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Molecule Parameter List for PP1A | 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. |
PP1A acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PP1A | Mammalian_cell_
cycle
Accession No. : 85 | Rb_grp
Pathway No. : 1071 | 0 | 200 | No |
PP1A 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 | 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 |
PP1A 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 | CycE /
k21_phiE | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99968 | 2500 | 4 | explicit E-S complex | Substrate
PP1A
Product
PP1
| | | Rate is just K21 * phiE * [CycE]. K21 = 1, phiE = 25. So rate= 25 * [CycE] MM rate = kcat * E.S/(Km + S) Let Km << S, then we get rate = kcat * E So if Km = 0.01, kcat = 25 7 Apr 2005. Actually should include substrate term. So, Km = 10, kcat = Km * K21 * phiE = 250 18 Apr 2005. Speeded up 10x. | | 2 | CycA /
k21_phiE_A | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 9.99968 | 2500 | 4 | explicit E-S complex | Substrate
PP1A
Product
PP1
| | | phiE is also used for the reaction catalyzed by A. So rates are identical to k21_phiE | | 3 | CycB /
k21_phiB | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 10 | 200 | 4 | explicit E-S complex | Substrate
PP1A
Product
PP1
| | | phiB = 2. See calculation for k21_phiE |
PP1A 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 | | k21b | Mammalian_cell_
cycle
Accession No. : 85 | Rb_grp
Pathway No. : 1071 | 10
(s^-1) | 0
(s^-1) | - | - | Substrate
PP1
Product
PP1A
| | A dummy back reaction, implicit in the form of equation 19 18 Apr 2005. Speeded up 10x. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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