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Molecule Parameter List for CaMCa4-CaNAB

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

CaMCa4-CaNAB 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	0	0	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Synaptic_ Network	16	Network	Shared_Object_Synaptic_Network,  PKC,  PLA2,   PLCbeta,  Gq,  MAPK,   Ras,  EGFR,  Sos,   PLC_g,  CaMKII,  CaM,   PP1,  PP2B,  PKA,   AC,  CaRegulation
This model is an annotated version of the synaptic signaling network. The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated. Bhalla US Biophys J. 2002 Aug;83(2):740-52 Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62

CaMCa4-CaNAB acting as a Molecule in  Synaptic_Network Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaMCa4-CaNAB	Synaptic_ Network Accession No. : 16	PP2B Pathway No. : 83	0	1000	No
Ca4.CaM.Ca4.CaNAB. This form is fullly loaded with Ca. Its activity is assumed to be the same as the lower Ca-bound forms of CaM.Ca4.CaNAB.

CaMCa4-CaNAB acting as a Summed Molecule in  Synaptic_Network Network

Accession Name	Pathway Name	Target	Input
Synaptic_ Network Accession No. : 16	Shared_Object_ Synaptic_ Network Pathway No. : 70	CaM(Ca)n-CaNAB	CaMCa4-CaNAB CaMCa3-CaNAB CaMCa2-CANAB
This pool sums the levels of the CaM.Ca2.CaNAB, CaM.Ca3.CaNAB and CaM.Ca4.CaNAB pools.

CaMCa4-CaNAB acting as a Product in a reaction in  Synaptic_Network 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
CaMCa4-bind-CaNA B	Synaptic_ Network Accession No. : 16	PP2B Pathway No. : 83	600 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0017(uM)	-	Substrate CaM-Ca4 CaNAB-Ca4 Product CaMCa4-CaNAB
This step is the starting point for calculating all the CaM-binding steps to CaNAB-Ca4. The calculation goes like this: From Stemmer and Klee 1994 Biochem 33 6859-6866 we have rates for Ca binding to CaM.Ca4.CaN. From detailed balance (Kd must be 1 around a loop) we can set ratios of Kds for CaMCa3 binding to CaN, and CaM-Ca2 binding to CaN. Thus those rates can come once we know the Kd for the current reaction of CaMCa4 binding to CaN. We'll ignore the Ca binding steps to CaM.Ca4.CaN since the reactions around the remaining part of the loop will settle pretty fast to the same levels. Finally, we estimate the kf=0.001 here from a series of simulations matching the curves in Stemmer and Klee.