| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | CaMK-thr286-bind
-CaM | CaMKII
Pathway No. 159 | 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. | | 2 | actIP3R | Othmer-Tang-mode
l
Pathway No. 171 | 1000.01
(uM^-2 s^-1) | 5
(s^-1) | Keq = 0.005(uM) | - | Substrate:
mirror_
Ca.IP3.IP3R
mirror_
Ca.IP3.IP3R
mirror_
Ca.IP3.IP3R
Products:
activeIP3R
|
| Rate set so that almost all Ca.IP3.IP3R complex (formed by Ca and IP3 binding to the IP3R) becomes the active Ca conducting channel | | 3 | 3k-CaM*-on | IP3-3K
Pathway No. 162 | 80.358
(uM^-1 s^-1) | 180
(s^-1) | Kd(bf) = 2.24(uM) | - | Substrate:
IP3(145)
IP3_3K_CaM*
Products:
3kCaM*_ip3_
cmplx
|
| Rates from Km of enzyme Communi et al, EMBO J 16(8) | | 4 | CaM-TR2-bind-Ca | CaM
Pathway No. 160 | 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 | | 5 | Antag-bind-Rec-G
q | Gq
Pathway No. 163 | 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. | | 6 | ip4-3k-on | IP4-system
Pathway No. 167 | 53.7501
(uM^-1 s^-1) | 17.2
(s^-1) | Kd(bf) = 0.32(uM) | - | Substrate:
IP4(1456)
IP4-3K
Products:
ip4_3k_cmplx
|
| Rates derived from Km for enzyme: Stephens et al, Biochem J 249; 1988. | | 7 | CaMKII-bind-CaM | CaMKII
Pathway No. 159 | 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. | | 8 | 3K*-bind-CaM | IP3-3K
Pathway No. 162 | 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) | | 9 | 3k-CaM*-off | IP3-3K
Pathway No. 162 | 45
(s^-1) | 0.4148
(uM^-1 s^-1) | Kd(cb) = 0.0092(uM) | - | Substrate:
3kCaM*_ip3_
cmplx
Products:
IP4(1345)
IP3_3K_CaM*
|
| Kf = Vmax for enzyme (Communi et al, EMBO J 16(8)) Vmax is such that enzyme activity is 9 fold above basal. Kb derived from Keq value when reaction free energy = -10 kJ/mol | | 10 | 4pase-off | 145_dephos
Pathway No. 166 | 39.33
(s^-1) | 0.0021
(uM^-1 s^-1) | Kd(cb) = 0.0001(uM) | - | Substrate:
ip1_4pase_cmplx
Products:
IP1_pase
inositol
|
| Kf = Vmax for Ins(4)P1 4-phosphatase: Gee et al, Biochem J 249, 1988. Kb adjusted to generate reported basal levels of Ins(4)P1 = 10% of Ins(1)P1 ~ 4uM | | 11 | IP1(3)_deg | 134_dephos
Pathway No. 165 | 35
(s^-1) | 0.336
(s^-1) | Keq = 0.0096(uM) | 0.028sec | Substrate:
IP1(3)
Products:
inositol
|
| Kf and Kb based on levels of Ins(3)P1. Kb necessary as energetics calculations show backflow from inositol to be significant. | | 12 | ip4-1k-on | IP4-system
Pathway No. 167 | 31.2001
(uM^-1 s^-1) | 2.496
(s^-1) | Kd(bf) = 0.08(uM) | - | Substrate:
IP4(3456)
IP3-56K_IP4-1K
Products:
ip4_1k_cmplx
|
| Rates derives from enzyme Km and Vmax values: Yang and Shears, Biochem J 2000, 351: 551-555. | | 13 | PLC-Gq-bind-Ca | PLCbeta
Pathway No. 164 | 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. | | 14 | Act-PLC-by-Gq | PLCbeta
Pathway No. 164 | 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 | | 15 | 3K-bind-CaM | IP3-3K
Pathway No. 162 | 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) | | 16 | 3k-CaM-on | IP3-3K
Pathway No. 162 | 18.7497
(uM^-1 s^-1) | 42.001
(s^-1) | Kd(bf) = 2.2401(uM) | - | Substrate:
IP3_3K_CaM
IP3(145)
Products:
3kCaM_ip3_cmplx
|
| rates from Km for enzyme: Erneux et al, Biochem 214; 1993 Enzyme is 2-2.5 fold more active than ip3-3k, but Km is doubled. | | 17 | RecLigandBinding | Gq
Pathway No. 163 | 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. | | 18 | Glu-bind-Rec-Gq | Gq
Pathway No. 163 | 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 | | 19 | bind_act_Ca | Othmer-Tang-mode
l
Pathway No. 171 | 15
(uM^-1 s^-1) | 1.65
(s^-1) | Kd(bf) = 0.11(uM) | - | Substrate:
IP3.IP3R
Ca
Products:
Ca.IP3.IP3R
|
| from the O-T model in Tang et al, Biophys J 70, 1996 | | 20 | bind_IP3 | Othmer-Tang-mode
l
Pathway No. 171 | 12
(uM^-1 s^-1) | 8
(s^-1) | Kd(bf) = 0.6667(uM) | - | Substrate:
IP3R
IP3
Products:
IP3.IP3R
|
| from the O-T model in Tang et al, Biophys J 70, 1996 |
and 
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