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Name Notes Model

Molecule Parameter List for Nucleotides

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

Nucleotides 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	0	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
mkp1_feedback_ effects	4	Network	Shared_Object_mkp1_feedback_effects,  Sos,  PKC,   MAPK,  PLA2,  Ras,   PDGFR
This is a network involving the MAPK-PKC feedback loop with input from the PDGFR in the synapse. The distinctive feature of this model is that it includes MKP-1 induction by MAPK, and the consequent inhibitory regulation of MAPK and the feedback loop. Lots of interesting dynamics arise from this. This link provides supplementary material for the paper Bhalla US et al. Science (2002) 297(5583):1018-23. In the form of several example simulations and demos for the figures in the paper.

Nucleotides acting as a Molecule in  mkp1_feedback_effects Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Nucleotides	mkp1_feedback_ effects Accession No. : 4	MAPK Pathway No. : 35	0.1	200	Yes
Infinite supply assumed for formation of mRNA.

Nucleotides acting as a Substrate for an Enzyme in  mkp1_feedback_effects Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
nuc_MAPK*  / act_ transcription	mkp1_feedback_ effects Accession No. : 4	MAPK Pathway No. : 35	4.00002	0.0008	4	explicit E-S complex	Substrate Nucleotides Product MKP1-RNA
This is a 'black box' representation of a lot of steps. Constraint provided by determining rate of formation of MKP-1.

Nucleotides acting as a Substrate in a reaction in  mkp1_feedback_effects 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
Basal_ transcription	mkp1_feedback_ effects Accession No. : 4	MAPK Pathway No. : 35	0 (s^-1)	0 (s^-1)	-	-	Substrate Nucleotides Product MKP1-RNA
This is just a basal rate of MKP-1 transcription scaled to give reasonable basal levels of the MKP-1.