Models
Navigation
Below is displayed the model view of the selected project. Model view is shown in the form of the model overview page for the currently selected model. The central feature of the model view is the model scheme that shows individual model components of selected model. The navigation panel on the left allows you to browse the biological structure of the model. Manipulation with the navigation panel is realized by unfolding the items in the navigation tree and clicking on a requested system level.
Annotations Tab
All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.
Components Tab
The Components Tab displays all the model species (state variables). More information for particular components are accessible after clicking on the requested component header.
Reactions Tab
Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.
Parameters Tab
All quantitative parameters are managed under Parameters Tab. Constants are separated from assigned quantities.
Simulation Tab
Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of initial conditions, parameters, options and datasets are listed in respective folders.
Analysis Tab
Conservation analysis, modes analysis and matrix analysis are available by clicking on appropriate buttons.
Experiments Tab
Experiments tab contains list of all experiments related to selected model.
Miyoshi et al. 2007
Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in Cyanobacteria. J Biol Rhythms 22:69-8
In the cyanobacterium, Synechococcus elongatus, most promoters are regulated by a circadian clock under continuous light (LL) conditions. Nevertheless, the basic circadian oscillation is primarily generated by alternating KaiC phosphorylation/dephosphorylation reactions at the posttranslational level. Indeed, the KaiC phosphorylation cycle was recently reconstituted in vitro by incubating KaiA, KaiB, and KaiC proteins with ATP. However, the molecular dynamics of this chemical oscillation and the mechanism that drives the circadian transcription/translation rhythms remain unknown. In this report, the KaiC phosphorylation cycle and the gene regulatory network in the cyanobacterial circadian system have been modeled. The model reproduces the robust KaiC phosphorylation cycle in the absence of de novo gene expression as is observed in vitro, as well as its coupling to transcriptional/translational feedback in LL conditions in vivo. Moreover, the model is consistent with most previous experiments, including various combinations of genetic knockout or overexpression of kai genes. It also predicts that multiple KaiC phosphorylation states and dynamic Kai protein interactions may be required for the cyanobacterial circadian system.
model:Miyoshi et al. (2007)
Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in Cyanobacteria. J Biol Rhythms 22:69-80.
publication:Miyoshi et al. (2007)
Function: Mass Action (irreversible)
Reaction rate: k12*KaiA2B4
| Kinetic rate constant | Value |
|---|---|
| k12 | 0.08788 |
Function: Mass action (two substrates) (reversible)
Reaction rate: k11*1*KaiB4*KaiA2
| Kinetic rate constant | Value |
|---|---|
| k11 | 0.0008756 |
| k2 | 1 |
Function: Mass Action (irreversible)
Reaction rate: k7*KaiA2
| Kinetic rate constant | Value |
|---|---|
| k7 | 0.162 |
Function: Mass Action 2nd order (irreversible)
Reaction rate: k8*KaiA*KaiA
| Kinetic rate constant | Value |
|---|---|
| k8 | 0.268 |
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg1*KaiA*L_
| Kinetic rate constant | Value |
|---|---|
| kpdeg1 | 0.008 |
| L_ | 1 |
Modifiers: kaiA_mRNA
Function: Light dependend inflow (irreversible)
Reaction rate: ktl1*L_*kaiA_mRNA
| Kinetic rate constant | Value |
|---|---|
| L_ | 1 |
| ktl1 | 0.008239 |
| k1 |
Function: Mass Action (irreversible)
Reaction rate: kmdeg1*kaiA_mRNA
| Kinetic rate constant | Value |
|---|---|
| kmdeg1 | 0.133 |
Modifiers: kaiBC_mRNA
Function: Light dependend inflow (irreversible)
Reaction rate: ktl2*L_*kaiBC_mRNA
| Kinetic rate constant | Value |
|---|---|
| ktl2 | 170.1 |
| L_ | 1 |
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg2*KaiB*L_
| Kinetic rate constant | Value |
|---|---|
| kpdeg2 | 0.49 |
| L_ | 1 |
Modifiers: CPKaiC6
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat_b2*CPKaiC6*KaiB4i)/(Km_b2 + KaiB4i)
| Kinetic rate constant | Value |
|---|---|
| kcat_b2 | 0.346 |
| Km_b2 | 66.75 |
Modifiers: PPKaiC6
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat_b1*PPKaiC6*KaiB4)/(Km_b1 + KaiB4)
| Kinetic rate constant | Value |
|---|---|
| Km_b1 | 0.602 |
| kcat_b1 | 2.423 |
Function: Mass Action (irreversible)
Reaction rate: k10*KaiB4
| Kinetic rate constant | Value |
|---|---|
| k10 | 0.0001615 |
Function: Mass Action 4th order (reversible)
Reaction rate: k9*KaiB*KaiB*KaiB*KaiB
| Kinetic rate constant | Value |
|---|---|
| k9 | 7.393e-17 |
Function: Mass Action (irreversible)
Reaction rate: k21*KaiC6
| Kinetic rate constant | Value |
|---|---|
| k21 | 1.079e-08 |
Function: Mass Action (irreversible)
Reaction rate: k1*KaiC6
| Kinetic rate constant | Value |
|---|---|
| k1 | 1.615 |
Function: Mass Action 6th order (reversible)
Reaction rate: k2*KaiC*KaiC*KaiC*KaiC*KaiC*KaiC
| Kinetic rate constant | Value |
|---|---|
| k2 | 2.039e-16 |
Modifiers: KaiA2
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat1*KaiA2*KaiC6)/(Km1 + KaiC6)
| Kinetic rate constant | Value |
|---|---|
| kcat1 | 0.539 |
| Km1 | 602 |
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg3*KaiC*L_
| Kinetic rate constant | Value |
|---|---|
| kpdeg3 | 1.3 |
| L_ | 1 |
Function: Mass Action (irreversible)
Reaction rate: k24*CPKaiC6
| Kinetic rate constant | Value |
|---|---|
| k24 | 1.079e-08 |
Modifiers: KaiA2B4
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat4*KaiA2B4*CPKaiC6)/(Km4 + CPKaiC6)
| Kinetic rate constant | Value |
|---|---|
| kcat4 | 0.89 |
| Km4 | 0.602 |
Function: Mass Action (irreversible)
Reaction rate: k5*CPKaiC6
| Kinetic rate constant | Value |
|---|---|
| k5 | 0.162 |
Function: Mass Action 6th order (reversible)
Reaction rate: k6*PKaiC*PKaiC*PKaiC*PKaiC*PKaiC*PKaiC
| Kinetic rate constant | Value |
|---|---|
| k6 | 1.019e-10 |
Modifiers: CPKaiC6, PPKaiC6
Function: Enzyme-modulated light-dependend transcription (irreversible)
Reaction rate: ka1*(kbts1*RNAP)/(1+kbts1*RNAP)*(CPKaiC6/PPKaiC6)*L_
| Kinetic rate constant | Value |
|---|---|
| RNAP | 5000 |
| ka1 | 10170000 |
| kbts1 | 3.657e-12 |
| L_ | 1 |
Function: Mass Action (irreversible)
Reaction rate: kmdeg2*kaiBC_mRNA
| Kinetic rate constant | Value |
|---|---|
| kmdeg2 | 0.178 |
Modifiers: CPKaiC6, PPKaiC6
Function: Enzyme-modulated light-dependend transcription (irreversible)
Reaction rate: ka2*(kbts2*RNAP)/(1+kbts2*RNAP)*(CPKaiC6/PPKaiC6)*L_
| Kinetic rate constant | Value |
|---|---|
| RNAP | 5000 |
| ka2 | 64580000 |
| kbts2 | 1e-12 |
| L_ | 1 |
Function: Mass Action (irreversible)
Reaction rate: k22*PPKaiC6
| Kinetic rate constant | Value |
|---|---|
| k22 | 1.079e-05 |
Function: Mass Action (irreversible)
Reaction rate: k23*PPKaiC6
| Kinetic rate constant | Value |
|---|---|
| k23 | 1.079e-06 |
Modifiers: KaiA2B4
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat2*KaiA2B4*PPKaiC6)/(Km2 + PPKaiC6)
| Kinetic rate constant | Value |
|---|---|
| kcat2 | 0.539 |
| Km2 | 602 |
Function: Mass Action (irreversible)
Reaction rate: k3*PPKaiC6
| Kinetic rate constant | Value |
|---|---|
| k3 | 0.0001615 |
Function: Specific hexamer formation (Myioshi) (reversible)
Reaction rate: k4*KaiC*KaiC*KaiC*PKaiC*PKaiC*PKaiC
| Kinetic rate constant | Value |
|---|---|
| k4 | 1.019e-14 |
Modifiers: KaiA2
Function: Michaelis-Menten irreversible (irreversible)
Reaction rate: (kcat3*KaiA2*PPKaiC6)/(Km3 + PPKaiC6)
| Kinetic rate constant | Value |
|---|---|
| kcat3 | 1.079 |
| Km3 | 0.602 |
Function: light-dependend Mass Action (irreversible)
Reaction rate: kpdeg4*PKaiC*L_
| Kinetic rate constant | Value |
|---|---|
| kpdeg4 | 0.2 |
| L_ | 1 |
Constant quantities
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Simulation type: fixed
Assigned quantities
Simulation type: assignment
Simulation type: assignment
| Description: | Dissolved oxygen was measured externally by PSI OxyCorder |
|---|
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI