Merge pull request #372 from HossFir/update-reportEnzymeUsage

Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes
SysBioChalmers · May 8, 2024 · cc8e449 · cc8e449
2 parents 883b40d + 86b8f3c
commit cc8e449
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Showing 2 changed files with 21 additions and 4 deletions.
diff --git a/src/geckomat/utilities/enzymeUsage.m b/src/geckomat/utilities/enzymeUsage.m
@@ -26,6 +26,7 @@
 %               absUsage    vector of absolute enzyme usages
 %               UB          vector of enzyme exchange reaction upper bounds
 %               protID      string array of matching protein IDs
+%               fluxes      vector of fluxes, copy of input fluxes
 %
 % Usage:
 %   usageData = enzymeUsage(ecModel,fluxes,zero)
@@ -42,6 +43,7 @@
 usageData.LB          = ecModel.lb(rxnIdx);
 usageData.absUsage    = abs(fluxes(rxnIdx));
 usageData.capUsage    = abs(usageData.absUsage./usageData.LB);
+usageData.fluxes      = fluxes;
 
 if ~zero
     nonzero               = usageData.absUsage<0;

diff --git a/src/geckomat/utilities/reportEnzymeUsage.m b/src/geckomat/utilities/reportEnzymeUsage.m
@@ -1,10 +1,10 @@
-function usageReport = topEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)
+function usageReport = reportEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)
 % reportEnzymeUsage
 %   Summarizes the results from enzymeUsage.
 %
 %  Input:
 %   ecModel         a GECKO3 ecModel
-%   usageData       output from reportEnzymeUsage
+%   usageData       output from enzymeUsage
 %   highCapUsage    minimum ratio of enzyme capacity usage to be considered
 %                   as high usage (Optional, default 0.9, refering to a 
 %                   minimum of 90% capacity usage)
@@ -61,7 +61,20 @@
 topUsage.rxnNames   = {};
 topUsage.grRules    = {};
 
-protPool = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'))/100;
+% Calculate the protein pool flux from the 'prot_pool_exchange' reaction
+protPoolExchangeFlux = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'));
+
+fluxValues = usageData.fluxes;
+
+% Sum fluxes for all 'usage_prot_' reactions, excluding the 'usage_prot_standard'
+usageProtIndices = startsWith(ecModel.rxns, 'usage_prot_') & ...
+                   ~contains(ecModel.rxns, 'standard');
+
+% Sum the absolute values of the usage fluxes
+totalUsageProtFlux = sum(abs(fluxValues(usageProtIndices)));
+
+% Define the new protein pool as the sum of prot_pool_exchange flux and total usage_prot fluxes
+protPool = (protPoolExchangeFlux + totalUsageProtFlux)/100;
 
 for i=1:numel(topEnzyme)
     [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
@@ -76,5 +89,7 @@
     topUsage.rxnNames(end+1:end+rxnNumber,1)    = rxnNames;
     topUsage.grRules(end+1:end+rxnNumber,1)     = grRules;
 end
-usageReport.topAbsUsage = struct2table(topUsage);
+usageReport.topAbsUsage     = struct2table(topUsage);
+usageReport.totalProtPool   = protPoolExchangeFlux;
+usageReport.totalUsageFlux  = totalUsageProtFlux;
 end