| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | Trimerize-G | Gq
Pathway No. 74 | 6
(uM^-1 s^-1) | 0
(s^-1) | - | - | Substrate:
G*GDP
BetaGamma
Products:
G-GDP
|
| kf == kg3 = 1e-5 /cell/sec. As usual, there is no back-reaction kb = 0 | | 2 | Shc_bind_
Sos.Grb2 | Sos
Pathway No. 78 | 0.5
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.2(uM) | - | Substrate:
Sos.Grb2
SHC*
Products:
Shc*.Sos.Grb2
|
| Sasaoka et al JBC 269:51 pp 32621 1994, table on pg 32623 indicates that this pathway accounts for about 50% of the GEF activation. (88% - 39%). Error is large, about 20%. Fig 1 is most useful in constraining rates. Chook et al JBC 271:48 pp 30472, 1996 say that the Kd is 0.2 uM for Shc binding to EGFR. The Kd for Grb direct binding is 0.7, so we'll ignore it. | | 3 | 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. | | 4 | Release-C2 | PKA
Pathway No. 84 | 60
(s^-1) | 18
(uM^-1 s^-1) | Kd(cb) = 0.3(uM) | - | Substrate:
R2C-cAMP4
Products:
PKA-active
R2-cAMP4
|
| Second catalytic subunit is now released. | | 5 | Release-C1 | PKA
Pathway No. 84 | 60
(s^-1) | 18
(uM^-1 s^-1) | Kd(cb) = 0.3(uM) | - | Substrate:
R2C2-cAMP4
Products:
PKA-active
R2C-cAMP4
|
| The complex starts to dissociate and release the catalytic subunit C. This has to be fast, as the activation of PKA by cAMP is also fast. | | 6 | RecLigandBinding | Gq
Pathway No. 74 | 16.8
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 0.5952(uM) | - | Substrate:
mGluR
Glu
Products:
Rec-Glu
|
| From Martin et al FEBS Lett 316:2 191-196 1993 we have Kd = 600 nM Assuming kb = 10/sec, we get kf = 10/(0.6 uM * 6e5) = 2.8e-5 1/sec/# The off time for Glu seems pretty slow: Nicoletti et al 1986 PNAS 83:1931-1935 and Schoepp and Johnson 1989 J Neurochem 53 1865-1870 indicate it is at least 30 sec. Here we are a little faster because this is only a small part of the off rate, the rest coming from the Rec-Gq complex. | | 7 | Rec-Glu-bind-Gq | Gq
Pathway No. 74 | 0.006
(uM^-1 s^-1) | 0.0001
(s^-1) | Kd(bf) = 0.0167(uM) | - | Substrate:
G-GDP
Rec-Glu
Products:
Rec-Glu-Gq
|
| This is the k1-k2 equivalent for enzyme complex formation in the binding of Rec-Glu to Gq. See Fay et al Biochem 30 5066-5075 1991. Closer reading of Fay et al suggests that kb <= 0.0001, so kf = 1e-8 by detailed balance. This reaction appears to be neglible. | | 8 | Rec-bind-Gq | Gq
Pathway No. 74 | 0.6
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 1.6667(uM) | - | Substrate:
G-GDP
mGluR
Products:
Rec-Gq
|
| From Berstein et al 1992 JBC 267(12):8081-8088 we know that 15-40% of Gq binds, GTP_gamma_S. Also about 20-30% of Gq is bound to GTP. To get to these values the receptor-Gq amount should be similar. These rates are designed to give that steady state with a fast tau of 1 sec. | | 9 | Ras-intrinsic-GT
Pase | Ras
Pathway No. 76 | 0.0001
(s^-1) | 0
(s^-1) | - | - | Substrate:
GTP-Ras
Products:
GDP-Ras
|
| This is extremely slow (kf = 1e-4), but it is significant as so little GAP actually gets complexed with it that the total GTP turnover rises only by 2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and Eccleston et al JBC 268(36) 27012-27019 There is no back reaction as we assume this to be a regular irreversible Michaelis-Menten zeroth order hydrolysis. | | 10 | 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 | | 11 | PLC-Gq-bind-Ca | PLCbeta
Pathway No. 73 | 30
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0333(uM) | - | Substrate:
Ca
PLC-Gq
Products:
PLC-Ca-Gq
|
| this step has a high affinity of 0.1 uM for Ca, from Smrcka et al 1991 Science 251:804-807 so kf /kb = 1/6e4 = 1.666e-5:1. See the Act-PLC-by-Gq reaction. Raised kf to 5e-5 based on match to conc-eff curves from Smrcka et al. | | 12 | PLC-bind-Gq | PLCbeta
Pathway No. 73 | 2.52
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.3968(uM) | - | Substrate:
PLC
G*GTP
Products:
PLC-Gq
|
| this binding does not produce active PLC. This step was needed to implement the described (Smrcka et al) increase in affinity for Ca by PLC once Gq was bound. The kinetics are the same as the binding step for Ca-PLC to Gq. Kd is constrained by detailed balance. | | 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 | 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. | | 15 | 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. | | 16 | 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. | | 17 | 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. | | 18 | 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. | | 19 | 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. | | 20 | 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 |
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