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Molecule Parameter List for E2FA.Rb | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Mammalian_cell_
cycle | 85 | Network |
Growth, CELLDIV, Rb_grp,
IE_GRP, CycB_Grp, Cdc20_Grp,
Cdh1_grp, E2F, CycA_Grp,
CycE_grp, Early_Response_Genes, Delayed_Response_Genes,
CycD_Grp | | This is a fairly complete mass-action reimplementation of the Novak and Tyson mammalian cell cycle model. It is inexact on two counts. First, it replaces many rather abstracted equations with mass action and Michaelis-Menten forms of enzymes. Second, it does not handle the halving of cellular volume at the division point. Within these limitations, the model does most of what the original paper shows including oscillation of the relevant molecules. |
E2FA.Rb acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | E2FA.Rb | Mammalian_cell_
cycle
Accession No. : 85 | E2F
Pathway No. : 1076 | 0 | 200 | No | | This is the active form of E2F. |
E2FA.Rb acting as a Substrate for an Enzyme in Mammalian_cell_cycle Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | CycD /
k20_lambdaD[2] | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100 | 3300 | 4 | explicit E-S complex | Substrate
E2FA.Rb
Product
E2FA
Rb_P
| | | With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330 The idea here is that these reactions phosphorylate the Rb protein attached to E2FA, so that Rb_P is released and E2FA is left. | | 2 | CycE /
k20_lambdaE[2] | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100.002 | 5000 | 4 | explicit E-S complex | Substrate
E2FA.Rb
Product
E2FA
Rb_P
| | | For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500 | | 3 | CycA /
A_phosph_
E2FA.Rb
| Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99992 | 10 | 4 | explicit E-S complex | Substrate
E2FA.Rb
Product
E2FAP.Rb
| | | Rate equn has form [CycA].[E2F].k23 k23 = 1 MM equn has form [CycA].[E2F].kcat/(Km + E2F) So, we set kcat = Km * k23 where Km >> E2F 25 March 2005 Use explicit form. rate = k23 = 1 = k3*k1/k2 where k3 << k2 So k3 = 1, k2 = 10, k1 = 10. 6 Apr 2005. Back to MM form because enz complex formation is depleting CycA, B etc. | | 4 | CycA /
k20_lambdaA[2] | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100 | 3000 | 4 | explicit E-S complex | Substrate
E2FA.Rb
Product
E2FA
Rb_P
| | | Km ~ 0, so rate ~ kcat. Here rate = k20 * lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300 | | 5 | CycB /
B_phosph_
E2FA.Rb
| Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99992 | 10 | 4 | explicit E-S complex | Substrate
E2FA.Rb
Product
E2FAP.Rb
| | | See A_phosph_E2F. Same rate of k23 = 1 applies. | | 6 | CycB /
k20_lambdaB[2] | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100.002 | 5000 | 4 | explicit E-S complex | Substrate
E2FA.Rb
Product
E2FA
Rb_P
| | | With Km ~ 0, rate ~ kcat. Here rate = k20 * lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500 |
E2FA.Rb acting as a Product in a reaction in Mammalian_cell_cycle Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | 1 | k22_23_prime.Rb | Mammalian_cell_
cycle
Accession No. : 85 | E2F
Pathway No. : 1076 | 1
(s^-1) | 0.005
(s^-1) | Keq = 0.005(uM) | 0.995sec | Substrate
E2FAP.Rb
Product
E2FA.Rb
| | | k22 is the forward rate of 1 k23_prime is the backward rate of 0.005 | | 2 | k26 | Mammalian_cell_
cycle
Accession No. : 85 | E2F
Pathway No. : 1076 | 10
(uM^-1 s^-1) | 200
(s^-1) | Kd(bf) = 20.0001(uM) | - | Substrate
E2FA
Rb
Product
E2FA.Rb
| | | k26 = 10, k26r =200 Unless k26 = 10000. There is a period in the paper but it may be a typo. The form of the equation is complex, but if k26 is large then there is more E2F:Rb, so that is the forward reaction here. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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