIp)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
3.0 [uM]
max reaction rate
Vmax
(kcat * PP1_act) [uM.s-1]
local
kcat
15.0 [s-1]
Expressions for ROCK activation by Rho
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]
Expressions for cdc42 GEF activation
reaction rate
J
((Vmax * Cdc42GEF) / (Km + Cdc42GEF)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * CaMKIIp) [uM.s-1]
local
kcat
0.01 [s-1]
Expressions for myosin phosphatase activation basal
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]
Expressions for MLC phosphorylation basal
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]
Expressions for ROCK inactivation 1
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]
Expressions for RhoGAP activation by CaMKII
reaction rate
J
((Vmax * RhoGAP) / (Km + RhoGAP)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
1.0 [uM]
max reaction rate
Vmax
(kcat * CaMKIIp) [uM.s-1]
local
kcat
0.01 [s-1]
Expressions for CaMKII sequestration of 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]
Expressions for SSH1 phosphorylation by CaMKIIp
reaction rate
J
((Vmax * SSH1_act) / (Km + SSH1_act)) [uM.s-1]
global
Km
2.0 [uM]
Km (1/2 max)
Km
127.0 [uM]
max reaction rate
Vmax
(0.34 * CaMKIIp) [uM.s-1]
Expressions for Actin growth
reaction rate
J
f_nuc [uM.s-1]
global
f_nuc
(k_nuc * arp23_act * l * F_actin * G_actin / (Km + arp23_act)) [tbd]
Structures
Name | Type | Electrical |
---|---|---|
plasma membrane | Membrane | Cytoplasm(+) c0(-) |
c0 | Compartment | (+) (-) |
Cytoplasm | Compartment | (+) (-) |
plasma membrane Universal ID's
plasma membrane Text Annotations
c0 Universal ID's
c0 Text Annotations
Cytoplasm Universal ID's
Cytoplasm Text Annotations
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
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 |
F_actin Universal ID's
F_actin Text Annotations
CaMKII_F_actin Universal ID's
CaMKII_F_actin Text Annotations
Il1_act Universal ID's
Il1_act Text Annotations
Myoppase Universal ID's
Myoppase Text Annotations
Myoppase_act Universal ID's
Myoppase_act Text Annotations
ROCK Universal ID's
ROCK Text Annotations
Il1 Universal ID's
Il1 Text Annotations
RhoGTP Universal ID's
RhoGTP Text Annotations
ROCK_act Universal ID's
ROCK_act Text Annotations
LIMK Universal ID's
LIMK Text Annotations
LIMK_P Universal ID's
LIMK_P Text Annotations
RhoGAP_act Universal ID's
RhoGAP_act Text Annotations
RhoGDP Universal ID's
RhoGDP Text Annotations
RhoGEF Universal ID's
RhoGEF Text Annotations
RhoGEF_act Universal ID's
RhoGEF_act Text Annotations
RhoGAP Universal ID's
RhoGAP Text Annotations
Ng Universal ID's
Ng Text Annotations
CaM_Ng Universal ID's
CaM_Ng Text Annotations
SSH1_act Universal ID's
SSH1_act Text Annotations
cdc42GTP Universal ID's
cdc42GTP Text Annotations
WASP Universal ID's
WASP Text Annotations
PP1 Universal ID's
PP1 Text Annotations
PP1_act Universal ID's
PP1_act Text Annotations
MLC Universal ID's
MLC Text Annotations
MLC_p Universal ID's
MLC_p Text Annotations
arp23 Universal ID's
arp23 Text Annotations
WASP_act Universal ID's
WASP_act Text Annotations
B Universal ID's
B Text Annotations
R Universal ID's
R Text Annotations
cdc42GDP Universal ID's
cdc42GDP Text Annotations
Ca_CaM Universal ID's
Ca_CaM Text Annotations
Bp Universal ID's
Bp Text Annotations
CaM Universal ID's
CaM Text Annotations
arp23_act Universal ID's
arp23_act Text Annotations
SSH1 Universal ID's
SSH1 Text Annotations
Ca Universal ID's
Ca Text Annotations
CaMKII Universal ID's
CaMKII Text Annotations
CaMKIIp Universal ID's
CaMKIIp Text Annotations
G_actin Universal ID's
G_actin Text Annotations
CaMKII_G_actin Universal ID's
CaMKII_G_actin Text Annotations
Calcineurin_act Universal ID's
Calcineurin_act Text Annotations
Cdc42GEF Universal ID's
Cdc42GEF Text Annotations
cdc42GEF_act Universal ID's
cdc42GEF_act Text Annotations
Cofilin_p Universal ID's
Cofilin_p Text Annotations
Calcineurin Universal ID's
Calcineurin Text Annotations
cofilin_act Universal ID's
cofilin_act Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Application0 |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
Application0 Universal ID's
Application0 Text Annotations
Specifications (Species) - Application0 go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
F_actin | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
CaMKII_F_actin | 10.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Il1_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Myoppase | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Myoppase_act | 0.1 [uM] | 0.0 [um2/s] | Cytoplasm |
ROCK | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Il1 | 1.8 [uM] | 0.0 [um2/s] | Cytoplasm |
RhoGTP | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
ROCK_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
LIMK | 2.0 [uM] | 0.0 [um2/s] | Cytoplasm |
LIMK_P | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
RhoGAP_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
RhoGDP | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
RhoGEF | 0.1 [uM] | 0.0 [um2/s] | Cytoplasm |
RhoGEF_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
RhoGAP | 0.1 [uM] | 0.0 [um2/s] | Cytoplasm |
Ng | 20.0 [uM] | 0.0 [um2/s] | Cytoplasm |
CaM_Ng | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
SSH1_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
cdc42GTP | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
WASP | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
PP1 | 0.36 [uM] | 0.0 [um2/s] | Cytoplasm |
PP1_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
MLC | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
MLC_p | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
arp23 | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
WASP_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
B | 30.0 [uM] | 0.0 [um2/s] | Cytoplasm |
R | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
cdc42GDP | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Ca_CaM | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Bp | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
CaM | 10.0 [uM] | 0.0 [um2/s] | Cytoplasm |
arp23_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
SSH1 | 2.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Ca | ((12.0 * (t > 1.0)) && (t < 5.0)) [uM] | 0.0 [um2/s] | Cytoplasm |
CaMKII | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
CaMKIIp | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
G_actin | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
CaMKII_G_actin | 10.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Calcineurin_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Cdc42GEF | 0.1 [uM] | 0.0 [um2/s] | Cytoplasm |
cdc42GEF_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Cofilin_p | 2.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Calcineurin | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
cofilin_act | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
Specifications (Reaction) - Application0 go to Simulations
Name | Enabled? |
---|---|
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 |
Simulations - Application0 go to Specifications
Name | End Time | Output Options |
---|---|---|
basic simulation | 300.0 |
OutputTimeStep 1.0 |
Arp23 variation | 300.0 |
OutputTimeStep 1.0 |
Nuc-Sev phase | 300.0 |
OutputTimeStep 1.0 |
cofilin variation | 300.0 |
OutputTimeStep 1.0 |
CaM variation | 300.0 |
OutputTimeStep 1.0 |
Ng variation | 300.0 |
OutputTimeStep 1.0 |
PP1 variation | 300.0 |
OutputTimeStep 1.0 |
CaN variation | 300.0 |
OutputTimeStep 1.0 |
Rho GTP level | 300.0 |
OutputTimeStep 1.0 |
sensitivity kage | 240.0 |
OutputTimeStep 1.0 |
sensitivity with cofilin | 240.0 |
OutputTimeStep 1.0 |
sensitivity with Arp2/3 | 240.0 |
OutputTimeStep 1.0 |
CaN sensitivity | 240.0 |
OutputTimeStep 1.0 |
CaMKII-f-actin | 240.0 |
OutputTimeStep 1.0 |
CaMKII-G-actin sensitivity | 240.0 |
OutputTimeStep 1.0 |
cdc42GTP sensitivity | 240.0 |
OutputTimeStep 1.0 |
Cdc42 GEF sensitivity | 240.0 |
OutputTimeStep 1.0 |
I1 sensitivity | 240.0 |
OutputTimeStep 1.0 |
LIMK sensitivity | 240.0 |
OutputTimeStep 1.0 |
MLC sensitivity | 240.0 |
OutputTimeStep 1.0 |
Myoppase active sens | 240.0 |
OutputTimeStep 1.0 |
Myoppase sens | 240.0 |
OutputTimeStep 1.0 |
Ng sens | 240.0 |
OutputTimeStep 1.0 |
phi sens | 240.0 |
OutputTimeStep 1.0 |
PP1 sens | 240.0 |
OutputTimeStep 1.0 |
Rho GAP sens | 240.0 |
OutputTimeStep 1.0 |
Rho GEF sens | 240.0 |
OutputTimeStep 1.0 |
Rho GDP sens | 240.0 |
OutputTimeStep 1.0 |
ROCK sens | 240.0 |
OutputTimeStep 1.0 |
SSH1 sens | 240.0 |
OutputTimeStep 1.0 |
VO sens | 240.0 |
OutputTimeStep 1.0 |
w sens | 240.0 |
OutputTimeStep 1.0 |
WASP sens | 240.0 |
OutputTimeStep 1.0 |
k-arp23 inactivation | 240.0 |
OutputTimeStep 1.0 |
k-calcineurin-activation-by-cam | 240.0 |
OutputTimeStep 1.0 |
kcap | 240.0 |
OutputTimeStep 1.0 |
kdeg | 240.0 |
OutputTimeStep 1.0 |
knuc | 240.0 |
OutputTimeStep 1.0 |
ksev | 240.0 |
OutputTimeStep 1.0 |
kshrink | 240.0 |
OutputTimeStep 1.0 |
KAPPA | 240.0 |
OutputTimeStep 1.0 |
kcat1 | 240.0 |
OutputTimeStep 1.0 |
kcat2 | 240.0 |
OutputTimeStep 1.0 |
kcat 3 | 240.0 |
OutputTimeStep 1.0 |
Kcat CaMKII activation by CAM | 240.0 |
OutputTimeStep 1.0 |
kcat camkii inactivation | 240.0 |
OutputTimeStep 1.0 |
kcat cd42 acticaion | 240.0 |
OutputTimeStep 1.0 |
kcat cdc42 gef activation | 240.0 |
OutputTimeStep 1.0 |
kcat cdc42 gef inactivation | 240.0 |
OutputTimeStep 1.0 |
kcat cdc42 hydrolysis | 240.0 |
OutputTimeStep 1.0 |
kcat cofilin activation through ssh1 | 240.0 |
OutputTimeStep 1.0 |
kcat cofilin inactivation through LIMK | 240.0 |
OutputTimeStep 1.0 |
kcat i1 inactivation | 240.0 |
OutputTimeStep 1.0 |
kcat limk rock | 240.0 |
OutputTimeStep 1.0 |
kcat mlc rock | 240.0 |
OutputTimeStep 1.0 |
kcat myoppase dephos | 240.0 |
OutputTimeStep 1.0 |
kcat myoppase rock1 | 240.0 |
OutputTimeStep 1.0 |
kcat myoppase rock | 240.0 |
OutputTimeStep 1.0 |
kcat pp1 by camkii | 240.0 |
OutputTimeStep 1.0 |
kcat rhogap camkii | 240.0 |
OutputTimeStep 1.0 |
kcat rho gef camkii | 240.0 |
OutputTimeStep 1.0 |
kcat Rho gtp by Rho gef | 240.0 |
OutputTimeStep 1.0 |
kf | 240.0 |
OutputTimeStep 1.0 |
kf arp23 activation | 240.0 |
OutputTimeStep 1.0 |
kf CaM NG | 240.0 |
OutputTimeStep 1.0 |
camkii f-actin | 240.0 |
OutputTimeStep 1.0 |
camkii g-actin | 240.0 |
OutputTimeStep 1.0 |
kf cdc42 wasp | 240.0 |
OutputTimeStep 1.0 |
kf MLC phosphorylation | 240.0 |
OutputTimeStep 1.0 |
kf myoppase basal | 240.0 |
OutputTimeStep 1.0 |
kf rock act by rho | 240.0 |
OutputTimeStep 1.0 |
kf rock inact | 240.0 |
OutputTimeStep 1.0 |
Km | 240.0 |
OutputTimeStep 1.0 |
km1 camkii activation by cam | 240.0 |
OutputTimeStep 1.0 |
km1 PP1 activation by i1 | 240.0 |
OutputTimeStep 1.0 |
km2 | 240.0 |
OutputTimeStep 1.0 |
km can cam | 240.0 |
OutputTimeStep 1.0 |
CaN inactivation | 240.0 |
OutputTimeStep 1.0 |
CaMKii activation by CaM | 240.0 |
OutputTimeStep 1.0 |
Km CaMKII inactivation | 240.0 |
OutputTimeStep 1.0 |
km cdc42 activation | 240.0 |
OutputTimeStep 1.0 |
km cdc42 gef activation | 240.0 |
OutputTimeStep 1.0 |
km cdc42 gef | 240.0 |
OutputTimeStep 1.0 |
km cdc42 hydrolysis | 240.0 |
OutputTimeStep 1.0 |
km cofilin actiation ssh1 | 240.0 |
OutputTimeStep 1.0 |
km i1 activation by CaN | 240.0 |
OutputTimeStep 1.0 |
Km i1 inactivation | 240.0 |
OutputTimeStep 1.0 |
km limk activation by rock | 240.0 |
OutputTimeStep 1.0 |
km limk inactivation by rock | 240.0 |
OutputTimeStep 1.0 |
km mlc dephosphorylation | 240.0 |
OutputTimeStep 1.0 |
km myoppase activation dephos | 240.0 |
OutputTimeStep 1.0 |
km myoppase inactivation rock | 240.0 |
OutputTimeStep 1.0 |
km pp1 inct by camkii | 240.0 |
OutputTimeStep 1.0 |
km rho gef inactivation | 240.0 |
OutputTimeStep 1.0 |
km rhogap camkii | 240.0 |
OutputTimeStep 1.0 |
km rho gap pp1 | 240.0 |
OutputTimeStep 1.0 |
km rhogef camkii | 240.0 |
OutputTimeStep 1.0 |
km rhogtp by rhogef | 240.0 |
OutputTimeStep 1.0 |
km rhogtp hhydrolysis | 240.0 |
OutputTimeStep 1.0 |
km ssh1 dephos | 240.0 |
OutputTimeStep 1.0 |
km ssh1 phos camkii | 240.0 |
OutputTimeStep 1.0 |
kr | 240.0 |
OutputTimeStep 1.0 |
kr arp activation | 240.0 |
OutputTimeStep 1.0 |
kr CaM binding NG | 240.0 |
OutputTimeStep 1.0 |
kr caMkii binding f-actin | 240.0 |
OutputTimeStep 1.0 |
kr camkii g-actin | 240.0 |
OutputTimeStep 1.0 |
kr cdc42 wasp | 240.0 |
OutputTimeStep 1.0 |
kr MLCp basal | 240.0 |
OutputTimeStep 1.0 |
kr myosin ppase basal | 240.0 |
OutputTimeStep 1.0 |
kr rock by rho | 240.0 |
OutputTimeStep 1.0 |
kr rock inacivation | 240.0 |
OutputTimeStep 1.0 |
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Assignments
Name | Variable | Assignment Function Expression |
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Events
Name | Trigger Type | Variable Assignment |
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Geometry non-spatial256678770
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | plasma membrane |
Events
Name | Variable | Rate Expression |
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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] |
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Downloads
Model Format | Model Downloads |
---|---|
Virtual Cell Markup Language | VCML File |
PDF Report | Report |
COMBINE Archive | OMEX File |
SEDML | SEDML File |
File Format | Application Downloads |
BNGL | Application0.bngl |
SBML | Application0.sbml |
Matlab | Application0.m |
NFSim XML | Application0.xml |