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Molecule Parameter List for GDP_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 |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Differential syn
thesis of mRNA | 95 | 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. |
GDP_dash_Ras acting as a Molecule in Differential synthesis of mRNA Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | GDP_dash_Ras | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.5 | 1000 | No | | GDP bound form. See Rosen et al Neuron 12 1207-1221 June 1994. the activation loop is based on Boguski and McCormick Nature 366 643-654 93 Assume Ras is present at about the same level as craf-1, 0.2 uM. Hallberg et al JBC 269:6 3913-3916 1994 estimate upto 5-10% of cellular Raf is assoc with Ras. Given that only 5-10% of Ras is GTP-bound, we need similar amounts of Ras as Raf. |
GDP_dash_Ras acting as a Substrate for an Enzyme in Differential synthesis of mRNA Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | GEF_dash_Gprot_
dash_bg /
GEF_dash_bg_
act_dash_ras
| Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.5051 | 0.02 | 4 | explicit E-S complex | Substrate
GDP_dash_Ras
Product
GTP_dash_Ras
| | | Kinetics based on the activation of Gq by the receptor complex in the Gq model (in turn based on the Mahama and Linderman model) k1 = 2e-5, k2 = 1e-10, k3 = 10 (I do not know why they even bother with k2). Lets put k1 at 2e-6 to get a reasonable equilibrium More specific values from, eg.g: Orita et al JBC 268(34) 25542-25546 from rasGRF and smgGDS: k1=3.3e-7; k2 = 0.08, k3 = 0.02 | | 2 | CaM_dash_GEF /
CaM_dash_GEF_
dash_act_dash_
ras
| Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.5051 | 0.02 | 4 | explicit E-S complex | Substrate
GDP_dash_Ras
Product
GTP_dash_Ras
| | | Kinetics same as GEF-bg_act-ras | | 3 | GEF_star /
GEF_star_dash_
act_dash_ras
| Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.5051 | 0.02 | 4 | explicit E-S complex | Substrate
GDP_dash_Ras
Product
GTP_dash_Ras
| | | Kinetics same as GEF-bg-act-ras | | 4 | Shc_
star.Sos.Grb2 /
Sos.Ras_GEF | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.0505 | 0.2 | 4 | explicit E-S complex | Substrate
GDP_dash_Ras
Product
GTP_dash_Ras
| | | |
GDP_dash_Ras acting as a Product of an Enzyme in Differential synthesis of mRNA Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | GAP /
GAP_dash_inact_
dash_ras
| Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 1.0104 | 10 | 4 | explicit E-S complex | Substrate
GTP_dash_Ras
Product
GDP_dash_Ras
| | From Eccleston et al JBC 268(36)pp27012-19 get Kd < 2uM, kcat - 10/sec From Martin et al Cell 63 843-849 1990 get Kd ~ 250 nM, kcat = 20/min I will go with the Eccleston figures as there are good error bars (10%). In general the values are reasonably close. k1 = 1.666e-3/sec, k2 = 1000/sec, k3 = 10/sec (note k3 is rate-limiting) 5 Nov 2002: Changed ratio term to 4 from 100. Now we have k1=8.25e-5; k2=40, k3=10. k3 is still rate-limiting. |
GDP_dash_Ras acting as a Product in a reaction in Differential synthesis of mRNA 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_
intrinsic_dash_
GTPase | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.0001
(s^-1) | 0
(s^-1) | - | - | Substrate
GTP_dash_Ras
Product
GDP_dash_Ras
| | This is extremely slow (1e-4), but it is significant as so little GAP actually gets complexed with it that the total GTP turnover rises only by 2-3 X (see Gibbs et al, JBC 265(33) 20437-20422) and Eccleston et al JBC 268(36) 27012-27019 kf = 1e-4 |
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