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Molecule Parameter List for DRG | 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. |
DRG acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | DRG | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 0 | 200 | No |
DRG acting as a Summed Molecule in Mammalian_cell_cycle Network
DRG 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 | DRG /
k9
| Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 1.00002 | 5 | 4 | explicit E-S complex | Substrate
AminoAcids
Product
CycD
| | Represented simply as [DRG]*k9, where k9 is 2.5. As AAs are at 1, we get rate = [AAs].[DRG].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 5 gives our desired equation. |
DRG 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 | ERG /
k_prime_17 | Mammalian_cell_
cycle
Accession No. : 85 | CELLDIV
Pathway No. : 1070 | 0.999989 | 0.7 | 4 | explicit E-S complex | Substrate
AminoAcids
Product
DRG
| | | k17_prime = 0.35. rate = epsilon * k17_prime * [ERG] Assume AA = 1, Km = 1. Then rate = kcat * AA * ERG / (Km + AA) gives kcat = 0.7 | | 2 | DRG_synth /
DRG_synth | Mammalian_cell_
cycle
Accession No. : 85 | Delayed_
Response_Genes
Pathway No. : 1080 | 0.0899986 | 10 | 4 | explicit E-S complex | Substrate
DRG_2A
Product
DRG
| | | k17 = 10 J17 = 0.3 This enz represents rate = k17([DRG]/J17)^2 / (1 + ([DRG]/J17)^2 ) Here we assume that the substrate conc = [DRG]^2. Then it expands into classical MM form: rate = k17.sub / (J17^2 + sub) provided [DRG_synth] = 1. |
DRG 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. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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