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Name Notes Model

Molecule Parameter List for IR*

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

IR* 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	1	1	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
simple_AMPAR_ traff_model2	61	Network	Shared_Object_simple_AMPAR_traff_model2,  Membrane,  Internal
This is a highly simplified model of the AMPAR trafficking cycle that exhibits bistability. It is model 2 from Hayer and Bhalla, PLoS 2005. Its main purpose it to illustrate how the bistability arises.

IR* acting as a Molecule in  simple_AMPAR_traff_model2 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
IR*	simple_AMPAR_ traff_model2 Accession No. : 61	Internal Pathway No. : 256	0	0.09	No

IR* acting as a Substrate for an Enzyme in  simple_AMPAR_traff_model2 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKA-active  / internal-PKA-act [1]	simple_AMPAR_ traff_model2 Accession No. : 61	Shared_Object_ simple_AMPAR_ traff_model2 Pathway No. : 254	3.74995	6	4	explicit E-S complex	Substrate IR* Product IR**
Note that Km is halved from the detailed model, as the reaction represents enzyme activity on 2 subunits.

IR* acting as a Product of an Enzyme in  simple_AMPAR_traff_model2 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKA-active  / internal-PKA-act	simple_AMPAR_ traff_model2 Accession No. : 61	Shared_Object_ simple_AMPAR_ traff_model2 Pathway No. : 254	3.74995	6	4	explicit E-S complex	Substrate IR Product IR*
Note that Km is halved from the main model, from 7.5 to 3.75. This is because here we lump two subunits into one, thus double the effective substrate conc that the enzyme must deal with. We thank an anonymous reviewer for pointing this out.

IR* acting as a Substrate in a reaction in  simple_AMPAR_traff_model2 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
degradation	simple_AMPAR_ traff_model2 Accession No. : 61	Shared_Object_ simple_AMPAR_ traff_model2 Pathway No. : 254	0 (s^-1)	0 (s^-1)	Not applicable**	-	Substrate IR* Product Bulk_AMPAR

** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration