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Molecule Parameter List for AminoAcids

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

AminoAcids participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	8	0	0	6	0	5	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.

AminoAcids acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	Growth Pathway No. : 1069	1	200	Yes
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	1	200	Yes
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	1	200	Yes
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	CycB_Grp Pathway No. : 1073	1	200	Yes
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	1	200	Yes
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	1	200	Yes
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	Early_Response_ Genes Pathway No. : 1079	1	200	Yes
Amino acid pool, Enters into system indirectly as a scaling factor. Set to 1.
AminoAcids	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	1	200	Yes

AminoAcids acting as a Substrate for 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	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
2	CycB  / k11	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	1	3	4	explicit E-S complex	Substrate AminoAcids Product Cdc20notA
	Represented simply as [CycB]*k11, where k11 is 1.5. As AAs are at 1, we get rate = [AAs].[CycB].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 3 gives our desired equation.
3	E2FA  / k7	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	1	1.2	4	explicit E-S complex	Substrate AminoAcids Product CycE
	Represented simply as [E2FA]*k7, where k7 is 0.6 As AAs are at 1, we get rate = [AAs].[E2FA].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 1.2 gives our desired equation.
4	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.
5	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
6	ERG_synth  / ERG_synth	Mammalian_cell_ cycle Accession No. : 85	Early_Response_ Genes Pathway No. : 1079	1.00002	0.5	4	explicit E-S complex	Substrate AminoAcids Product ERG
	kcat = 2 * k15 = 0.5 Km = 1 [AA] = 1

AminoAcids 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
1	k33	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	0.05 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product PPX
2	k11_prime	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	0 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product Cdc20notA
	Kind of a silly reaction, with all terms zero, but it is there in the Novak and Tyson equations.
3	k1_prime	Mammalian_cell_ cycle Accession No. : 85	CycB_Grp Pathway No. : 1073	0.1 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product CycB
	k1_prime = 0.1
4	k5	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	20 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product Kip1
5	k_prime7	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product CycE
	This is set to zero in the paper, so this reaction isn't really doing anything.