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Molecule Parameter List for Capped

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

*Capped* 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	1	0

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.

Capped acting as a Molecule in CaMKII Network

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

Capped 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

Capped 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_T305	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	1.27325	10	0	explicit E-S complex	Substrate Autonomous Product Capped
This enzyme also represents an intra-holoenzyme reaction. So it is not really treated as an enzyme in Holme's model, more like a probability of reaction that scales according to the number of active CaMKII neighboring subunits. Here we approximate it as an enzyme rate limited by the k1=0.1 step, no back reaction, and with a scaling from Total_CaMKII such that the effective forward rate will simply be the fraction of CaMKII that are active, times 1/10 for nearest neigbors, times k1.

Capped 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
dephosph_T305	CaMKII Accession No. : 33	CaMKII Pathway No. : 174	0.01 (s^-1)	0 (s^-1)	-	-	Substrate Capped Product Autonomous
This is treated as a separate reaction because it is independent of the CaMKII concentration or activation state, unlike the forward reaction in the Holmes paper. Holmes tries a range of rates for this step, and says it doesn't matter much.

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