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Molecule Parameter List for mass | 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. |
mass acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | mass | Mammalian_cell_
cycle
Accession No. : 85 | Growth
Pathway No. : 1069 | 1 | 200 | No |
mass acting as a Summed Molecule in Mammalian_cell_cycle Network
mass 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 | 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 |
mass 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 | 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 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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