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Molecule Parameter List for PPN | 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 | | SOCS1_knockout | 67 | Pathway |
SOCS1_knockout | This model was taken from the Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6
This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. This is the knockout version of Jak-Stat pathway in this model the SOCS1 has been knocked out i.e it formation is not shown.
The graphs are almost similar to the graphs as shown in the paper but STAT1n graph has some ambiguities. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in the simulations. |
PPN acting as a Molecule in SOCS1_knockout Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PPN | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 0.06 | 0.0016667 | No | | PPX: Unidentified phosphatase in the nucleus PPX = 60nM = 0.06uM Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
PPN acting as a Substrate in a reaction in SOCS1_knockout 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 | | 1 | PPN_binding | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 1
(uM^-1 s^-1) | 0.2
(s^-1) | Kd(bf) = 0.2(uM) | - | Substrate
PPN
STAT1n*
Product
PPN-STAT1n*
| | | Binding of PPN to phosphorylated STAT1n Kf = 1*10e+06 /M/sec = 1/uM/sec Kb = 0.2 /sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 | | 2 | PPN_binding[1] | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 1
(uM^-1 s^-1) | 0.2
(s^-1) | Kd(bf) = 0.2(uM) | - | Substrate
PPN
STAT1n*-STAT1n*
Product
PPN-STAT1n*-STAT
1n*
| | | Binding of PPN to phosphorylated STAT1n dimer Kf = 1*10e+06 /M/sec = 1/uM/sec Kb = 0.2 /sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
PPN acting as a Product in a reaction in SOCS1_knockout 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 | | 1 | STAT1n*_
dephosphorylatio
n | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 0.005
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
PPN-STAT1n*
Product
PPN
STAT1n
| | | Nucleoplasmic phosphatase (PPN) dephosphorylates STAT1n Kf = 0.005 /sec Kb = 0 /uM/sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 | | 2 | STAT1n*_
dephosphorylatio
n[1] | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 0.005
(s^-1) | 0
(uM^-2 s^-1) | - | - | Substrate
PPN-STAT1n*-STAT
1n*
Product
PPN
STAT1n
STAT1n*
| | | Nucleoplasmic phosphatase (PPN) dephosphorylates STAT1n Kf = 0.005 /sec Kb = 0 /uM/sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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