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Molecule Parameter List for 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. |
Rb acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Rb | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 10 | 200 | No | | Rbtot = 10, assigned to CoInit |
Rb acting as a Summed Molecule in Mammalian_cell_cycle Network
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 | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100 | 3300 | 4 | explicit E-S complex | Substrate
Rb
Product
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 | | 2 | CycE /
k20_lambdaE | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100.002 | 5000 | 4 | explicit E-S complex | Substrate
Rb
Product
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 | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100 | 3000 | 4 | explicit E-S complex | Substrate
Rb
Product
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 | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 100.002 | 5000 | 4 | explicit E-S complex | Substrate
Rb
Product
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 |
Rb 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 | PP1 /
k19_prime | Mammalian_cell_
cycle
Accession No. : 85 | Rb_grp
Pathway No. : 1071 | 99.9992 | 0.1 | 4 | explicit E-S complex | Substrate
Rb_P
Product
Rb
| | | k19_prime is actually zero, but I do not want NaNs (numerical errors due to divide-by-zero) so I set kcat to a very small value. 7 Apr 2005. Same reasoning, now set Km to 10. | | 2 | PP1A /
k19 | Mammalian_cell_
cycle
Accession No. : 85 | Rb_grp
Pathway No. : 1071 | 100 | 2000 | 4 | explicit E-S complex | Substrate
Rb_P
Product
Rb
| | | This is part of Eqn 20. k19 = 20. It is meant to represent a dephosph step of Rb_p. rate is k19*PP1A. rate in MM form is kcat * PP1A * Rb_P / (Km + Rb_P) Assume Km << Rb_P. To do so, Km = 0.01 Then kcat = k19. 7 Apr 2005. Actually should include substrate term. Take Km = 10 >> sub. Then kcat = Km * k19 = 200 18 April. Actually substrate levels are near 10. So need to scale up. Km = 100, kcat = Km * k19 = 2000 |
Rb 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 | | 1 | 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. | | 2 | k26_P | Mammalian_cell_
cycle
Accession No. : 85 | E2F
Pathway No. : 1076 | 10
(uM^-1 s^-1) | 200
(s^-1) | Kd(bf) = 20.0001(uM) | - | Substrate
E2FAP
Rb
Product
E2FAP.Rb
| | | Same as k26, but acting on the phosph form. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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