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Name Notes Model

Molecule Parameter List for CaM_dash_GEF

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_dash_GEF 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	1	0	0	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Differential syn thesis of mRNA	95	Network	kinetics,  compartment_1,  compartment_2
The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway.

CaM_dash_GEF acting as a Molecule in  Differential synthesis of mRNA Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM_dash_GEF	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0	1000	No
See Farnsworth et al Nature 376 524-527 1995

CaM_dash_GEF acting as an Enzyme in  Differential synthesis of mRNA Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
CaM_dash_GEF / CaM_dash_GEF_ dash_act_dash_ ras	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.5051	0.02	4	explicit E-S complex	Substrate GDP_dash_Ras Product GTP_dash_Ras
Kinetics same as GEF-bg_act-ras

CaM_dash_GEF acting as a Product in a reaction in  Differential synthesis of mRNA 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
CaM_dash_bind_ dash_GEF	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	60 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0167(uM)	-	Substrate CaM_dash_Ca4 inact_dash_GEF Product CaM_dash_GEF
We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995