| |
Name | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | DAG | Pathway | 11.66 | 0 | No | - |
| | Baseline in model is 11.661 uM. DAG is pretty nasty to estimate. In this model we just hold it fixed at this baseline level. Data sources are many and varied and sometimes difficult to reconcile. Welsh and Cabot 1987 JCB 35:231-245: DAG degradation Bocckino et al JBC 260(26):14201-14207: hepatocytes stim with vasopressin: 190 uM. Bocckino et al 1987 JBC 262(31):15309-15315: DAG rises from 70 to 200 ng/mg wet weight, approx 150 to 450 uM. Prescott and Majerus 1983 JBC 258:764-769: Platelets: 6 uM. Also see Rittenhouse-Simmons 1979 J Clin Invest 63. Sano et al JBC 258(3):2010-2013: Report a nearly 10 fold rise. Habenicht et al 1981 JBC 256(23)12329-12335: 3T3 cells with PDGF stim: 27 uM Cornell and Vance 1987 BBA 919:23-36: 10x rise from 10 to 100 uM. Summary: I see much lower rises in my PLC models, but the baseline could be anywhere from 5 to 100 uM. I have chosen about 11 uM based on the stimulus -response characteristics from the Schaechter and Benowitz paper and the Shinomura et al papers. |
| 2 | AA | Pathway | 5.5 | 0 | No | - |
| | Arachidonic Acid. This messenger diffuses through membranes as well as cytosolically, has been suggested as a possible retrograde messenger at synapses. Based on simulations the AA settles to around 5.5 uM under resting conditions. |
| 3 | PKC-cytosolic | Pathway | 1 | 0 | No | - |
| | Marquez et al J. Immun 149,2560(92) est 1e6/cell for chromaffin cells Kikkawa et al 1982 JBC 257(22):13341 have PKC levels in brain at about 1 uM. The cytosolic form is the inactive PKC. This is really a composite of three isoforms: alpha, beta and gamma which have slightly different properties and respond to different combinations of Ca, AA and DAG. |
| 4 | PKC-RNA | Pathway | 1 | 0 | Yes | - |
| | Just a unity concentration for convenience. The rate limiting step is the PKC-synthesis reaction. |
| 5 | Ca | Pathway | 0.08 | 0 | No | - |
| | This calcium pool is treated as being buffered to a steady 0.08 uM, which is the resting level. |
| 6 | PKC-Ca | Pathway | 0 | 0 | No | - |
| | This intermediate is strongly indicated by the synergistic activation of PKC by combinations of DAG and Ca, as well as AA and Ca. PKC by definition also has a direct Ca-activation, to which this also contributes. |
| 7 | PKC-DAG-AA | Pathway | 0 | 0 | No | - |
| | Complex of PKC, DAG and AA giving rise to synergistic activation of PKC by DAG and AA at resting Ca. |
| 8 | PKC-Ca-DAG | Pathway | 0 | 0 | No | - |
| | This is the active PKC form involving Ca and DAG. It has to translocate to the membrane. |
| 9 | PKC-DAG-AA* | Pathway | 0 | 0 | No | - |
| | Membrane translocated form of PKC-DAG-AA complex. |
| 10 | PKC-Ca-AA* | Pathway | 0 | 0 | No | - |
| | Membrane bound and active complex of PKC, Ca and AA. |
| 11 | PKC-Ca-memb* | Pathway | 0 | 0 | No | - |
| | This is the direct Ca-stimulated activity of PKC. |
| 12 | PKC-DAG-memb* | Pathway | 0 | 0 | No | - |
| | Active, membrane attached form of Ca.DAG.PKC complex. |
| 13 | PKC-basal* | Pathway | 0 | 0 | No | - |
| | This is the basal PKC activity which contributes about 2% to the maximum. |
| 14 | PKC-AA* | Pathway | 0 | 0 | No | - |
| | This is the membrane-bound and active form of the PKC-AA complex. |
| 15 | PKC-DAG | Pathway | 0 | 0 | No | - |
| | This is a DAG-bound intermediate used in synergistic activation of PKC by DAG and AA. |
| 16 | PKC-substrate | Pathway | 0 | 0 | No | - |
| | This molecule represents a generic PKC substrate. |
| 17 | PKC-substrate* | Pathway | 0 | 0 | No | - |
| | This is the phosphorylated form of a generic PKC substrate. |
| 18 | degraded-PKC | Pathway | 0 | 0 | Yes | - |
| | This represents the ubiquitination and eventual removal of the PKC. See Lu et al 1998 Mol Cell Biol 18(2):839-845 |
| 19 | PKC-active | Pathway | 0 | 0 | No | 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. |
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