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Reaction List for pathway Shared_Object_AMPAR_CaMKII_strong_coupling (Pathway Number 271) |
| 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 reactions is not considered. |
| Name | Kf | Kb | Kd | tau | Substrate | Product | |
| 1 | back_1 | 0.3 (s^-1) | 0 (#^-1 s^-1) | Not applicable** | - | CaMKII-PSD | CaMKII NMDAR |
| Rates set by the translocation experiments of Shen and Meyer, Science 1999. | |||||||
| 2 | back_2 | 0.3 (s^-1) | 0 (#^-1 s^-1) | Not applicable** | - | D | CaMK-thr305 NMDAR |
| Same as for back_1 | |||||||
| 3 | CaM-Ca3-bind-Ca | 0.465 (uM^-1 s^-1) | 10 (s^-1) | Kd(bf) = 21.5054(uM) | - | CaM-Ca3 Ca | 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 | |||||||
| 4 | CaMKII-bind-CaM- PSD | 49.9998 (uM^-1 s^-1) | 0 (s^-1) | - | - | CaMKII-PSD CaM-Ca4-PSD | CaMKII-CaM-PSD |
| 5 | CaMKII-diss-CaM | 5 (s^-1) | 0 (uM^-1 s^-1) | - | - | CaMKII-CaM-PSD | CaM-Ca4-PSD CaMKII-PSD |
| 6 | CaMKII-thr286-bi nd-CaM-PSD | 1000.02 (uM^-1 s^-1) | 0.1 (s^-1) | Kd(bf) = 0.0001(uM) | - | D CaM-Ca4-PSD | M-PSD |
| Same values as for the main compartment Can the main compartment pool of Ca/CaM be used? | |||||||
| 7 | Ca_stoch_cyt | 100 (s^-1) | 100 (s^-1) | Keq = 1(uM) | 0.005sec | Ca_control_cyt | Ca |
| 8 | Ca_stoch_PSD | 100 (s^-1) | 100 (s^-1) | Keq = 1(uM) | 0.005sec | Ca_control_PSD | Ca-PSD |
| 9 | endo_const | 0.0004 (s^-1) | 0.0014 (s^-1) | Not applicable** | - | GluR23_M | GluR23_I |
| 10 | equilib | 540 (s^-1) | 60 (s^-1) | Not applicable** | - | CaM-Ca4-PSD | CaM-Ca4 |
| Diffusional equilibrium between PSD- and cytosolic compartment. According to D. Bary in Cell Movements 2nd ed 2001 D for proteins is 5e-7 cm^2/s giving 10 ms for a translocation of 1 um. | |||||||
| 11 | Inact-PP1 | 499.98 (uM^-1 s^-1) | 0.1 (s^-1) | Kd(bf) = 0.0002(uM) | - | I1* PP1-active_PSD | PP1-I1* |
| K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4 | |||||||
| 12 | PKC-stoch-input | 2.5 (s^-1) | 2.5 (s^-1) | Keq = 1(uM) | 0.2sec | PKC-control | PKC-active |
| 13 | Stoch_Basal_ CaMKII_PSD | 1 (s^-1) | 1 (s^-1) | Keq = 1(uM) | 0.5sec | PSD_control | PSD |
| 14 | transloc_1 | 0 (#^-1 s^-1) | 0 (s^-1) | Not applicable** | - | CaMKII-CaM NMDAR | CaMKII-CaM-PSD |
| Rates to match curve in fig2 from Shen and Meyer, Science 284:162-166(1999), calculated for 6:1 alpha:beta CaMKII heterodimers | |||||||
| 15 | transloc_2 | 0 (#^-1 s^-1) | 0 (s^-1) | Not applicable** | - | aM NMDAR | M-PSD |
| Same as for transloc_1 | |||||||
| 16 | turnover | 0.018 (s^-1) | 1 (s^-1) | Not applicable** | - | AMPAR_bulk | A_B |
| Represents both synthesis and degradation of the receptor. The rate is set to be rather fast for now. The forward rate also includes scaling terms because the AMPAR_bulk is in the dendritic volume of 5e-18. This means that we need to lower Kf to account for the difference in volumes. Effectively Kf is 1/sec, but the scaled version becomes 9e-20/5e-18 = 0.018 | |||||||
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