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Molecule Parameter List for Kip1

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

*Kip1* 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	0	3	4	4	3

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.

Kip1 acting as a Molecule in Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0	200	No

Kip1 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	Tot_Kip1	CycE_Kip1 Kip1 CycA_Kip1 CycD_Kip1

Kip1 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	CycE / k6_kip1_E	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate Kip1 Product degraded_kip
	Rate = V6 * [CycD_Kip1]. k3.k1/k2 = rate = k6 * etaE = 50. 6 Apr 2005. Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1. Need to go back to MM form because the above explict rates give a very low Km, ie, lots of E.S complex. k6 = 100, etaE = 0.5, Let Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaE = 500.
2	CycA / k6_kip1_A	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate Kip1 Product degraded_kip
	k3.k1/k2 = k6.etaA = 1000.5 = 50 Also k3 << k2. Assume ratio is 10. Let k3 be reasonable, say 1. Then k2 = 10, k1 = 500. 6 April 2005: The above rates are bad because they give a very low Km and too much E.S. complex. So, back to MM: Km >> substrate, so Km = 10. Then kcat = Km k6 * etaA = 10 * 100 * 0.5 = 500.
3	CycB / k6_kip1_B	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate Kip1 Product degraded_kip
	6 Apr 2005. Using MM form: k6 = 100 Let Km = 10 >> substrate. Then kcat = Km k6 * eta_B = 1000*

Kip1 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	CycE / k8_CycE_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
	Autocatalysis step equation 5. Unfortunately cannot exactly represent the math of Equation 26. Note that we cannot merge this enzyme with k6_etaE because this is in the explicit form to get a little closer to the mathematical form.
2	CycA / k8_CycA_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
3	CycB / k8_CycB_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0999992	0.1	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
	k8 = 0.2, psiB = 0.05, so kcat = 0.1. J8 = 0.1
4	Cdc20 / Cdc20_deg_CycA_ Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	4	explicit E-S complex	Substrate CycA_Kip1 Product Kip1 degraded
	Rate comes in as k30 = 20 Same rate as for CycA alone. Rate = [Cdc20][CycA_Kip1] k30. To put in MM form: Rate = [Cdc20][CycA_Kip1] kcat / (Km + [CycA_Kip1]) where kcat = k30 * Km and Km >> [CycA_Kip1]. Put Km = 1000, so kcat = 20000 Similar to CycA alone, we instead get k2 = 10, k3 = 1, so k1 = 200. 19 Apr 2005: Go back to MM form because of low Km. Let Km = 10, then kcat = Km * k30 = 200.

Kip1 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	k25	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	999.996 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 0.01(uM)	-	Substrate CycA Kip1 Product CycA_Kip1
2	k_prime_6_kip1	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	10 (s^-1)	0 (s^-1)	-	-	Substrate Kip1 Product degraded_kip
3	k25	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	999.996 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 0.01(uM)	-	Substrate CycE Kip1 Product CycE_Kip1
4	k24	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	999.996 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 0.01(uM)	-	Substrate CycD Kip1 Product CycD_Kip1
	k24 = 1000 k24r = 10

Kip1 acting as a Product in a reaction in Mammalian_cell_cycle Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	k5	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	20 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product Kip1
2	k_prime_8_kip1	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0.1 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycE_Kip1 Product Kip1 degraded
	k_prime_8 = 0.1
3	k10_b	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	5 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycD_Kip1 Product Kip1 degraded
	This is another degradation step for CycD, but it happens while the CycD is bound to Kip1. Same rate as k10.

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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