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Molecule Parameter List for PKC-active | 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-active 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 | 3 | 0 | 0 | 0 | 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. |
PKC-active acting as a Molecule in mkp1_feedback_effects Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PKC-active | mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 0.02 | 1000 | No | | 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-active acting as a Summed Molecule in mkp1_feedback_effects Network
| Accession Name | Pathway Name | Target | Input | mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | PKC-active | PKC-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-active acting as an Enzyme in mkp1_feedback_effects Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PKC-active /
PKC-act-raf
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 66.6667 | 4 | 4 | explicit E-S complex | Substrate
craf-1
Product
craf-1*
| | | Rate constants are from Chen SJ, Klann E, Gower MC, Powell CM, Sessoms JS, Sweatt JD. (1993) Biochemistry 32(4):1032-1039. k3 = 4 Km for this substrate is trickier. Specific substrates are in the uM range, so we use a higher Km here. This may be too conservative in which case PKC would have a still higher effect on raf. The presence of this phosphorylation and activation step is from Kolch W, Heidecker G, Kochs G, Hummel R, Vahidi H, Mischak H, Finkenzeller G, Marme D, Rapp UR. (1993) Nature 364(6434):249-52. | | 2 | PKC-active /
PKC-inact-GAP
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 66.6667 | 25 | 4 | explicit E-S complex | Substrate
GAP
Product
GAP*
| | | Rate constants are generic PKC rates. This reaction inactivates GAP. The reaction is from Boguski MS and McCormick F (1993) Nature 366(6456):643-54. The phosphorylation Vmax is 6x higher to account for balance of GDP-Ras:GDP-Ras. | | 3 | PKC-active /
PKC-act-GEF
| mkp1_feedback_
effects
Accession No. : 4 | Shared_Object_
mkp1_feedback_
effects
Pathway No. : 32 | 66.6667 | 4 | 4 | explicit E-S complex | Substrate
inact-GEF
Product
GEF*
| | | Rate constants are generic PKC rates. See Chen SJ, Klann E, Gower MC, Powell CM, Sessoms JS, Sweatt JD. (1993) Biochemistry 32(4):1032-9. This reaction activates GEF. Gives >= 2X stim of ras, and a 2X stim of MAPK over amount from direct phosph of c-raf. Note that it is a push-pull reaction, and also get effect through phosph and inact of GAPs. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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