%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MODEL 1 - GENERAL % Author: Anze Zupanic % Date: September 2014 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % PottersWheel model definition file % This file is constructed as a Matlab function. % The returned variable "m" contains all required information of the model. % For more information visit www.potterswheel.de function m = UPFstudy_Model1_general() m = pwGetEmptyModel(); % General information: % ID fields require no blanks and only A-Za-z_0-9. % Use [] in order to get default values for a field. % You can use an arbitrary number of strings in arrays like {'string1','string2', ...}. %% Meta information m.name = 'UPFstudy_Model1_general'; m.description = 'a'; m.authors = {'Anze Zupanic'}; m.dates = {'2014-02-05'}; m.modelFormat = 3.0; %% Default sampling time points % m.t = 0:10:200; %% X - Dynamic variables % Model 1 for every selenoprotein has the same dynamic variables initiated % to the same values % gene - there is one copy of the selenoprotein gene % mRNA - initially there are no mRNAs in the cell % mRNA_UGA - also no mRNAs with ribosome at UGA codon % mRNA_sec - and no mRNAs with tRNA bound m = pwAddX(m, 'Gene' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); %% K - Dynamic parameters % Model 1 for every selenoprotein has the same dynamic variables: % transcription - rate of transcription of a mRNA from the gene % translation_UGA - rate of ribosome moving from start codon to UGA codon % secbinding - rate of binding a tRNAsec molecules % translation_END - rate of ribosome moving from UGA to stop codon % NMD - rate of NMD based degradation of the mRNA % degradation - rate of normal degradation of mRNAs % Translation_UGA, translation_END and degradation were set according to % the values from the literature for each selenoprotein. (Since very little % known about degradation rates for individual selenoproteins, we assume % that normal degradation is the same for all). The used values are: % Gpx1: 0.52, 0.23, 0.00025 % Gpx2: 0.64, 0.22, 0.00025 % Gpx4: 0.35, 0.46, 0.00025 % TR1: 0.05, 12.5, 0.00025 % TR2: 0.05, 8.33, 0.00025 % SelK: 0.27, 6.25, 0.00025 % SelH: 0.58, 0.31, 0.00025 % Sep15:0.26, 0.36, 0.00025 % Sepp1:0.43, 0.09, 0.00025 % Sepw1:2.08, 0.36, 0.00025 % SPS2: 0.42, 0.06, 0.00025 % see Table S3 for fitted values for each selenoprotein. m = pwAddK(m, 'transcription' , 1.56973046441431e-05, 'global'); m = pwAddK(m, 'translation_UGA', 0.520833333333333 , 'fix' ); m = pwAddK(m, 'secBinding' , 0.000138998427400249, 'global'); m = pwAddK(m, 'translation_END', 0.231481481481481 , 'fix' ); m = pwAddK(m, 'NMD' , 0.0005969375730224 , 'global'); m = pwAddK(m, 'degradation' , 0.00025 , 'fix' ); %% R - Reactions % these reaction are the same for all selenoproteins m = pwAddR(m, 'R01', {'Gene'} ,{'Gene','mRNA'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription'}); m = pwAddR(m, 'R02', {'mRNA'} ,{'mRNA_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R03', {'mRNA_UGA'} ,{'mRNA_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R04', {'mRNA_sec'} ,{'mRNA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R05', {'mRNA_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R06', {'mRNA_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation'}); m = pwAddR(m, 'R07', {'mRNA_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation'}); m = pwAddR(m, 'R08', {'mRNA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation'}); %% C - Compartments m = pwAddC(m, 'cytoplasm', 1); %% U - Driving inputs m = pwAddU(m, 'tRNAsec', 'steps', [-1 0] , [0 0] , 'cytoplasm'); %% Y - Observables m = pwAddY(m, 'mRNA_total', 'mRNA+mRNA_UGA+mRNA_sec'); %% Time m.t = 0:100:100000; %% Designer layout properties m.designerPropsM = [1 1 1 0 0 0 400 250 600 400 1 1 1 0 0 0 0 0 0]; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MODEL 1b % Author: Anze Zupanic % Date: September 2014 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % PottersWheel model definition file % This file is constructed as a Matlab function. % The returned variable "m" contains all required information of the model. % For more information visit www.potterswheel.de function m = UPFstudy_Model1b() m = pwGetEmptyModel(); % General information: % ID fields require no blanks and only A-Za-z_0-9. % Use [] in order to get default values for a field. % You can use an arbitrary number of strings in arrays like {'string1','string2', ...}. %% Meta information m.name = 'UPFstudy_Model1b'; m.description = 'a'; m.authors = {'Anze Zupanic'}; m.dates = {'2014-03-27'}; m.modelFormat = 3.0; %% Default sampling time points % m.t = 0:10:200; %% X - Dynamic variables % all selenoproteins are listed below with same initial values % gene - there is one copy of the selenoprotein gene % mRNA - initially there are no mRNAs in the cell % mRNA_UGA - also no mRNAs with ribosome at UGA codon % mRNA_sec - and no mRNAs with tRNA bound m = pwAddX(m, 'Gene_Gpx1' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_Gpx1' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_Gpx1', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_Gpx1', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_Gpx2' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_Gpx2' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_Gpx2', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_Gpx2', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_Gpx4' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_Gpx4' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_Gpx4', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_Gpx4', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_TR1' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_TR1' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_TR1', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_TR1', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_TR2' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_TR2' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_TR2', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_TR2', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_Sepp' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_Sepp' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_Sepp', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_Sepp', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_SelH' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_SelH' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_SelH', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_SelH', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_SelK' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_SelK' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_SelK', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_SelK', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_Sep15' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_Sep15' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_Sep15', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_Sep15', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_SPS2' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_SPS2' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_SPS2', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_SPS2', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'Gene_Sepw1' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_Sepw1' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec_Sepw1', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA_Sepw1', 0, 'fix', 0, [], [], 'cytoplasm'); %% K - Dynamic parameters % transcription - rate of transcription of a mRNA from the gene % translation_UGA - rate of ribosome moving from start codon to UGA codon % secbinding - rate of binding a tRNAsec molecules % translation_END - rate of ribosome moving from UGA to stop codon % NMD - rate of NMD based degradation of the mRNA % degradation - rate of normal degradation of mRNAs m = pwAddK(m, 'transcription_Gpx1' , 1.56973046441431e-05, 'global'); m = pwAddK(m, 'translation_UGA_Gpx1', 0.520833333333333 , 'fix' ); m = pwAddK(m, 'secBinding_Gpx1' , 0.000138998427400249, 'global'); m = pwAddK(m, 'translation_END_Gpx1', 0.231481481481481 , 'fix' ); m = pwAddK(m, 'NMD_Gpx1' , 0.0005969375730224 , 'global'); m = pwAddK(m, 'degradation_Gpx1' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_Gpx2' , 8.24499176659036e-06, 'global'); m = pwAddK(m, 'translation_UGA_Gpx2', 0.641025641025641 , 'fix' ); m = pwAddK(m, 'secBinding_Gpx2' , 1.00072786905447e-07, 'global'); m = pwAddK(m, 'translation_END_Gpx2', 0.221238938053097 , 'fix' ); m = pwAddK(m, 'NMD_Gpx2' , 1.00004698499661e-07, 'global'); m = pwAddK(m, 'degradation_Gpx2' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_Gpx4' , 0.000238629893984257, 'global'); m = pwAddK(m, 'translation_UGA_Gpx4', 0.347222222222222 , 'fix' ); m = pwAddK(m, 'secBinding_Gpx4' , 5.02184402801871e-05, 'global'); m = pwAddK(m, 'translation_END_Gpx4', 0.462962962962963 , 'fix' ); m = pwAddK(m, 'NMD_Gpx4' , 9.54450039786469e-05, 'global'); m = pwAddK(m, 'degradation_Gpx4' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_TR1' , 2.08325856313204e-05, 'global'); m = pwAddK(m, 'translation_UGA_TR1', 0.0454545454545455 , 'fix' ); m = pwAddK(m, 'secBinding_TR1' , 1.00000166905053e-07, 'global'); m = pwAddK(m, 'translation_END_TR1', 12.5, 'fix' ); m = pwAddK(m, 'NMD_TR1' , 1.08649728341266e-05, 'global'); m = pwAddK(m, 'degradation_TR1' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_TR2' , 0.000124568247642679, 'global'); m = pwAddK(m, 'translation_UGA_TR2', 0.0478927203065134 , 'fix' ); m = pwAddK(m, 'secBinding_TR2' , 3.71761806885377e-06, 'global'); m = pwAddK(m, 'translation_END_TR2', 8.33333333333333 , 'fix' ); m = pwAddK(m, 'NMD_TR2' , 7.71848315031509e-05, 'global'); m = pwAddK(m, 'degradation_TR2' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_Sepp' , 6.13130752772913e-06, 'global'); m = pwAddK(m, 'translation_UGA_Sepp', 0.431034482758621 , 'fix' ); m = pwAddK(m, 'secBinding_Sepp' , 7.57842445949248e-07, 'global'); m = pwAddK(m, 'translation_END_Sepp', 0.093984962406015 , 'fix' ); m = pwAddK(m, 'NMD_Sepp' , 0.000749990911259673, 'global'); m = pwAddK(m, 'degradation_Sepp' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_SelH' , 0.000238550203254256, 'global'); m = pwAddK(m, 'translation_UGA_SelH', 0.581395348837209 , 'fix' ); m = pwAddK(m, 'secBinding_SelH' , 7.10594229941777e-05, 'global'); m = pwAddK(m, 'translation_END_SelH', 0.3125 , 'fix' ); m = pwAddK(m, 'NMD_SelH' , 0.000333861152175014, 'global'); m = pwAddK(m, 'degradation_SelH' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_SelK' , 4.39591354749738e-05, 'global'); m = pwAddK(m, 'translation_UGA_SelK', 0.274725274725275 , 'fix' ); m = pwAddK(m, 'secBinding_SelK' , 31713.7730921325 , 'global'); m = pwAddK(m, 'translation_END_SelK', 6.25 , 'fix' ); m = pwAddK(m, 'NMD_SelK' , 1.01190508455211e-05, 'global'); m = pwAddK(m, 'degradation_SelK' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_Sep15' , 5.08972312767377e-06, 'global'); m = pwAddK(m, 'translation_UGA_Sep15', 0.263157894736842 , 'fix' ); m = pwAddK(m, 'secBinding_Sep15' , 1.00000000000883e-07, 'global'); m = pwAddK(m, 'translation_END_Sep15', 0.357142857142857 , 'fix' ); m = pwAddK(m, 'NMD_Sep15' , 1.00000000000002e-07, 'global'); m = pwAddK(m, 'degradation_Sep15' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_SPS2' , 0.000222401182591302, 'global'); m = pwAddK(m, 'translation_UGA_SPS2', 0.423728813559322 , 'fix' ); m = pwAddK(m, 'secBinding_SPS2' , 1.00000003122079e-07, 'global'); m = pwAddK(m, 'translation_END_SPS2', 0.0641025641025641 , 'fix' ); m = pwAddK(m, 'NMD_SPS2' , 1.00000000000511e-07, 'global'); m = pwAddK(m, 'degradation_SPS2' , 0.00025 , 'fix' ); m = pwAddK(m, 'transcription_Sepw1' , 9.35776267746978e-05, 'global'); m = pwAddK(m, 'translation_UGA_Sepw1', 2.08333333333333 , 'fix' ); m = pwAddK(m, 'secBinding_Sepw1' , 0.000154356859181462, 'global'); m = pwAddK(m, 'translation_END_Sepw1', 0.36231884057971 , 'fix' ); m = pwAddK(m, 'NMD_Sepw1' , 0.000528647446847041, 'global'); m = pwAddK(m, 'degradation_Sepw1' , 0.00025 , 'fix' ); % m = pwAddK(m, 'protein_degradation' , 2.5e-6, 'fix'); %% R - Reactions m = pwAddR(m, 'R01', {'Gene_Gpx1'} ,{'Gene_Gpx1','mRNA_Gpx1'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_Gpx1'}); m = pwAddR(m, 'R02', {'mRNA_Gpx1'} ,{'mRNA_UGA_Gpx1'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_Gpx1'}); m = pwAddR(m, 'R03', {'mRNA_UGA_Gpx1'} ,{'mRNA_sec_Gpx1'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_Gpx1'}); m = pwAddR(m, 'R04', {'mRNA_sec_Gpx1'} ,{'mRNA_Gpx1'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_Gpx1'}); m = pwAddR(m, 'R05', {'mRNA_UGA_Gpx1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_Gpx1'}); m = pwAddR(m, 'R06', {'mRNA_UGA_Gpx1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx1'}); m = pwAddR(m, 'R07', {'mRNA_sec_Gpx1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx1'}); m = pwAddR(m, 'R08', {'mRNA_Gpx1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx1'}); m = pwAddR(m, 'R09', {'Gene_Gpx2'} ,{'Gene_Gpx2','mRNA_Gpx2'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_Gpx2'}); m = pwAddR(m, 'R10', {'mRNA_Gpx2'} ,{'mRNA_UGA_Gpx2'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_Gpx2'}); m = pwAddR(m, 'R11', {'mRNA_UGA_Gpx2'} ,{'mRNA_sec_Gpx2'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_Gpx2'}); m = pwAddR(m, 'R12', {'mRNA_sec_Gpx2'} ,{'mRNA_Gpx2'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_Gpx2'}); m = pwAddR(m, 'R13', {'mRNA_UGA_Gpx2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_Gpx2'}); m = pwAddR(m, 'R14', {'mRNA_UGA_Gpx2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx2'}); m = pwAddR(m, 'R15', {'mRNA_sec_Gpx2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx2'}); m = pwAddR(m, 'R16', {'mRNA_Gpx2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx2'}); m = pwAddR(m, 'R17', {'Gene_Gpx4'} ,{'Gene_Gpx4','mRNA_Gpx4'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_Gpx4'}); m = pwAddR(m, 'R18', {'mRNA_Gpx4'} ,{'mRNA_UGA_Gpx4'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_Gpx4'}); m = pwAddR(m, 'R19', {'mRNA_UGA_Gpx4'} ,{'mRNA_sec_Gpx4'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_Gpx4'}); m = pwAddR(m, 'R20', {'mRNA_sec_Gpx4'} ,{'mRNA_Gpx4'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_Gpx4'}); m = pwAddR(m, 'R21', {'mRNA_UGA_Gpx4'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_Gpx4'}); m = pwAddR(m, 'R22', {'mRNA_UGA_Gpx4'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx4'}); m = pwAddR(m, 'R23', {'mRNA_sec_Gpx4'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx4'}); m = pwAddR(m, 'R24', {'mRNA_Gpx4'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Gpx4'}); m = pwAddR(m, 'R25', {'Gene_TR1'} ,{'Gene_TR1','mRNA_TR1'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_TR1'}); m = pwAddR(m, 'R26', {'mRNA_TR1'} ,{'mRNA_UGA_TR1'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_TR1'}); m = pwAddR(m, 'R27', {'mRNA_UGA_TR1'} ,{'mRNA_sec_TR1'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_TR1'}); m = pwAddR(m, 'R28', {'mRNA_sec_TR1'} ,{'mRNA_TR1'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_TR1'}); m = pwAddR(m, 'R29', {'mRNA_UGA_TR1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_TR1'}); m = pwAddR(m, 'R30', {'mRNA_UGA_TR1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_TR1'}); m = pwAddR(m, 'R31', {'mRNA_sec_TR1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_TR1'}); m = pwAddR(m, 'R32', {'mRNA_TR1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_TR1'}); m = pwAddR(m, 'R33', {'Gene_TR2'} ,{'Gene_TR2','mRNA_TR2'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_TR2'}); m = pwAddR(m, 'R34', {'mRNA_TR2'} ,{'mRNA_UGA_TR2'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_TR2'}); m = pwAddR(m, 'R35', {'mRNA_UGA_TR2'} ,{'mRNA_sec_TR2'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_TR2'}); m = pwAddR(m, 'R36', {'mRNA_sec_TR2'} ,{'mRNA_TR2'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_TR2'}); m = pwAddR(m, 'R37', {'mRNA_UGA_TR2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_TR2'}); m = pwAddR(m, 'R38', {'mRNA_UGA_TR2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_TR2'}); m = pwAddR(m, 'R39', {'mRNA_sec_TR2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_TR2'}); m = pwAddR(m, 'R40', {'mRNA_TR2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_TR2'}); m = pwAddR(m, 'R41', {'Gene_Sepp'} ,{'Gene_Sepp','mRNA_Sepp'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_Sepp'}); m = pwAddR(m, 'R42', {'mRNA_Sepp'} ,{'mRNA_UGA_Sepp'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_Sepp'}); m = pwAddR(m, 'R43', {'mRNA_UGA_Sepp'} ,{'mRNA_sec_Sepp'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_Sepp'}); m = pwAddR(m, 'R44', {'mRNA_sec_Sepp'} ,{'mRNA_Sepp'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_Sepp'}); m = pwAddR(m, 'R45', {'mRNA_UGA_Sepp'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_Sepp'}); m = pwAddR(m, 'R46', {'mRNA_UGA_Sepp'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sepp'}); m = pwAddR(m, 'R47', {'mRNA_sec_Sepp'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sepp'}); m = pwAddR(m, 'R48', {'mRNA_Sepp'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sepp'}); m = pwAddR(m, 'R49', {'Gene_SelH'} ,{'Gene_SelH','mRNA_SelH'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_SelH'}); m = pwAddR(m, 'R50', {'mRNA_SelH'} ,{'mRNA_UGA_SelH'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_SelH'}); m = pwAddR(m, 'R51', {'mRNA_UGA_SelH'} ,{'mRNA_sec_SelH'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_SelH'}); m = pwAddR(m, 'R52', {'mRNA_sec_SelH'} ,{'mRNA_SelH'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_SelH'}); m = pwAddR(m, 'R53', {'mRNA_UGA_SelH'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_SelH'}); m = pwAddR(m, 'R54', {'mRNA_UGA_SelH'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SelH'}); m = pwAddR(m, 'R55', {'mRNA_sec_SelH'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SelH'}); m = pwAddR(m, 'R56', {'mRNA_SelH'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SelH'}); m = pwAddR(m, 'R57', {'Gene_SelK'} ,{'Gene_SelK','mRNA_SelK'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_SelK'}); m = pwAddR(m, 'R58', {'mRNA_SelK'} ,{'mRNA_UGA_SelK'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_SelK'}); m = pwAddR(m, 'R59', {'mRNA_UGA_SelK'} ,{'mRNA_sec_SelK'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_SelK'}); m = pwAddR(m, 'R60', {'mRNA_sec_SelK'} ,{'mRNA_SelK'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_SelK'}); m = pwAddR(m, 'R61', {'mRNA_UGA_SelK'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_SelK'}); m = pwAddR(m, 'R62', {'mRNA_UGA_SelK'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SelK'}); m = pwAddR(m, 'R63', {'mRNA_sec_SelK'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SelK'}); m = pwAddR(m, 'R64', {'mRNA_SelK'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SelK'}); m = pwAddR(m, 'R65', {'Gene_Sep15'} ,{'Gene_Sep15','mRNA_Sep15'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_Sep15'}); m = pwAddR(m, 'R66', {'mRNA_Sep15'} ,{'mRNA_UGA_Sep15'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_Sep15'}); m = pwAddR(m, 'R67', {'mRNA_UGA_Sep15'} ,{'mRNA_sec_Sep15'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_Sep15'}); m = pwAddR(m, 'R68', {'mRNA_sec_Sep15'} ,{'mRNA_Sep15'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_Sep15'}); m = pwAddR(m, 'R69', {'mRNA_UGA_Sep15'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_Sep15'}); m = pwAddR(m, 'R70', {'mRNA_UGA_Sep15'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sep15'}); m = pwAddR(m, 'R71', {'mRNA_sec_Sep15'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sep15'}); m = pwAddR(m, 'R72', {'mRNA_Sep15'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sep15'}); m = pwAddR(m, 'R73', {'Gene_SPS2'} ,{'Gene_SPS2','mRNA_SPS2'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_SPS2'}); m = pwAddR(m, 'R74', {'mRNA_SPS2'} ,{'mRNA_UGA_SPS2'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_SPS2'}); m = pwAddR(m, 'R75', {'mRNA_UGA_SPS2'} ,{'mRNA_sec_SPS2'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_SPS2'}); m = pwAddR(m, 'R76', {'mRNA_sec_SPS2'} ,{'mRNA_SPS2'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_SPS2'}); m = pwAddR(m, 'R77', {'mRNA_UGA_SPS2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_SPS2'}); m = pwAddR(m, 'R78', {'mRNA_UGA_SPS2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SPS2'}); m = pwAddR(m, 'R79', {'mRNA_sec_SPS2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SPS2'}); m = pwAddR(m, 'R80', {'mRNA_SPS2'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_SPS2'}); m = pwAddR(m, 'R81', {'Gene_Sepw1'} ,{'Gene_Sepw1','mRNA_Sepw1'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription_Sepw1'}); m = pwAddR(m, 'R82', {'mRNA_Sepw1'} ,{'mRNA_UGA_Sepw1'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA_Sepw1'}); m = pwAddR(m, 'R83', {'mRNA_UGA_Sepw1'} ,{'mRNA_sec_Sepw1'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding_Sepw1'}); m = pwAddR(m, 'R84', {'mRNA_sec_Sepw1'} ,{'mRNA_Sepw1'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END_Sepw1'}); m = pwAddR(m, 'R85', {'mRNA_UGA_Sepw1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD_Sepw1'}); m = pwAddR(m, 'R86', {'mRNA_UGA_Sepw1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sepw1'}); m = pwAddR(m, 'R87', {'mRNA_sec_Sepw1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sepw1'}); m = pwAddR(m, 'R88', {'mRNA_Sepw1'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_Sepw1'}); %% C - Compartments m = pwAddC(m, 'cytoplasm', 1); %% U - Driving inputs % the only driving input is tRNAsec, which is define here. The values of % tRNAsec in the model range from 0 (0 nM added sodium selenite) to 200000 % (40 nM added sodium selenite) - linear scale is used m = pwAddU(m, 'tRNAsec', 'steps', [-1 0] , [0 200000] , 'cytoplasm'); %% Y - Observables % the only observables are total mRNAs for each selenoprotein m = pwAddY(m, 'mRNA_total_Gpx1', 'mRNA_Gpx1+mRNA_UGA_Gpx1+mRNA_sec_Gpx1'); m = pwAddY(m, 'mRNA_total_Gpx2', 'mRNA_Gpx2+mRNA_UGA_Gpx2+mRNA_sec_Gpx2'); m = pwAddY(m, 'mRNA_total_Gpx4', 'mRNA_Gpx4+mRNA_UGA_Gpx4+mRNA_sec_Gpx4'); m = pwAddY(m, 'mRNA_total_TR1', 'mRNA_TR1+mRNA_UGA_TR1+mRNA_sec_TR1'); m = pwAddY(m, 'mRNA_total_TR2', 'mRNA_TR2+mRNA_UGA_TR2+mRNA_sec_TR2'); m = pwAddY(m, 'mRNA_total_Sepp', 'mRNA_Sepp+mRNA_UGA_Sepp+mRNA_sec_Sepp'); m = pwAddY(m, 'mRNA_total_SelH', 'mRNA_SelH+mRNA_UGA_SelH+mRNA_sec_SelH'); m = pwAddY(m, 'mRNA_total_SelK', 'mRNA_SelK+mRNA_UGA_SelK+mRNA_sec_SelK'); m = pwAddY(m, 'mRNA_total_Sep15', 'mRNA_Sep15+mRNA_UGA_Sep15+mRNA_sec_Sep15'); m = pwAddY(m, 'mRNA_total_SPS2', 'mRNA_SPS2+mRNA_UGA_SPS2+mRNA_sec_SPS2'); m = pwAddY(m, 'mRNA_total_Sepw1', 'mRNA_Sepw1+mRNA_UGA_Sepw1+mRNA_sec_Sepw1'); %% Observation parameters %% Designer layout properties m.designerPropsM = [1 1 1 0 0 0 400 250 600 400 1 1 1 0 0 0 0 0 0]; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MODEL 2 - GENERAL % Author: Anze Zupanic % Date: September 2014 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % PottersWheel model definition file % This file is constructed as a Matlab function. % The returned variable "m" contains all required information of the model. % For more information visit www.potterswheel.de function m = UPFstudy_Model2_general() m = pwGetEmptyModel(); % General information: % ID fields require no blanks and only A-Za-z_0-9. % Use [] in order to get default values for a field. % You can use an arbitrary number of strings in arrays like {'string1','string2', ...}. %% Meta information m.name = 'UPFstudy_Model2_general'; m.description = 'a'; m.authors = {'Anze Zupanic'}; m.dates = {'2014-02-05'}; m.modelFormat = 3.0; %% Default sampling time points % m.t = 0:10:200; %% X - Dynamic variables % Model 1 for every selenoprotein has the same dynamic variables initiated % to the same values % gene - there is one copy of the selenoprotein gene % mRNA - initially there are no mRNAs in the cell % mRNA_UGA - also no mRNAs with ribosome at UGA codon % mRNA_sec - and no mRNAs with tRNA bound m = pwAddX(m, 'Gene' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); % m = pwAddX(m, 'protein' , 0, 'fix'); %% K - Dynamic parameters % Model 2 for every selenoprotein has the same dynamic variables: % transcription - rate of transcription of a mRNA from the gene % translation_UGA - rate of ribosome moving from start codon to UGA codon % secbinding - rate of binding a tRNAsec molecules % translation_END - rate of ribosome moving from UGA to stop codon % NMD - rate of NMD based degradation of the mRNA % degradation - rate of normal degradation of mRNAs % dropoff - rate of ribosome dropoff at UGA codon (without % resulting degradation) - EXTRA COMPARED TO MODEL1 % translation_UGA, translation_END and degradation were set according to % the values from the literature for each selenoprotein. (Since very little % known about degradation rates for indiviudla selenoproteins, we assume % that normal degradation is the same for all). The used values are: % Gpx1: 0.52, 0.23, 0.00025 % Gpx2: 0.64, 0.22, 0.00025 % Gpx4: 0.35, 0.46, 0.00025 % TR1: 0.05, 12.5, 0.00025 % TR2: 0.05, 8.33, 0.00025 % SelK: 0.27, 6.25, 0.00025 % SelH: 0.58, 0.31, 0.00025 % Sep15:0.26, 0.36, 0.00025 % Sepp1:0.43, 0.09, 0.00025 % Sepw1:2.08, 0.36, 0.00025 % SPS2: 0.42, 0.06, 0.00025 % see Table S3 for fitted values for each selenoprotein. m = pwAddK(m, 'transcription' , 1.56973046441431e-05, 'global'); m = pwAddK(m, 'translation_UGA', 0.520833333333333 , 'fix' ); m = pwAddK(m, 'secBinding' , 0.000138998427400249, 'global'); m = pwAddK(m, 'translation_END', 0.231481481481481 , 'fix' ); m = pwAddK(m, 'NMD' , 0.0005969375730224 , 'global'); m = pwAddK(m, 'dropoff' , 1.08649728341266e-05 , 'global'); m = pwAddK(m, 'degradation' , 0.00025 , 'fix' ); % m = pwAddK(m, 'protein_degradation' , 2.5e-6, 'fix'); %% R - Reactions % these reaction are the same for all selenoproteinsm = pwAddR(m, 'R01', {'Gene'} ,{'Gene','mRNA'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription'}); m = pwAddR(m, 'R02', {'mRNA'} ,{'mRNA_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R03', {'mRNA_UGA'} ,{'mRNA_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R04', {'mRNA_sec'} ,{'mRNA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R05', {'mRNA_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R06', {'mRNA_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation'}); m = pwAddR(m, 'R07', {'mRNA_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation'}); m = pwAddR(m, 'R08', {'mRNA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation'}); % extra reaction compared to model1 m = pwAddR(m, 'R09', {'mRNA_UGA'} ,{'mRNA'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); %% C - Compartments m = pwAddC(m, 'cytoplasm', 1); %% U - Driving inputs % the only driving input is tRNAsec, which is define here. The values of % tRNAsec in the model range from 0 (0 nM added sodium selenite) to 200000 % (40 nM added sodium selenite) - linear scale is used m = pwAddU(m, 'tRNAsec', 'steps', [-1 0] , [0 25000] , 'cytoplasm'); %% Y - Observables % the only observable is total_mRNA m = pwAddY(m, 'mRNA_total', 'mRNA+mRNA_UGA+mRNA_sec'); %% Time m.t = 0:100:100000; %% Designer layout properties m.designerPropsM = [1 1 1 0 0 0 400 250 600 400 1 1 1 0 0 0 0 0 0]; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % MODEL 3 - GENERAL % Author: Anze Zupanic % Date: September 2014 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % PottersWheel model definition file % This file is constructed as a Matlab function. % The returned variable "m" contains all required information of the model. % For more information visit www.potterswheel.de function m = UPFstudy_Model3_general() m = pwGetEmptyModel(); % General information: % ID fields require no blanks and only A-Za-z_0-9. % Use [] in order to get default values for a field. % You can use an arbitrary number of strings in arrays like {'string1','string2', ...}. %% Meta information m.name = 'UPFstudy__Model3_general'; m.description = 'a'; m.authors = {'Anze Zupanic'}; m.dates = {'2014-02-05'}; m.modelFormat = 3.0; %% Default sampling time points % m.t = 0:10:200; %% X - Dynamic variables % Model 3 for every selenoprotein has the same dynamic variables initiated % to the same values % gene - there is one copy of the selenoprotein gene % mRNA - initially there are no mRNAs in the cell % mRNA_UGA - also no mRNAs with ribosome at UGA codon % mRNA_sec - and no mRNAs with tRNA bound % % mRNA, mRNA_UGA and mRNA_sec are all present with different length of % the polyadenylated tail (from 70 to 20 for mRNA_UGA and mRNA_sec and % for 70 to 10 for mRNA) m = pwAddX(m, 'Gene' , 1, 'fix', [], [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA70' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA60' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA50' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA40' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA30' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA20' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA10' , 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA70_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA60_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA50_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA40_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA30_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA20_sec', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA70_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA60_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA50_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA40_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA30_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); m = pwAddX(m, 'mRNA20_UGA', 0, 'fix', 0, [], [], 'cytoplasm'); %% K - Dynamic parameters % Model 3 for every selenoprotein has the same dynamic variables: % transcription - rate of transcription of a mRNA from the gene % translation_UGA - rate of ribosome moving from start codon to UGA codon % secbinding - rate of binding a tRNAsec molecules % translation_END - rate of ribosome moving from UGA to stop codon % NMD - rate of NMD based degradation of the mRNA % degradation_background - rate of normal degradation of mRNAs % dropoff - rate of ribosome dropoff at UGA codon (without % resulting degradation) - EXTRA COMPARED TO MODEL1 % degradation_polyA - rate of degradation when polyA tail reaches % minimum size EXTRA COMPARED TO MODEL1 % translation_UGA, translation_END, degradation_background and % degradation_polyA were set according to the values from the literature % for each selenoprotein. (Since very little known about degradation rates % for indiviudla selenoproteins, we assume that normal degradation and poly % A degradation is the same for all). The used values are: % Gpx1: 0.52, 0.23, 0.00025, 100 % Gpx2: 0.64, 0.22, 0.00025, 100 % Gpx4: 0.35, 0.46, 0.00025, 100 % TR1: 0.05, 12.5, 0.00025, 100 % TR2: 0.05, 8.33, 0.00025, 100 % SelK: 0.27, 6.25, 0.00025, 100 % SelH: 0.58, 0.31, 0.00025, 100 % Sep15:0.26, 0.36, 0.00025, 100 % Sepp1:0.43, 0.09, 0.00025, 100 % Sepw1:2.08, 0.36, 0.00025, 100 % SPS2: 0.42, 0.06, 0.00025, 100 % see Table S3 for fitted values for each selenoprotein. m = pwAddK(m, 'transcription' , 0.00170933288810836 , 'global'); m = pwAddK(m, 'translation_UGA' , 0.520833333333333 , 'fix' ); m = pwAddK(m, 'secBinding' , 7.70718729214138e-05, 'global'); m = pwAddK(m, 'translation_END' , 0.231481481481481 , 'fix' ); m = pwAddK(m, 'NMD' , 0.111663210458388 , 'global'); m = pwAddK(m, 'dropoff' , 0.000338087308164937, 'global'); m = pwAddK(m, 'degradation_background', 0.00025 , 'fix' ); m = pwAddK(m, 'degradation_polyA' , 100 , 'fix' ); %% R - Reactions % these reaction are the same for all selenoproteins m = pwAddR(m, 'R01', {'Gene'} ,{'Gene','mRNA70'} ,{} ,'C' ,[] ,'k1*r1' ,{'transcription'}); m = pwAddR(m, 'R02', {'mRNA70'} ,{'mRNA70_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R03', {'mRNA70_UGA'} ,{'mRNA70_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R04', {'mRNA70_sec'} ,{'mRNA60'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R05', {'mRNA70_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R06', {'mRNA70_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R07', {'mRNA70_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R08', {'mRNA70'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R09', {'mRNA70_UGA'} ,{'mRNA70'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); % -10 polyA m = pwAddR(m, 'R10', {'mRNA60'} ,{'mRNA60_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R11', {'mRNA60_UGA'} ,{'mRNA60_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R12', {'mRNA60_sec'} ,{'mRNA50'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R13', {'mRNA60_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R14', {'mRNA60_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R15', {'mRNA60_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R16', {'mRNA60'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R17', {'mRNA60_UGA'} ,{'mRNA60'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); % -20 polyA m = pwAddR(m, 'R18', {'mRNA50'} ,{'mRNA50_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R19', {'mRNA50_UGA'} ,{'mRNA50_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R20', {'mRNA50_sec'} ,{'mRNA40'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R21', {'mRNA50_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R22', {'mRNA50_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R23', {'mRNA50_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R24', {'mRNA50'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R25', {'mRNA50_UGA'} ,{'mRNA50'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); % -30 polyA m = pwAddR(m, 'R26', {'mRNA40'} ,{'mRNA40_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R27', {'mRNA40_UGA'} ,{'mRNA40_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R28', {'mRNA40_sec'} ,{'mRNA30'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R29', {'mRNA40_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R30', {'mRNA40_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R31', {'mRNA40_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R32', {'mRNA40'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R33', {'mRNA40_UGA'} ,{'mRNA40'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); % -40 polyA m = pwAddR(m, 'R34', {'mRNA30'} ,{'mRNA30_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R35', {'mRNA30_UGA'} ,{'mRNA30_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R36', {'mRNA30_sec'} ,{'mRNA20'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R37', {'mRNA30_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R38', {'mRNA30_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R39', {'mRNA30_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R40', {'mRNA30'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R41', {'mRNA30_UGA'} ,{'mRNA30'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); % -50 polyA m = pwAddR(m, 'R42', {'mRNA20'} ,{'mRNA20_UGA'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_UGA'}); m = pwAddR(m, 'R43', {'mRNA20_UGA'} ,{'mRNA20_sec'} ,{'tRNAsec'} ,'C' ,[] ,'k1*r1*m1' ,{'secBinding'}); m = pwAddR(m, 'R44', {'mRNA20_sec'} ,{'mRNA10'} ,{} ,'C' ,[] ,'k1*r1' ,{'translation_END'}); m = pwAddR(m, 'R45', {'mRNA20_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'NMD'}); m = pwAddR(m, 'R46', {'mRNA20_UGA'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R47', {'mRNA20_sec'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R48', {'mRNA20'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_background'}); m = pwAddR(m, 'R49', {'mRNA20_UGA'} ,{'mRNA20'} ,{} ,'C' ,[] ,'k1*r1' ,{'dropoff'}); % -60 polyA m = pwAddR(m, 'R50', {'mRNA10'} ,{} ,{} ,'C' ,[] ,'k1*r1' ,{'degradation_polyA'}); %% C - Compartments m = pwAddC(m, 'cytoplasm', 1); %% U - Driving inputs % the only driving input is tRNAsec, which is define here. The values of % tRNAsec in the model range from 0 (0 nM added sodium selenite) to 200000 % (40 nM added sodium selenite) - linear scale is used m = pwAddU(m, 'tRNAsec', 'steps', [-1 0] , [0 25000] , 'cytoplasm'); %% Y - Observables % the only observable is total_mRNA m = pwAddY(m, 'mRNA_total', 'mRNA70+mRNA70_UGA+mRNA70_sec + mRNA60+mRNA60_UGA+mRNA60_sec + mRNA50+mRNA50_UGA+mRNA50_sec + mRNA40+mRNA40_UGA+mRNA40_sec + mRNA30+mRNA30_UGA+mRNA30_sec + mRNA20+mRNA20_UGA+mRNA20_sec + mRNA10'); %% Observation parameters m.t = 0:100:100000; %% Designer layout properties m.designerPropsM = [1 1 1 0 0 0 400 250 600 400 1 1 1 0 0 0 0 0 0];