Location: BG_GiProtein @ 388451396a71 / BG_GPCR_sneyd.cellml
- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-26 08:45:13+12:00
- Desc:
- Adding MATLAB script to call function to find kinetic parameters. One for each module.
- Permanent Source URI:
- https://models.cellml.org/workspace/6f9/rawfile/388451396a719f4944f3bdbc3b121ce2855589df/BG_GPCR_sneyd.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_GPCR" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<!-- def unit per_sec as
unit second {expo: -1};
enddef;-->
<!-- def unit J_per_K_per_mol as
unit joule;
unit kelvin {expo: -1};
unit mole {expo: -1};
enddef;-->
<!-- def unit C_per_mol as
unit coulomb;
unit mole {expo: -1};
enddef;-->
<!-- def unit fmol as
unit mole {pref: femto};
enddef;-->
<!-- def unit fmol_per_L as
unit mole {pref: femto};
unit litre {expo: -1};
enddef;-->
<!-- def unit fmol_per_L_per_sec as
unit fmol_per_L;
unit second {expo: -1};
enddef;-->
<!-- def unit per_sec_per_fmol_per_L as
unit second {expo: -1};
unit fmol_per_L {expo: -1};
enddef;-->
<!-- def unit per_fmol as
unit fmol {expo: -1};
enddef;-->
<!-- def unit fmol_per_sec as
unit fmol;
unit second {expo: -1};
enddef;-->
<!-- def unit J_per_mol as
unit joule;
unit mole {expo: -1};
enddef;-->
<!-- def unit mM as
unit mole {pref: milli};
unit litre {expo: -1};
enddef;-->
<!-- def unit uM as
unit mole {pref: micro};
unit litre {expo: -1};
enddef;-->
<!-- def unit mM_per_sec as
unit mM;
unit second {expo: -1.0};
enddef;-->
<!-- def unit uM_per_sec as
unit uM;
unit second {expo: -1.0};
enddef;-->
<!-- def unit pL as
unit litre {pref: pico};
enddef;-->
<!-- def unit m_to_u as
unit second {pref: micro};
unit second {pref: milli};
enddef;-->
<component name="GPCR_sneyd">
<variable name="t" public_interface="in" units="second"/>
<!-- Physical parameters-->
<variable initial_value="8.31" name="R" units="J_per_K_per_mol"/>
<variable initial_value="310" name="T" units="kelvin"/>
<variable initial_value="96485" name="F" units="C_per_mol"/>
<!-- 21july FKC with all 3 constraints, and detailed bal for ksig4m and for scheme2 kP2p. Merged GsabyGDP into G. R and LR in scheme 4. new constraint of R + L to LR using Gibbs free energy -->
<variable initial_value="45.2032" name="kappa_bind" units="fmol_per_sec"/>
<variable initial_value="0.000736499" name="kappa_act" units="fmol_per_sec"/>
<variable initial_value="0.0778247" name="kappa_hyd" units="fmol_per_sec"/>
<variable initial_value="0.000712931" name="kappa_reassoc" units="fmol_per_sec"/>
<variable initial_value="3.34204" name="K_L" units="per_fmol"/>
<variable initial_value="1.53743e-07" name="K_R" units="per_fmol"/>
<variable initial_value="1.69722e-06" name="K_G" units="per_fmol"/>
<variable initial_value="3.34204" name="K_LR" units="per_fmol"/>
<variable initial_value="10.2795" name="K_a_GTP" units="per_fmol"/>
<variable initial_value="0.132085" name="K_beta_gamma" units="per_fmol"/>
<variable initial_value="0.0128494" name="K_a_GDP" units="per_fmol"/>
<!-- States (and initial conditions)
8jul21 original kinetic concs + equal division of enzyme states-->
<variable initial_value="0.000167285" name="q_L" units="fmol"/>
<variable initial_value="1.697e-06" name="q_LR" public_interface="out" units="fmol"/>
<variable initial_value="0.000219725" name="q_R" units="fmol"/>
<variable initial_value="0.145305" name="q_G" units="fmol"/>
<variable initial_value="0.0009519" name="q_a_GTP" units="fmol"/>
<variable initial_value="0.00097622" name="q_beta_gamma" units="fmol"/>
<variable initial_value="2.44948e-05" name="q_a_GDP" units="fmol"/>
<variable name="q_LR_global" public_interface="in" units="fmol"/>
<!-- Bond variables-->
<variable name="vbind" units="fmol_per_sec"/>
<variable name="vAct" units="fmol_per_sec"/>
<variable name="vHyd" units="fmol_per_sec"/>
<variable name="vReassoc" units="fmol_per_sec"/>
<variable name="mu_L" units="J_per_mol"/>
<variable name="mu_R" units="J_per_mol"/>
<variable name="mu_G" units="J_per_mol"/>
<variable name="mu_LR" units="J_per_mol"/>
<variable name="mu_a_GTP" units="J_per_mol"/>
<variable name="mu_beta_gamma" units="J_per_mol"/>
<variable name="mu_a_GDP" units="J_per_mol"/>
<!-- Concentrations - for plotting-->
<variable name="c_L" public_interface="out" units="uM"/>
<variable name="c_R" public_interface="out" units="uM"/>
<variable name="c_G" public_interface="out" units="uM"/>
<variable name="c_LR" public_interface="out" units="uM"/>
<variable name="c_a_GTP" public_interface="out" units="uM"/>
<variable name="c_beta_gamma" public_interface="out" units="uM"/>
<variable name="c_a_GDP" public_interface="out" units="uM"/>
<variable initial_value="38.0" name="vol" units="pL"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>c_L</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_L</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_R</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_R</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_G</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_G</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_LR</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_LR_global</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_a_GTP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_a_GTP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_beta_gamma</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_beta_gamma</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_a_GDP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_a_GDP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<!-- Constitutive equations-->
<apply>
<eq/>
<ci>mu_L</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_L</ci>
<ci>q_L</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R</ci>
<ci>q_R</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_G</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_G</ci>
<ci>q_G</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR</ci>
<ci>q_LR_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_a_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_a_GTP</ci>
<ci>q_a_GTP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_beta_gamma</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_beta_gamma</ci>
<ci>q_beta_gamma</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_a_GDP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_a_GDP</ci>
<ci>q_a_GDP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vbind</ci>
<apply>
<times/>
<ci>kappa_bind</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_L</ci>
<ci>mu_R</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vAct</ci>
<apply>
<times/>
<ci>kappa_Act</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_a_GTP</ci>
<ci>mu_beta_gamma</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vHyd</ci>
<apply>
<times/>
<ci>kappa_Hyd</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_a_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_a_GDP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vReassoc</ci>
<apply>
<times/>
<ci>kappa_Reassoc</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_a_GDP</ci>
<ci>mu_beta_gamma</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_G</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
<!-- velocity in uM_per_sec-->
<variable name="vAct_kinetic" units="uM_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>vAct_kinetic</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>vAct</ci>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_L</ci>
</apply>
<apply>
<minus/>
<ci>vbind</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_R</ci>
</apply>
<apply>
<minus/>
<ci>vbind</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_G</ci>
</apply>
<apply>
<minus/>
<ci>vReassoc</ci>
<ci>vAct</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_LR</ci>
</apply>
<apply>
<minus/>
<ci>vbind</ci>
<ci>vAct</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_a_GTP</ci>
</apply>
<apply>
<minus/>
<ci>vAct</ci>
<ci>vHyd</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_beta_gamma</ci>
</apply>
<apply>
<minus/>
<ci>vAct</ci>
<ci>vReassoc</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_a_GDP</ci>
</apply>
<apply>
<minus/>
<ci>vHyd</ci>
<ci>vReassoc</ci>
</apply>
</apply>
</math>
</component>
</model>