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Ajay_Bhalla_
2004_PKM_Tuning
PKC
Shared_Object_
Ajay_Bhalla_
2004_PKM_tuning
PLA2
PLCbeta
Gq
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MAPK
Ras
EGFR
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PLC_g
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Reaction List for pathway Gq (Pathway Number 316)

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 reactions is not considered.
  Name KfKbKdtauSubstrateProduct
1 Activate-Gqkf
(s^-1)
0
(uM^-2 s^-1)
--Rec-Glu-Gq
G*GTP
BetaGamma
Rec-Glu
  This is the kcat==k3 stage of the Rec-Glu ezymatic activation of Gq. From Berstein et al actiation is at .35 - 0.7/min From Fay et al Biochem 30 5066-5075 1991 kf = .01/sec From Nakamura et al J physiol Lond 474:1 35-41 1994 see time courses. Also (Berstein) 15-40% of gprot is in GTP-bound form on stim.
2 Antag-bind-Rec-G
q
kf
(uM^-1 s^-1)
0.01
(s^-1)
Kd(bf) = 0.0002(uM)-Rec-Gq
mGluRAntag
Blocked-rec-Gq
  The rate consts give a total binding affinity of only
3 Basal-Act-Gkf
(s^-1)
0
(uM^-1 s^-1)
--G-GDP
G*GTP
BetaGamma
  kf = kg1 = 0.01/sec, kb = 0. This is the basal exchange of GTP for GDP.
4 Glu-bind-Rec-Gqkf
(uM^-1 s^-1)
0.1
(s^-1)
Kd(bf) = 0.006(uM)-Glu
Rec-Gq
Rec-Glu-Gq
  From Fay et al kb3 = kb = 1.06e-3 which is rather slow. k+1 = kf = 2.8e7 /M/sec= 4.67e-5/sec use 5e-5. However, the Kd from Martin et al may be more appropriate, as this is Glu not the system from Fay. kf = 2.8e-5, kb = 10 Let us compromise. since we have the Fay model, keep kf = k+1 = 2.8e-5. But kb (k-3) is .01 * k-1 from Fay. Scaling by .01, kb = .01 * 10 = 0.1
5 Inact-Gkf
(s^-1)
0
(s^-1)
--G*GTP
G*GDP
  From Berstein et al JBC 267:12 8081-8088 1992, kcat for GTPase activity of Gq is only 0.8/min
6 Rec-bind-Gqkf
(uM^-1 s^-1)
1
(s^-1)
Kd(bf) = 1.6667(uM)-G-GDP
mGluR
Rec-Gq
  Lets try out the same kinetics as the Rec-Glu-bind-Gq This is much too forward. We know that the steady-state amount of Rec-Gq should be 40% of the total amount of receptor. This is for a different receptor, still we can try to match the value. kf = 1e-6 and kb = 1 give 0.333:0.8 which is pretty close.
7 Rec-Glu-bind-Gqkf
(uM^-1 s^-1)
0.0001
(s^-1)
Kd(bf) = 0.0167(uM)-G-GDP
Rec-Glu
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. kf = 5e-5 which is nearly the same as calculated by Fay et al. (4.67e-5) kb = .04 June 1996: 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 RecLigandBindingkf
(uM^-1 s^-1)
10
(s^-1)
Kd(bf) = 0.5952(uM)-mGluR
Glu
Rec-Glu
  kf = kf from text = 1e7 / M / sec = 10 /uM/sec = 10 / 6e5 / # / sec = 1.67e-5 kb = kr from text = 60 / sec Note that we continue to use uM here since [phenylephrine] is also in uM. 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/#
9 Trimerize-Gkf
(uM^-1 s^-1)
0
(s^-1)
--G*GDP
BetaGamma
G-GDP
  kf == kg3 = 1e-5 /cell/sec. As usual, there is no back-reaction kb = 0


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