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Molecule Parameter List for degraded_kip

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

degraded_kip 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	0	0	0	3	0	1

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.

degraded_kip acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
degraded_kip	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	0	200	Yes

degraded_kip 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  / 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 = 100*0.5 = 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

degraded_kip acting as a Product 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
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