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Molecule Parameter List for Ca | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Ca 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 | 0 | 0 | 0 | 5 | 0 |
Accession and Pathway Details |
| Accession Name | Accession No. | Accession Type | Pathway Link |
| mTOR_pathway | 92 | Network | Shared_Object_mTOR_pathway, AKT_mod, S6Kinase, PI3K_mod, TrKB_mod, mTOR_model, MAPK, PKC, 4E-BP_mod, Ras, Sos, 43S_complex, CaM |
| This model consists of various sub-modules. They are as follows: 1) BDNF receptor signaling 2) AKT signaling 3) 4E-BP model 4) S6 Kinase model 5) CaMKIII model 6) Protein synthesis model 7) CaM 8) PKC 9) MAPK model. | |||
Ca acting as a Molecule in mTOR_pathway Network
| Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered |
| Ca | mTOR_pathway Accession No. : 92 | mTOR_pathway Pathway No. : 1097 | 0.08 | 1000 | No |
Ca acting as a Substrate in a reaction in mTOR_pathway 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 | |
| 1 | CaM-Ca3-bind-Ca | mTOR_pathway Accession No. : 92 | CaM Pathway No. : 1109 | 0.465 (uM^-1 s^-1) | 10 (s^-1) | Kd(bf) = 21.5051(uM) | - | Substrate Ca CaM-Ca3 Product CaM-Ca4 |
| Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 | ||||||||
| 2 | CaM-bind-Ca | mTOR_pathway Accession No. : 92 | CaM Pathway No. : 1109 | 8.4846 (uM^-1 s^-1) | 8.4853 (s^-1) | Kd(bf) = 1.0001(uM) | - | Substrate Ca CaM Product CaM-Ca |
| Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 | ||||||||
| 3 | CaM-Ca2-bind-Ca | mTOR_pathway Accession No. : 92 | CaM Pathway No. : 1109 | 3.6001 (uM^-1 s^-1) | 10 (s^-1) | Kd(bf) = 2.7777(uM) | - | Substrate Ca CaM-Ca2 Product CaM-Ca3 |
| K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 | ||||||||
| 4 | CaM-Ca-bind-Ca | mTOR_pathway Accession No. : 92 | CaM Pathway No. : 1109 | 8.4846 (uM^-1 s^-1) | 8.4853 (s^-1) | Kd(bf) = 1.0001(uM) | - | Substrate Ca CaM-Ca Product CaM-Ca2 |
| Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 | ||||||||
| 5 | PKC-act-by-Ca | mTOR_pathway Accession No. : 92 | PKC Pathway No. : 1104 | 0.6 (uM^-1 s^-1) | 0.5 (s^-1) | Kd(bf) = 0.8333(uM) | - | Substrate Ca PKC-cytosolic Product PKC-Ca |
| Need est of rate of assoc of Ca and PKC. Assume it is fast The original parameter-searched kf of 439.4 has been scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085 Raised kf to 1e-6 to match Ca curve, kb to .5 | ||||||||