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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

mass participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	1	1	0	1	0	0

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

Accession Name	Pathway Name	Target	Input
Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	Mass_dup	mass

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