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Molecule Parameter List for PP1-active | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Synaptic_
Network | 16 | Network |
Shared_Object_Synaptic_Network, PKC, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, CaRegulation | This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
Bhalla US Biophys J. 2002 Aug;83(2):740-52
Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62 |
PP1-active acting as a Molecule in Synaptic_Network Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PP1-active | Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 1.8 | 1000 | No | | Cohen et al Meth Enz 159 390-408 is main source of info concentration of enzyme = 1.8 uM |
PP1-active acting as an Enzyme in Synaptic_Network Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PP1-active /
Deph-thr286
| Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 5.09907 | 0.35 | 4 | explicit E-S complex | Substrate
CaMKII-thr286*-C
aM
Product
CaMKII-CaM
| | | The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35. This gives the final Km of 5.1, and Vmax of 0.35/sec. | | 2 | PP1-active /
Deph-thr305
| Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 5.09907 | 0.35 | 4 | explicit E-S complex | Substrate
CaMKII***
Product
CaMKII-thr286
| | | Dephosphorylation kinetics are assumed to be the same for all phosphorylation sites on CaMKII. The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35. This gives the final Km of 5.1, and Vmax of 0.35/sec. | | 3 | PP1-active /
Deph-thr306
| Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 5.09907 | 0.35 | 4 | explicit E-S complex | Substrate
CaMK-thr306
Product
CaMKII
| | | Dephosphorylation kinetics are assumed to be the same for all phosphorylation sites on CaMKII. The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35. This gives the final Km of 5.1, and Vmax of 0.35/sec. | | 4 | PP1-active /
Deph-thr286c
| Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 5.09907 | 0.35 | 4 | explicit E-S complex | Substrate
CaMKII***
Product
CaMK-thr306
| | | Dephosphorylation kinetics are assumed to be the same for all phosphorylation sites on CaMKII. The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35. This gives the final Km of 5.1, and Vmax of 0.35/sec. | | 5 | PP1-active /
Deph_thr286b
| Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 5.09907 | 0.35 | 4 | explicit E-S complex | Substrate
CaMKII-thr286
Product
CaMKII
| | | Rates are assumed to be the same for all phosphorylation sites on CaMKII. The rates are from Stralfors et al Eur J Biochem 149 295-303 giving Vmax = 5.7 umol/min giving k3 = 3.5/sec and k2 = 14. Foulkes et al Eur J Biochem 132 309-313 1983 give Km = 5.1 uM so k1 becomes 5.72e-6 Simonelli 1984 (Grad Thesis, CUNY) showed that other substrates are about 1/10 rate of phosphorylase a, so we reduce k1,k2,k3 by 10 to 5.72e-7, 1.4, 0.35. This gives the final Km of 5.1, and Vmax of 0.35/sec. |
PP1-active acting as a Substrate in a reaction in Synaptic_Network Network
| 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 reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | Inact-PP1 | Synaptic_
Network
Accession No. : 16 | PP1
Pathway No. : 82 | 499.98
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0002(uM) | - | Substrate
I1*
PP1-active
Product
PP1-I1*
| | K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4 The Kd used here is 0.2 nM. This is small, but unlikely to matter much as the affinity is so strong that the reaction will be all the way forward in either case. Tau < 1 min for inhibition. Stralfors 1985 Eur J Biochem 149:295-303 fig 8 pg 201. |
PP1-active acting as a Product in a reaction in Synaptic_Network Network
| 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 reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | dissoc-PP1-I1 | Synaptic_
Network
Accession No. : 16 | PP1
Pathway No. : 82 | 1
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
PP1-I1
Product
I1
PP1-active
| | Assumption is that the affinity of the unphosphorylated form of I1 for PP1 is extremely weak and that the reaction is essentially all the way forward. The tau is fast at 1 sec. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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