| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | Ca-bind-to-Trans
p | CaRegulation
Pathway No. 110 | 3600
(uM^-2 s^-1) | 144
(s^-1) | Kd(af) = 0.2(uM) | - | Substrate:
Ca
Ca
CaTransp
Products:
CaTransp-2Ca
|
| Rates from Lauffenburger abd Linderman 1993 Receptors pg 200. Kd = KCa2 = 0.2 uM | | 2 | CaMK-thr286-bind
-CaM | CaMKII
Pathway No. 106 | 1000.2
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0001(uM) | - | Substrate:
CaMKII-thr286
CaM-Ca4
Products:
CaMKII-thr286*-C
aM
|
| Affinity is up 1000X over the unphosphorylated CaMKII, which makes the Kd of 0.1 nM. See Hanson et al 1994 Neuron 12:943-956. Time to release is about 20 sec, so the kb is OK at 0.1/sec. as tested by a few runs. | | 3 | CaM-TR2-bind-Ca | CaM
Pathway No. 107 | 72
(uM^-2 s^-1) | 72
(s^-1) | Kd(af) = 1(uM) | - | Substrate:
CaM
Ca
Ca
Products:
CaM-TR2-Ca2
|
| We use the Martin et al 1985 Eur J Biochem 151(3):543-550 rates here, plus the Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 binding consts. All are scaled by 3X to cell temperature. kf = 2e-10 kb = 72 Stemmer & Klee 1994 Biochem 33:6859-6866 have values of : K1=.9, K2=1.1. Assume 1.0uM for both | | 4 | Antag-bind-Rec-G
q | Gq
Pathway No. 111 | 60
(uM^-1 s^-1) | 0.01
(s^-1) | Kd(bf) = 0.0002(uM) | - | Substrate:
Rec-Gq
mGluRAntag
Products:
Blocked-rec-Gq
|
| The rate consts give a total binding affinity of under 0.2 nM, good for a strong antagonist. | | 5 | CaMKII-bind-CaM | CaMKII
Pathway No. 106 | 49.9998
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.1(uM) | - | Substrate:
CaM-Ca4
CaMKII
Products:
CaMKII-CaM
|
| This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kd = 0.1 uM. Rate is fast (see Hanson et al Neuron 12 943-956 1994) Hanson and Schulman 1992 AnnRev Biochem 61:559-601 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol. | | 6 | 3K*-bind-CaM | IP3-3K
Pathway No. 109 | 49.9998
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.002(uM) | - | Substrate:
IP3_3K*
CaM-Ca4
Products:
IP3_3K_CaM*
|
| Communi et al, EMBO J 16; 1997 phosphorylated 3kinase has 25 fold greater sensitivity to CaM binding than the non-phosphorylated enzyme (Kd of 2nM) | | 7 | IP1(3)_deg | 134_dephos
Pathway No. 113 | 35
(s^-1) | 0
(s^-1) | - | - | Substrate:
IP1(3)
Products:
inositol
|
| rate based on levels of Ins(3)P1 | | 8 | PLC-Gq-bind-Ca | PLCbeta
Pathway No. 112 | 30
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0333(uM) | - | Substrate:
PLC-Gq
Ca
Products:
PLC-Ca-Gq
|
| this step has a high affinity for Ca, from Smrcka et al. 0.1uM 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. | | 9 | Act-PLC-by-Gq | PLCbeta
Pathway No. 112 | 25.2
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0397(uM) | - | Substrate:
PLC-Ca
G*GTP
Products:
PLC-Ca-Gq
|
| Affinity for Gq is > 20 nM (Smrcka et al Science251 804-807 1991) so [Gq].kf = kb so 40nM * 6e5 = kb/kf = 24e3 so kf = 4.2e-5, kb =1 | | 10 | CaTraspATPase | CaRegulation
Pathway No. 110 | 25
(s^-1) | 0
(#^-2 s^-1) | Not applicable** | - | Substrate:
CaTransp-2Ca
Products:
CaTransp
Ca-sequester
Ca-sequester
|
| kCa3 = 2 * Ca transporter rate since each step has 2 Ca++. = 0.5 uM/sec from Lauffenburger and Linderman 1993 Receptors pg200 The amount of the activated transporter is about 0.01 uM = 6e3#. from runs. So 0.01uM * kf * 2 = 0.5 uM/sec (no back reaction) so kf = 25, kb = 0 Alternatively, 6e3 * kf = 0.25 * 6e5, giving the same kf | | 11 | 3K-bind-CaM | IP3-3K
Pathway No. 109 | 19.2312
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.052(uM) | - | Substrate:
IP3_3K
CaM-Ca4
Products:
IP3_3K_CaM
|
| Communi et al, EMBO J 16; 1997 non-phosphorylated 3kinase with low sensitivity to CaM binding (Kd = 52nM) | | 12 | RecLigandBinding | Gq
Pathway No. 111 | 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. | | 13 | Glu-bind-Rec-Gq | Gq
Pathway No. 111 | 16.8
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.006(uM) | - | Substrate:
Glu
Rec-Gq
Products:
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 | | 14 | Trimerize-G | Gq
Pathway No. 111 | 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 | | 15 | CaM-TR2-Ca2-bind
-Ca | CaM
Pathway No. 107 | 3.6
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7778(uM) | - | Substrate:
CaM-TR2-Ca2
Ca
Products:
CaM-Ca3
|
| Stemmer and Klee 1994 Biochem 33:6859-6866 K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 | | 16 | IP3-Kcmplx-on | IP4-system
Pathway No. 115 | 3
(uM^-1 s^-1) | 0.192
(s^-1) | Kd(bf) = 0.064(uM) | - | Substrate:
IP3(134)
IP3-56K
Products:
IP3-56Kcmplx
|
| Kf and Kb are equivalent to k1 and k2 for InsP3 56-K, calculated from Km and Vmax values provided by Wilson and Majerus, JBC 271; 1996 | | 17 | Act-PLC-Ca | PLCbeta
Pathway No. 112 | 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 so [Ca].kf = kb so kb/kf = 1 * 6e5 = 1/1.66e-6 Assigned affinity to a Kd of 0.333 to maintain balance. | | 18 | PLC-bind-Gq | PLCbeta
Pathway No. 112 | 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 tempkin are the same as the binding step for Ca-PLC to Gq. Kd is constrained by detailed balance. | | 19 | PKC-act-by-DAG-A
A | PKC
Pathway No. 108 | 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 | | 20 | Inact-PLC-Gq | PLCbeta
Pathway No. 112 | 1.6667
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate:
PLC-Ca-Gq
Products:
PLC-Ca
G*GDP
|
| Rate of 100/min to account for GAP activity of PLC: Biddlecome et al, JBC, 271, 14, 7999-8007, 1996 |
and 
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