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Molecule Parameter List for CaM-PSD

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

CaM-PSD 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	1	2	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
AMPAR_traff_ model1	60	Network	Shared_Object_AMPAR_traff_model1,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD,   PKA,  AC,  AMPAR,   AMPAR_memb
This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable.

CaM-PSD acting as a Molecule in  AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM-PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	26.3333	0.01	No
There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels.

CaM-PSD acting as a Product of an Enzyme in  AMPAR_traff_model1 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKC-active  / PKC-phosph-ng-Ca M_ PSD	AMPAR_traff_ model1 Accession No. : 60	Shared_Object_ AMPAR_traff_ model1 Pathway No. : 244	28.5956	0.35	4	explicit E-S complex	Substrate neurogranin-CaM_ PSD Product CaM-PSD neurogranin*_ PSD
Rates are 60% those of PKC-phosph-neurogranin. See Huang et al ABB 305:2 570-580 1993

CaM-PSD acting as a Substrate in a reaction in  AMPAR_traff_model1 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	CaM-TR2-bind-Ca- PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	72 (uM^-2 s^-1)	72 (s^-1)	Kd(af) = 1(uM)	-	Substrate Ca-PSD Ca-PSD CaM-PSD Product CaM-TR2-Ca2-PSD
	Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !)....
2	neurogranin-bind -CaM_ PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	0.3 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 3.3333(uM)	-	Substrate CaM-PSD neurogranin_PSD Product neurogranin-CaM_ PSD
	Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987