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Molecule Parameter List for PKC-Ca-memb*

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
PKC-Ca-memb* participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1100011

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
PKC_turnover26Pathway
PKC 
This model is a superset of the PKC model presented in Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. The current version includes PKC turnover. This version includes the stimulating pools Ca, AA and DAG as well as the PKC activity within the synaptic signaling pathway since it is meant to be a self-contained pathway model rather than part of a network.

PKC-Ca-memb* acting as a Molecule in  
PKC_turnover Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
PKC-Ca-memb*PKC_turnover
Accession No. : 26
PKC
Pathway No. : 138
01000No
This is the direct Ca-stimulated activity of PKC.

PKC-Ca-memb* acting as a Summed Molecule in  
PKC_turnover Network
Accession NamePathway NameTargetInput
PKC_turnover
Accession No. : 26
PKC
Pathway No. : 138
PKC-activePKC-DAG-AA*
PKC-Ca-memb*
PKC-Ca-AA*
PKC-DAG-memb*
PKC-basal*
PKC-AA*
This is the total active PKC. It is the sum of the respective activities of PKC-basal* PKC-Ca-memb* PKC-DAG-memb* PKC-Ca-AA* PKC-DAG-AA* PKC-AA* I treat PKC here in a two-state manner: Either it is in an active state (any one of the above list) or it is inactive. No matter what combination of stimuli activate the PKC, I treat it as having the same activity. The scaling comes in through the relative amounts of PKC which bind to the respecive stimuli. The justification for this is the mode of action of PKC, which like most Ser/Thr kinases has a kinase domain normally bound to and blocked by a regulatory domain. I assume that all the activators simply free up the kinase domain. A more general model would incorporate a different enzyme activity for each combination of activating inputs, as well as for each substrate. The current model seems to be a decent and much simpler approximation for the available data. One caveat of this way of representing PKC is that the summation procedure assumes that PKC does not saturate with its substrates. If this assumption fails, then the contributing PKC complexes would experience changes in availability which would affect their balance. Given the relatively low percentage of PKC usually activated, and its high throughput as an enzyme, this is a safe assumption under physiological conditions.

PKC-Ca-memb* acting as a Substrate in a reaction in  
PKC_turnover 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.
NameAccession NamePathway NameKfKbKdtauReagents
PKC-Ca_downregPKC_turnover
Accession No. : 26
PKC
Pathway No. : 138
0
(s^-1)
0
(s^-1)
--Substrate
PKC-Ca-memb*

Product
degraded-PKC
Typical rate for downreg is 6 hours. The downregulation appears to occur by a suicide mechanism in which the active PKC gets ubiquinated and degraded. The reference for this is Lu Z, Liu D, Hornia A, Devonish W, Pagana M and Foster DA 1998 Mol Cell Biol 18(2):839-845. I assume all activated forms of PKC downreg at the same rate.

PKC-Ca-memb* acting as a Product in a reaction in  
PKC_turnover 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.
NameAccession NamePathway NameKfKbKdtauReagents
PKC-Ca-to-membPKC_turnover
Accession No. : 26
PKC
Pathway No. : 138
1.2705
(s^-1)
3.5026
(s^-1)
Keq = 2.7569(uM)0.21secSubstrate
PKC-Ca

Product
PKC-Ca-memb*
Membrane translocation is a standard step in PKC activation. It also turns out to be necessary to replicate the curves from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and Shonomura et al 1991 PNAS 88:5149-5153. These rates are constrained by matching the curves in the above papers and by fixing a rather fast (sub-second) tau for PKC activation.



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