/* ===========================================================
Author: Daniel Keller
Institution: Ecole Polytechnique Federale de Lausanne
Reference: Keller D, Babai N, Kochubey O, Han Y, Markram H, Schürmann F, et al. (2015) An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse. PLoS Comput Biol 11(5): e1004253. doi:10.1371/journal.pcbi.1004253
============================================================= */
/* ------ Inserts unchanging mechanisms ----- */
/* generic calcium removal */
DEFINE_REACTIONS{
generic_pump.U' + Ca, -> generic_pump.B' [3e6]
generic_pump.B' -> generic_pump.U' [1e8]
}
/* Hodgkin Huxley models */
/*based on Borst and Sakmann 1998 */
/*J physiology 506.1 p 143-157 */
sprintf(file_str19,"%s%s",data_header_str,"twoalpham.dat")
sprintf(file_str20,"%s%s",data_header_str,"alpham.dat")
sprintf(file_str21,"%s%s",data_header_str,"twobetam.dat")
sprintf(file_str22,"%s%s",data_header_str,"betam.dat")
sprintf(file_kopencurrent,"%s%s",data_header_str,"kCav2_2calciumchannelcurrent.dat")
DEFINE_REACTIONS {
Ca_HH.C0 ' ->Ca_HH.C1' [file_str19]
Ca_HH.C1 ' ->Ca_HH.O' [file_str20]
Ca_HH.O ' ->Ca_HH.C1' [file_str21]
Ca_HH.C1 ' ->Ca_HH.C0' [file_str22]
Ca_HH.O ' ->Ca_HH.O' + Ca, [file_kopencurrent] : io_hh
}
/* --------- LVA Calcium channels ---------- */
sprintf(file_str3,"%s%s",data_header_str,"LVA_activation_rate.dat")
sprintf(file_str4,"%s%s",data_header_str,"lva_IV.dat")
DEFINE_REACTIONS {
Ca_LVA_head.C' ->Ca_LVA_head.O'[file_str3]
Ca_LVA_head.O' ->Ca_LVA_head.O' +Ca,[file_str4]
Ca_LVA_head.O' ->Ca_LVA_head.C'[1000]
Ca_LVA_neck.C' ->Ca_LVA_neck.O'[file_str3]
Ca_LVA_neck.O' ->Ca_LVA_neck.O' +Ca,[file_str4]
Ca_LVA_neck.O' ->Ca_LVA_neck.C'[1000]
}
/* -------- HVA Calcium channels ---------- */
/* based on Bischofberger and Jonas 2002 */
sprintf(file_str10,"%s%s",data_header_str,"hva_a1.dat")
sprintf(file_str11,"%s%s",data_header_str,"hva_b1.dat")
sprintf(file_str12,"%s%s",data_header_str,"hva_a2.dat")
sprintf(file_str13,"%s%s",data_header_str,"hva_b2.dat")
sprintf(file_str14,"%s%s",data_header_str,"hva_a3.dat")
sprintf(file_str15,"%s%s",data_header_str,"hva_b3.dat")
sprintf(file_str16,"%s%s",data_header_str,"hva_a4.dat")
sprintf(file_str17,"%s%s",data_header_str,"hva_b4.dat")
sprintf(file_str18,"%s%s",data_header_str,"hva_IV_2.5.dat")
DEFINE_REACTIONS {
Ca_HVA.C1' ->Ca_HVA.C2'[file_str10]
Ca_HVA.C2' ->Ca_HVA.C1'[file_str11]
Ca_HVA.C2' ->Ca_HVA.C3'[file_str12]
Ca_HVA.C3' ->Ca_HVA.C2'[file_str13]
Ca_HVA.C3' ->Ca_HVA.C4'[file_str14]
Ca_HVA.C4' ->Ca_HVA.C3'[file_str15]
Ca_HVA.C4' ->Ca_HVA.O5'[file_str16]
Ca_HVA.O5' ->Ca_HVA.C4'[file_str17]
Ca_HVA.O5' ->Ca_HVA.O5'+Ca,[file_str18] :hva_create
}
/* release events according to Schneggennerger */
DEFINE_REACTIONS {
release_sensor0.a.x0 -> release_sensor0.a.x6 [kx06]
release_sensor0.a.x0 +Ca <-> release_sensor0.a.x1 [>kx01,<kx10]
release_sensor0.a.x1 -> release_sensor0.a.x6 [kx16]
release_sensor0.a.x1 +Ca <-> release_sensor0.a.x2 [>kx12,<kx21]
release_sensor0.a.x2 -> release_sensor0.a.x6 [kx26]
release_sensor0.a.x2 +Ca <-> release_sensor0.a.x3 [>kx23,<kx32]
release_sensor0.a.x3 -> release_sensor0.a.x6 [kx36]
release_sensor0.a.x3 +Ca <-> release_sensor0.a.x4 [>kx34,<kx43]
release_sensor0.a.x4 -> release_sensor0.a.x6 [kx46]
release_sensor0.a.x4 +Ca <-> release_sensor0.a.x5 [>kx45,<kx54]
release_sensor0.a.x5 -> release_sensor0.a.x6 [kx56]
release_sensor1.a.x0 -> release_sensor1.a.x6 [kx06]
release_sensor1.a.x0 +Ca <-> release_sensor1.a.x1 [>kx01,<kx10]
release_sensor1.a.x1 -> release_sensor1.a.x6 [kx16]
release_sensor1.a.x1 +Ca <-> release_sensor1.a.x2 [>kx12,<kx21]
release_sensor1.a.x2 -> release_sensor1.a.x6 [kx26]
release_sensor1.a.x2 +Ca <-> release_sensor1.a.x3 [>kx23,<kx32]
release_sensor1.a.x3 -> release_sensor1.a.x6 [kx36]
release_sensor1.a.x3 +Ca <-> release_sensor1.a.x4 [>kx34,<kx43]
release_sensor1.a.x4 -> release_sensor1.a.x6 [kx46]
release_sensor1.a.x4 +Ca <-> release_sensor1.a.x5 [>kx45,<kx54]
release_sensor1.a.x5 -> release_sensor1.a.x6 [kx56]
release_sensor2.a.x0 -> release_sensor2.a.x6 [kx06]
release_sensor2.a.x0 +Ca <-> release_sensor2.a.x1 [>kx01,<kx10]
release_sensor2.a.x1 -> release_sensor2.a.x6 [kx16]
release_sensor2.a.x1 +Ca <-> release_sensor2.a.x2 [>kx12,<kx21]
release_sensor2.a.x2 -> release_sensor2.a.x6 [kx26]
release_sensor2.a.x2 +Ca <-> release_sensor2.a.x3 [>kx23,<kx32]
release_sensor2.a.x3 -> release_sensor2.a.x6 [kx36]
release_sensor2.a.x3 +Ca <-> release_sensor2.a.x4 [>kx34,<kx43]
release_sensor2.a.x4 -> release_sensor2.a.x6 [kx46]
release_sensor2.a.x4 +Ca <-> release_sensor2.a.x5 [>kx45,<kx54]
release_sensor2.a.x5 -> release_sensor2.a.x6 [kx56]
release_sensor3.a.x0 -> release_sensor3.a.x6 [kx06]
release_sensor3.a.x0 +Ca <-> release_sensor3.a.x1 [>kx01,<kx10]
release_sensor3.a.x1 -> release_sensor3.a.x6 [kx16]
release_sensor3.a.x1 +Ca <-> release_sensor3.a.x2 [>kx12,<kx21]
release_sensor3.a.x2 -> release_sensor3.a.x6 [kx26]
release_sensor3.a.x2 +Ca <-> release_sensor3.a.x3 [>kx23,<kx32]
release_sensor3.a.x3 -> release_sensor3.a.x6 [kx36]
release_sensor3.a.x3 +Ca <-> release_sensor3.a.x4 [>kx34,<kx43]
release_sensor3.a.x4 -> release_sensor3.a.x6 [kx46]
release_sensor3.a.x4 +Ca <-> release_sensor3.a.x5 [>kx45,<kx54]
release_sensor3.a.x5 -> release_sensor3.a.x6 [kx56]
release_sensor4.a.x0 -> release_sensor4.a.x6 [kx06]
release_sensor4.a.x0 +Ca <-> release_sensor4.a.x1 [>kx01,<kx10]
release_sensor4.a.x1 -> release_sensor4.a.x6 [kx16]
release_sensor4.a.x1 +Ca <-> release_sensor4.a.x2 [>kx12,<kx21]
release_sensor4.a.x2 -> release_sensor4.a.x6 [kx26]
release_sensor4.a.x2 +Ca <-> release_sensor4.a.x3 [>kx23,<kx32]
release_sensor4.a.x3 -> release_sensor4.a.x6 [kx36]
release_sensor4.a.x3 +Ca <-> release_sensor4.a.x4 [>kx34,<kx43]
release_sensor4.a.x4 -> release_sensor4.a.x6 [kx46]
release_sensor4.a.x4 +Ca <-> release_sensor4.a.x5 [>kx45,<kx54]
release_sensor4.a.x5 -> release_sensor4.a.x6 [kx56]
release_sensor5.a.x0 -> release_sensor5.a.x6 [kx06]
release_sensor5.a.x0 +Ca <-> release_sensor5.a.x1 [>kx01,<kx10]
release_sensor5.a.x1 -> release_sensor5.a.x6 [kx16]
release_sensor5.a.x1 +Ca <-> release_sensor5.a.x2 [>kx12,<kx21]
release_sensor5.a.x2 -> release_sensor5.a.x6 [kx26]
release_sensor5.a.x2 +Ca <-> release_sensor5.a.x3 [>kx23,<kx32]
release_sensor5.a.x3 -> release_sensor5.a.x6 [kx36]
release_sensor5.a.x3 +Ca <-> release_sensor5.a.x4 [>kx34,<kx43]
release_sensor5.a.x4 -> release_sensor5.a.x6 [kx46]
release_sensor5.a.x4 +Ca <-> release_sensor5.a.x5 [>kx45,<kx54]
release_sensor5.a.x5 -> release_sensor5.a.x6 [kx56]
release_sensor6.a.x0 -> release_sensor6.a.x6 [kx06]
release_sensor6.a.x0 +Ca <-> release_sensor6.a.x1 [>kx01,<kx10]
release_sensor6.a.x1 -> release_sensor6.a.x6 [kx16]
release_sensor6.a.x1 +Ca <-> release_sensor6.a.x2 [>kx12,<kx21]
release_sensor6.a.x2 -> release_sensor6.a.x6 [kx26]
release_sensor6.a.x2 +Ca <-> release_sensor6.a.x3 [>kx23,<kx32]
release_sensor6.a.x3 -> release_sensor6.a.x6 [kx36]
release_sensor6.a.x3 +Ca <-> release_sensor6.a.x4 [>kx34,<kx43]
release_sensor6.a.x4 -> release_sensor6.a.x6 [kx46]
release_sensor6.a.x4 +Ca <-> release_sensor6.a.x5 [>kx45,<kx54]
release_sensor6.a.x5 -> release_sensor6.a.x6 [kx56]
release_sensor7.a.x0 -> release_sensor7.a.x6 [kx06]
release_sensor7.a.x0 +Ca <-> release_sensor7.a.x1 [>kx01,<kx10]
release_sensor7.a.x1 -> release_sensor7.a.x6 [kx16]
release_sensor7.a.x1 +Ca <-> release_sensor7.a.x2 [>kx12,<kx21]
release_sensor7.a.x2 -> release_sensor7.a.x6 [kx26]
release_sensor7.a.x2 +Ca <-> release_sensor7.a.x3 [>kx23,<kx32]
release_sensor7.a.x3 -> release_sensor7.a.x6 [kx36]
release_sensor7.a.x3 +Ca <-> release_sensor7.a.x4 [>kx34,<kx43]
release_sensor7.a.x4 -> release_sensor7.a.x6 [kx46]
release_sensor7.a.x4 +Ca <-> release_sensor7.a.x5 [>kx45,<kx54]
release_sensor7.a.x5 -> release_sensor7.a.x6 [kx56]
release_sensor8.a.x0 -> release_sensor8.a.x6 [kx06]
release_sensor8.a.x0 +Ca <-> release_sensor8.a.x1 [>kx01,<kx10]
release_sensor8.a.x1 -> release_sensor8.a.x6 [kx16]
release_sensor8.a.x1 +Ca <-> release_sensor8.a.x2 [>kx12,<kx21]
release_sensor8.a.x2 -> release_sensor8.a.x6 [kx26]
release_sensor8.a.x2 +Ca <-> release_sensor8.a.x3 [>kx23,<kx32]
release_sensor8.a.x3 -> release_sensor8.a.x6 [kx36]
release_sensor8.a.x3 +Ca <-> release_sensor8.a.x4 [>kx34,<kx43]
release_sensor8.a.x4 -> release_sensor8.a.x6 [kx46]
release_sensor8.a.x4 +Ca <-> release_sensor8.a.x5 [>kx45,<kx54]
release_sensor8.a.x5 -> release_sensor8.a.x6 [kx56]
release_sensor9.a.x0 -> release_sensor9.a.x6 [kx06]
release_sensor9.a.x0 +Ca <-> release_sensor9.a.x1 [>kx01,<kx10]
release_sensor9.a.x1 -> release_sensor9.a.x6 [kx16]
release_sensor9.a.x1 +Ca <-> release_sensor9.a.x2 [>kx12,<kx21]
release_sensor9.a.x2 -> release_sensor9.a.x6 [kx26]
release_sensor9.a.x2 +Ca <-> release_sensor9.a.x3 [>kx23,<kx32]
release_sensor9.a.x3 -> release_sensor9.a.x6 [kx36]
release_sensor9.a.x3 +Ca <-> release_sensor9.a.x4 [>kx34,<kx43]
release_sensor9.a.x4 -> release_sensor9.a.x6 [kx46]
release_sensor9.a.x4 +Ca <-> release_sensor9.a.x5 [>kx45,<kx54]
release_sensor9.a.x5 -> release_sensor9.a.x6 [kx56]
release_sensor10.a.x0 -> release_sensor10.a.x6 [kx06]
release_sensor10.a.x0 +Ca <-> release_sensor10.a.x1 [>kx01,<kx10]
release_sensor10.a.x1 -> release_sensor10.a.x6 [kx16]
release_sensor10.a.x1 +Ca <-> release_sensor10.a.x2 [>kx12,<kx21]
release_sensor10.a.x2 -> release_sensor10.a.x6 [kx26]
release_sensor10.a.x2 +Ca <-> release_sensor10.a.x3 [>kx23,<kx32]
release_sensor10.a.x3 -> release_sensor10.a.x6 [kx36]
release_sensor10.a.x3 +Ca <-> release_sensor10.a.x4 [>kx34,<kx43]
release_sensor10.a.x4 -> release_sensor10.a.x6 [kx46]
release_sensor10.a.x4 +Ca <-> release_sensor10.a.x5 [>kx45,<kx54]
release_sensor10.a.x5 -> release_sensor10.a.x6 [kx56]
release_sensor11.a.x0 -> release_sensor11.a.x6 [kx06]
release_sensor11.a.x0 +Ca <-> release_sensor11.a.x1 [>kx01,<kx10]
release_sensor11.a.x1 -> release_sensor11.a.x6 [kx16]
release_sensor11.a.x1 +Ca <-> release_sensor11.a.x2 [>kx12,<kx21]
release_sensor11.a.x2 -> release_sensor11.a.x6 [kx26]
release_sensor11.a.x2 +Ca <-> release_sensor11.a.x3 [>kx23,<kx32]
release_sensor11.a.x3 -> release_sensor11.a.x6 [kx36]
release_sensor11.a.x3 +Ca <-> release_sensor11.a.x4 [>kx34,<kx43]
release_sensor11.a.x4 -> release_sensor11.a.x6 [kx46]
release_sensor11.a.x4 +Ca <-> release_sensor11.a.x5 [>kx45,<kx54]
release_sensor11.a.x5 -> release_sensor11.a.x6 [kx56]
release_sensor12.a.x0 -> release_sensor12.a.x6 [kx06]
release_sensor12.a.x0 +Ca <-> release_sensor12.a.x1 [>kx01,<kx10]
release_sensor12.a.x1 -> release_sensor12.a.x6 [kx16]
release_sensor12.a.x1 +Ca <-> release_sensor12.a.x2 [>kx12,<kx21]
release_sensor12.a.x2 -> release_sensor12.a.x6 [kx26]
release_sensor12.a.x2 +Ca <-> release_sensor12.a.x3 [>kx23,<kx32]
release_sensor12.a.x3 -> release_sensor12.a.x6 [kx36]
release_sensor12.a.x3 +Ca <-> release_sensor12.a.x4 [>kx34,<kx43]
release_sensor12.a.x4 -> release_sensor12.a.x6 [kx46]
release_sensor12.a.x4 +Ca <-> release_sensor12.a.x5 [>kx45,<kx54]
release_sensor12.a.x5 -> release_sensor12.a.x6 [kx56]
release_sensor13.a.x0 -> release_sensor13.a.x6 [kx06]
release_sensor13.a.x0 +Ca <-> release_sensor13.a.x1 [>kx01,<kx10]
release_sensor13.a.x1 -> release_sensor13.a.x6 [kx16]
release_sensor13.a.x1 +Ca <-> release_sensor13.a.x2 [>kx12,<kx21]
release_sensor13.a.x2 -> release_sensor13.a.x6 [kx26]
release_sensor13.a.x2 +Ca <-> release_sensor13.a.x3 [>kx23,<kx32]
release_sensor13.a.x3 -> release_sensor13.a.x6 [kx36]
release_sensor13.a.x3 +Ca <-> release_sensor13.a.x4 [>kx34,<kx43]
release_sensor13.a.x4 -> release_sensor13.a.x6 [kx46]
release_sensor13.a.x4 +Ca <-> release_sensor13.a.x5 [>kx45,<kx54]
release_sensor13.a.x5 -> release_sensor13.a.x6 [kx56]
release_sensor14.a.x0 -> release_sensor14.a.x6 [kx06]
release_sensor14.a.x0 +Ca <-> release_sensor14.a.x1 [>kx01,<kx10]
release_sensor14.a.x1 -> release_sensor14.a.x6 [kx16]
release_sensor14.a.x1 +Ca <-> release_sensor14.a.x2 [>kx12,<kx21]
release_sensor14.a.x2 -> release_sensor14.a.x6 [kx26]
release_sensor14.a.x2 +Ca <-> release_sensor14.a.x3 [>kx23,<kx32]
release_sensor14.a.x3 -> release_sensor14.a.x6 [kx36]
release_sensor14.a.x3 +Ca <-> release_sensor14.a.x4 [>kx34,<kx43]
release_sensor14.a.x4 -> release_sensor14.a.x6 [kx46]
release_sensor14.a.x4 +Ca <-> release_sensor14.a.x5 [>kx45,<kx54]
release_sensor14.a.x5 -> release_sensor14.a.x6 [kx56]
release_sensor15.a.x0 -> release_sensor15.a.x6 [kx06]
release_sensor15.a.x0 +Ca <-> release_sensor15.a.x1 [>kx01,<kx10]
release_sensor15.a.x1 -> release_sensor15.a.x6 [kx16]
release_sensor15.a.x1 +Ca <-> release_sensor15.a.x2 [>kx12,<kx21]
release_sensor15.a.x2 -> release_sensor15.a.x6 [kx26]
release_sensor15.a.x2 +Ca <-> release_sensor15.a.x3 [>kx23,<kx32]
release_sensor15.a.x3 -> release_sensor15.a.x6 [kx36]
release_sensor15.a.x3 +Ca <-> release_sensor15.a.x4 [>kx34,<kx43]
release_sensor15.a.x4 -> release_sensor15.a.x6 [kx46]
release_sensor15.a.x4 +Ca <-> release_sensor15.a.x5 [>kx45,<kx54]
release_sensor15.a.x5 -> release_sensor15.a.x6 [kx56]
release_sensor16.a.x0 -> release_sensor16.a.x6 [kx06]
release_sensor16.a.x0 +Ca <-> release_sensor16.a.x1 [>kx01,<kx10]
release_sensor16.a.x1 -> release_sensor16.a.x6 [kx16]
release_sensor16.a.x1 +Ca <-> release_sensor16.a.x2 [>kx12,<kx21]
release_sensor16.a.x2 -> release_sensor16.a.x6 [kx26]
release_sensor16.a.x2 +Ca <-> release_sensor16.a.x3 [>kx23,<kx32]
release_sensor16.a.x3 -> release_sensor16.a.x6 [kx36]
release_sensor16.a.x3 +Ca <-> release_sensor16.a.x4 [>kx34,<kx43]
release_sensor16.a.x4 -> release_sensor16.a.x6 [kx46]
release_sensor16.a.x4 +Ca <-> release_sensor16.a.x5 [>kx45,<kx54]
release_sensor16.a.x5 -> release_sensor16.a.x6 [kx56]
release_sensor17.a.x0 -> release_sensor17.a.x6 [kx06]
release_sensor17.a.x0 +Ca <-> release_sensor17.a.x1 [>kx01,<kx10]
release_sensor17.a.x1 -> release_sensor17.a.x6 [kx16]
release_sensor17.a.x1 +Ca <-> release_sensor17.a.x2 [>kx12,<kx21]
release_sensor17.a.x2 -> release_sensor17.a.x6 [kx26]
release_sensor17.a.x2 +Ca <-> release_sensor17.a.x3 [>kx23,<kx32]
release_sensor17.a.x3 -> release_sensor17.a.x6 [kx36]
release_sensor17.a.x3 +Ca <-> release_sensor17.a.x4 [>kx34,<kx43]
release_sensor17.a.x4 -> release_sensor17.a.x6 [kx46]
release_sensor17.a.x4 +Ca <-> release_sensor17.a.x5 [>kx45,<kx54]
release_sensor17.a.x5 -> release_sensor17.a.x6 [kx56]
release_sensor18.a.x0 -> release_sensor18.a.x6 [kx06]
release_sensor18.a.x0 +Ca <-> release_sensor18.a.x1 [>kx01,<kx10]
release_sensor18.a.x1 -> release_sensor18.a.x6 [kx16]
release_sensor18.a.x1 +Ca <-> release_sensor18.a.x2 [>kx12,<kx21]
release_sensor18.a.x2 -> release_sensor18.a.x6 [kx26]
release_sensor18.a.x2 +Ca <-> release_sensor18.a.x3 [>kx23,<kx32]
release_sensor18.a.x3 -> release_sensor18.a.x6 [kx36]
release_sensor18.a.x3 +Ca <-> release_sensor18.a.x4 [>kx34,<kx43]
release_sensor18.a.x4 -> release_sensor18.a.x6 [kx46]
release_sensor18.a.x4 +Ca <-> release_sensor18.a.x5 [>kx45,<kx54]
release_sensor18.a.x5 -> release_sensor18.a.x6 [kx56]
release_sensor19.a.x0 -> release_sensor19.a.x6 [kx06]
release_sensor19.a.x0 +Ca <-> release_sensor19.a.x1 [>kx01,<kx10]
release_sensor19.a.x1 -> release_sensor19.a.x6 [kx16]
release_sensor19.a.x1 +Ca <-> release_sensor19.a.x2 [>kx12,<kx21]
release_sensor19.a.x2 -> release_sensor19.a.x6 [kx26]
release_sensor19.a.x2 +Ca <-> release_sensor19.a.x3 [>kx23,<kx32]
release_sensor19.a.x3 -> release_sensor19.a.x6 [kx36]
release_sensor19.a.x3 +Ca <-> release_sensor19.a.x4 [>kx34,<kx43]
release_sensor19.a.x4 -> release_sensor19.a.x6 [kx46]
release_sensor19.a.x4 +Ca <-> release_sensor19.a.x5 [>kx45,<kx54]
release_sensor19.a.x5 -> release_sensor19.a.x6 [kx56]
release_sensor20.a.x0 -> release_sensor20.a.x6 [kx06]
release_sensor20.a.x0 +Ca <-> release_sensor20.a.x1 [>kx01,<kx10]
release_sensor20.a.x1 -> release_sensor20.a.x6 [kx16]
release_sensor20.a.x1 +Ca <-> release_sensor20.a.x2 [>kx12,<kx21]
release_sensor20.a.x2 -> release_sensor20.a.x6 [kx26]
release_sensor20.a.x2 +Ca <-> release_sensor20.a.x3 [>kx23,<kx32]
release_sensor20.a.x3 -> release_sensor20.a.x6 [kx36]
release_sensor20.a.x3 +Ca <-> release_sensor20.a.x4 [>kx34,<kx43]
release_sensor20.a.x4 -> release_sensor20.a.x6 [kx46]
release_sensor20.a.x4 +Ca <-> release_sensor20.a.x5 [>kx45,<kx54]
release_sensor20.a.x5 -> release_sensor20.a.x6 [kx56]
release_sensor21.a.x0 -> release_sensor21.a.x6 [kx06]
release_sensor21.a.x0 +Ca <-> release_sensor21.a.x1 [>kx01,<kx10]
release_sensor21.a.x1 -> release_sensor21.a.x6 [kx16]
release_sensor21.a.x1 +Ca <-> release_sensor21.a.x2 [>kx12,<kx21]
release_sensor21.a.x2 -> release_sensor21.a.x6 [kx26]
release_sensor21.a.x2 +Ca <-> release_sensor21.a.x3 [>kx23,<kx32]
release_sensor21.a.x3 -> release_sensor21.a.x6 [kx36]
release_sensor21.a.x3 +Ca <-> release_sensor21.a.x4 [>kx34,<kx43]
release_sensor21.a.x4 -> release_sensor21.a.x6 [kx46]
release_sensor21.a.x4 +Ca <-> release_sensor21.a.x5 [>kx45,<kx54]
release_sensor21.a.x5 -> release_sensor21.a.x6 [kx56]
release_sensor22.a.x0 -> release_sensor22.a.x6 [kx06]
release_sensor22.a.x0 +Ca <-> release_sensor22.a.x1 [>kx01,<kx10]
release_sensor22.a.x1 -> release_sensor22.a.x6 [kx16]
release_sensor22.a.x1 +Ca <-> release_sensor22.a.x2 [>kx12,<kx21]
release_sensor22.a.x2 -> release_sensor22.a.x6 [kx26]
release_sensor22.a.x2 +Ca <-> release_sensor22.a.x3 [>kx23,<kx32]
release_sensor22.a.x3 -> release_sensor22.a.x6 [kx36]
release_sensor22.a.x3 +Ca <-> release_sensor22.a.x4 [>kx34,<kx43]
release_sensor22.a.x4 -> release_sensor22.a.x6 [kx46]
release_sensor22.a.x4 +Ca <-> release_sensor22.a.x5 [>kx45,<kx54]
release_sensor22.a.x5 -> release_sensor22.a.x6 [kx56]
release_sensor23.a.x0 -> release_sensor23.a.x6 [kx06]
release_sensor23.a.x0 +Ca <-> release_sensor23.a.x1 [>kx01,<kx10]
release_sensor23.a.x1 -> release_sensor23.a.x6 [kx16]
release_sensor23.a.x1 +Ca <-> release_sensor23.a.x2 [>kx12,<kx21]
release_sensor23.a.x2 -> release_sensor23.a.x6 [kx26]
release_sensor23.a.x2 +Ca <-> release_sensor23.a.x3 [>kx23,<kx32]
release_sensor23.a.x3 -> release_sensor23.a.x6 [kx36]
release_sensor23.a.x3 +Ca <-> release_sensor23.a.x4 [>kx34,<kx43]
release_sensor23.a.x4 -> release_sensor23.a.x6 [kx46]
release_sensor23.a.x4 +Ca <-> release_sensor23.a.x5 [>kx45,<kx54]
release_sensor23.a.x5 -> release_sensor23.a.x6 [kx56]
release_sensor24.a.x0 -> release_sensor24.a.x6 [kx06]
release_sensor24.a.x0 +Ca <-> release_sensor24.a.x1 [>kx01,<kx10]
release_sensor24.a.x1 -> release_sensor24.a.x6 [kx16]
release_sensor24.a.x1 +Ca <-> release_sensor24.a.x2 [>kx12,<kx21]
release_sensor24.a.x2 -> release_sensor24.a.x6 [kx26]
release_sensor24.a.x2 +Ca <-> release_sensor24.a.x3 [>kx23,<kx32]
release_sensor24.a.x3 -> release_sensor24.a.x6 [kx36]
release_sensor24.a.x3 +Ca <-> release_sensor24.a.x4 [>kx34,<kx43]
release_sensor24.a.x4 -> release_sensor24.a.x6 [kx46]
release_sensor24.a.x4 +Ca <-> release_sensor24.a.x5 [>kx45,<kx54]
release_sensor24.a.x5 -> release_sensor24.a.x6 [kx56]
release_sensor25.a.x0 -> release_sensor25.a.x6 [kx06]
release_sensor25.a.x0 +Ca <-> release_sensor25.a.x1 [>kx01,<kx10]
release_sensor25.a.x1 -> release_sensor25.a.x6 [kx16]
release_sensor25.a.x1 +Ca <-> release_sensor25.a.x2 [>kx12,<kx21]
release_sensor25.a.x2 -> release_sensor25.a.x6 [kx26]
release_sensor25.a.x2 +Ca <-> release_sensor25.a.x3 [>kx23,<kx32]
release_sensor25.a.x3 -> release_sensor25.a.x6 [kx36]
release_sensor25.a.x3 +Ca <-> release_sensor25.a.x4 [>kx34,<kx43]
release_sensor25.a.x4 -> release_sensor25.a.x6 [kx46]
release_sensor25.a.x4 +Ca <-> release_sensor25.a.x5 [>kx45,<kx54]
release_sensor25.a.x5 -> release_sensor25.a.x6 [kx56]
release_sensor26.a.x0 -> release_sensor26.a.x6 [kx06]
release_sensor26.a.x0 +Ca <-> release_sensor26.a.x1 [>kx01,<kx10]
release_sensor26.a.x1 -> release_sensor26.a.x6 [kx16]
release_sensor26.a.x1 +Ca <-> release_sensor26.a.x2 [>kx12,<kx21]
release_sensor26.a.x2 -> release_sensor26.a.x6 [kx26]
release_sensor26.a.x2 +Ca <-> release_sensor26.a.x3 [>kx23,<kx32]
release_sensor26.a.x3 -> release_sensor26.a.x6 [kx36]
release_sensor26.a.x3 +Ca <-> release_sensor26.a.x4 [>kx34,<kx43]
release_sensor26.a.x4 -> release_sensor26.a.x6 [kx46]
release_sensor26.a.x4 +Ca <-> release_sensor26.a.x5 [>kx45,<kx54]
release_sensor26.a.x5 -> release_sensor26.a.x6 [kx56]
release_sensor27.a.x0 -> release_sensor27.a.x6 [kx06]
release_sensor27.a.x0 +Ca <-> release_sensor27.a.x1 [>kx01,<kx10]
release_sensor27.a.x1 -> release_sensor27.a.x6 [kx16]
release_sensor27.a.x1 +Ca <-> release_sensor27.a.x2 [>kx12,<kx21]
release_sensor27.a.x2 -> release_sensor27.a.x6 [kx26]
release_sensor27.a.x2 +Ca <-> release_sensor27.a.x3 [>kx23,<kx32]
release_sensor27.a.x3 -> release_sensor27.a.x6 [kx36]
release_sensor27.a.x3 +Ca <-> release_sensor27.a.x4 [>kx34,<kx43]
release_sensor27.a.x4 -> release_sensor27.a.x6 [kx46]
release_sensor27.a.x4 +Ca <-> release_sensor27.a.x5 [>kx45,<kx54]
release_sensor27.a.x5 -> release_sensor27.a.x6 [kx56]
release_sensor28.a.x0 -> release_sensor28.a.x6 [kx06]
release_sensor28.a.x0 +Ca <-> release_sensor28.a.x1 [>kx01,<kx10]
release_sensor28.a.x1 -> release_sensor28.a.x6 [kx16]
release_sensor28.a.x1 +Ca <-> release_sensor28.a.x2 [>kx12,<kx21]
release_sensor28.a.x2 -> release_sensor28.a.x6 [kx26]
release_sensor28.a.x2 +Ca <-> release_sensor28.a.x3 [>kx23,<kx32]
release_sensor28.a.x3 -> release_sensor28.a.x6 [kx36]
release_sensor28.a.x3 +Ca <-> release_sensor28.a.x4 [>kx34,<kx43]
release_sensor28.a.x4 -> release_sensor28.a.x6 [kx46]
release_sensor28.a.x4 +Ca <-> release_sensor28.a.x5 [>kx45,<kx54]
release_sensor28.a.x5 -> release_sensor28.a.x6 [kx56]
release_sensor29.a.x0 -> release_sensor29.a.x6 [kx06]
release_sensor29.a.x0 +Ca <-> release_sensor29.a.x1 [>kx01,<kx10]
release_sensor29.a.x1 -> release_sensor29.a.x6 [kx16]
release_sensor29.a.x1 +Ca <-> release_sensor29.a.x2 [>kx12,<kx21]
release_sensor29.a.x2 -> release_sensor29.a.x6 [kx26]
release_sensor29.a.x2 +Ca <-> release_sensor29.a.x3 [>kx23,<kx32]
release_sensor29.a.x3 -> release_sensor29.a.x6 [kx36]
release_sensor29.a.x3 +Ca <-> release_sensor29.a.x4 [>kx34,<kx43]
release_sensor29.a.x4 -> release_sensor29.a.x6 [kx46]
release_sensor29.a.x4 +Ca <-> release_sensor29.a.x5 [>kx45,<kx54]
release_sensor29.a.x5 -> release_sensor29.a.x6 [kx56]
release_sensor30.a.x0 -> release_sensor30.a.x6 [kx06]
release_sensor30.a.x0 +Ca <-> release_sensor30.a.x1 [>kx01,<kx10]
release_sensor30.a.x1 -> release_sensor30.a.x6 [kx16]
release_sensor30.a.x1 +Ca <-> release_sensor30.a.x2 [>kx12,<kx21]
release_sensor30.a.x2 -> release_sensor30.a.x6 [kx26]
release_sensor30.a.x2 +Ca <-> release_sensor30.a.x3 [>kx23,<kx32]
release_sensor30.a.x3 -> release_sensor30.a.x6 [kx36]
release_sensor30.a.x3 +Ca <-> release_sensor30.a.x4 [>kx34,<kx43]
release_sensor30.a.x4 -> release_sensor30.a.x6 [kx46]
release_sensor30.a.x4 +Ca <-> release_sensor30.a.x5 [>kx45,<kx54]
release_sensor30.a.x5 -> release_sensor30.a.x6 [kx56]
release_sensor31.a.x0 -> release_sensor31.a.x6 [kx06]
release_sensor31.a.x0 +Ca <-> release_sensor31.a.x1 [>kx01,<kx10]
release_sensor31.a.x1 -> release_sensor31.a.x6 [kx16]
release_sensor31.a.x1 +Ca <-> release_sensor31.a.x2 [>kx12,<kx21]
release_sensor31.a.x2 -> release_sensor31.a.x6 [kx26]
release_sensor31.a.x2 +Ca <-> release_sensor31.a.x3 [>kx23,<kx32]
release_sensor31.a.x3 -> release_sensor31.a.x6 [kx36]
release_sensor31.a.x3 +Ca <-> release_sensor31.a.x4 [>kx34,<kx43]
release_sensor31.a.x4 -> release_sensor31.a.x6 [kx46]
release_sensor31.a.x4 +Ca <-> release_sensor31.a.x5 [>kx45,<kx54]
release_sensor31.a.x5 -> release_sensor31.a.x6 [kx56]
release_sensor32.a.x0 -> release_sensor32.a.x6 [kx06]
release_sensor32.a.x0 +Ca <-> release_sensor32.a.x1 [>kx01,<kx10]
release_sensor32.a.x1 -> release_sensor32.a.x6 [kx16]
release_sensor32.a.x1 +Ca <-> release_sensor32.a.x2 [>kx12,<kx21]
release_sensor32.a.x2 -> release_sensor32.a.x6 [kx26]
release_sensor32.a.x2 +Ca <-> release_sensor32.a.x3 [>kx23,<kx32]
release_sensor32.a.x3 -> release_sensor32.a.x6 [kx36]
release_sensor32.a.x3 +Ca <-> release_sensor32.a.x4 [>kx34,<kx43]
release_sensor32.a.x4 -> release_sensor32.a.x6 [kx46]
release_sensor32.a.x4 +Ca <-> release_sensor32.a.x5 [>kx45,<kx54]
release_sensor32.a.x5 -> release_sensor32.a.x6 [kx56]
release_sensor33.a.x0 -> release_sensor33.a.x6 [kx06]
release_sensor33.a.x0 +Ca <-> release_sensor33.a.x1 [>kx01,<kx10]
release_sensor33.a.x1 -> release_sensor33.a.x6 [kx16]
release_sensor33.a.x1 +Ca <-> release_sensor33.a.x2 [>kx12,<kx21]
release_sensor33.a.x2 -> release_sensor33.a.x6 [kx26]
release_sensor33.a.x2 +Ca <-> release_sensor33.a.x3 [>kx23,<kx32]
release_sensor33.a.x3 -> release_sensor33.a.x6 [kx36]
release_sensor33.a.x3 +Ca <-> release_sensor33.a.x4 [>kx34,<kx43]
release_sensor33.a.x4 -> release_sensor33.a.x6 [kx46]
release_sensor33.a.x4 +Ca <-> release_sensor33.a.x5 [>kx45,<kx54]
release_sensor33.a.x5 -> release_sensor33.a.x6 [kx56]
release_sensor_surface0.a.x0' -> release_sensor_surface0.a.x6' [kx06]
release_sensor_surface0.a.x0' +Ca, <-> release_sensor_surface0.a.x1' [>kx01,<kx10]
release_sensor_surface0.a.x1' -> release_sensor_surface0.a.x6' [kx16]
release_sensor_surface0.a.x1' +Ca, <-> release_sensor_surface0.a.x2' [>kx12,<kx21]
release_sensor_surface0.a.x2' -> release_sensor_surface0.a.x6' [kx26]
release_sensor_surface0.a.x2' +Ca, <-> release_sensor_surface0.a.x3' [>kx23,<kx32]
release_sensor_surface0.a.x3' -> release_sensor_surface0.a.x6' [kx36]
release_sensor_surface0.a.x3' +Ca, <-> release_sensor_surface0.a.x4' [>kx34,<kx43]
release_sensor_surface0.a.x4' -> release_sensor_surface0.a.x6' [kx46]
release_sensor_surface0.a.x4' +Ca, <-> release_sensor_surface0.a.x5' [>kx45,<kx54]
release_sensor_surface0.a.x5' -> release_sensor_surface0.a.x6' [kx56]
}
/* ------- AMPA mechanism from Jonas et al. J Physiol. 1993 Dec;472:615-63 -------- */
DEFINE_REACTIONS {
AMPA.C0' +Glu'->AMPA.C1'[AMPA_kC0C1]
AMPA.C1' +Glu'->AMPA.C2'[AMPA_kC1C2]
AMPA.C1' ->AMPA.C3'[AMPA_kC1C3]
AMPA.C1' ->AMPA.C0'+Glu'[AMPA_kC1C0]
AMPA.C2' ->AMPA.O'[AMPA_kC2O]
AMPA.C2' ->AMPA.C4'[AMPA_kC2C4]
AMPA.C2' ->AMPA.C1'+Glu'[AMPA_kC2C1]
AMPA.C3' +Glu'->AMPA.C4'[AMPA_kC3C4]
AMPA.C3' ->AMPA.C1'[AMPA_kC3C1]
AMPA.C4' ->AMPA.C5'[AMPA_kC4C5]
AMPA.C4' ->AMPA.C2'[AMPA_kC4C2]
AMPA.C4' ->AMPA.C3'+Glu'[AMPA_kC4C3]
AMPA.C5' ->AMPA.C4'[AMPA_kC5C4]
AMPA.C5' ->AMPA.O'[AMPA_kC5O]
AMPA.O' ->AMPA.C2'[AMPA_kOC2]
AMPA.O' ->AMPA.C5'[AMPA_kOC5]
}
/* A model based on Popescu Robert Howe Auerbach Nature 2004 */
DEFINE_REACTIONS {
NMDA_H.CU' + Glu' -> NMDA_H.CM'[NMDA_H_CU_CM ]
NMDA_H.CM' + Glu' -> NMDA_H.C1'[NMDA_H_CM_C1 ]
NMDA_H.CM' -> NMDA_H.CU'[NMDA_H_CM_CU ]
NMDA_H.C1' -> NMDA_H.CM'[NMDA_H_C1_CM ]
NMDA_H.C1' -> NMDA_H.C2'[NMDA_H_C1_C2 ]
NMDA_H.C2' -> NMDA_H.C1'[NMDA_H_C2_C1 ]
NMDA_H.C2' -> NMDA_H.C3'[NMDA_H_C2_C3 ]
NMDA_H.C3' -> NMDA_H.C2'[NMDA_H_C3_C2 ]
NMDA_H.C3' -> NMDA_H.O1'[NMDA_H_C3_O1 ]
NMDA_H.O1' -> NMDA_H.O2'[NMDA_H_O1_O2 ]
NMDA_H.O1' -> NMDA_H.C3'[NMDA_H_O1_C3 ]
NMDA_H.O2' -> NMDA_H.O1'[NMDA_H_O2_O1 ]
NMDA_H.O1' -> NMDA_H.O1'+Ca,[NMDA_GENERATE_CA]
NMDA_H.O2' -> NMDA_H.O2'+Ca,[NMDA_GENERATE_CA]
NMDA_M.CU' + Glu' -> NMDA_M.CM'[NMDA_M_CU_CM ]
NMDA_M.CM' + Glu' -> NMDA_M.C1'[NMDA_M_CM_C1 ]
NMDA_M.CM' -> NMDA_M.CU'[NMDA_M_CM_CU ]
NMDA_M.C1' -> NMDA_M.CM'[NMDA_M_C1_CM ]
NMDA_M.C1' -> NMDA_M.C2'[NMDA_M_C1_C2 ]
NMDA_M.C2' -> NMDA_M.C1'[NMDA_M_C2_C1 ]
NMDA_M.C2' -> NMDA_M.C3'[NMDA_M_C2_C3 ]
NMDA_M.C3' -> NMDA_M.C2'[NMDA_M_C3_C2 ]
NMDA_M.C3' -> NMDA_M.O1'[NMDA_M_C3_O1 ]
NMDA_M.O1' -> NMDA_M.O2'[NMDA_M_O1_O2 ]
NMDA_M.O1' -> NMDA_M.C3'[NMDA_M_O1_C3 ]
NMDA_M.O2' -> NMDA_M.O1'[NMDA_M_O2_O1 ]
NMDA_M.O1' -> NMDA_M.O1'+Ca,[NMDA_GENERATE_CA]
NMDA_M.O2' -> NMDA_M.O2'+Ca,[NMDA_GENERATE_CA]
NMDA_L.CU' + Glu' -> NMDA_L.CM'[NMDA_L_CU_CM ]
NMDA_L.CM' + Glu' -> NMDA_L.C1'[NMDA_L_CM_C1 ]
NMDA_L.CM' -> NMDA_L.CU'[NMDA_L_CM_CU ]
NMDA_L.C1' -> NMDA_L.CM'[NMDA_L_C1_CM ]
NMDA_L.C1' -> NMDA_L.C2'[NMDA_L_C1_C2 ]
NMDA_L.C1' -> NMDA_L.D'[NMDA_L_C1_D ]
NMDA_L.D' -> NMDA_L.C1'[NMDA_L_D_C1 ]
NMDA_L.C2' -> NMDA_L.C1'[NMDA_L_C2_C1 ]
NMDA_L.C2' -> NMDA_L.C3'[NMDA_L_C2_C3 ]
NMDA_L.C3' -> NMDA_L.C2'[NMDA_L_C3_C2 ]
NMDA_L.C3' -> NMDA_L.O1'[NMDA_L_C3_O1 ]
NMDA_L.O1' -> NMDA_L.O2'[NMDA_L_O1_O2 ]
NMDA_L.O1' -> NMDA_L.C3'[NMDA_L_O1_C3 ]
NMDA_L.O2' -> NMDA_L.O1'[NMDA_L_O2_O1 ]
NMDA_L.O1' -> NMDA_L.O1'+Ca,[NMDA_GENERATE_CA]
NMDA_L.O2' -> NMDA_L.O2'+Ca,[NMDA_GENERATE_CA]
NMDA_L.CUB' + Glu' -> NMDA_L.CMB'[NMDA_L_CU_CM ]
NMDA_L.CMB' + Glu' -> NMDA_L.C1B'[NMDA_L_CM_C1 ]
NMDA_L.CMB' -> NMDA_L.CUB'[NMDA_L_CM_CU ]
NMDA_L.C1B' -> NMDA_L.CMB'[NMDA_L_C1_CM ]
NMDA_L.C1B' -> NMDA_L.C2B'[NMDA_L_C1_C2 ]
NMDA_L.C1B' -> NMDA_L.DB'[NMDA_L_C1_D ]
NMDA_L.DB' -> NMDA_L.C1B'[NMDA_L_D_C1 ]
NMDA_L.C2B' -> NMDA_L.C1B'[NMDA_L_C2_C1 ]
NMDA_L.C2B' -> NMDA_L.C3B'[NMDA_L_C2_C3 ]
NMDA_L.C3B' -> NMDA_L.C2B'[NMDA_L_C3_C2 ]
NMDA_L.C3B' -> NMDA_L.O1B'[NMDA_L_C3_O1 ]
NMDA_L.O1B' -> NMDA_L.O2B'[NMDA_L_O1_O2 ]
NMDA_L.O1B' -> NMDA_L.C3B'[NMDA_L_O1_C3 ]
NMDA_L.O2B' -> NMDA_L.O1B'[NMDA_L_O2_O1 ]
NMDA_L.CU' -> NMDA_L.CUB'[NMDA_kB]
NMDA_L.CM' -> NMDA_L.CMB'[NMDA_kB]
NMDA_L.C1' -> NMDA_L.C1B'[NMDA_kB]
NMDA_L.C2' -> NMDA_L.C2B'[NMDA_kB]
NMDA_L.C3' -> NMDA_L.C3B'[NMDA_kB]
NMDA_L.O1' -> NMDA_L.O1B'[NMDA_kB]
NMDA_L.O2' -> NMDA_L.O2B'[NMDA_kB]
NMDA_L.D' -> NMDA_L.DB'[NMDA_kB]
NMDA_L.CUB' -> NMDA_L.CU'[NMDA_kU]
NMDA_L.CMB' -> NMDA_L.CM'[NMDA_kU]
NMDA_L.C1B' -> NMDA_L.C1'[NMDA_kU]
NMDA_L.C2B' -> NMDA_L.C2'[NMDA_kU]
NMDA_L.C3B' -> NMDA_L.C3'[NMDA_kU]
NMDA_L.O1B' -> NMDA_L.O1'[NMDA_kU]
NMDA_L.O2B' -> NMDA_L.O2'[NMDA_kU]
NMDA_L.DB' -> NMDA_L.D'[NMDA_kU]
}
/*A reduced Lester and Jahr mechanism */
DEFINE_REACTIONS {
NMDA_ljsimple.C2' ->NMDA_ljsimple.O'[91.6]
NMDA_ljsimple.O' ->NMDA_ljsimple.C2'[46.5]
NMDA_ljsimple.O' ->NMDA_ljsimple.O'+Ca,[1.42e6/15]
NMDA_ljsimple.O' ->NMDA_ljsimple.C1'[2*4.7]
NMDA_ljsimple.C2' ->NMDA_ljsimple.C1'[2*4.7]
}
/* ----- NMDA mechanism Destexhe et al., Comput Neurosci. 1994 Aug;1(3):195-230 -------- */
DEFINE_REACTIONS {
NMDA_simple.C0' +Glu' ->NMDA_simple.C1'[NMDA_kC0C1]
NMDA_simple.C1' +Glu' ->NMDA_simple.C2'[NMDA_kC1C2]
NMDA_simple.C1' ->NMDA_simple.C0'+Glu'[NMDA_kC1C0]
NMDA_simple.C2' ->NMDA_simple.O'[NMDA_kC2O]
NMDA_simple.C2' ->NMDA_simple.C1'+Glu'[NMDA_kC2C1]
NMDA_simple.C2' ->NMDA_simple.D'[NMDA_kC2D]
NMDA_simple.D' ->NMDA_simple.C2'[NMDA_kDC2]
NMDA_simple.O' ->NMDA_simple.C2'[NMDA_kOC2]
}
/* ----- NMDA mechanism w/ Mg2+-block ------*/
DEFINE_REACTIONS {
NMDA.C0'+Glu'->NMDA.C1'[NMDA_kC0C1]
NMDA.C1'+Glu'->NMDA.C2'[NMDA_kC1C2]
NMDA.C1' ->NMDA.C0'+Glu'[NMDA_kC1C0]
NMDA.C2' ->NMDA.O'[NMDA_kC2O]
NMDA.C2' ->NMDA.C1'+Glu'[NMDA_kC2C1]
NMDA.C2' ->NMDA.D'[NMDA_kC2D]
NMDA.D' ->NMDA.C2'[NMDA_kDC2]
NMDA.O' ->NMDA.C2'[NMDA_kOC2]
NMDA.O' ->NMDA.OB'[NMDA_kB]
NMDA.O' ->NMDA.O'+Ca,[NMDA_GENERATE_CA]
NMDA.C0B'+Glu' ->NMDA.C1B'[NMDA_kC0C1]
NMDA.C1B'+Glu' ->NMDA.C2B'[NMDA_kC1C2]
NMDA.C1B' ->NMDA.C0B'+Glu'[NMDA_kC1C0]
NMDA.C2B' ->NMDA.OB'[NMDA_kC2Ob]
NMDA.C2B' ->NMDA.C1B'+Glu'[NMDA_kC2C1]
NMDA.C2B'->NMDA.DB'[NMDA_kC2D]
NMDA.DB' ->NMDA.C2B'[NMDA_kDC2]
NMDA.OB' ->NMDA.C2B'[NMDA_kOC2b]
NMDA.OB' ->NMDA.O'[NMDA_kU]
}
/* NR2B Banke and Traynelis, 2003 */
DEFINE_REACTIONS {
NR2B.R' + Glu' ->NR2B.RA' [kRRA]
NR2B.RA' -> NR2B.R' + Glu' [kRAR]
NR2B.RA' + Glu' -> NR2B.RA2' [kRARA2]
NR2B.RA2' -> NR2B.RA' + Glu'[kRA2RA]
NR2B.RA2' -> NR2B.RA2d1' [kRA2RA2d1]
NR2B.RA2' -> NR2B.RA2d2' [kRA2RA2d2]
NR2B.RA2' -> NR2B.RA2f' [kRA2RA2f]
NR2B.RA2' -> NR2B.RA2s'[kRA2RA2s]
NR2B.RA2d1' -> NR2B.RA2' [kRA2d1RA2]
NR2B.RA2d2' -> NR2B.RA2' [kRA2d2RA2]
NR2B.RA2f' -> NR2B.RA2' [kRA2fRA2]
NR2B.RA2f' -> NR2B.RA2o' [kRA2fRA2o]
NR2B.RA2s' -> NR2B.RA2' [kRA2sRA2]
NR2B.RA2s' -> NR2B.RA2o' [kRA2sRA2o]
NR2B.RA2o' -> NR2B.RA2f' [kRA2oRA2f]
NR2B.RA2o' -> NR2B.RA2s' [kRA2oRA2s]
NR2B.RA2o' -> NR2B.RA2o'+Ca,[NMDA_GENERATE_CA]
NR2B.B.R' + Glu' ->NR2B.B.RA' [kRRA]
NR2B.B.RA' -> NR2B.B.R' + Glu' [kRAR]
NR2B.B.RA' + Glu' -> NR2B.B.RA2' [kRARA2]
NR2B.B.RA2' -> NR2B.B.RA' + Glu'[kRA2RA]
NR2B.B.RA2' -> NR2B.B.RA2d1' [kRA2RA2d1]
NR2B.B.RA2' -> NR2B.B.RA2d2' [kRA2RA2d2]
NR2B.B.RA2' -> NR2B.B.RA2f' [kRA2RA2f]
NR2B.B.RA2' -> NR2B.B.RA2s'[kRA2RA2s]
NR2B.B.RA2d1' -> NR2B.B.RA2' [kRA2d1RA2]
NR2B.B.RA2d2' -> NR2B.B.RA2' [kRA2d2RA2]
NR2B.B.RA2f' -> NR2B.B.RA2' [kRA2fRA2]
NR2B.B.RA2f' -> NR2B.B.RA2o' [kRA2fRA2o]
NR2B.B.RA2s' -> NR2B.B.RA2' [kRA2sRA2]
NR2B.B.RA2s' -> NR2B.B.RA2o' [kRA2sRA2o]
NR2B.B.RA2o' -> NR2B.B.RA2f' [kRA2oRA2f]
NR2B.B.RA2o' -> NR2B.B.RA2s' [kRA2oRA2s]
NR2B.R' -> NR2B.B.R' [NMDA_kB]
NR2B.RA' -> NR2B.B.RA' [NMDA_kB]
NR2B.RA2' -> NR2B.B.RA2' [NMDA_kB]
NR2B.RA2d1' -> NR2B.B.RA2d1' [NMDA_kB]
NR2B.RA2d2' -> NR2B.B.RA2d2' [NMDA_kB]
NR2B.RA2f' -> NR2B.B.RA2f' [NMDA_kB]
NR2B.RA2s' -> NR2B.B.RA2s' [NMDA_kB]
NR2B.RA2o' -> NR2B.B.RA2o' [NMDA_kB]
NR2B.B.R' -> NR2B.R' [NMDA_kU]
NR2B.B.RA' -> NR2B.RA' [NMDA_kU]
NR2B.B.RA2' -> NR2B.RA2' [NMDA_kU]
NR2B.B.RA2d1' -> NR2B.RA2d1' [NMDA_kU]
NR2B.B.RA2d2' -> NR2B.RA2d2' [NMDA_kU]
NR2B.B.RA2f' -> NR2B.RA2f' [NMDA_kU]
NR2B.B.RA2s' -> NR2B.RA2s' [NMDA_kU]
NR2B.B.RA2o' -> NR2B.RA2o' [NMDA_kU]
}
/* ----- Glutamate uptake mechanism after Diamond and Jahr J Neurosci. 1997 Jun 15;17(12):4672-87.-------- */
DEFINE_REACTIONS {
GluT.T1' +Glu'->GluT.T2'[GluT_kT1T2]
GluT.T2' ->GluT.T3'[GluT_kT2T3]
GluT.T2' ->GluT.T1'+Glu'[GluT_kT2T1]
GluT.T3' ->GluT.T1'[GluT_kT3T1]
}
/* -------- Calcium Binding Protein Calbindin ------ */
DEFINE_REACTIONS {
calbindin.high0medium0+Ca->calbindin.high1medium0[calbindin_high_on]
calbindin.high1medium0->calbindin.high0medium0+Ca[calbindin_high_off]
calbindin.high1medium0+Ca->calbindin.high2medium0[calbindin_high_on]
calbindin.high2medium0->calbindin.high1medium0+Ca[calbindin_high_off]
calbindin.high0medium1+Ca->calbindin.high1medium1[calbindin_high_on]
calbindin.high1medium1->calbindin.high0medium1+Ca[calbindin_high_off]
calbindin.high1medium1+Ca->calbindin.high2medium1[calbindin_high_on]
calbindin.high2medium1->calbindin.high1medium1+Ca[calbindin_high_off]
calbindin.high0medium2+Ca->calbindin.high1medium2[calbindin_high_on]
calbindin.high1medium2->calbindin.high0medium2+Ca[calbindin_high_off]
calbindin.high1medium2+Ca->calbindin.high2medium2[calbindin_high_on]
calbindin.high2medium2->calbindin.high1medium2+Ca[calbindin_high_off]
calbindin.high0medium0+Ca->calbindin.high0medium1[calbindin_medium_on]
calbindin.high0medium1->calbindin.high0medium0+Ca[calbindin_medium_off]
calbindin.high0medium1+Ca->calbindin.high0medium2[calbindin_medium_on]
calbindin.high0medium2->calbindin.high0medium1+Ca[calbindin_medium_off]
calbindin.high1medium0+Ca->calbindin.high1medium1[calbindin_medium_on]
calbindin.high1medium1->calbindin.high1medium0+Ca[calbindin_medium_off]
calbindin.high1medium1+Ca->calbindin.high1medium2[calbindin_medium_on]
calbindin.high1medium2->calbindin.high1medium1+Ca[calbindin_medium_off]
calbindin.high2medium0+Ca->calbindin.high2medium1[calbindin_medium_on]
calbindin.high2medium1->calbindin.high2medium0+Ca[calbindin_medium_off]
calbindin.high2medium1+Ca->calbindin.high2medium2[calbindin_medium_on]
calbindin.high2medium2->calbindin.high2medium1+Ca[calbindin_medium_off]
}
DEFINE_REACTIONS{
caremover+Ca->caremover[1e9]
}
/* --------- CBPs; fast, medium, slow & v_slow -------- */
DEFINE_REACTIONS{
fast_sp.U+Ca->fast_sp.B[fast_on]
fast_sp.B->fast_sp.U+Ca[fast_off]
}
DEFINE_REACTIONS {
medium_sp.U+Ca->medium_sp.B[medium_on]
medium_sp.B->medium_sp.U+Ca[medium_off]
}
DEFINE_REACTIONS {
slow_sp.U+Ca->slow_sp.B[slow_on]
slow_sp.B->slow_sp.U+Ca[slow_off]
}
DEFINE_REACTIONS {
parvalbumin.U+Ca->parvalbumin.B[4e8]
parvalbumin.U->parvalbumin.M[Mgbase * (1e6)]
parvalbumin.B->parvalbumin.U+Ca[4]
parvalbumin.M->parvalbumin.U[30]
}
DEFINE_REACTIONS {
v_slow_sp.U+Ca->v_slow_sp.B[v_slow_on]
v_slow_sp.B->v_slow_sp.U+Ca[v_slow_off]
}
DEFINE_REACTIONS {
fluo_four_ff.U+Ca->fluo_four_ff.B[fluo_four_ff_on]
fluo_four_ff.B->fluo_four_ff.U+Ca[fluo_four_ff_off]
}
DEFINE_REACTIONS {
fluo_four_ff.10xmobile.U+Ca->fluo_four_ff.10xmobile.B[fluo_four_ff_on]
fluo_four_ff.10xmobile.B->fluo_four_ff.10xmobile.U+Ca[fluo_four_ff_off]
}
/* -------- Calcium sensor; Fluo-4ff ------ */
DEFINE_REACTIONS {
fluo_four_sp.U+Ca->fluo_four_sp.B[fluo_four_on]
fluo_four_sp.B->fluo_four_sp.U+Ca[fluo_four_off]
}
/* -------- Calcium sensor; Calcium Green ------ */
DEFINE_REACTIONS {
cal_green_sp.U+Ca->cal_green_sp.B[cal_green_on]
cal_green_sp.B->cal_green_sp.U+Ca[cal_green_off]
}
/* -------- Calcium sensor; Oregon Green - BAPTA-2 ------ */
DEFINE_REACTIONS {
OG_B_1_sp.U+Ca->OG_B_1_sp.B[OG_B_1_on]
OG_B_1_sp.B->OG_B_1_sp.U+Ca[OG_B_1_off]
}
DEFINE_REACTIONS {
OG_B_1_sp.10xmobile.U+Ca->OG_B_1_sp.10xmobile.B[OG_B_1_on]
OG_B_1_sp.10xmobile.B->OG_B_1_sp.10xmobile.U+Ca[OG_B_1_off]
}
DEFINE_REACTIONS {
OG_B_5_sp.U+Ca->OG_B_5_sp.B[OG_B_5_on]
OG_B_5_sp.B->OG_B_5_sp.U+Ca[OG_B_5_off]
}
DEFINE_REACTIONS {
NCX_pump_spine.U'+Ca,->NCX_pump_spine.B'[NCX_pump_for]
NCX_pump_spine.B'->NCX_pump_spine.U'+Ca,[NCX_pump_back]
NCX_pump_spine.B' ->NCX_pump_spine.U'[NCX_pump_kill] :ncxex
NCX_pump_spine.U' ->NCX_pump_spine.U'+Ca,[I_leak_NCX] :ncxin
NCX_pump_neck.U'+Ca,->NCX_pump_neck.B'[NCX_pump_for]
NCX_pump_neck.B'->NCX_pump_neck.U'+Ca,[NCX_pump_back]
NCX_pump_neck.B' ->NCX_pump_neck.U'[NCX_pump_kill]
NCX_pump_neck.U' ->NCX_pump_neck.U'+Ca,[I_leak_NCX]
NCX_pump_dendrite.U'+Ca,->NCX_pump_dendrite.B'[NCX_pump_for]
NCX_pump_dendrite.B'->NCX_pump_dendrite.U'+Ca,[NCX_pump_back]
NCX_pump_dendrite.B' ->NCX_pump_dendrite.U'[NCX_pump_kill]
NCX_pump_dendrite.U' ->NCX_pump_dendrite.U'+Ca,[I_leak_NCX]
}
/* ------ Extracellular extrusion pumps -------- */
DEFINE_REACTIONS {
ex_Ca_pump_spine.U'+Ca,->ex_Ca_pump_spine.B'[pump_for]
ex_Ca_pump_spine.B'->ex_Ca_pump_spine.U'+Ca,[pump_back]
ex_Ca_pump_spine.B' ->ex_Ca_pump_spine.U'[pump_kill] : pmcaex
ex_Ca_pump_spine.U' ->ex_Ca_pump_spine.U'+Ca,[I_leak_PMCA] : pmcain
ex_Ca_pump_neck.U'+Ca,->ex_Ca_pump_neck.B'[pump_for]
ex_Ca_pump_neck.B'->ex_Ca_pump_neck.U'+Ca,[pump_back]
ex_Ca_pump_neck.B' ->ex_Ca_pump_neck.U'[pump_kill]
ex_Ca_pump_neck.U' ->ex_Ca_pump_neck.U'+Ca,[I_leak_PMCA]
}
/* -------- Intracellular sequestration pump ------*/
/* 6-step Buffering SERCA Pump */
/* From Higgins et al, 2006, Biophys. J. */
/* Note: ignores Ca in the ER, assume constant Ca in ER */
DEFINE_REACTIONS {
Ca' + SERCA_X1' <-> SERCA_X1A' [>2*k_SERCA_X1_X1A, <k_SERCA_X1A_X1]
Ca' + SERCA_X1A' <-> SERCA_X2' [>k_SERCA_X1A_X2, <2*k_SERCA_X2_X1A]
SERCA_X2' <-> SERCA_Y2' [>k_SERCA_X2_Y2, <k_SERCA_Y2_X2]
SERCA_Y2' <-> SERCA_Y1A' [>2*k_SERCA_Y2_Y1A, <k_SERCA_Y1A_Y2]
SERCA_Y1A' <-> SERCA_Y1' [>k_SERCA_Y1A_Y1, <2*k_SERCA_Y1_Y1A]
SERCA_Y1' -> SERCA_X1' [k_SERCA_Y1_X1] :finalreturn
SERCA_X1' -> SERCA_Y1' [k_SERCA_X1_Y1]
SERCA_X1' -> SERCA_X1' + Ca' [k_ER_leak]
SERCA_X1A' -> SERCA_X1A' + Ca' [k_ER_leak]
SERCA_X2' -> SERCA_X2' + Ca' [k_ER_leak]
SERCA_Y2' -> SERCA_Y2' + Ca' [k_ER_leak]
SERCA_Y1' -> SERCA_Y1' + Ca' [k_ER_leak]
SERCA_Y1A' -> SERCA_Y1A' + Ca' [k_ER_leak]
}
/*simpler SERCA model */
DEFINE_REACTIONS {
SERCA.U'+Ca,->SERCA.B'[k_SERCA_for]
SERCA.B'->SERCA.U'+Ca,[k_SERCA_back]
SERCA.B' ->SERCA.U'[k_SERCA_kill]
SERCA.U' ->SERCA.U'+Ca,[k_SERCA_leak]
SERCA.B' ->SERCA.B'+Ca,[k_SERCA_leak]
}
DEFINE_REACTIONS{
ATP.U+Ca->ATP.CaB[katpCafor]
ATP.CaB->ATP.U+Ca[katpCaback]
ATP.U->ATP.MgB[Mgbase * katpMgfor]
ATP.MgB->ATP.U[katpMgback]
}
/* -------- Intracellular sequestration pump ------*/
DEFINE_REACTIONS {
int_Ca_pump_spine.U,+Ca,->int_Ca_pump_spine.B,[pump_for]
int_Ca_pump_spine.B,->int_Ca_pump_spine.U,+Ca,[pump_back]
int_Ca_pump_spine.B, ->int_Ca_pump_spine.K,[pump_kill]
int_Ca_pump_spine.K,->int_Ca_pump_spine.U,[pump_return]
int_Ca_pump_neck.U,+Ca,->int_Ca_pump_neck.B,[pump_for]
int_Ca_pump_neck.B,->int_Ca_pump_neck.U,+Ca,[pump_back]
int_Ca_pump_neck.B, ->int_Ca_pump_neck.K,[pump_kill]
int_Ca_pump_neck.K,->int_Ca_pump_neck.U,[pump_return]
}
/* Calcium leak mechanism */
DEFINE_REACTIONS {
Ca_leak.O' ->Ca_leak.O'+Ca,[I_leak]
}
/* ------- Define Calmodulin Reaction ------- */
DEFINE_REACTIONS {
calmodulin.B0+Ca ->calmodulin.B1[cam_for_1]
calmodulin.B1 ->calmodulin.B0+Ca[cam_back_1]
calmodulin.B1 +Ca ->calmodulin.B2[cam_for_2]
calmodulin.B2 ->calmodulin.B1+Ca[cam_back_2]
calmodulin.B2 +Ca ->calmodulin.B3[cam_for_3]
calmodulin.B3 ->calmodulin.B2+Ca[cam_back_3]
calmodulin.B3 +Ca ->calmodulin.B4[cam_for_4]
calmodulin.B4 ->calmodulin.B3+Ca[cam_back_4]
}
DEFINE_REACTIONS {
calmodulin_immobile.B0+Ca ->calmodulin_immobile.B1[cam_for_1]
calmodulin_immobile.B1 ->calmodulin_immobile.B0+Ca[cam_back_1]
calmodulin_immobile.B1 +Ca ->calmodulin_immobile.B2[cam_for_2]
calmodulin_immobile.B2 ->calmodulin_immobile.B1+Ca[cam_back_2]
calmodulin_immobile.B2 +Ca ->calmodulin_immobile.B3[cam_for_3]
calmodulin_immobile.B3 ->calmodulin_immobile.B2+Ca[cam_back_3]
calmodulin_immobile.B3 +Ca ->calmodulin_immobile.B4[cam_for_4]
calmodulin_immobile.B4 ->calmodulin_immobile.B3+Ca[cam_back_4]
}
DEFINE_REACTIONS {
EGTA.U + Ca ->EGTA.B [EGTA_on]
EGTA.B -> EGTA.U + Ca [EGTA_off]
}
DEFINE_REACTIONS {
EGTAimmobile.U + Ca ->EGTAimmobile.B [EGTA_on]
EGTAimmobile.B -> EGTAimmobile.U + Ca [EGTA_off]
}
DEFINE_REACTIONS {
BAPTA.U + Ca -> BAPTA.B [BAPTA_on]
BAPTA.B -> BAPTA.U + Ca [BAPTA_off]
}