| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | Ras-act-craf | Shared_Object_
Synaptic_
Network
Pathway No. 70 | 24
(uM^-1 s^-1) | 0.5
(s^-1) | Kd(bf) = 0.0208(uM) | - | Substrate:
craf-1*
GTP-Ras
Products:
Raf-GTP-Ras*
|
| Assume binding is fast and limited only by available Ras*. So kf = kb/[craf-1] If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 * 6e5) = 8.3e-6 Later: Raise it by 10 X to about 1e-4, giving a Kf of 60 for Kb of 0.5 and a tau of approx 2 sec. Based on: Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414. Also see Koide et al 1993 PNAS USA 90(18):8683-8686 | | 2 | remove_glu | Shared_Object_
Synaptic_
Network
Pathway No. 70 | 500
(s^-1) | 1000
(s^-1) | Keq = 2(uM) | 0.001sec | Substrate:
Glu
Products:
synapse
|
| This reaction doubles for arrival as well as removal of glu from the synapse. Assume tau for removal of glu is ~1 msec. We know that diffusion time for arrival of glu from presynaptic side is < 50 usec. Most of the actual synaptic delay has to do with binding to the receptors. | | 3 | PKC-act-by-Ca | PKC
Pathway No. 71 | 0.6
(uM^-1 s^-1) | 0.5
(s^-1) | Kd(bf) = 0.8333(uM) | - | Substrate:
PKC-cytosolic
Ca
Products:
PKC-Ca
|
| This Kd is a straightforward result from the Schaechter and Benowitz 1993 J Neurosci 13(10):4361 curves. The time-course is based on the known rapid activation of PKC and also the fact that Ca association with proteins is typically quite fast. My guess is that this tau of 2 sec is quite conservative and the actualy rate may be much faster. The parameter is quite insensitive for most stimuli. | | 4 | PKC-act-by-DAG | PKC
Pathway No. 71 | 0.008
(uM^-1 s^-1) | 8.6348
(s^-1) | Kd(bf) = 1079.377(uM) | - | Substrate:
DAG
PKC-Ca
Products:
PKC-Ca-DAG
|
| Ca.PKC interaction with DAG is modeled by this reaction. Kf based on Shinomura et al PNAS 88 5149-5153 1991 and Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and uses the constraining procedure referred to in the general notes for PKC. | | 5 | PKC-Ca-to-memb | PKC
Pathway No. 71 | 1.2705
(s^-1) | 3.5026
(s^-1) | Keq = 2.7569(uM) | 0.21sec | Substrate:
PKC-Ca
Products:
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. | | 6 | PKC-DAG-to-memb | PKC
Pathway No. 71 | 1
(s^-1) | 0.1
(s^-1) | Keq = 0.1(uM) | 0.909sec | Substrate:
PKC-Ca-DAG
Products:
PKC-DAG-memb*
|
| membrane translocation step for Ca.DAG.PKC complex. Rates constrained from Shinomura et al 1991 PNAS 88:5149-5153 and Schaechter and Benowitz 1993 J Neurosci 13(10):4361 as derived in the references cited in PKC general notes. | | 7 | PKC-act-by-Ca-AA | PKC
Pathway No. 71 | 0.0012
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 83.3333(uM) | - | Substrate:
PKC-Ca
AA
Products:
PKC-Ca-AA*
|
| Ca-dependent AA activation of PKC. Note that this step combines the AA activation and also the membrane translocation. From Schaechter and Benowitz 1993 J Neurosci 13(10):4361 | | 8 | PKC-act-by-DAG-A
A | PKC
Pathway No. 71 | 2
(s^-1) | 0.2
(s^-1) | Keq = 0.1(uM) | 0.455sec | Substrate:
PKC-DAG-AA
Products:
PKC-DAG-AA*
|
| Membrane translocation step for PKC-DAG-AA complex. Rates from matching concentration-effect data in our two main references: Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and Shinomura et al 1988 PNAS 88: 5149-5153 | | 9 | PKC-basal-act | PKC
Pathway No. 71 | 1
(s^-1) | 50
(s^-1) | Keq = 50(uM) | 0.02sec | Substrate:
PKC-cytosolic
Products:
PKC-basal*
|
| Basal activity of PKC is quite high, about 10% of max. See Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and Shinomura et al 1991 PNAS 88:5149-5153. This is partly due to basal levels of DAG, AA and Ca, but even when these are taken into account (see the derivations as per the PKC general notes) there is a small basal activity still to be accounted for. This reaction handles it by giving a 2% activity at baseline. | | 10 | PKC-act-by-AA | PKC
Pathway No. 71 | 0.0001
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 833.3333(uM) | - | Substrate:
AA
PKC-cytosolic
Products:
PKC-AA*
|
| AA stimulates PKC activity even at rather low Ca. Schaechter and Benowitz 1993 J Neurosci 13(10):4361 Note that this one reaction combines the initial interaction and also membrane translocation. | | 11 | PKC-n-DAG | PKC
Pathway No. 71 | 0.0006
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 166.6667(uM) | - | Substrate:
PKC-cytosolic
DAG
Products:
PKC-DAG
|
| Binding of PKC to DAG, non-Ca dependent. Kf based on Shinomura et al PNAS 88 5149-5153 1991 Tau estimated as fast and here it is about the same time-course as the formation of DAG so it will not be rate-limiting. | | 12 | PKC-n-DAG-AA | PKC
Pathway No. 71 | 0.018
(uM^-1 s^-1) | 2
(s^-1) | Kd(bf) = 111.1111(uM) | - | Substrate:
PKC-DAG
AA
Products:
PKC-DAG-AA
|
| This is one of the more interesting steps. Mechanistically it does not seem necessary at first glance. Turns out that one needs this step to quantitatively match the curves in Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and Shinomura et al 1991 PNAS 88:5149-5153. There is a synergy between DAG and AA activation even at low Ca levels, which is most simply represented by this reaction. Tau is assumed to be fast. Kd comes from matching the experimental curves. | | 13 | PLA2-Ca-act | PLA2
Pathway No. 72 | 1
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.1(uM) | - | Substrate:
PLA2-cytosolic
Ca
Products:
PLA2-Ca*
|
| Direct activation of PLA2 by Ca. From Leslie and Channon BBA 1045 (1990) 261-270 fig6 pp267. | | 14 | PIP2-PLA2-act | PLA2
Pathway No. 72 | 0.0012
(uM^-1 s^-1) | 0.5
(s^-1) | Kd(bf) = 416.6667(uM) | - | Substrate:
temp-PIP2
PLA2-cytosolic
Products:
PIP2-PLA2*
|
| Activation of PLA2 by PIP2. From Leslie and Channon 1990 BBA 1045:261 the stimulation of PLA2 activity by high PIP2 is 7x. In this model we don't really expect any PIP2 stimulus. | | 15 | PIP2-Ca-PLA2-act | PLA2
Pathway No. 72 | 0.012
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 8.3333(uM) | - | Substrate:
temp-PIP2
PLA2-Ca*
Products:
PIP2-Ca-PLA2*
|
| Synergistic activation of PLA2 by Ca and PIP2. Again from Leslie and Channon 1990 BBA 1045:261 | | 16 | DAG-Ca-PLA2-act | PLA2
Pathway No. 72 | 0.003
(uM^-1 s^-1) | 4
(s^-1) | Kd(bf) = 1333.3333(uM) | - | Substrate:
DAG
PLA2-Ca*
Products:
DAG-Ca-PLA2*
|
| Synergistic activation of PLA2 by Ca and DAG. Based on Leslie and Channon 1990 BBA 1045:261 The Kd is rather large and may reflect the complications in measuring DAG. For this model it is not critical since DAG is held fixed. | | 17 | Degrade-AA | PLA2
Pathway No. 72 | 0.4
(s^-1) | 0
(s^-1) | - | - | Substrate:
AA
Products:
APC
|
| Degradation pathway for AA. APC is a convenient buffered pool to dump it back into, though the actual metabolism is probably far more complex. For the purposes of the full model we use a rate of degradation of 0.4/sec to give a dynamic range of AA comparable to what is seen experimentally. Wijkander and Sundler 1991 Eur J Biochem 202:873 Leslie and Channon 1990 BBA 1045:261 | | 18 | PLA2*-Ca-act | PLA2
Pathway No. 72 | 6
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0167(uM) | - | Substrate:
PLA2*
Ca
Products:
PLA2*-Ca
|
| Nemenoff et al 1993 JBC 268:1960 report a 2X to 4x activation of PLA2 by MAPK, which seems dependent on Ca as well. This reaction represents this activation. Rates are scaled to give appropriate fold activation. | | 19 | dephosphorylate-
PLA2* | PLA2
Pathway No. 72 | 0.17
(s^-1) | 0
(s^-1) | - | - | Substrate:
PLA2*
Products:
PLA2-cytosolic
|
| Dephosphorylation reaction to balance MAPK phosphorylation of PLA2. This is probably mediated by PP2A. Rates determined to keep the balance of phosphorylated and non-phosphorylated PLA2 reasonable. The constraining factor is the fold activation of PLA2 by MAPK. | | 20 | Act-PLC-Ca | PLCbeta
Pathway No. 73 | 3
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.3333(uM) | - | Substrate:
Ca
PLC
Products:
PLC-Ca
|
| Affinity for Ca = 1uM without AlF, 0.1 with: from Smrcka et al science 251 pp 804-807 1991 Assigned affinity to a Kd of 0.333 to maintain detailed balance. |
and 
color.
indicates that ordering is done according to ascending or descending order.