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Molecule Parameter List for GAP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| GAP 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 | 1 | 1 | 0 | 0 | 1 |
Accession and Pathway Details |
| Accession Name | Accession No. | Accession Type | Pathway Link |
| 3d_fold_model | 8 | Network | Shared_Object_3d_fold_model, PKC, MAPK, PLA2, Ras |
| 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, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23. | |||
GAP acting as a Molecule in 3d_fold_model Network
| Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | |
| GAP | 3d_fold_model Accession No. : 8 | Ras Pathway No. : 58 | 0.002 | 1000 | No | |
| GTPase-activating proteins. See Boguski and McCormick. Turn off Ras by helping to hydrolyze bound GTP. This one is probably NF1, ie., Neurofibromin as it is inhibited by AA and lipids, and expressed in neural cells. p120-GAP is also a possible candidate, but is less regulated. Both may exist at similar levels. See Eccleston et al JBC 268(36) pp27012-19 Level=.002 | ||||||
GAP acting as an Enzyme in 3d_fold_model Network
| Enzyme Molecule / Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents |
| GAP / GAP-inact-ras | 3d_fold_model Accession No. : 8 | Ras Pathway No. : 58 | 1.0104 | 10 | 100 | explicit E-S complex | Substrate GTP-Ras Product GDP-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) | |||||||
GAP acting as a Substrate for an Enzyme in 3d_fold_model Network
| Enzyme Molecule / Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents |
| PKC-active / PKC-inact-GAP | 3d_fold_model Accession No. : 8 | 3d_fold_model Pathway No. : 54 | 3.33333 | 4 | 4 | explicit E-S complex | Substrate GAP Product GAP* |
| Rate consts copied from PCK-act-raf This reaction inactivates GAP. The idea is from the Boguski and McCormick review. | |||||||
GAP acting as a Product in a reaction in 3d_fold_model 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 |
| dephosph-GAP | 3d_fold_model Accession No. : 8 | Ras Pathway No. : 58 | 0.1 (s^-1) | 0 (s^-1) | - | - | Substrate GAP* Product GAP |
| Assume a reasonably good rate for dephosphorylating it, 1/sec | |||||||