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Molecule Parameter List for GM | 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. |
GM acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | GM | Mammalian_cell_
cycle
Accession No. : 85 | Growth
Pathway No. : 1069 | 0 | 200 | No | | Stands for General Machinery, presumably for synthesis. |
GM 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 | GM /
mu
| Mammalian_cell_
cycle
Accession No. : 85 | Growth
Pathway No. : 1069 | 1.00001 | 0.122 | 4 | explicit E-S complex | Substrate
AminoAcids
Product
mass
| | Rate = E.S.kcat/(Km + S) We want to represent dmass/dt = epsilon.mu.GM. Epsilon is 1 for now. mu = 0.061 S here is AA, buffered to 1. We assign Km = 1 for simplicity. Then kcat = 2 * mu = 0.122 |
GM 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 | mass /
k27 | Mammalian_cell_
cycle
Accession No. : 85 | Growth
Pathway No. : 1069 | 10 | 2 | 4 | explicit E-S complex | Substrate
Heaviside_dup
Product
GM
| | Equation 17 dGM/dt = k27 * mass * Heaviside_out. k27 = 0.2 If k3 << k2, we have ES ~ E.S.k1/k2 and rate = k3 * ES. So we assume k2 = 1, k3 = 0.1, then k1 = 10 * k27 so k1 = 2. This gives a rather low Km, leading to much complex formation. Let us use MM form, and assume Km >> Heaviside_out. Take Km = 10, then kcat = Km * k27 = 2 |
GM 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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