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Molecule Parameter List for craf_dash_1_star | 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 | | mRNA synthesis | 94 | Network |
kinetics, compartment_1, compartment_2 | | The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway. |
craf_dash_1_star acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | craf_dash_1_star | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0 | 1000 | No | | |
craf_dash_1_star acting as a Substrate for an Enzyme in mRNA synthesis Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PPhosphatase2A /
craf_dash_deph | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 15.6568 | 6 | 4 | explicit E-S complex | Substrate
craf_dash_1_
star
Product
craf_dash_1
| | | See parent PPhosphatase2A for parms | | 2 | MAPK_star /
MAPK_star_dash_
feedback
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 25.641 | 10 | 4 | explicit E-S complex | Substrate
craf_dash_1_
star
Product
craf_dash_1_
star_star
| | | 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. |
craf_dash_1_star acting as a Product of an Enzyme in mRNA synthesis Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PKC_dash_active /
PKC_dash_act_
dash_raf
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 66.668 | 4 | 4 | explicit E-S complex | Substrate
craf_dash_1
Product
craf_dash_1_
star
| | | | | 2 | PPhosphatase2A /
craf_star_star_
dash_deph
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 15.6568 | 6 | 4 | explicit E-S complex | Substrate
craf_dash_1_
star_star
Product
craf_dash_1_
star
| | | 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 not known to me, but it may be PP2A like the rest, so I have made it so. |
craf_dash_1_star acting as a Substrate in a reaction in mRNA synthesis 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_dash_act_
dash_craf | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 9.9996
(uM^-1 s^-1) | 0.5
(s^-1) | Kd(bf) = 0.05(uM) | - | Substrate
GTP_dash_Ras
craf_dash_1_
star
Product
Raf_star_dash_
GTP_dash_Ras
| | Assume the binding is fast and limited only by the amount of Ras* available. 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 4e-5 From Hallberg et al JBC 269:6 3913-3916 1994, 3% of cellular Raf is complexed with Ras. So we raise kb 4x to 4 This step needed to memb-anchor and activate Raf: Leevers et al Nature 369 411-414 May 16, 2003 Changed Ras and Raf to synaptic levels, an increase of about 2x for each. To maintain the percentage of complexed Raf, reduced the kf by 2.4 fold to 10. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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