Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Myoppase_actMyoppase Myoppase inactivation by ROCK Cytoplasm HMMIrreversible
cofilin_actCofilin_p Cofilin inactivation by LIMK Cytoplasm GeneralKinetics
PP1_actPP1 PP1 inactivation by CaMKII Cytoplasm HMMIrreversible
Ca+CaMCa_CaM calcium binding calmodulin Cytoplasm GeneralKinetics
Calcineurin_actCalcineurin calcinuerin inactivation Cytoplasm HMMIrreversible
Cofilin_pcofilin_act Cofilin activation through SSH1 dephosphorylation Cytoplasm HMMIrreversible
RhoGTPRhoGDP RhoGTP hydrolysis Cytoplasm HMMIrreversible
SSH1SSH1_act SSH1 dephosphorylation by CaN Cytoplasm HMMIrreversible
cdc42GTP+WASPWASP_act cdc42 activates WASP Cytoplasm MassAction
cdc42GTPcdc42GDP cdc42 hydrolysis Cytoplasm HMMIrreversible
LIMKLIMK_P LIMK activation by ROCK Cytoplasm HMMIrreversible
MLCMLC_p MLC Phosphorylation by ROCK Cytoplasm HMMIrreversible
cdc42GEF_actCdc42GEF Cdc42 GEF inactivation Cytoplasm HMMIrreversible
arp23_actarp23 Arp23 inactivation Cytoplasm GeneralKinetics
B Barbed ends Cytoplasm GeneralKinetics
RhoGEFRhoGEF_act RhoGEF activation by CaMKII Cytoplasm HMMIrreversible
Il1_actIl1 Il1 inactivation Cytoplasm HMMIrreversible
Il1Il1_act Il1 activation by CaN Cytoplasm HMMIrreversible
arp23+WASP_actarp23_act Arp23 activation Cytoplasm MassAction
F_actinG_actin severing Cytoplasm GeneralKinetics
CaMKIICaMKIIp CaMKII activation by CaM Cytoplasm GeneralKinetics
PP1PP1_act PP1 activation by IL1 Cytoplasm GeneralKinetics
cdc42GDPcdc42GTP cdc42 activation Cytoplasm HMMIrreversible
Bp pushing barbed ends Cytoplasm GeneralKinetics
CaMKII+G_actinCaMKII_G_actin CaMKII sequestration of G-actin Cytoplasm MassAction
Ng+CaMCaM_Ng Calmodulin binding neurogranin Cytoplasm MassAction
R Radius Cytoplasm GeneralKinetics
RhoGAP_actRhoGAP RhoGAP inactivation by PP1 Cytoplasm HMMIrreversible
RhoGDPRhoGTP RhoGTP activation by RhoGEF Cytoplasm HMMIrreversible
MyoppaseMyoppase_act Myoppase activation by autodephosphorylation Cytoplasm HMMIrreversible
RhoGEF_actRhoGEF Rho GEF inactivation Cytoplasm HMMIrreversible
CalcineurinCalcineurin_act Calcineurin activation by CaM Cytoplasm GeneralKinetics
LIMK_PLIMK LIMK inactivation by ROCK Cytoplasm HMMIrreversible
MLC_pMLC MLC dephosphorylation Cytoplasm HMMIrreversible
CaMKIIpCaMKII CaMKII inactivation Cytoplasm HMMIrreversible
ROCK+RhoGTPROCK_act ROCK activation by Rho Cytoplasm MassAction
Cdc42GEFcdc42GEF_act cdc42 GEF activation Cytoplasm HMMIrreversible
MyoppaseMyoppase_act myosin phosphatase activation basal Cytoplasm MassAction
MLCMLC_p MLC phosphorylation basal Cytoplasm MassAction
ROCK_act ROCK inactivation 1 Cytoplasm MassAction
RhoGAPRhoGAP_act RhoGAP activation by CaMKII Cytoplasm HMMIrreversible
CaMKII+F_actinCaMKII_F_actin CaMKII sequestration of F-actin Cytoplasm MassAction
SSH1_actSSH1 SSH1 phosphorylation by CaMKIIp Cytoplasm HMMIrreversible
F_actin+arp23_act+G_actinF_actin Actin growth Cytoplasm GeneralKinetics

Structures

Name
Type
Electrical
plasma membrane Membrane Cytoplasm(+)   c0(-)
c0 Compartment (+)   (-)
Cytoplasm Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
F_actin Cytoplasm Cytoplasm
CaMKII_F_actin Cytoplasm Cytoplasm
Il1_act Cytoplasm Cytoplasm
Myoppase Cytoplasm Cytoplasm
Myoppase_act Cytoplasm Cytoplasm
ROCK Cytoplasm Cytoplasm
Il1 Cytoplasm Cytoplasm
RhoGTP Cytoplasm Cytoplasm
ROCK_act Cytoplasm Cytoplasm
LIMK Cytoplasm Cytoplasm
LIMK_P Cytoplasm Cytoplasm
RhoGAP_act Cytoplasm Cytoplasm
RhoGDP Cytoplasm Cytoplasm
RhoGEF Cytoplasm Cytoplasm
RhoGEF_act Cytoplasm Cytoplasm
RhoGAP Cytoplasm Cytoplasm
Ng Cytoplasm Cytoplasm
CaM_Ng Cytoplasm Cytoplasm
SSH1_act Cytoplasm Cytoplasm
cdc42GTP Cytoplasm Cytoplasm
WASP Cytoplasm Cytoplasm
PP1 Cytoplasm Cytoplasm
PP1_act Cytoplasm Cytoplasm
MLC Cytoplasm Cytoplasm
MLC_p Cytoplasm Cytoplasm
arp23 Cytoplasm Cytoplasm
WASP_act Cytoplasm Cytoplasm
B Cytoplasm Cytoplasm
R Cytoplasm Cytoplasm
cdc42GDP Cytoplasm Cytoplasm
Ca_CaM Cytoplasm Cytoplasm
Bp Cytoplasm Cytoplasm
CaM Cytoplasm Cytoplasm
arp23_act Cytoplasm Cytoplasm
SSH1 Cytoplasm Cytoplasm
Ca Cytoplasm Cytoplasm
CaMKII Cytoplasm Cytoplasm
CaMKIIp Cytoplasm Cytoplasm
G_actin Cytoplasm Cytoplasm
CaMKII_G_actin Cytoplasm Cytoplasm
Calcineurin_act Cytoplasm Cytoplasm
Cdc42GEF Cytoplasm Cytoplasm
cdc42GEF_act Cytoplasm Cytoplasm
Cofilin_p Cytoplasm Cytoplasm
Calcineurin Cytoplasm Cytoplasm
cofilin_act Cytoplasm Cytoplasm

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Compartmental

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

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

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

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]

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