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Molecule Parameter List for degraded

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* participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	9	0	0	0	20	0	13

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 acting as a Molecule in Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
degraded	Mammalian_cell_ cycle Accession No. : 85	CycB_Grp Pathway No. : 1073	0	200	No
degraded	Mammalian_cell_ cycle Accession No. : 85	Growth Pathway No. : 1069	0	200	Yes
degraded	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	0	200	Yes
degraded	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	0	200	Yes
degraded	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	0	200	Yes
degraded	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0	200	Yes
degraded	Mammalian_cell_ cycle Accession No. : 85	Early_Response_ Genes Pathway No. : 1079	0	200	Yes
Degraded products of Early Response Genes. Just a place- filler pool, does not enter elsewhere.
degraded	Mammalian_cell_ cycle Accession No. : 85	Delayed_ Response_Genes Pathway No. : 1080	0	200	Yes
Degraded products of Early Response Genes. Just a place- filler pool, does not enter elsewhere.
degraded	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	0	200	Yes

degraded 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 / Ak6_etaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	Rate = V6 [CycD_Kip1]. 6 Apr 2005. Rates were k1 = 500, k2 = 10, k3 = 1 in explicit E.S reaction form. Changed to MM as Km was too low. New values: Km = 10 kcat = Km * k6 * etaE = 500.*
2	CycE / k8_CycE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE Product 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.
3	CycE / k6_E_etaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	k6 = 100, etaE = 0.5 Assume a large Km of 1000 so that the conc of the enzyme is negligible. Then rate is E.S.Vmax/Km. 6 April 2006 I had changed it over to an explict form earlier. Those values were k1 = 500, k2 = 10, k3 = 1. Cannot use as effective Km is very small so we would end up with lots of E.S complex. Change back to MM: Km = 10, kcat = Km * k6 * etaE = 500.
4	CycE / k6_D_etaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	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.
5	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.
6	CycA / Ak6_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	See Ak6_etaE
7	CycA / k8_CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE Product degraded
8	CycA / k6_E_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	See notes for k6_E_etaE. Explicit rates had been k1 = 500, k2 = 10, k3 = 1 but this gave a very low Km. So, back to MM: etaA = 0.5 so kcat = 500, Km = 10 as for k6_E_etaE
9	CycA / k6_D_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	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.
10	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
11	CycB / Ak6_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	See Ak6_etaE
12	CycB / k8_CycB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0999992	0.1	4	explicit E-S complex	Substrate CycE Product degraded
13	CycB / k6_E_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	See notes for k6_E_etaE. Here etaB = 1 so kcat = 1000, Km as before is 10
14	CycB / k6_D_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	6 Apr 2005. Earlier used explicit E.S complex form with k1 = 1000, k2 = 10, k3 = 1. This gave low Km and lots of E.S. complex. So shift to MM form: k6 = 100, etaB = 1. Let Km = 10 >> substrate. Then kcat = Km * k6 * etaB = 1000
15	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
16	Cdc20 / k2_prime_prime	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	99.9992	100	4	explicit E-S complex	Substrate CycB Product degraded
	k2_prime_prime = 1. rate = k2_prime_prime Cdc20 * CycB Using MM: rate = kcat * Cdc20 * CycB / (CycB + Km) Let Km >> CycB, ie, around 100. Then kcat = k2_prime_prime * Km = 100.*
17	Cdc20 / Cdc20_deg_CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	4	explicit E-S complex	Substrate CycA Product degraded
	Rate comes in as k30 = 20 Rate = [Cdc20][CycA] k30. To put in MM form: Rate = [Cdc20][CycA] kcat / (Km + [CycA]) where kcat = k30 * Km and Km >> [CycA]. Put Km = 1000, so kcat = 20000 25 March: use explicit enz form. Use rate = k3*k1/k2 = 20, which works if k2 >> k3. Then let k3 = 1, k2 = 10, k1 becomes 200 7 Apr 2005: Above won't work because of low Km consuming too much of the Cdc20 in the complex form. So use Km = 10, kcat = 200.
18	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.
19	Cdh1_i / Cdh1_i_k2_prime	Mammalian_cell_ cycle Accession No. : 85	Cdh1_grp Pathway No. : 1075	100.002	5	4	explicit E-S complex	Substrate CycB Product degraded
	k2_prime = 0.05. so actually this reaction is pretty negligible. rate = k2_prime * Cdh1_i * CycB From MM kinetics, rate = kcat * Cdh1_i * CycB / (CycB + Km). Let Km >>CycB, so Km = 10. Then kcat = k2_prime * Km = 0.5
20	Cdh1 / Cdh1_k2	Mammalian_cell_ cycle Accession No. : 85	Cdh1_grp Pathway No. : 1075	100	2000	4	explicit E-S complex	Substrate CycB Product degraded
	k2 = 20 Let Km = 100, so it is >> substrate. Then kcat = Km k2 = 2000*

degraded 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
1	k28	Mammalian_cell_ cycle Accession No. : 85	Growth Pathway No. : 1069	0.2 (s^-1)	0 (s^-1)	-	-	Substrate GM Product degraded
	k28 = 0.2
2	k34	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	0.05 (s^-1)	0 (s^-1)	-	-	Substrate PPX Product degraded
3	k12	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	1.5 (s^-1)	0 (s^-1)	-	-	Substrate Cdc20 Product degraded
4	k12A	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	1.5 (s^-1)	0 (s^-1)	-	-	Substrate Cdc20notA Product degraded
5	k_prime6	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	10 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycA_Kip1 Product CycA degraded
6	k_prime6	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	10 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycE_Kip1 Product CycE degraded
7	k_prime_8	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0.1 (s^-1)	0 (s^-1)	-	-	Substrate CycE Product degraded
	k_prime_8 = 0.1
8	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
9	k16	Mammalian_cell_ cycle Accession No. : 85	Early_Response_ Genes Pathway No. : 1079	0.25 (s^-1)	0 (s^-1)	-	-	Substrate ERG Product degraded
	k16 from paper = 0.25, unidirectional degradation step.
10	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
11	k10	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	5 (s^-1)	0 (s^-1)	-	-	Substrate CycD Product degraded
12	k_prime6	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	10 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycD_Kip1 Product CycD degraded
13	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.

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