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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. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | | CaMKIII | 90 | Network |
Shared_Object_CaMKIII, CaM | | CaMKIII is activated by Ca2+ and inactivated by S6K. Since CaMKIII inhibits eEF2, the net effect of Ca2+ on elongation is inhibitory and of S6K is excitatory |
Ca acting as a Molecule in CaMKIII Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Ca | CaMKIII
Accession No. : 90 | Shared_Object_
CaMKIII
Pathway No. : 1093 | 0.08 | 1000 | No |
Ca acting as a Substrate in a reaction in CaMKIII 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 | CaMKIII
Accession No. : 90 | CaM
Pathway No. : 1094 | 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 | CaMKIII
Accession No. : 90 | CaM
Pathway No. : 1094 | 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 | CaMKIII
Accession No. : 90 | CaM
Pathway No. : 1094 | 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 | CaMKIII
Accession No. : 90 | CaM
Pathway No. : 1094 | 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 |
Ca acting as a Product in a reaction in CaMKIII 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 | | Ca_diff | CaMKIII
Accession No. : 90 | Shared_Object_
CaMKIII
Pathway No. : 1093 | 300
(s^-1) | 300
(s^-1) | Keq = 1(uM) | 0.002sec | Substrate
Ca_sum
Product
Ca
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| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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