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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

DRG 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	2	1	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.

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

Accession Name	Pathway Name	Target	Input
Mammalian_cell_ cycle Accession No. : 85	Delayed_ Response_Genes Pathway No. : 1080	DRG_dup	DRG

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.

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
k18	Mammalian_cell_ cycle Accession No. : 85	Delayed_ Response_Genes Pathway No. : 1080	10 (s^-1)	0 (s^-1)	-	-	Substrate DRG Product degraded
k18 = 10