| Citation |
|---|
| Novak B, tyson JJ (1997) Modeling the control of DNA replication in fission yeast, PNAS, USA, 94:9147-9152. http://www.pnas.org/cgi/content/abstract/ 94/17/9147 |
| Description |
|---|
| A cell cycle model with 13 dynamic variables ( Cdc25,G1K,G1R=[Cig2/Cdc2/Rum1],G2K=[Cdc13/Cdc2],G2R=[Cdc13/Cdc2/Rum1],IE=[ Intermediary enzyme],mass,PG2=[Cdc13/P-Cdc2],PG2R=[Cdc13/P-Cdc2/Rum1],R=[ Rum1],UbE,UbE2, Wee1} and two auxilllary variables MPF = G2K+ beta*PG2, SPF=MPF+alpha*G1K+Cig1, (alpha, beta, Cig1 constants) . NOTE: The following switches in the published model are NOT described by the SBML: "Switches(i) When SPF crosses 0.1 from below, S phase is initiated (Start).(ii) When UbE crosses 0.1 from above, the cell divides functionally (mass->mass/2), although visible cytokinesis may be delayed.(iii) 60 min after Start,kp is divided by 2, and at cell division kp is multiplied by 2." ( from Table 1 of the cited reference). |
| Rate constant | Reaction |
|---|---|
| 0 | G1R -> R |
| 0.00175 | EmptySet -> G1K |
| 0.00495*mass[t] | EmptySet -> mass |
| 0.0075*(1 - UbE[t]) + 0.25*UbE[t] | G2K -> EmptySet |
| 0.0075*(1 - UbE[t]) + 0.25*UbE[t] | PG2 -> EmptySet |
| 0.015 | EmptySet -> G2K |
| 0.025*(1 - Cdc25[t]) + 0.5*Cdc25[t] | PG2 -> G2K |
| 0.035*(1 - Wee1[t]) + 0.35*Wee1[t] | G2K -> PG2 |
| 0.0375*(1 - UbE2[t]) + 7.5*UbE2[t] | G1K -> EmptySet |
| 0.05 + 0.0075*(1 - UbE[t]) + 0.25*UbE[t] | G2R -> R |
| 0.05 + 0.0075*(1 - UbE[t]) + 0.25*UbE[t] | PG2R -> R |
| 0.09375 | EmptySet -> R |
| 0.1 | G1R -> G1K + R |
| 0.1 | G2R -> G2K + R |
| 0.1 | PG2R -> PG2 + R |
| 0.1875 | G1R -> G1K |
| 0.1875 | G2R -> G2K |
| 0.1875 | PG2R -> PG2 |
| 0.1875 | R -> EmptySet |
| 0.4 (G2K[t] + 0.05 PG2[t]) = unassigned ( hill vmax) | 1 - IE |-> IE |
| 10 | G1K + R -> G1R |
| 100 | G2K + R -> G2R |
| 100 | PG2 + R -> PG2R |
| 3.25 (0.25 G1K[t] + G2K[t] + 0.05 PG2[t]) = unassigned (hill vmax) | mass + R |-> mass + EmptySet |
| G2K[t] + 0.05 PG2[t] = unassigned ( hill vmax) | 1 - Cdc25 |-> Cdc25 |
| G2K[t] + 0.05 PG2[t] = unassigned ( hill vmax) | 1 - UbE2 |-> UbE2 |
| G2K[t] + 0.05 PG2[t] = unassigned ( hill vmax) | Wee1 |-> EmptySet |
| Variable | IC | ODE |
|---|---|---|
| Cdc25 | 0 | Cdc25'[t] == -((kcr*Cdc25[t])/(Kmcr + Cdc25[t])) + (kc*(1 - Cdc25[t])*(G2K[t] + beta*PG2[t]))/(1 + Kmc - Cdc25[t]) |
| G1K | 0 | G1K'[t] == k5 + k4*G1R[t] + k8r*G1R[t] - k8*G1K[t]*R[t] - G1K[t]*(V6p*(1 - UbE2[t]) + V6*UbE2[t]) |
| G1R | 0 | G1R'[t] == -(k4*G1R[t]) - k6p*G1R[t] - k8r* G1R[t] + k8*G1K[t]*R[t] |
| G2K | 0 | G2K'[t] == k1 + k4*G2R[t] + k7r*G2R[t] + (V25p*(1 - Cdc25[t]) + V25*Cdc25[t])*PG2[t] - k7*G2K[t]*R[t] - G2K[t]*(V2p*(1 - UbE[t]) + V2*UbE[t]) - G2K[t]*(Vwp*(1 - Wee1[t]) + Vw* Wee1[t]) |
| G2R | 0 | G2R'[t] == -(k4*G2R[t]) - k7r*G2R[t] + k7*G2K[ t]*R[t] - G2R[t]*(k2p + V2p*(1 - UbE[t]) + V2*UbE[t]) |
| IE | 0 | IE'[t] == -((kir*IE[t])/(Kmir + IE[t])) + (ki* (1 - IE[t])*(G2K[t] + beta*PG2[t]))/(1 + Kmi - IE[t]) |
| mass | 0.4 | mass'[t] == mu*mass[t] |
| PG2 | 0 | PG2'[t] == -((V25p*(1 - Cdc25[t]) + V25*Cdc25[ t])*PG2[t]) + k4*PG2R[t] + k7r*PG2R[t] - k7*PG2[t] *R[t] - PG2[t]*(V2p*(1 - UbE[t]) + V2*UbE[t]) + G2K[t]*(Vwp*(1 - Wee1[t]) + Vw*Wee1[t]) |
| PG2R | 0 | PG2R'[t] == -(k4*PG2R[t]) - k7r*PG2R[t] + k7* PG2[t]*R[t] - PG2R[t]*(k2p + V2p*(1 - UbE[t]) + V2*UbE[t]) |
| R | 0 | R'[t] == k3 + k6p*G1R[t] + k8r*G1R[t] + k7r*G2R[t] + k7r*PG2R[t] - k4*R[t] - k8*G1K[ t]*R[t] - k7*G2K[t]*R[t] - k7*PG2[t]*R[t] - (kp* mass[t]*(Cig1 + alpha*G1K[t] + G2K[t] + beta*PG2[t])*R[t] )/(Kmp + R[t]) + G2R[t]*(k2p + V2p*(1 - UbE[t]) + V2*UbE[t]) + PG2R[t]*(k2p + V2p*( 1 - UbE[t]) + V2*UbE[t]) |
| UbE | 0 | UbE'[t] == (ku*IE[t]*(1 - UbE[t]))/(1 + Kmu - UbE[t]) - (kur*UbE[t])/(Kmur + UbE[t]) |
| UbE2 | 0 | UbE2'[t] == (ku2*(G2K[t] + beta*PG2[t])*(1 - UbE2[t]))/(1 + Kmu2 - UbE2[t]) - (kur2*UbE2[ t])/(Kmur2 + UbE2[t]) |
| Wee1 | 0 | Wee1'[t] == (kwr*(1 - Wee1[t]))/(1 + Kmwr - Wee1[t]) - (kw*(G2K[t] + beta*PG2[t])* Wee1[t])/(Kmw + Wee1[t]) |