Table 4. Model reactions (rate parameters provided in S1 Table).
| Reaction number | Reaction | Rate |
|---|---|---|
| AMPAR Binding Interactions at PSD and the Endosome † | ||
| 1 | AMPAR + GRIP → AMPAR-GRIP | k.ampar-grip.on |
| 2 | AMPAR-GRIP → AMPAR + GRIP1 | k.ampar-grip.off 1 |
| AMPARpS-GRIP → AMPARpS + GRIP2 | k.ampar-grip.offpS 2 | |
| 3 | AMPAR + PICK1 → AMPAR-PICK1 | k.ampar-pick.on |
| 4 | AMPAR-PICK1 → AMPAR + PICK1 | k.ampar-pick.off |
| 5 | AMPAR + PICK1-PKC* → AMPAR-PICK1-PKC* | k.ampar-pick.on* |
| 6 | AMPAR-PICK1-PKC* → AMPAR + PICK1-PKC* | k.ampar-pick.off |
| 7 | AMPAR-GRIP + PICK1 → AMPAR-GRIP-PICK1 | k.grip-pick.on |
| 8 | AMPAR-GRIP-PICK1 → AMPAR-GRIP + PICK1 | k.grip-pick.off |
| 9 | AMPAR-GRIP + PICK1-PKC* → AMPAR-GRIP-PICK1-PKC* | k.grip-pick.on |
| 10 | AMPAR-GRIP-PICK1-PKC* → AMPAR-GRIP + PICK1-PKC* | k.grip-pick.off |
| 11 | AMPAR-GRIP-PICK1 → AMPAR + GRIP + PICK1 | k.ampar-grip.off |
| 12 | AMPAR-GRIP-PICK1-PKC* → AMPAR + GRIP + PICK1-PKC* | k.ampar-grip.off |
| 13 | AMPAR + NSF → AMPAR-NSF (endosome only) | k.ansf.on |
| 14 | AMPAR-NSF → AMPAR + NSF (endosome only) | k.ansf.off |
| AMPAR Lateral Diffusion (between PSD and extra-synaptic area, X) | ||
| 15 | AMPAR → AMPAR(X) | k.diff.psd-x |
| 16 | AMPAR-PICK1 → AMPAR-PICK1(X) | k.diff.psd-x |
| 17 | AMPAR-PICK1-PKC* → AMPAR-PICK1-PKC*(X) | k.diff.psd-x |
| 18 | AMPAR(X) → AMPAR | k.diff.x-psd |
| 19 | AMPAR-PICK1(X) → AMPAR-PICK1 | k.diff.x-psd |
| 20 | AMPAR-PICK1-PKC*(X) → AMPAR-PICK1-PKC* | k.diff.x-psd |
| AMPAR Lateral Diffusion (between extra-synaptic area, X, and endocytic zone, EZ) | ||
| 21 | AMPAR(X) → AMPAR(EZ) | k.diff.x-ez |
| 22 | AMPAR-PICK1(X) → AMPAR-PICK1(EZ) | k.diff.x-ez |
| 23 | AMPAR-PICK1-PKC*(X) → AMPAR-PICK1-PKC*(EZ) | k.diff.x-ez |
| 24 | AMPAR(EZ) → AMPAR(X) | k.diff.ez-x |
| 25 | AMPAR-PICK1(EZ) → AMPAR-PICK1(X) | k.diff.ez-x |
| 26 | AMPAR-PICK1-PKC*(EZ) → AMPAR-PICK1-PKC*(X) | k.diff.ez-x |
| AMPAR Endocytosis and Exocytosis | ||
| 27 | AMPAR-PICK1(EZ) → AMPAR-PICK1(endosome) | k.endo |
| 28 | AMPAR-PICK1-PKC*(EZ) → AMPAR-PICK1-PKC*(endosome) | k.endo |
| 29 | AMPAR-NSF → AMPAR(X) | k.exo |
| Activation/inactivation of PKC | ||
| 30 | PKC → PKC* | pkc.act |
| 31 | PKC* → PKC | pkc.deact |
| PICK-PKC Interactions | ||
| 32 | PICK1 + PKC* → PICK1-PKC* | k.pick-pkc.on |
| 33 | PICK1-PKC* → PICK1 + PKC* | k.pick-pkc.off |
| PKC Phosphorylation at GluA2-S880 | ||
| 34 | AMPAR + PKC* → AMPARpS + PKC* | kcat.pkc, km.pkc |
| 35 | AMPAR-GRIP + PKC* → AMPARpS-GRIP + PKC* | kcat.pkc, km.pkc |
| 36 | AMPAR-PICK1 + PKC* → AMPApS-PICK1 + PKC* | kcat.pkc, km.pkc |
| 37 | AMPAR-GRIP-PICK1 + PKC* → AMPARpS-GRIP-PICK1 + PKC* | kcat.pkc, km.pkc |
| 38 | AMPAR-PICK1-PKC* → AMPARpS-PICK1-PKC* | kcat.pkc |
| 39 | AMPAR-GRIP-PICK1-PKC* → AMPARpS-GRIP-PICK1-PKC* | kcat.pkc |
| AMPARpS(880) Dephosphorylation | ||
| 40 | AMPARpS + PP2A → AMPAR + PP2A | kcat.pp2a, km.pp2a |
| 41 | AMPARpS-GRIP + PP2A → AMPAR-GRIP + PP2A | kcat.pp2a, km.pp2a |
| 42 | AMPARpS-PICK + PP2A → AMPAR-PICK + PP2A | kcat.pp2a, km.pp2a |
| 43 | AMPARpS-PICK-PKC* + PP2A → AMPAR-PICK-PKC* + PP2A | kcat.pp2a, km.pp2a |
| 44 | AMPARpS-GRIP-PICK + PP2A → AMPAR-GRIP-PICK + PP2A | kcat.pp2a, km.pp2a |
| 45 | AMPARpS-GRIP-PICK-PKC* + PP2A → AMPAR-GRIP-PICK-PKC* + PP2A | kcat.pp2a, km.pp2a |
| SFK Phosphorylation at GluA2-Y876 | ||
| 46 | AMPAR + SFK → AMPARpY + SFK | kcat.sfk, km.sfk |
| 47 | AMPAR-GRIP + SFK → AMPARpY-GRIP + SFK | kcat.sfk, km.sfk |
| 48 | AMPAR-PICK + SFK → AMPARpY-PICK + SFK | kcat.sfk, km.sfk |
| 49 | AMPAR-PICK-PKC* + SFK → AMPARpY-PICK-PKC* + SFK | kcat.sfk, km.sfk |
| 50 | AMPAR-GRIP-PICK1 + SFK → AMPARpY-GRIP-PICK1 + SFK | kcat.sfk, km.sfk |
| 51 | AMPAR-GRIP-PICK1-PKC* + SFK → AMPARpY-GRIP-PICK1-PCK* + SFK | kcat.sfk, km.sfk |
| AMPARpY(876) Dephosphorylation | ||
| 52 | AMPARpY + PTPMEG → AMPAR + PTPMEG | kcat.ptpmeg, km.ptpmeg |
| 53 | AMPARpY-GRIP + PTPMEG → AMPAR-GRIP + PTPMEG | kcat.ptpmeg, km.ptpmeg |
| 54 | AMPARpY-PICK1 + PTPMEG → AMPAR-PICK1 + PTPMEG | kcat.ptpmeg, km.ptpmeg |
| 55 | AMPARpY-PICK1-PKC* + PTPMEG → AMPAR-PICK1-PKC* + PTPMEG | kcat.ptpmeg, km.ptpmeg |
| 56 | AMPARpY-GRIP-PICK1 + PTPMEG → AMPAR-GRIP-PICK1 + PTPMEG | kcat.ptpmeg, km.ptpmeg |
| 57 | AMPARpY-GRIP-PICK1-PKC* + PTPMEG → AMPAR-GRIP-PICK1-PKC* + PTPMEG | kcat.ptpmeg, km.ptpmeg |
† Barring reaction 3 (dissociation of AMPARpS880 from GRIP), ‘AMPAR’ denotes any of AMPAR, AMPARpS880 or AMPARpY876 that can participate in each reaction.
1rate for AMPAR species other than AMPARpS880
2rate for AMPARpS880