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Molecule Parameter List for E2FA | 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 acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | E2FA | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 5 | 200 | No | | This is the active form of E2F. E2FTot = 5, and this is used for the CoInit. |
E2FA acting as 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 | E2FA /
k29
| Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 1000.02 | 50 | 4 | explicit E-S complex | Substrate
Mass_dup
Product
CycA
| | | Represented as eps*k29*[E2FA]*[mass], where k29 is 0.05 Split into two steps, this one deals with the E2FA term. rate = Mass_dup * E2FA * kcat / (Km + Mass_dup) Note that Mass_dup will not change. Let Km >> Mass_dup and kcat = k29 * Km. then rate ~ Mass_dup * E2FA * k29 * Km / Km | | 2 | E2FA /
k7
| Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 1 | 1.2 | 4 | explicit E-S complex | Substrate
AminoAcids
Product
CycE
| | | Represented simply as [E2FA]*k7, where k7 is 0.6 As AAs are at 1, we get rate = [AAs].[E2FA].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 1.2 gives our desired equation. |
E2FA 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 | CycA /
A_phosph_E2F | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99992 | 10 | 4 | explicit E-S complex | Substrate
E2FA
Product
E2FAP
| | | 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 Mar. Better: Use explicit enz form. rate = k3.k1/k2 if k3 << k2. Let k3 = 1, k2 = 10, so we get k1 = k23 * 10 = 10. 6 Apr. Problem with explicit form is that the enz-substrate complex may affect the levels of the CycA, B etc. Back to MM. | | 2 | CycB /
B_phosph_E2FA | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99992 | 10 | 4 | explicit E-S complex | Substrate
E2FA
Product
E2FAP
| | | See A_phosph_E2F. Same rate of k23 = 1 applies. |
E2FA acting as a Product of 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 /
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 | | 4 | 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 acting as a Substrate 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 | | 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. |
E2FA 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 | | k22_23_prime | 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
Product
E2FA
| | k22 is the forward rate of 1 k23_prime is the backward rate of 0.005 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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