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Molecule Parameter List for craf-1* | 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 |
craf-1* acting as a Molecule in Synaptic_Network Network
Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | craf-1* | Synaptic_ Network Accession No. : 16 | MAPK Pathway No. : 75 | 0 | 1000 | No | Singly phosphorylated form of c-raf-1. This is the form that gets best activated by GTP.Ras. |
craf-1* acting as a Substrate for an Enzyme in Synaptic_Network Network
| Enzyme Molecule / Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | 1 | MAPK* / MAPK*-feedback | Synaptic_ Network Accession No. : 16 | Shared_Object_ Synaptic_ Network Pathway No. : 70 | 25.641 | 10 | 4 | explicit E-S complex | Substrate craf-1*
Product craf-1**
| | Ueki et al JBC 269(22):15756-15761 show the presence of this step, but not the rate consts, which are derived from Sanghera et al JBC 265(1):52-57, 1990, see the deriv in the MAPK* notes. | 2 | PPhosphatase2A / craf-deph | Synaptic_ Network Accession No. : 16 | Shared_Object_ Synaptic_ Network Pathway No. : 70 | 15.6566 | 6 | 4.16667 | explicit E-S complex | Substrate craf-1*
Product craf-1
| | See parent PPhosphatase2A for parms |
craf-1* acting as a Product of an Enzyme in Synaptic_Network Network
| Enzyme Molecule / Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | 1 | PKC-active / PKC-act-raf | Synaptic_ Network Accession No. : 16 | Shared_Object_ Synaptic_ Network Pathway No. : 70 | 66.6667 | 4 | 4 | explicit E-S complex | Substrate craf-1
Product craf-1*
| | Rate consts from Chen et al Biochem 32, 1032 (1993) k3 = 4 Km for this substrate is trickier. Specific substrates are in the uM range, so we use a higher Km here. This may be too conservative in which case PKC would have a still higher effect on raf. The presence of this phosphorylation and activation step is from Kolch et al 1993 Nature 364:249 | 2 | PPhosphatase2A / craf**-deph | Synaptic_ Network Accession No. : 16 | Shared_Object_ Synaptic_ Network Pathway No. : 70 | 15.6566 | 6 | 4.16667 | explicit E-S complex | Substrate craf-1**
Product craf-1*
| | Ueki et al JBC 269(22) pp 15756-15761 1994 show hyperphosphorylation of craf, so this is there to dephosphorylate it. Identity of phosphatase is assumed to be PP2A. |
craf-1* 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 | Ras-act-craf | Synaptic_ Network Accession No. : 16 | Shared_Object_ Synaptic_ Network Pathway No. : 70 | 24 (uM^-1 s^-1) | 0.5 (s^-1) | Kd(bf) = 0.0208(uM) | - | Substrate GTP-Ras craf-1*
Product Raf-GTP-Ras*
| Assume binding is fast and limited only by available Ras*. So kf = kb/[craf-1] If kb is 1/sec, then kf = 1/0.2 uM = 1/(0.2 * 6e5) = 8.3e-6 Later: Raise it by 10 X to about 1e-4, giving a Kf of 60 for Kb of 0.5 and a tau of approx 2 sec. Based on: Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414. Also see Koide et al 1993 PNAS USA 90(18):8683-8686 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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