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Molecule Parameter List for Raf_star_dash_GTP_dash_Ras | 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 |
| Raf_star_dash_GTP_dash_Ras participated as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction | | No. of occurrences | 1 | 0 | 2 | 0 | 0 | 0 | 1 |
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. |
Raf_star_dash_GTP_dash_Ras acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Raf_star_dash_GTP_dash_Ras | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0 | 1000 | No | | |
Raf_star_dash_GTP_dash_Ras acting as an Enzyme in mRNA synthesis Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | Raf_star_dash_
GTP_dash_Ras /
Raf_star_dash_
GTP_dash_Ras.2
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0.1591 | 0.3 | 4 | explicit E-S complex | Substrate
MAPKK_dash_ser
Product
MAPKK_star
| | | Same kinetics as other c-raf activated forms. See Force et al PNAS 91 1270-1274 1994. k1 = 1.1e-6, k2 = .42, k3 = 1.05 raise k1 to 5.5e-6 | | 2 | Raf_star_dash_
GTP_dash_Ras /
Raf_star_dash_
GTP_dash_Ras.1
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0.1591 | 0.3 | 4 | explicit E-S complex | Substrate
MAPKK
Product
MAPKK_dash_ser
| | | Kinetics are the same as for the craf-1* activity, ie., k1=1.1e-6, k2=.42, k3 =0.105 These are based on Force et al PNAS USA 91 1270-1274 1994. These parms cannot reach the observed 4X stim of MAPK. So lets increase the affinity, ie, raise k1 10X to 1.1e-5 Lets take it back down to where it was. Back up to 5X: 5.5e-6 |
Raf_star_dash_GTP_dash_Ras acting as a Product 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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