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Molecule Parameter List for CaMKII-CaM

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

*CaMKII-CaM* 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	2	1	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Ajay_Bhalla_ 2004_PKM_Tuning	76	Network	PKC, Shared_Object_Ajay_Bhalla_2004_PKM_tuning, PLA2, PLCbeta, Gq, MAPK, Ras, EGFR, Sos, PLC_g, CaMKII, CaM, PP1, PP2B, PKA, AC, PKM
This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.

CaMKII-CaM acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaMKII-CaM	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaMKII Pathway No. : 322	0	1.5	No

CaMKII-CaM acting as a Summed Molecule in Ajay_Bhalla_2004_PKM_Tuning Network

Accession Name	Pathway Name	Target	Input
Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaMKII Pathway No. : 322	tot_CaM_CaMKII	CaMKII-CaM CaMKII-thr286*-C aM

CaMKII-CaM acting as a Substrate for an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	tot_CaM_CaMKII / CaM_act_286	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaMKII Pathway No. : 322	113.601	0.5	4	explicit E-S complex	Substrate CaMKII-CaM Product CaMKII-thr286*-C aM

2	tot_autonomous_ CaMKII / auton_286	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaMKII Pathway No. : 322	175	0.5	4	explicit E-S complex	Substrate CaMKII-CaM Product CaMKII-thr286*-C aM

CaMKII-CaM acting as a Product of an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PP1-active / Deph-thr286	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Shared_Object_ Ajay_Bhalla_ 2004_PKM_tuning Pathway No. : 312	5.09911	0.35	4	explicit E-S complex	Substrate CaMKII-thr286-C aM Product* CaMKII-CaM
The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35

CaMKII-CaM acting as a Product in a reaction in Ajay_Bhalla_2004_PKM_Tuning 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
CaMKII-bind-CaM	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaMKII Pathway No. : 322	49.9995 (uM^-1 s^-1)	5 (s^-1)	Kd(bf) = 0.1(uM)	-	Substrate CaM-Ca4 CaMKII Product CaMKII-CaM
This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol.

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