Table 1.
Molecular concentration
| Molecule | Concentration (μm) | Previous version | Notes and references |
|---|---|---|---|
| Ca2+ | 0.1 | Same | See Kitagawa et al. (2009). |
| Glu | 0.001 | — | Assumed to produce a basal cAMP concentration around 0.14 μm (Sugiyama et al. 2008). |
| GABA | 0.01 | Same | See Kitagawa et al. (2009). |
| NO | 0.05 | — | Assumed to produce the basal cGMP concentration around 50 nm (Francis et al. 2010). |
| CaM | 60 | Same | See Kitagawa et al. (2009). |
| CaN | 10 | Same | See Kawaguchi et al. (2011). |
| CaMKII | 20 | Same | See Kitagawa et al. (2009). |
| PKC | 2 | 1 | The PKC amount was assumed to be slightly larger. |
| PP-1 | 0.4 | 0.54 | Assumed to balance the level of CaMKII phosphorylation. |
| PP-2A | 0.4 | 0.2 | PP-2A amount was increased to inhibit CaMKII, AMPARs, DARPP-32, G-substrate, MEK and Raf. |
| AMPAR | 1 | 0.5 | The ratio of phosphorylated and dephosphorylated AMPARs reflects the LTD establishment. Thus, the absolute amount of AMPARs is not important here. |
| GABAAR | 1 | Same | See Kitagawa et al. (2009). |
| DARPP-32 | 0.7 | 1.1 | According to the decrease of PP-1 in the model, amount of DARPP-32 was also reduced. |
| R2C2-PKA | 0.25 | Same | See Kawaguchi et al. (2011). |
| GABABR | 0.5 | Same | See Kitagawa et al. (2009). |
| GDPαiβγ | 1.5 | Same | See Kawaguchi et al. (2011). |
| AC | 0.02 | Same | See Kawaguchi et al. (2011). |
| cAMP | 0.1 | Same | See Kitagawa et al. (2009). |
| ATP | 2000 (constant) | Same | See Kitagawa et al. (2009). |
| PDE1 | 0.6 | Same | See Kawaguchi et al. (2011). |
| PDE4 | 0.6 | 0.4 | To enable rapid regulation of cAMP concentration, the amount of PDE4 was increased. |
| PDE5 | 0.6 | Newly defined | The amount of PDE5 was assumed to be similar to that of PDE1 or PDE4 in a Purkinje cell. |
| G-substrate | 0.7 | 10.8 | Because the affinity between phospho-G substrate and PP-2A was set much higher based on Endo et al. (2003), the amounts of PKG and G-substrate were reduced. |
| PKG | 0.1 | 2.445 | |
| cGMP | 0 | Same | Kuroda et al. (2001). |
| GTP | 100 | Same | Kitagawa et al. (2009). |
| GC | 0.02 | 3 | The amount of soluble guanylyl cyclase was assumed to be identical to that of adenylyl cyclase, producing a basal cGMP concentration around 50 nm (Francis et al. 2010). |
| Raf | 0.2 | 0.5 | The amounts of proteins in MAPK cascades were slightly reduced to balance the strength of the positive feedback loop and that of PP-2A activity. |
| MAPKK | 0.1 | 0.5 | The amounts of proteins in MAPK cascades were slightly reduced to balance the strength of the positive feedback loop and that of PP-2A activity. |
| MAPK | 0.2 | 1 | The amounts of proteins in MAPK cascades were slightly reduced to balance the strength of the positive feedback loop and that of PP-2A activity. |
| MKP-1 (MAPK phosphatase 1) | 0.005 | 0.0032 | The amounts of proteins in MAPK cascades were slightly reduced to balance the strength of the positive feedback loop and that of PP-2A activity. |
| PLA2 | 0.4 | Same | Tanaka et al. (2007). |
| AA | 0 | Same | Kuroda et al. (2001). |
| APC (aracholonyl-phosphatidylcholine) | 3 | 30 | Tanaka et al. (2007). |
| PIP2 (phosphati-dylinositol 4,5-bisphosphate) | 3 | 10 | Tanaka et al. (2007). |
| DAG | 0 | Same | Kuroda et al. (2001). |
| mGluR1 | 0.5 | 0.19524 | Adjusted to be identical to that of GABABRs. |
| Gq | 1.5 | 0.89513 | Adjusted to be identical to that of Gi protein. |
| Gs | 1.5 | — | Adjusted to be identical to that of Gi protein. |
| PLC | 0.2 | 0.8 | Assumption |