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CA_PRi.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright Xin-Guang Zhu, Yu Wang, Donald R. ORT and Stephen P. LONG
%CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
%China Institute of Genomic Biology and Department of Plant Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
%University of Illinois at Urbana Champaign
%Global Change and Photosynthesis Research Unit, USDA/ARS, 1406 Institute of Genomic Biology, Urbana, IL 61801, USA.
% This file is part of e-photosynthesis.
% e-photosynthesis is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation;
% e-photosynthesis is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
% You should have received a copy of the GNU General Public License (GPL)
% along with this program. If not, see <http://www.gnu.org/licenses/>.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function PrS = CA_PRi(BE)
global NADHc;
global NADc;
global ADPc;
global ATPc;
global GLUc;
global KGc;
global PR_ADP;
global PR_ATP;
NADHc = 0.47;
NADc = 0.4;
ADPc = 0.64;
ATPc= 0.35;
GLUc=24;
KGc=0.4;
PR_ADP = 0.82;
PR_ATP = 0.68;
SERc= 7.5; % Serine in cytosol; 7.5 original value
GLYc = 1.8; % Glycine in cytosol; 1.8 original vlaue
PGA = 4.3; % PGA in chloroplast;4.3 is the original value;
GOAc = 0.028; % Glyoxylate in cytosol; 0.028; EXPERIMENTAL DATA;
GCAc = 0.36; % See the note for GCA.
GCA = 0.36; % Derived from radioactive labelling experiment; assuem equal concenatration
% inside and outshide chloroplast
PGCA= 0.0029; % Phosphoglycolate in chloroplast derived based on the Km112; orignal value is : 0.0029;
GCEA =0.1812; % Glycerate in chloroplast; derived based on V113
GCEAc = 0.1812; % Glycerate in cytosol; assume at equilibrium with GCEA initially.
HPRc = 0.0035; % HydroxylPyruvate; derived from equation 123;
RUBP = 2; % RuBP concentration
CO2 = 0.012; % CO2 concentration(mM)
O2 = 0.264; % O2 concentration(mM)
PrS = zeros(10,1);
PrS(1) = GCEA;
PrS(2) = GCA;
PrS(3) = PGA;
PrS(4) = PGCA;
PrS(5) = GCAc;
PrS(6) = GOAc;
PrS(7) = SERc;
PrS(8) = GLYc;
PrS(9) = HPRc;
PrS(10) = GCEAc;
PrS(11) = RUBP;
PrS(12) = CO2;
PrS(13) = O2;
CE = 1;
CEV111 = 1;
CE122 = 1;
% Reaction: 111: RUBP+O2<-->PGlycolate + PGA
global V111;
global KO;
global KC;
global KR;
global gp2V111;
V111 = gp2V111;
KO = 0.48; % Michaelis constant for O2
KC = 0.014; % Michaelis constant for CO2
KR = 0.02; % Michaelis constant for RUBP
% Reaction: 112: PGlycolate-->Pi+Glycolate;
global V112;
global KM112; % Km112 for PGlycolate;
global KI1122; % Inhibition constant for Glycolate;
global KI1121; % The competitive Pi inhibition for PGlycolate
KM112 = 0.026;
KI1122 = 94;
KI1121 = 2.55;
% Reaction 113 : Gcea+ATP<-->ADP + PGA
global V113;
global KM1131; % Km for ATP;
global KM1132; % Km for Gcea;
global KI113; % Ki for ATP BY pga;
global KE113; % New
KM1131 = 0.21;
KM1132 = 0.25;
KI113 = 0.36; %%%%%%%%%%%%%%%%%%%%%%%%% Competitive inhibition for ATP; in original paper it is 0.36;
KE113 = 300; % New Kleczkowski et al . 1985 Archives of Biochemistry and Biophysics
% Reactoin 121; Glycolate +O2<-->H2O2+Glyoxylate
global V121;
global KM121;
KM121 = 0.1;
% Reaction 122 : Glyoxylate + Serine<--> Hydoxypyruvate + Glycine;
global V122;
global KM1221; % Michaelis constant for glyoxylate;
global KM1222; % Michaelis constant for serinie;
global KI1221; % Inhibition constant for Glycine;
global KE122; % nEW
KM1221 = 0.15;
KM1222 = 2.7;
KI1221 = 33;
KE122 = 0.24; % New: Guynn, R.W.; Arch. Biochem. Biophys.; 218, 14 (1982).; 0.24. At 25 degree.
% Reaction 123: HydroxylPyruvate + NAD <--> NADH + Glycerate
global V123;
global KM123; % Michaelis constant for hydroxylpyruvate;
global KI123;
global KE123; % New
KM123 = 0.09;
KI123 = 12; % Inhibition constant for hydroxypyruvate;
KE123 = 1/(4*10^(-6)); % Guynn, R.W.; Arch. Biochem. Biophys.; 218, 14 (1982).; 1/(4*10^(-6);
% Reaction 124: Glyoxylate + Glu <--> KG + Glycine;
global V124;
global KM1241; % Michaelis constant for glyoxylate
global KM1242; % Michaelis constant for Glu
global KI124; % This KI is one guessed.
global KE124; % New Cooper, A.J.L.; Meister, A.; Biochemistry; 11, 661 (1972).; K' 607.
KM1241 = 0.15;
KM1242 = 1.7;
KI124 = 2;
KE124 = 607;
% Reaction 131: NAD+Glycine <--> CO2+ NADH + NH3
global V131;
global KM1311; % Michaelis constant for Glycine;
global KI1311; % Inhibition constant for Serine
KM1311 = 6;
KI1311 = 4;
global KI1312; % Inhibition constant for NADH; Since in the current program, we assume that P protein limit the
% rate of the overall glycin decarboxylase; the KI1312 and KM1312 were not used.
global KM1312; % Michaelis constant for NAD;
KM1312 = 0.075;
KI1312 = 0.015;
% The consant for calculating the glycerate uptake.
global V1T;
global KM1011;
global KI1011;
V1T = 0.25*CE *10;
KM1011 = 0.39;
KI1011 = 0.28;
% The constant for calculating the glycolate uptake
global V2T;
global KM1012;
global KI1012;
V2T = 0.32*CE * 10;
KM1012 = 0.2;
KI1012 = 0.22;
global J;
J=1;
global VmaxXValue;
V111 = VmaxXValue(21,J);
V112 = VmaxXValue(22,J);
V113 = VmaxXValue(23,J);
V121 = VmaxXValue(24,J);
V122 = VmaxXValue(25,J);
V123 = VmaxXValue(26,J);
V124 = VmaxXValue(27,J);
V131 = VmaxXValue(28,J);
V1T = VmaxXValue(29,J);
V2T = VmaxXValue(30,J);
KO = VmaxXValue ( 121 , J ) ;
KC = VmaxXValue ( 122 , J ) ;
KR = VmaxXValue ( 123 , J ) ;
KM112 = VmaxXValue ( 124 , J ) ;
KI1122 = VmaxXValue ( 125 , J ) ;
KI1121 = VmaxXValue ( 126 , J ) ;
KM1131 = VmaxXValue ( 127 , J ) ;
KM1132 = VmaxXValue ( 128 , J ) ;
KI113 = VmaxXValue ( 129 , J ) ;
KE113 = VmaxXValue ( 130 , J ) ;
KM121 = VmaxXValue ( 131 , J ) ;
KM1221 = VmaxXValue ( 132 , J ) ;
KM1222 = VmaxXValue ( 133 , J ) ;
KI1221 = VmaxXValue ( 134 , J ) ;
KE122 = VmaxXValue ( 135 , J ) ;
KM123 = VmaxXValue ( 136 , J ) ;
KI123 = VmaxXValue ( 137 , J ) ;
KE123 = VmaxXValue ( 138 , J ) ;
KM1241 = VmaxXValue ( 139 , J ) ;
KM1242 = VmaxXValue ( 140 , J ) ;
KI124 = VmaxXValue ( 141 , J ) ;
KE124 = VmaxXValue ( 142 , J ) ;
KM1311 = VmaxXValue ( 143 , J ) ;
KI1311 = VmaxXValue ( 144 , J ) ;
KI1312 = VmaxXValue ( 145 , J ) ;
KM1312 = VmaxXValue ( 146 , J ) ;
KM1011 = VmaxXValue ( 147 , J ) ;
KI1011 = VmaxXValue ( 148 , J ) ;
KM1012 = VmaxXValue ( 149 , J ) ;
KI1012 = VmaxXValue ( 150 , J ) ;