- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-10-01 15:50:20+13:00
- Desc:
- Separate G from R in stoichiometry
- Permanent Source URI:
- https://models.cellml.org/workspace/6f8/rawfile/a3a885d3814c7115f5cc7522e31ed089571a7f01/BG_GsProtein.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_GsProtein" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="units_and_constants/units_BG.cellml">
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="fmol" units_ref="fmol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="mM" units_ref="mM"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!--Initial conditions-->
<variable initial_value="0.000219725" name="q_R_B1_init" units="fmol"/>
<variable initial_value="0.145305" name="q_Gs_init" units="fmol"/>
<variable initial_value="1e-6" name="q_R_B1Gs_init" units="fmol"/>
<variable initial_value="1.697e-06" name="q_LR_B1_init" units="fmol"/>
<variable initial_value="1e-6" name="q_LR_B1Gs_init" units="fmol"/>
<variable initial_value="0.0009519" name="q_aGs_GTP_init" units="fmol"/>
<variable initial_value="0.00097622" name="q_beta_gamma_Gs_init" units="fmol"/>
<variable initial_value="2.44948e-05" name="q_aGs_GDP_init" units="fmol"/>
<!-- Global value-->
<variable name="q_R_B1" public_interface="out" units="fmol"/>
<variable name="q_Gs" public_interface="out" units="fmol"/>
<variable name="q_R_B1Gs" public_interface="out" units="fmol"/>
<variable name="q_LR_B1" public_interface="out" units="fmol"/>
<variable name="q_LR_B1Gs" public_interface="out" units="fmol"/>
<variable name="q_aGs_GTP" public_interface="out" units="fmol"/>
<variable name="q_beta_gamma_Gs" public_interface="out" units="fmol"/>
<variable name="q_aGs_GDP" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="q_R_B1_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_Gs_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_R_B1Gs_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_LR_B1_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_LR_B1Gs_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_aGs_GTP_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_beta_gamma_Gs_mGsProtein" public_interface="in" units="fmol"/>
<variable name="q_aGs_GDP_mGsProtein" public_interface="in" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_R_B1</ci>
<apply>
<plus/>
<ci>q_R_B1_mGsProtein</ci>
<ci>q_R_B1_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Gs</ci>
<apply>
<plus/>
<ci>q_Gs_mGsProtein</ci>
<ci>q_Gs_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R_B1Gs</ci>
<apply>
<plus/>
<ci>q_R_B1Gs_mGsProtein</ci>
<ci>q_R_B1Gs_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_B1</ci>
<apply>
<plus/>
<ci>q_LR_B1_mGsProtein</ci>
<ci>q_LR_B1_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_B1Gs</ci>
<apply>
<plus/>
<ci>q_LR_B1Gs_mGsProtein</ci>
<ci>q_LR_B1Gs_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_aGs_GTP</ci>
<apply>
<plus/>
<ci>q_aGs_GTP_mGsProtein</ci>
<ci>q_aGs_GTP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_beta_gamma_Gs</ci>
<apply>
<plus/>
<ci>q_beta_gamma_Gs_mGsProtein</ci>
<ci>q_beta_gamma_Gs_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_aGs_GDP</ci>
<apply>
<plus/>
<ci>q_aGs_GDP_mGsProtein</ci>
<ci>q_aGs_GDP_init</ci>
</apply>
</apply>
</math>
</component>
<component name="GsProtein_parameters">
<variable initial_value="0.0598586" name="kappa_act1_Gs" units="fmol_per_sec"/>
<variable initial_value="0.0598586" name="kappa_act2_Gs" units="fmol_per_sec"/>
<variable initial_value="0.0204713" name="kappa_hyd_Gs" units="fmol_per_sec"/>
<variable initial_value="12975.8" name="kappa_reassoc_Gs" units="fmol_per_sec"/>
<variable initial_value="6.5099e-06" name="K_R_B1" units="per_fmol"/>
<variable initial_value="2.71077e-06" name="K_Gs" units="per_fmol"/>
<variable initial_value="7.77025" name="K_R_B1Gs" units="per_fmol"/>
<variable initial_value="6.5099e-06" name="K_LR_B1" units="per_fmol"/>
<variable initial_value="7.77025" name="K_LR_B1Gs" units="per_fmol"/>
<variable initial_value="1.13602" name="K_aGs_GTP" units="per_fmol"/>
<variable initial_value="0.0554931" name="K_beta_gamma_Gs" units="per_fmol"/>
<variable initial_value="0.00142002" name="K_aGs_GDP" units="per_fmol"/>
</component>
<component name="GsProtein">
<variable name="time" public_interface="in" units="second"/>
<!-- Physical parameters-->
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- BG parameters-->
<variable name="kappa_act1_Gs" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_act2_Gs" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_hyd_Gs" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_reassoc_Gs" public_interface="in" units="fmol_per_sec"/>
<variable name="K_R_B1" public_interface="in" units="per_fmol"/>
<variable name="K_Gs" public_interface="in" units="per_fmol"/>
<variable name="K_R_B1Gs" public_interface="in" units="per_fmol"/>
<variable name="K_LR_B1" public_interface="in" units="per_fmol"/>
<variable name="K_LR_B1Gs" public_interface="in" units="per_fmol"/>
<variable name="K_aGs_GTP" public_interface="in" units="per_fmol"/>
<variable name="K_beta_gamma_Gs" public_interface="in" units="per_fmol"/>
<variable name="K_aGs_GDP" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_R_B1_global" public_interface="in" units="fmol"/>
<variable name="q_Gs_global" public_interface="in" units="fmol"/>
<variable name="q_R_B1Gs_global" public_interface="in" units="fmol"/>
<variable name="q_LR_B1_global" public_interface="in" units="fmol"/>
<variable name="q_LR_B1Gs_global" public_interface="in" units="fmol"/>
<variable name="q_aGs_GTP_global" public_interface="in" units="fmol"/>
<variable name="q_beta_gamma_Gs_global" public_interface="in" units="fmol"/>
<variable name="q_aGs_GDP_global" public_interface="in" units="fmol"/>
<!-- Output to global environment-->
<variable initial_value="1e-16" name="q_R_B1" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Gs" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_R_B1Gs" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_B1" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_B1Gs" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_aGs_GTP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_beta_gamma_Gs" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_aGs_GDP" public_interface="out" units="fmol"/>
<!-- Bond variables-->
<variable name="vact1_Gs" units="fmol_per_sec"/>
<variable name="vact2_Gs" units="fmol_per_sec"/>
<variable name="vhyd_Gs" units="fmol_per_sec"/>
<variable name="vreassoc_Gs" units="fmol_per_sec"/>
<variable name="mu_R_B1" units="J_per_mol"/>
<variable name="mu_Gs" units="J_per_mol"/>
<variable name="mu_R_B1Gs" units="J_per_mol"/>
<variable name="mu_LR_B1" units="J_per_mol"/>
<variable name="mu_LR_B1Gs" units="J_per_mol"/>
<variable name="mu_aGs_GTP" units="J_per_mol"/>
<variable name="mu_beta_gamma_Gs" units="J_per_mol"/>
<variable name="mu_aGs_GDP" units="J_per_mol"/>
<!-- Constitutive equations-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_R_B1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_B1</ci>
<ci>q_R_B1_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Gs</ci>
<ci>q_Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_B1Gs</ci>
<ci>q_R_B1Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_B1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_B1</ci>
<ci>q_LR_B1_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_B1Gs</ci>
<ci>q_LR_B1Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_aGs_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_aGs_GTP</ci>
<ci>q_aGs_GTP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_beta_gamma_Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_beta_gamma_Gs</ci>
<ci>q_beta_gamma_Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_aGs_GDP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_aGs_GDP</ci>
<ci>q_aGs_GDP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vact1_Gs</ci>
<apply>
<times/>
<ci>kappa_act1_Gs</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_R_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGs_GTP</ci>
<ci>mu_beta_gamma_Gs</ci>
<ci>mu_R_B1</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vact2_Gs</ci>
<apply>
<times/>
<ci>kappa_act2_Gs</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGs_GTP</ci>
<ci>mu_beta_gamma_Gs</ci>
<ci>mu_LR_B1</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vhyd_Gs</ci>
<apply>
<times/>
<ci>kappa_hyd_Gs</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_aGs_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_aGs_GDP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vreassoc_Gs</ci>
<apply>
<times/>
<ci>kappa_reassoc_Gs</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGs_GDP</ci>
<ci>mu_beta_gamma_Gs</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_B1</ci>
</apply>
<ci>vact1_Gs</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_B1Gs</ci>
</apply>
<apply>
<minus/>
<ci>vact1_Gs</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Gs</ci>
</apply>
<ci>vreassoc_Gs</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_B1</ci>
</apply>
<ci>vact2_Gs</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_B1Gs</ci>
</apply>
<apply>
<minus/>
<ci>vact2_Gs</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_aGs_GTP</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>vact1_Gs</ci>
<ci>vact2_Gs</ci>
</apply>
<ci>vhyd_Gs</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_beta_gamma_Gs</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>vact1_Gs</ci>
<ci>vact2_Gs</ci>
</apply>
<ci>vreassoc_Gs</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_aGs_GDP</ci>
</apply>
<apply>
<minus/>
<ci>vhyd_Gs</ci>
<ci>vreassoc_Gs</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="GsProtein"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_R_B1_mGsProtein" variable_2="q_R_B1"/>
<map_variables variable_1="q_R_B1" variable_2="q_R_B1_global"/>
<map_variables variable_1="q_Gs_mGsProtein" variable_2="q_Gs"/>
<map_variables variable_1="q_Gs" variable_2="q_Gs_global"/>
<map_variables variable_1="q_R_B1Gs_mGsProtein" variable_2="q_R_B1Gs"/>
<map_variables variable_1="q_R_B1Gs" variable_2="q_R_B1Gs_global"/>
<map_variables variable_1="q_LR_B1_mGsProtein" variable_2="q_LR_B1"/>
<map_variables variable_1="q_LR_B1" variable_2="q_LR_B1_global"/>
<map_variables variable_1="q_LR_B1Gs_mGsProtein" variable_2="q_LR_B1Gs"/>
<map_variables variable_1="q_LR_B1Gs" variable_2="q_LR_B1Gs_global"/>
<map_variables variable_1="q_aGs_GTP_mGsProtein" variable_2="q_aGs_GTP"/>
<map_variables variable_1="q_aGs_GTP" variable_2="q_aGs_GTP_global"/>
<map_variables variable_1="q_beta_gamma_Gs_mGsProtein" variable_2="q_beta_gamma_Gs"/>
<map_variables variable_1="q_beta_gamma_Gs" variable_2="q_beta_gamma_Gs_global"/>
<map_variables variable_1="q_aGs_GDP_mGsProtein" variable_2="q_aGs_GDP"/>
<map_variables variable_1="q_aGs_GDP" variable_2="q_aGs_GDP_global"/>
</connection>
<connection>
<map_components component_1="GsProtein_parameters" component_2="GsProtein"/>
<map_variables variable_1="kappa_act1_Gs" variable_2="kappa_act1_Gs"/>
<map_variables variable_1="kappa_act2_Gs" variable_2="kappa_act2_Gs"/>
<map_variables variable_1="kappa_hyd_Gs" variable_2="kappa_hyd_Gs"/>
<map_variables variable_1="kappa_reassoc_Gs" variable_2="kappa_reassoc_Gs"/>
<map_variables variable_1="K_R_B1" variable_2="K_R_B1"/>
<map_variables variable_1="K_Gs" variable_2="K_Gs"/>
<map_variables variable_1="K_R_B1Gs" variable_2="K_R_B1Gs"/>
<map_variables variable_1="K_LR_B1" variable_2="K_LR_B1"/>
<map_variables variable_1="K_LR_B1Gs" variable_2="K_LR_B1Gs"/>
<map_variables variable_1="K_aGs_GTP" variable_2="K_aGs_GTP"/>
<map_variables variable_1="K_beta_gamma_Gs" variable_2="K_beta_gamma_Gs"/>
<map_variables variable_1="K_aGs_GDP" variable_2="K_aGs_GDP"/>
</connection>
<connection>
<map_components component_1="constants" component_2="GsProtein"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
