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Molecule Parameter List for Trapped-T286

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

Trapped-T286 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	1	2	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
CaMKII	33	Network	Shared_Object_CaMKII,  CaM,  CaMKII,   CaN
This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in William R. Holmes J Comput Neurosci. (2000) 8(1):65-85. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original.

Trapped-T286 acting as a Molecule in  CaMKII Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Trapped-T286	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	0	0.1309	No

Trapped-T286 acting as a Summed Molecule in  CaMKII Network

Accession Name	Pathway Name	Target	Input
CaMKII Accession No. : 33	CaMKII Pathway No. : 174	Tot-active-CaMKII	CaMKII-CaMCa4 Trapped-T286 Capped Autonomous

Trapped-T286 acting as a Product of an Enzyme in  CaMKII Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
Tot-active-CaMKI I  / phosph_T286	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	0.254651	10	0	explicit E-S complex	Substrate CaMKII-CaMCa4 Product Trapped-T286
This enzyme represents an intra-holoenzyme reaction from one active subunit to its neighbor. k1 is now in units of 1/sec. The Km, Ratio and Vmax terms are pretty meaningless. The enzyme really is there just to represent the forward rate of 0.5 from CaMKII-CaMCa4 to Trapped-T285. We have a high k3 so that the reac is limited only by k1. The enzyme itself does not have much purpose other than to allow scaling of the overall rate by the proportion of adjacent molecules in the appropriate state.

Trapped-T286 acting as a Substrate in a reaction in  CaMKII 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	Dephosph_ trapped_T286	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	0.003 (s^-1)	0 (s^-1)	-	-	Substrate Trapped-T286 Product CaMKII-CaMCa4
	This rate is for the back reaction for the step represented here as a separate enzyme, but by Holmes as a single reversible reaction. Here it is treated as separate because the forward reaction is dependent on activity levels of the CaMKII, whereas the back reaction is not. Holmes tries a range of values for this back-reaction and says that it doesn't matter much.
2	Autonomous_ lose_CaMCa4	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	0.02 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate Trapped-T286 Product Autonomous CaMCa4
	Holmes says that this rate is variable, and depends on Ca conc. It is 0.1 when [Ca] = 10 nM, and 0.00355/sec when [Ca] is 1.0 For our purposes, we assume a good steady approx to this rate is 0.02.

Trapped-T286 acting as a Product in a reaction in  CaMKII 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
Autonomous-bind- CaMCa4	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	33.2998 (uM^-1 s^-1)	0 (s^-1)	-	-	Substrate Autonomous CaMCa4 Product Trapped-T286