(************** Content-type: application/mathematica ************** CreatedBy='Mathematica 4.2' Mathematica-Compatible Notebook This notebook can be used with any Mathematica-compatible application, such as Mathematica, MathReader or Publicon. The data for the notebook starts with the line containing stars above. To get the notebook into a Mathematica-compatible application, do one of the following: * Save the data starting with the line of stars above into a file with a name ending in .nb, then open the file inside the application; * Copy the data starting with the line of stars above to the clipboard, then use the Paste menu command inside the application. Data for notebooks contains only printable 7-bit ASCII and can be sent directly in email or through ftp in text mode. Newlines can be CR, LF or CRLF (Unix, Macintosh or MS-DOS style). 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For more information on notebooks and Mathematica-compatible applications, contact Wolfram Research: web: http://www.wolfram.com email: info@wolfram.com phone: +1-217-398-0700 (U.S.) Notebook reader applications are available free of charge from Wolfram Research. *******************************************************************) (*CacheID: 232*) (*NotebookFileLineBreakTest NotebookFileLineBreakTest*) (*NotebookOptionsPosition[ 490994, 12846]*) (*NotebookOutlinePosition[ 492059, 12880]*) (* CellTagsIndexPosition[ 492015, 12876]*) (*WindowFrame->Normal*) Notebook[{ Cell[TextData[{ StyleBox["Supplementary Figure 1. \nA Mathematical Model for the Flow of \ Carbon Through the Branched Chain Amino Acid Pathways of ", FontSize->18], StyleBox["Escherichia coli", FontSize->18, FontSlant->"Italic"], StyleBox[" K12.", FontSize->18] }], "Input", Evaluatable->False], Cell[CellGroupData[{ Cell[BoxData[ RowBox[{ StyleBox[\( (*\ call\ Cellerator\ and\ kMech\ into\ Mathematica\ Kernel\ *) \), FontSize->14], "\[IndentingNewLine]", "\[IndentingNewLine]", RowBox[{\(<< myPadRight.m;\), "\n", \(<< cellerator.m;\), "\[IndentingNewLine]", \(<< kMech.m;\), "\[IndentingNewLine]", RowBox[{ RowBox[{"Off", "[", StyleBox[\(General::"\"\), "TI"], "]"}], StyleBox[";", "MR"]}], "\[IndentingNewLine]", RowBox[{ RowBox[{"Off", "[", StyleBox[\(General::"\"\), "TI"], "]"}], StyleBox[";", "MR"]}]}]}]], "Input"], Cell[BoxData[ \("myPadRight Version 0.3 for Cellerator Loaded."\)], "Print"], Cell[BoxData[ \("Cellerator\[Trademark] Version 1.0 update 3.1002, loaded at Oct. 27, \ 2003, 10:02:47\n\[Copyright]2001,2002 Jet Propulsion Laboratory, California \ Institute of Technology. U.S. Government Sponsorship Acknowledged. All \ rights reserved. \nPatent Pending (USPTO App 09993291).\nThe contents of this \ file may not be copied, distributed or transferred without written \ permission."\)], "Print"], Cell[BoxData[ InterpretationBox[\("Cellerator\[Trademark] 1.0 update 3.1002 load (using \ Mathematica Version 4.2 for Microsoft Windows (June 5, 2002)) complete at "\ \[InvisibleSpace]"October 27, 2003 10:02:49"\), SequenceForm[ "Cellerator\[Trademark] 1.0 update 3.1002 load (using Mathematica \ Version 4.2 for Microsoft Windows (June 5, 2002)) complete at ", "October 27, 2003 10:02:49"], Editable->False]], "Print"], Cell[BoxData[ \(" "\)], "Print"], Cell[BoxData[ \(" kMech is loaded "\)], "Print"] }, Open ]], Cell[BoxData[ RowBox[{ StyleBox[\( (*\ kMech\ Input\ of\ Enzyme\ Mechanisms\ for\ the\ Mathematical\ \ Modeling\ of\ \ L - isoleucine\ \((ILE)\), \ L - valine\ \((VAL)\), \ and\ L - leucine\ \((LEU)\)\ Biosynthesis\ *) \), FontSize->14], "\[IndentingNewLine]", "\[IndentingNewLine]", RowBox[{ RowBox[{ 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rkcat$TC$Pyr}, {$Complex$Val$TB$ \[ShortRightArrow] aKIV + TBNH2, rkcat$TB$Val}, {$Complex$Val$TC$ \[ShortRightArrow] aKIV + TCNH2, rkcat$TC$Val}, {\({Thr}\[DoubleLongRightArrow]{aKB, NH3}\)\+\({{Val}, \ {Ile}}\)\%TDA, GMWC[nGMWC \[Rule] nTDA, cGMWC \[Rule] cTDA, LGMWC \[Rule] L0TDA, vmax \[Rule] kcat$TDA, KGMWC \[Rule] {KmThr, KaVal, KiIle}]}, {AHASICH3CO + aKB \[RightArrowLeftArrow] $Complex$aKB$AHASICH3CO$, kfAHASIaKB, krAHASIaKB}, {AHASIICH3CO + aKB \[RightArrowLeftArrow] $Complex$aKB$AHASIICH3CO$, kfAHASIIaKB, krAHASIIaKB}, {AHASIIICH3CO + aKB \[RightArrowLeftArrow] $Complex$aKB$AHASIIICH3CO$, kfAHASIIIaKB, krAHASIIIaKB}, {acetylCoA + IPMS \[RightArrowLeftArrow] $Complex$acetylCoA$IPMS$, kfIPMSacetylCoA, krIPMSacetylCoA}, {aKIV + IPMSacetyl \[RightArrowLeftArrow] $Complex$aKIV$IPMSacetyl$, kfIPMSaKIV, krIPMSaKIV}, {IPMS + Leu \[RightArrowLeftArrow] $Complex$IPMS$Leu$, kfiIPMSLeu, kriIPMSLeu}, {IPMSacetyl + Leu \[RightArrowLeftArrow] $Complex$IPMSacetyl$Leu$, kfiIPMSacetylLeu, kriIPMSacetylLeu}, {bIPM + IPMDH + NAD \[RightArrowLeftArrow] $Complex$IPMDH$bIPM$NAD$, kfIPMDHbIPM, krIPMDHbIPM}, {aAHB + IR + NADPH \[RightArrowLeftArrow] $Complex$IR$aAHB$NADPH$, kfIRaAHB, krIRaAHB}, {aAL + IR + NADPH \[RightArrowLeftArrow] $Complex$IR$aAL$NADPH$, kfIRaAL, krIRaAL}, {AHASI + Pyr \[RightArrowLeftArrow] $Complex$Pyr$AHASI$, kfAHASIPyr, krAHASIPyr}, {AHASICH3CO + Pyr \[RightArrowLeftArrow] $Complex$Pyr$AHASICH3CO$, kfAHASIPyr2, krAHASIPyr2}, {AHASII + Pyr \[RightArrowLeftArrow] $Complex$Pyr$AHASII$, kfAHASIIPyr, krAHASIIPyr}, {AHASIICH3CO + Pyr \[RightArrowLeftArrow] $Complex$Pyr$AHASIICH3CO$, kfAHASIIPyr2, krAHASIIPyr2}, {AHASIII + Pyr \[RightArrowLeftArrow] $Complex$Pyr$AHASIII$, kfAHASIIIPyr, krAHASIIIPyr}, {AHASIIICH3CO + Pyr \[RightArrowLeftArrow] $Complex$Pyr$AHASIIICH3CO$, kfAHASIIIPyr2, krAHASIIIPyr2}, {Glu + TB \[RightArrowLeftArrow] $Complex$Glu$TB$, fkfTBGlu, fkrTBGlu}, {Ile + TB \[RightArrowLeftArrow] $Complex$Ile$TB$, rkfTBIle, rkrTBIle}, {Leu + TB \[RightArrowLeftArrow] $Complex$Leu$TB$, rkfTBLeu, rkrTBLeu}, {aKG + TBNH2 \[RightArrowLeftArrow] $Complex$aKG$TBNH2$, rkfTBaKG, rkrTBaKG}, {aKIC + TBNH2 \[RightArrowLeftArrow] $Complex$aKIC$TBNH2$, fkfTBaKIC, fkrTBaKIC}, {aKIV + TBNH2 \[RightArrowLeftArrow] $Complex$aKIV$TBNH2$, fkfTBaKIV, fkrTBaKIV}, {aKMV + TBNH2 \[RightArrowLeftArrow] $Complex$aKMV$TBNH2$, fkfTBaKMV, fkrTBaKMV}, {Ala + TC \[RightArrowLeftArrow] $Complex$Ala$TC$, fkfTCAla, fkrTCAla}, {aKIV + TCNH2 \[RightArrowLeftArrow] $Complex$aKIV$TCNH2$, fkfTCaKIV, fkrTCaKIV}, {Pyr + TCNH2 \[RightArrowLeftArrow] $Complex$Pyr$TCNH2$, rkfTCPyr, rkrTCPyr}, {AHASI + Val \[RightArrowLeftArrow] $Complex$AHASI$Val$, kfiAHASIPyrVal, kriAHASIPyrVal}, {AHASICH3CO + Val \[RightArrowLeftArrow] $Complex$AHASICH3CO$Val$, kfiAHASIaKBVal, kriAHASIaKBVal}, {AHASICH3CO + Val \[RightArrowLeftArrow] $Complex$AHASICH3CO$Val$, kfiAHASIPyr2Val, kriAHASIPyr2Val}, {AHASIII + Val \[RightArrowLeftArrow] $Complex$AHASIII$Val$, kfiAHASIIIPyrVal, kriAHASIIIPyrVal}, {AHASIIICH3CO + Val \[RightArrowLeftArrow] $Complex$AHASIIICH3CO$Val$, kfiAHASIIIaKBVal, kriAHASIIIaKBVal}, {AHASIIICH3CO + Val \[RightArrowLeftArrow] $Complex$AHASIIICH3CO$Val$, kfiAHASIIIPyr2Val, kriAHASIIIPyr2Val}, {TB + Val \[RightArrowLeftArrow] $Complex$Val$TB$, rkfTBVal, rkrTBVal}, {TC + Val \[RightArrowLeftArrow] $Complex$Val$TC$, rkfTCVal, rkrTCVal}, {aKB + $Complex$AHASICH3CO$Val$ \[RightArrowLeftArrow] \ $Complex$aKB$AHASICH3CO$Val$, kfAHASIaKB, krAHASIaKB}, {Pyr + $Complex$AHASICH3CO$Val$ \[RightArrowLeftArrow] \ $Complex$Pyr$AHASICH3CO$Val$, kfAHASIPyr2, krAHASIPyr2}, {aKB + $Complex$AHASIIICH3CO$Val$ \ \[RightArrowLeftArrow] $Complex$aKB$AHASIIICH3CO$Val$, kfAHASIIIaKB, krAHASIIIaKB}, {Pyr + $Complex$AHASIIICH3CO$Val$ \ \[RightArrowLeftArrow] $Complex$Pyr$AHASIIICH3CO$Val$, kfAHASIIIPyr2, krAHASIIIPyr2}, {Pyr + $Complex$AHASIII$Val$ \[RightArrowLeftArrow] \ $Complex$Pyr$AHASIII$Val$, kfAHASIIIPyr, krAHASIIIPyr}, {Pyr + $Complex$AHASI$Val$ \[RightArrowLeftArrow] \ $Complex$Pyr$AHASI$Val$, kfAHASIPyr, krAHASIPyr}, {Val + $Complex$aKB$AHASICH3CO$ \[RightArrowLeftArrow] \ $Complex$aKB$AHASICH3CO$Val$, kfiAHASIaKBVal, kriAHASIaKBVal}, {Val + $Complex$aKB$AHASIIICH3CO$ \ \[RightArrowLeftArrow] $Complex$aKB$AHASIIICH3CO$Val$, kfiAHASIIIaKBVal, kriAHASIIIaKBVal}, {Leu + $Complex$aKIV$IPMSacetyl$ \ \[RightArrowLeftArrow] $Complex$aKIV$IPMSacetyl$Leu$, kfiIPMSacetylLeu, kriIPMSacetylLeu}, {aKIV + $Complex$IPMSacetyl$Leu$ \ \[RightArrowLeftArrow] $Complex$aKIV$IPMSacetyl$Leu$, kfIPMSaKIV, krIPMSaKIV}, {Val + $Complex$Pyr$AHASICH3CO$ \[RightArrowLeftArrow] \ $Complex$Pyr$AHASICH3CO$Val$, kfiAHASIPyr2Val, kriAHASIPyr2Val}, {Val + $Complex$Pyr$AHASIIICH3CO$ \ \[RightArrowLeftArrow] $Complex$Pyr$AHASIIICH3CO$Val$, kfiAHASIIIPyr2Val, kriAHASIIIPyr2Val}, {Val + $Complex$Pyr$AHASIII$ \ \[RightArrowLeftArrow] $Complex$Pyr$AHASIII$Val$, kfiAHASIIIPyrVal, kriAHASIIIPyrVal}, {Val + $Complex$Pyr$AHASI$ \[RightArrowLeftArrow] \ $Complex$Pyr$AHASI$Val$, kfiAHASIPyrVal, kriAHASIPyrVal}, {\(aDHIV \[RightArrowLeftArrow] aKIV\)\&DAD, kfDADaDHIV, krDADaDHIV, kcat$DAD$aDHIV}, {\(aDMV \[RightArrowLeftArrow] aKMV\)\&DAD, kfDADaDMV, krDADaDMV, kcat$DAD$aDMV}, {\(aIPM \[RightArrowLeftArrow] bIPM\)\&IPMI, kfIPMIaIPM, krIPMIaIPM, kcat$IPMI$aIPM}, {\(aKB \[RightArrowLeftArrow] propionylCoA\)\&KDC, kfKDCaKB, krKDCaKB, kcat$KDC$aKB}, {\(bIPM \[RightArrowLeftArrow] aIPM\)\&IPMI, kfIPMIbIPM, krIPMIbIPM, kcat$IPMI$bIPM}, {\(exIle \[RightArrowLeftArrow] Ile\)\&LIVI, kfLIVIexIle, krLIVIexIle, kcat$LIVI$exIle}, {\(exIle \[RightArrowLeftArrow] Ile\)\&LIVII, kfLIVIIexIle, krLIVIIexIle, kcat$LIVII$exIle}, {\(exLeu \[RightArrowLeftArrow] Leu\)\&LIVI, kfLIVIexLeu, krLIVIexLeu, kcat$LIVI$exLeu}, {\(exLeu \[RightArrowLeftArrow] Leu\)\&LIVII, kfLIVIIexLeu, krLIVIIexLeu, kcat$LIVII$exLeu}, {\(exLeu \[RightArrowLeftArrow] Leu\)\&LS, kfLSexLeu, krLSexLeu, kcat$LS$exLeu}, {\(exVal \[RightArrowLeftArrow] Val\)\&LIVI, kfLIVIexVal, krLIVIexVal, kcat$LIVI$exVal}, {\(exVal \[RightArrowLeftArrow] Val\)\&LIVII, kfLIVIIexVal, krLIVIIexVal, kcat$LIVII$exVal}}\)], "Output"] }, Open ]], Cell[BoxData[ RowBox[{ StyleBox[\( (*\ Cellerator - interpreted\ Ordinary\ Differential\ Equations\ \((ODEs)\) and\ Equations\ for\ the\ MWC\ Model\ and\ Substrate\ \ \(\(Generators\)\(\ \)\(.\)\)\ *) \), FontSize->14], "\[IndentingNewLine]", "\[IndentingNewLine]", \(interpret[ILE$VAL$LEU$Synthesis]\)}]], "Input"], Cell[BoxData[ StyleBox[ RowBox[{"(*", " ", "\[IndentingNewLine]", RowBox[{\(Modifications\ for\ Substrate\ \(Generators : \ \[IndentingNewLine]The\ generated\ ODEs\ require\ some\ modifications\ to\ \ include\ the\ constant\ substrate\ fluxes\ for\ the\ steady\ state\ \ simulation\[IndentingNewLine]\[IndentingNewLine] \ 1. Substrate\ \(Generators : \ \[IndentingNewLine]\ \ \ \ \ \ \ Set\ the\ first\ derivatives\ of\ the\ following\ substrates\ to\ 0\ \[IndentingNewLine] \ \ \ \ to\ simulate\ constant\ flux\[IndentingNewLine] \t\(Thr'\)[t] \[Equal] 0\)\)\), ",", " ", \(\(Pyr'\)[t] \[Equal] 0\), ",", " ", \(\(NADPH'\)[t] \[Equal] 0\), ",", " ", \(\(Glu'\)[t] \[Equal] 0\), ",", "\[IndentingNewLine]", "\t\t", \(\(Ala'\)[t] \[Equal] 0\), ",", " ", RowBox[{ RowBox[{ SuperscriptBox["exIle", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", " ", RowBox[{ RowBox[{ SuperscriptBox["exVal", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", " ", RowBox[{ RowBox[{ SuperscriptBox["exLeu", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", "\t\t", RowBox[{ RowBox[{ SuperscriptBox["acetylCoA", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", RowBox[{ RowBox[{ SuperscriptBox["NAD", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ","}], "\[IndentingNewLine]", "*)"}], FontSize->14]], "Input"], Cell[BoxData[ RowBox[{ RowBox[{\({myODEs, myVars}\), "=", "\[IndentingNewLine]", RowBox[{"{", RowBox[{ RowBox[{"{", RowBox[{ RowBox[{ RowBox[{ SuperscriptBox["aAHB", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIRaAHB\)\ aAHB[t]\ IR[t]\ NADPH[t] + kcat$AHASI$aKB\ $Complex$aKB$AHASICH3CO$[t] + kcat$AHASI$aKB\ residualRateAHASIValaKB\ \ $Complex$aKB$AHASICH3CO$Val$[t] + kcat$AHASII$aKB\ $Complex$aKB$AHASIICH3CO$[t] + kcat$AHASIII$aKB\ $Complex$aKB$AHASIIICH3CO$[t] + kcat$AHASIII$aKB\ residualRateAHASIIIValaKB\ \ $Complex$aKB$AHASIIICH3CO$Val$[t] + krIRaAHB\ $Complex$IR$aAHB$NADPH$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aAL", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIRaAL\)\ aAL[t]\ IR[t]\ NADPH[t] + krIRaAL\ $Complex$IR$aAL$NADPH$[t] + kcat$AHASI$Pyr2\ $Complex$Pyr$AHASICH3CO$[t] + kcat$AHASI$Pyr2\ residualRateAHASIValPyr2\ \ $Complex$Pyr$AHASICH3CO$Val$[t] + kcat$AHASII$Pyr2\ $Complex$Pyr$AHASIICH3CO$[t] + kcat$AHASIII$Pyr2\ $Complex$Pyr$AHASIIICH3CO$[t] + kcat$AHASIII$Pyr2\ residualRateAHASIIIValPyr2\ \ $Complex$Pyr$AHASIIICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["acetylCoA", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", RowBox[{ RowBox[{ SuperscriptBox["aDHIV", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfDADaDHIV\)\ aDHIV[t]\ DAD[t] + krDADaDHIV\ $Complex$aDHIV$DAD$[t] + kcat$IR$aAL\ $Complex$IR$aAL$NADPH$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aDMV", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfDADaDMV\)\ aDMV[t]\ DAD[t] + krDADaDMV\ $Complex$aDMV$DAD$[t] + kcat$IR$aAHB\ $Complex$IR$aAHB$NADPH$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["AHASI", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIPyr\)\ AHASI[t]\ Pyr[t] - kfiAHASIPyrVal\ AHASI[t]\ Val[t] + kriAHASIPyrVal\ $Complex$AHASI$Val$[t] + kcat$AHASI$aKB\ $Complex$aKB$AHASICH3CO$[t] + kcat$AHASI$Pyr2\ $Complex$Pyr$AHASICH3CO$[t] + krAHASIPyr\ $Complex$Pyr$AHASI$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["AHASICH3CO", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIaKB\)\ AHASICH3CO[t]\ aKB[t] - kfAHASIPyr2\ AHASICH3CO[t]\ Pyr[t] - kfiAHASIaKBVal\ AHASICH3CO[t]\ Val[t] + kriAHASIaKBVal\ $Complex$AHASICH3CO$Val$[t] + krAHASIaKB\ $Complex$aKB$AHASICH3CO$[t] + krAHASIPyr2\ $Complex$Pyr$AHASICH3CO$[t] + kcat$AHASI$Pyr\ $Complex$Pyr$AHASI$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["AHASII", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIIPyr\)\ AHASII[t]\ Pyr[t] + kcat$AHASII$aKB\ $Complex$aKB$AHASIICH3CO$[t] + kcat$AHASII$Pyr2\ $Complex$Pyr$AHASIICH3CO$[t] + krAHASIIPyr\ $Complex$Pyr$AHASII$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["AHASIICH3CO", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIIaKB\)\ AHASIICH3CO[t]\ aKB[t] - kfAHASIIPyr2\ AHASIICH3CO[t]\ Pyr[t] + krAHASIIaKB\ $Complex$aKB$AHASIICH3CO$[t] + krAHASIIPyr2\ $Complex$Pyr$AHASIICH3CO$[t] + kcat$AHASII$Pyr\ $Complex$Pyr$AHASII$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["AHASIII", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIIIPyr\)\ AHASIII[t]\ Pyr[t] - kfiAHASIIIPyrVal\ AHASIII[t]\ Val[t] + kriAHASIIIPyrVal\ $Complex$AHASIII$Val$[t] + kcat$AHASIII$aKB\ $Complex$aKB$AHASIIICH3CO$[t] + kcat$AHASIII$Pyr2\ $Complex$Pyr$AHASIIICH3CO$[t] + krAHASIIIPyr\ $Complex$Pyr$AHASIII$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["AHASIIICH3CO", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIIIaKB\)\ AHASIIICH3CO[t]\ aKB[t] - kfAHASIIIPyr2\ AHASIIICH3CO[t]\ Pyr[t] - kfiAHASIIIaKBVal\ AHASIIICH3CO[t]\ Val[t] + kriAHASIIIaKBVal\ $Complex$AHASIIICH3CO$Val$[t] + krAHASIIIaKB\ $Complex$aKB$AHASIIICH3CO$[t] + krAHASIIIPyr2\ $Complex$Pyr$AHASIIICH3CO$[t] + kcat$AHASIII$Pyr\ $Complex$Pyr$AHASIII$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aIPM", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIPMIaIPM\)\ aIPM[t]\ IPMI[t] + krIPMIaIPM\ $Complex$aIPM$IPMI$[t] + kcat$IPMS$aKIV\ $Complex$aKIV$IPMSacetyl$[t] + kcat$IPMI$bIPM\ $Complex$bIPM$IPMI$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aKB", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfAHASIaKB\)\ AHASICH3CO[t]\ aKB[t] - kfAHASIIaKB\ AHASIICH3CO[t]\ aKB[t] - kfAHASIIIaKB\ AHASIIICH3CO[t]\ aKB[t] - kfKDCaKB\ aKB[t]\ KDC[ t] + \((kcat$TDA\ TDA[ t]\ \((\(cTDA\ L0TDA\ \((1 + \ Ile[t]\/KiIle)\)\^nTDA\ Thr[t]\ \((1 + \(cTDA\ Thr[t]\)\/KmThr)\)\^\(\(-1\) + \ nTDA\)\)\/KmThr + \(Thr[t]\ \((1 + Thr[t]\/KmThr)\)\^\(\(-1\) + nTDA\)\ \((1 \ + Val[t]\/KaVal)\)\^nTDA\)\/KmThr)\))\)/\((L0TDA\ \((1 + \ Ile[t]\/KiIle)\)\^nTDA\ \((1 + \(cTDA\ Thr[t]\)\/KmThr)\)\^nTDA + \((1 + \ Thr[t]\/KmThr)\)\^nTDA\ \((1 + Val[t]\/KaVal)\)\^nTDA)\) - kfAHASIaKB\ aKB[t]\ $Complex$AHASICH3CO$Val$[t] - kfAHASIIIaKB\ aKB[t]\ $Complex$AHASIIICH3CO$Val$[t] + krAHASIaKB\ $Complex$aKB$AHASICH3CO$[t] + krAHASIaKB\ $Complex$aKB$AHASICH3CO$Val$[t] + krAHASIIaKB\ $Complex$aKB$AHASIICH3CO$[t] + krAHASIIIaKB\ $Complex$aKB$AHASIIICH3CO$[t] + krAHASIIIaKB\ $Complex$aKB$AHASIIICH3CO$Val$[t] + krKDCaKB\ $Complex$aKB$KDC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aKG", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-rkfTBaKG\)\ aKG[t]\ TBNH2[t] + rkrTBaKG\ $Complex$aKG$TBNH2$[t] + fkcat$TB$Glu\ $Complex$Glu$TB$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aKIC", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kcat$aKIC\)\ aKIC[t] - fkfTBaKIC\ aKIC[t]\ TBNH2[t] + fkrTBaKIC\ $Complex$aKIC$TBNH2$[t] + kcat$IPMDH$bIPM\ $Complex$IPMDH$bIPM$NAD$[t] + rkcat$TB$Leu\ $Complex$Leu$TB$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aKIV", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kcat$aKIV\)\ aKIV[t] - kfIPMSaKIV\ aKIV[t]\ IPMSacetyl[t] - fkfTBaKIV\ aKIV[t]\ TBNH2[t] - fkfTCaKIV\ aKIV[t]\ TCNH2[t] + kcat$DAD$aDHIV\ $Complex$aDHIV$DAD$[t] + krIPMSaKIV\ $Complex$aKIV$IPMSacetyl$[t] + krIPMSaKIV\ $Complex$aKIV$IPMSacetyl$Leu$[t] + fkrTBaKIV\ $Complex$aKIV$TBNH2$[t] + fkrTCaKIV\ $Complex$aKIV$TCNH2$[t] - kfIPMSaKIV\ aKIV[t]\ $Complex$IPMSacetyl$Leu$[t] + rkcat$TB$Val\ $Complex$Val$TB$[t] + rkcat$TC$Val\ $Complex$Val$TC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["aKMV", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kcat$aKMV\)\ aKMV[t] - fkfTBaKMV\ aKMV[t]\ TBNH2[t] + kcat$DAD$aDMV\ $Complex$aDMV$DAD$[t] + fkrTBaKMV\ $Complex$aKMV$TBNH2$[t] + rkcat$TB$Ile\ $Complex$Ile$TB$[t]\)}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["Ala", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["bIPM", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIPMIbIPM\)\ bIPM[t]\ IPMI[t] - kfIPMDHbIPM\ bIPM[t]\ IPMDH[t]\ NAD[t] + kcat$IPMI$aIPM\ $Complex$aIPM$IPMI$[t] + krIPMIbIPM\ $Complex$bIPM$IPMI$[t] + krIPMDHbIPM\ $Complex$IPMDH$bIPM$NAD$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["CO2", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$AHASIII$Pyr\ $Complex$Pyr$AHASIII$[t] + kcat$AHASIII$Pyr\ residualRateAHASIIIValaKB\ \ $Complex$Pyr$AHASIII$Val$[t] + kcat$AHASII$Pyr\ $Complex$Pyr$AHASII$[t] + kcat$AHASI$Pyr\ $Complex$Pyr$AHASI$[t] + kcat$AHASI$Pyr\ residualRateAHASIValaKB\ \ $Complex$Pyr$AHASI$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["CoA", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$IPMS$acetylCoA\ $Complex$acetylCoA$IPMS$[ t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["DAD", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfDADaDHIV\)\ aDHIV[t]\ DAD[t] - kfDADaDMV\ aDMV[t]\ DAD[t] + kcat$DAD$aDHIV\ $Complex$aDHIV$DAD$[t] + krDADaDHIV\ $Complex$aDHIV$DAD$[t] + kcat$DAD$aDMV\ $Complex$aDMV$DAD$[t] + krDADaDMV\ $Complex$aDMV$DAD$[t]\)}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["exIle", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["exLeu", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["exVal", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["Glu", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["glutarylCoA", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$aKIC\ aKIC[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["Ile", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kcat$Ile\)\ Ile[t] - rkfTBIle\ Ile[t]\ TB[t] + fkcat$TB$aKMV\ $Complex$aKMV$TBNH2$[t] + kcat$LIVII$exIle\ $Complex$exIle$LIVII$[t] + kcat$LIVI$exIle\ $Complex$exIle$LIVI$[t] + rkrTBIle\ $Complex$Ile$TB$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["IPMDH", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIPMDHbIPM\)\ bIPM[t]\ IPMDH[t]\ NAD[t] + kcat$IPMDH$bIPM\ $Complex$IPMDH$bIPM$NAD$[t] + krIPMDHbIPM\ $Complex$IPMDH$bIPM$NAD$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["IPMI", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIPMIaIPM\)\ aIPM[t]\ IPMI[t] - kfIPMIbIPM\ bIPM[t]\ IPMI[t] + kcat$IPMI$aIPM\ $Complex$aIPM$IPMI$[t] + krIPMIaIPM\ $Complex$aIPM$IPMI$[t] + kcat$IPMI$bIPM\ $Complex$bIPM$IPMI$[t] + krIPMIbIPM\ $Complex$bIPM$IPMI$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["IPMS", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIPMSacetylCoA\)\ acetylCoA[t]\ IPMS[t] - kfiIPMSLeu\ IPMS[t]\ Leu[t] + krIPMSacetylCoA\ $Complex$acetylCoA$IPMS$[t] + kcat$IPMS$aKIV\ $Complex$aKIV$IPMSacetyl$[t] + kriIPMSLeu\ $Complex$IPMS$Leu$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["IPMSacetyl", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIPMSaKIV\)\ aKIV[t]\ IPMSacetyl[t] - kfiIPMSacetylLeu\ IPMSacetyl[t]\ Leu[t] + kcat$IPMS$acetylCoA\ $Complex$acetylCoA$IPMS$[t] + krIPMSaKIV\ $Complex$aKIV$IPMSacetyl$[t] + kriIPMSacetylLeu\ $Complex$IPMSacetyl$Leu$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["IR", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfIRaAHB\)\ aAHB[t]\ IR[t]\ NADPH[t] - kfIRaAL\ aAL[t]\ IR[t]\ NADPH[t] + kcat$IR$aAHB\ $Complex$IR$aAHB$NADPH$[t] + krIRaAHB\ $Complex$IR$aAHB$NADPH$[t] + kcat$IR$aAL\ $Complex$IR$aAL$NADPH$[t] + krIRaAL\ $Complex$IR$aAL$NADPH$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["KDC", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfKDCaKB\)\ aKB[t]\ KDC[t] + kcat$KDC$aKB\ $Complex$aKB$KDC$[t] + krKDCaKB\ $Complex$aKB$KDC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["Leu", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kcat$Leu\)\ Leu[t] - kfiIPMSLeu\ IPMS[t]\ Leu[t] - kfiIPMSacetylLeu\ IPMSacetyl[t]\ Leu[t] - rkfTBLeu\ Leu[t]\ TB[t] + fkcat$TB$aKIC\ $Complex$aKIC$TBNH2$[t] - kfiIPMSacetylLeu\ Leu[t]\ $Complex$aKIV$IPMSacetyl$[t] + kriIPMSacetylLeu\ $Complex$aKIV$IPMSacetyl$Leu$[t] + kcat$LIVII$exLeu\ $Complex$exLeu$LIVII$[t] + kcat$LIVI$exLeu\ $Complex$exLeu$LIVI$[t] + kcat$LS$exLeu\ $Complex$exLeu$LS$[t] + kriIPMSacetylLeu\ $Complex$IPMSacetyl$Leu$[t] + kriIPMSLeu\ $Complex$IPMS$Leu$[t] + rkrTBLeu\ $Complex$Leu$TB$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["LIVI", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfLIVIexIle\)\ exIle[t]\ LIVI[t] - kfLIVIexLeu\ exLeu[t]\ LIVI[t] - kfLIVIexVal\ exVal[t]\ LIVI[t] + kcat$LIVI$exIle\ $Complex$exIle$LIVI$[t] + krLIVIexIle\ $Complex$exIle$LIVI$[t] + kcat$LIVI$exLeu\ $Complex$exLeu$LIVI$[t] + krLIVIexLeu\ $Complex$exLeu$LIVI$[t] + kcat$LIVI$exVal\ $Complex$exVal$LIVI$[t] + krLIVIexVal\ $Complex$exVal$LIVI$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["LIVII", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfLIVIIexIle\)\ exIle[t]\ LIVII[t] - kfLIVIIexLeu\ exLeu[t]\ LIVII[t] - kfLIVIIexVal\ exVal[t]\ LIVII[t] + kcat$LIVII$exIle\ $Complex$exIle$LIVII$[t] + krLIVIIexIle\ $Complex$exIle$LIVII$[t] + kcat$LIVII$exLeu\ $Complex$exLeu$LIVII$[t] + krLIVIIexLeu\ $Complex$exLeu$LIVII$[t] + kcat$LIVII$exVal\ $Complex$exVal$LIVII$[t] + krLIVIIexVal\ $Complex$exVal$LIVII$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["LS", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kfLSexLeu\)\ exLeu[t]\ LS[t] + kcat$LS$exLeu\ $Complex$exLeu$LS$[t] + krLSexLeu\ $Complex$exLeu$LS$[t]\)}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["NAD", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["NADH", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$IPMDH$bIPM\ $Complex$IPMDH$bIPM$NAD$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["NADP", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$IR$aAHB\ $Complex$IR$aAHB$NADPH$[t] + kcat$IR$aAL\ $Complex$IR$aAL$NADPH$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["NADPH", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", RowBox[{ RowBox[{ SuperscriptBox["NH3", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\((kcat$TDA\ TDA[ t]\ \((\(cTDA\ L0TDA\ \((1 + Ile[t]\/KiIle)\)\^nTDA\ \ Thr[t]\ \((1 + \(cTDA\ Thr[t]\)\/KmThr)\)\^\(\(-1\) + nTDA\)\)\/KmThr + \ \(Thr[t]\ \((1 + Thr[t]\/KmThr)\)\^\(\(-1\) + nTDA\)\ \((1 + Val[t]\/KaVal)\)\ \^nTDA\)\/KmThr)\))\)/\((L0TDA\ \((1 + Ile[t]\/KiIle)\)\^nTDA\ \((1 + \(cTDA\ \ Thr[t]\)\/KmThr)\)\^nTDA + \((1 + Thr[t]\/KmThr)\)\^nTDA\ \((1 + \ Val[t]\/KaVal)\)\^nTDA)\)\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["pantothenate", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$aKIV\ aKIV[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["propionylCoA", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$KDC$aKB\ $Complex$aKB$KDC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["protein", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kcat$Ile\ Ile[t] + kcat$Leu\ Leu[t] + kcat$Val\ Val[t]\)}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["Pyr", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["TB", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-fkfTBGlu\)\ Glu[t]\ TB[t] - rkfTBIle\ Ile[t]\ TB[t] - rkfTBLeu\ Leu[t]\ TB[t] - rkfTBVal\ TB[t]\ Val[t] + rkcat$TB$aKG\ $Complex$aKG$TBNH2$[t] + fkcat$TB$aKIC\ $Complex$aKIC$TBNH2$[t] + fkcat$TB$aKIV\ $Complex$aKIV$TBNH2$[t] + fkcat$TB$aKMV\ $Complex$aKMV$TBNH2$[t] + fkrTBGlu\ $Complex$Glu$TB$[t] + rkrTBIle\ $Complex$Ile$TB$[t] + rkrTBLeu\ $Complex$Leu$TB$[t] + rkrTBVal\ $Complex$Val$TB$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["TBNH2", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-rkfTBaKG\)\ aKG[t]\ TBNH2[t] - fkfTBaKIC\ aKIC[t]\ TBNH2[t] - fkfTBaKIV\ aKIV[t]\ TBNH2[t] - fkfTBaKMV\ aKMV[t]\ TBNH2[t] + rkrTBaKG\ $Complex$aKG$TBNH2$[t] + fkrTBaKIC\ $Complex$aKIC$TBNH2$[t] + fkrTBaKIV\ $Complex$aKIV$TBNH2$[t] + fkrTBaKMV\ $Complex$aKMV$TBNH2$[t] + fkcat$TB$Glu\ $Complex$Glu$TB$[t] + rkcat$TB$Ile\ $Complex$Ile$TB$[t] + rkcat$TB$Leu\ $Complex$Leu$TB$[t] + rkcat$TB$Val\ $Complex$Val$TB$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["TC", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-fkfTCAla\)\ Ala[t]\ TC[t] - rkfTCVal\ TC[t]\ Val[t] + fkcat$TC$aKIV\ $Complex$aKIV$TCNH2$[t] + fkrTCAla\ $Complex$Ala$TC$[t] + rkcat$TC$Pyr\ $Complex$Pyr$TCNH2$[t] + rkrTCVal\ $Complex$Val$TC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["TCNH2", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-fkfTCaKIV\)\ aKIV[t]\ TCNH2[t] - rkfTCPyr\ Pyr[t]\ TCNH2[t] + fkrTCaKIV\ $Complex$aKIV$TCNH2$[t] + fkcat$TC$Ala\ $Complex$Ala$TC$[t] + rkrTCPyr\ $Complex$Pyr$TCNH2$[t] + rkcat$TC$Val\ $Complex$Val$TC$[t]\)}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["TDA", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["Thr", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "\[Equal]", "0"}], ",", "\[IndentingNewLine]", RowBox[{ RowBox[{ SuperscriptBox["Val", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(\(-kcat$Val\)\ Val[t] - kfiAHASIPyrVal\ AHASI[t]\ Val[t] - kfiAHASIaKBVal\ AHASICH3CO[t]\ Val[t] - kfiAHASIIIPyrVal\ AHASIII[t]\ Val[t] - kfiAHASIIIaKBVal\ AHASIIICH3CO[t]\ Val[t] - rkfTBVal\ TB[t]\ Val[t] - rkfTCVal\ TC[t]\ Val[t] + kriAHASIaKBVal\ $Complex$AHASICH3CO$Val$[t] + kriAHASIIIaKBVal\ $Complex$AHASIIICH3CO$Val$[t] + kriAHASIIIPyrVal\ $Complex$AHASIII$Val$[t] + kriAHASIPyrVal\ $Complex$AHASI$Val$[t] - kfiAHASIaKBVal\ Val[t]\ $Complex$aKB$AHASICH3CO$[t] + kriAHASIaKBVal\ $Complex$aKB$AHASICH3CO$Val$[t] - kfiAHASIIIaKBVal\ Val[t]\ $Complex$aKB$AHASIIICH3CO$[t] + kriAHASIIIaKBVal\ $Complex$aKB$AHASIIICH3CO$Val$[t] + fkcat$TB$aKIV\ $Complex$aKIV$TBNH2$[t] + fkcat$TC$aKIV\ $Complex$aKIV$TCNH2$[t] + kcat$LIVII$exVal\ $Complex$exVal$LIVII$[t] + kcat$LIVI$exVal\ $Complex$exVal$LIVI$[t] - kfiAHASIPyr2Val\ Val[t]\ $Complex$Pyr$AHASICH3CO$[t] + kriAHASIPyr2Val\ $Complex$Pyr$AHASICH3CO$Val$[t] - kfiAHASIIIPyr2Val\ Val[t]\ $Complex$Pyr$AHASIIICH3CO$[ t] + kriAHASIIIPyr2Val\ \ $Complex$Pyr$AHASIIICH3CO$Val$[t] - kfiAHASIIIPyrVal\ Val[t]\ $Complex$Pyr$AHASIII$[t] + kriAHASIIIPyrVal\ $Complex$Pyr$AHASIII$Val$[t] - kfiAHASIPyrVal\ Val[t]\ $Complex$Pyr$AHASI$[t] + kriAHASIPyrVal\ $Complex$Pyr$AHASI$Val$[t] + rkrTBVal\ $Complex$Val$TB$[t] + rkrTCVal\ $Complex$Val$TC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$acetylCoA$IPMS$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfIPMSacetylCoA\ acetylCoA[t]\ IPMS[t] - kcat$IPMS$acetylCoA\ $Complex$acetylCoA$IPMS$[t] - krIPMSacetylCoA\ $Complex$acetylCoA$IPMS$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aDHIV$DAD$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfDADaDHIV\ aDHIV[t]\ DAD[t] - kcat$DAD$aDHIV\ $Complex$aDHIV$DAD$[t] - krDADaDHIV\ $Complex$aDHIV$DAD$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aDMV$DAD$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfDADaDMV\ aDMV[t]\ DAD[t] - kcat$DAD$aDMV\ $Complex$aDMV$DAD$[t] - krDADaDMV\ $Complex$aDMV$DAD$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$AHASICH3CO$Val$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfiAHASIaKBVal\ AHASICH3CO[t]\ Val[t] - kriAHASIaKBVal\ $Complex$AHASICH3CO$Val$[t] - kfAHASIaKB\ aKB[t]\ $Complex$AHASICH3CO$Val$[t] - kfAHASIPyr2\ Pyr[t]\ $Complex$AHASICH3CO$Val$[t] + krAHASIaKB\ $Complex$aKB$AHASICH3CO$Val$[t] + kcat$AHASI$aKB\ residualRateAHASIValaKB\ \ $Complex$aKB$AHASICH3CO$Val$[t] + krAHASIPyr2\ $Complex$Pyr$AHASICH3CO$Val$[t] + kcat$AHASI$Pyr2\ residualRateAHASIValPyr2\ \ $Complex$Pyr$AHASICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$AHASIIICH3CO$Val$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfiAHASIIIaKBVal\ AHASIIICH3CO[t]\ Val[t] - kriAHASIIIaKBVal\ $Complex$AHASIIICH3CO$Val$[t] - kfAHASIIIaKB\ aKB[t]\ $Complex$AHASIIICH3CO$Val$[t] - kfAHASIIIPyr2\ Pyr[t]\ $Complex$AHASIIICH3CO$Val$[t] + krAHASIIIaKB\ $Complex$aKB$AHASIIICH3CO$Val$[t] + kcat$AHASIII$aKB\ residualRateAHASIIIValaKB\ \ $Complex$aKB$AHASIIICH3CO$Val$[t] + krAHASIIIPyr2\ $Complex$Pyr$AHASIIICH3CO$Val$[t] + kcat$AHASIII$Pyr2\ residualRateAHASIIIValPyr2\ \ $Complex$Pyr$AHASIIICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$AHASIII$Val$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfiAHASIIIPyrVal\ AHASIII[t]\ Val[t] - kriAHASIIIPyrVal\ $Complex$AHASIII$Val$[t] - kfAHASIIIPyr\ Pyr[t]\ $Complex$AHASIII$Val$[t] + krAHASIIIPyr\ $Complex$Pyr$AHASIII$Val$[t] + kcat$AHASIII$Pyr\ residualRateAHASIIIValaKB\ \ $Complex$Pyr$AHASIII$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$AHASI$Val$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfiAHASIPyrVal\ AHASI[t]\ Val[t] - kriAHASIPyrVal\ $Complex$AHASI$Val$[t] - kfAHASIPyr\ Pyr[t]\ $Complex$AHASI$Val$[t] + krAHASIPyr\ $Complex$Pyr$AHASI$Val$[t] + kcat$AHASI$Pyr\ residualRateAHASIValaKB\ \ $Complex$Pyr$AHASI$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aIPM$IPMI$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfIPMIaIPM\ aIPM[t]\ IPMI[t] - kcat$IPMI$aIPM\ $Complex$aIPM$IPMI$[t] - krIPMIaIPM\ $Complex$aIPM$IPMI$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKB$AHASICH3CO$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfAHASIaKB\ AHASICH3CO[t]\ aKB[t] - kcat$AHASI$aKB\ $Complex$aKB$AHASICH3CO$[t] - krAHASIaKB\ $Complex$aKB$AHASICH3CO$[t] - kfiAHASIaKBVal\ Val[t]\ $Complex$aKB$AHASICH3CO$[t] + kriAHASIaKBVal\ $Complex$aKB$AHASICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKB$AHASICH3CO$Val$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfAHASIaKB\ aKB[t]\ $Complex$AHASICH3CO$Val$[t] + kfiAHASIaKBVal\ Val[t]\ $Complex$aKB$AHASICH3CO$[t] - krAHASIaKB\ $Complex$aKB$AHASICH3CO$Val$[t] - kriAHASIaKBVal\ $Complex$aKB$AHASICH3CO$Val$[t] - kcat$AHASI$aKB\ residualRateAHASIValaKB\ \ $Complex$aKB$AHASICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKB$AHASIICH3CO$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfAHASIIaKB\ AHASIICH3CO[t]\ aKB[t] - kcat$AHASII$aKB\ $Complex$aKB$AHASIICH3CO$[t] - krAHASIIaKB\ $Complex$aKB$AHASIICH3CO$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKB$AHASIIICH3CO$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfAHASIIIaKB\ AHASIIICH3CO[t]\ aKB[t] - kcat$AHASIII$aKB\ $Complex$aKB$AHASIIICH3CO$[t] - krAHASIIIaKB\ $Complex$aKB$AHASIIICH3CO$[t] - kfiAHASIIIaKBVal\ Val[t]\ $Complex$aKB$AHASIIICH3CO$[t] + kriAHASIIIaKBVal\ $Complex$aKB$AHASIIICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKB$AHASIIICH3CO$Val$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfAHASIIIaKB\ aKB[t]\ $Complex$AHASIIICH3CO$Val$[ t] + kfiAHASIIIaKBVal\ Val[ t]\ $Complex$aKB$AHASIIICH3CO$[t] - krAHASIIIaKB\ $Complex$aKB$AHASIIICH3CO$Val$[t] - kriAHASIIIaKBVal\ $Complex$aKB$AHASIIICH3CO$Val$[t] - kcat$AHASIII$aKB\ residualRateAHASIIIValaKB\ \ $Complex$aKB$AHASIIICH3CO$Val$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKB$KDC$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfKDCaKB\ aKB[t]\ KDC[t] - kcat$KDC$aKB\ $Complex$aKB$KDC$[t] - krKDCaKB\ $Complex$aKB$KDC$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKG$TBNH2$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(rkfTBaKG\ aKG[t]\ TBNH2[t] - rkcat$TB$aKG\ $Complex$aKG$TBNH2$[t] - rkrTBaKG\ $Complex$aKG$TBNH2$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKIC$TBNH2$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(fkfTBaKIC\ aKIC[t]\ TBNH2[t] - fkcat$TB$aKIC\ $Complex$aKIC$TBNH2$[t] - fkrTBaKIC\ $Complex$aKIC$TBNH2$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKIV$IPMSacetyl$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfIPMSaKIV\ aKIV[t]\ IPMSacetyl[t] - kcat$IPMS$aKIV\ $Complex$aKIV$IPMSacetyl$[t] - krIPMSaKIV\ $Complex$aKIV$IPMSacetyl$[t] - kfiIPMSacetylLeu\ Leu[t]\ $Complex$aKIV$IPMSacetyl$[t] + kriIPMSacetylLeu\ $Complex$aKIV$IPMSacetyl$Leu$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKIV$IPMSacetyl$Leu$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(kfiIPMSacetylLeu\ Leu[t]\ $Complex$aKIV$IPMSacetyl$[ t] - kriIPMSacetylLeu\ $Complex$aKIV$IPMSacetyl$Leu$[ t] - krIPMSaKIV\ $Complex$aKIV$IPMSacetyl$Leu$[t] + kfIPMSaKIV\ aKIV[t]\ $Complex$IPMSacetyl$Leu$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKIV$TBNH2$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(fkfTBaKIV\ aKIV[t]\ TBNH2[t] - fkcat$TB$aKIV\ $Complex$aKIV$TBNH2$[t] - fkrTBaKIV\ $Complex$aKIV$TBNH2$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKIV$TCNH2$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(fkfTCaKIV\ aKIV[t]\ TCNH2[t] - fkcat$TC$aKIV\ $Complex$aKIV$TCNH2$[t] - fkrTCaKIV\ $Complex$aKIV$TCNH2$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$aKMV$TBNH2$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", \(fkfTBaKMV\ aKMV[t]\ TBNH2[t] - fkcat$TB$aKMV\ $Complex$aKMV$TBNH2$[t] - fkrTBaKMV\ $Complex$aKMV$TBNH2$[t]\)}], ",", RowBox[{ RowBox[{ SuperscriptBox["$Complex$Ala$TC$", "\[Prime]", MultilineFunction->None], "[", "t", "]"}], "==", 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FontSlant->"Italic"]}]], "."}], FontSize->14]}]}], StyleBox["\[IndentingNewLine]", FontSize->14], StyleBox["*)", FontSize->14]}], "\[IndentingNewLine]", "\[IndentingNewLine]", \(\(Lamda = 100;\)\n \(Omega = 1;\)\[IndentingNewLine] \(myKs = {\n\ \ \ \ \ \ \ nTDA \[Rule] \ 4, \[IndentingNewLine]cTDA \[Rule] \ 0.013, \[IndentingNewLine]L0TDA \[Rule] 1.05, \[IndentingNewLine]kcat$TDA \[Rule] 6000, \[IndentingNewLine]KmThr \[Rule] \ 2700, \[IndentingNewLine]KaVal \[Rule] \ 550, \[IndentingNewLine]KiIle \[Rule] \ 15, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (*\ TDA\ feedback\ resistant\ mutant, \ KiIle = 100000\ \ *) \[IndentingNewLine]\[IndentingNewLine]KmKDCaKB = 1000; \ kcat$KDC$aKB = 3000; \[IndentingNewLine]kfKDCaKB \[Rule] Kf[KmKDCaKB, kcat$KDC$aKB, Lamda], \[IndentingNewLine]krKDCaKB \[Rule] Kr[kcat$KDC$aKB, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIPyr = 10; kcat$AHASI$Pyr = 7000; \[IndentingNewLine]kfAHASIPyr \[Rule] Kf[KmAHASIPyr, kcat$AHASI$Pyr, Lamda], \[IndentingNewLine]krAHASIPyr \[Rule] Kr[kcat$AHASI$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIaKB = 5000; kcat$AHASI$aKB = 7000; \[IndentingNewLine]kfAHASIaKB \[Rule] Kf[KmAHASIaKB, kcat$AHASI$aKB, Lamda], \[IndentingNewLine]krAHASIaKB \[Rule] Kr[kcat$AHASI$aKB, Lamda], \[IndentingNewLine]residualRateAHASIValaKB \[Rule] 0, \[IndentingNewLine]\[IndentingNewLine]KiAHASIVal = 200; \[IndentingNewLine]kfiAHASIPyrVal \[Rule] Kfi[KmAHASIPyr, kcat$AHASI$Pyr, Lamda, Omega], \[IndentingNewLine]kriAHASIPyrVal \[Rule] Kri[KmAHASIPyr, kcat$AHASI$Pyr, Lamda, Omega, KiAHASIVal], \[IndentingNewLine]kfiAHASIaKBVal \[Rule] Kfi[KmAHASIaKB, kcat$AHASI$aKB, Lamda, Omega], \[IndentingNewLine]kriAHASIaKBVal \[Rule] Kri[KmAHASIaKB, kcat$AHASI$aKB, Lamda, Omega, KiAHASIVal], \ \[IndentingNewLine]\[IndentingNewLine]KmAHASIIPyr = 10; kcat$AHASII$Pyr = 7000; \[IndentingNewLine]kfAHASIIPyr \[Rule] Kf[KmAHASIIPyr, kcat$AHASII$Pyr, Lamda], \[IndentingNewLine]krAHASIIPyr \[Rule] Kr[kcat$AHASII$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIIaKB = 150; kcat$AHASII$aKB = 7000; \[IndentingNewLine]kfAHASIIaKB \[Rule] Kf[KmAHASIIaKB, kcat$AHASII$aKB, Lamda], \[IndentingNewLine]krAHASIIaKB \[Rule] Kr[kcat$AHASII$aKB, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIIIPyr = 10; kcat$AHASIII$Pyr = 7000; \[IndentingNewLine]kfAHASIIIPyr \[Rule] Kf[KmAHASIIIPyr, kcat$AHASIII$Pyr, Lamda], \[IndentingNewLine]krAHASIIIPyr \[Rule] Kr[kcat$AHASIII$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIIIaKB = 150; kcat$AHASIII$aKB = 7000; \[IndentingNewLine]kfAHASIIIaKB \[Rule] Kf[KmAHASIIIaKB, kcat$AHASIII$aKB, Lamda], \[IndentingNewLine]krAHASIIIaKB \[Rule] Kr[kcat$AHASIII$aKB, Lamda], \[IndentingNewLine]residualRateAHASIIIValaKB \[Rule] 0.15, \[IndentingNewLine]\[IndentingNewLine]KiAHASIIIVal = 20; \[IndentingNewLine]kfiAHASIIIPyrVal \[Rule] Kfi[KmAHASIIIPyr, kcat$AHASIII$Pyr, Lamda, Omega], \[IndentingNewLine]kriAHASIIIPyrVal \[Rule] Kri[KmAHASIIIPyr, kcat$AHASIII$Pyr, Lamda, Omega, KiAHASIIIVal], \[IndentingNewLine]kfiAHASIIIaKBVal \[Rule] Kfi[KmAHASIIIaKB, kcat$AHASIII$aKB, Lamda, Omega], \[IndentingNewLine]kriAHASIIIaKBVal \[Rule] Kri[KmAHASIIIaKB, kcat$AHASIII$aKB, Lamda, Omega, KiAHASIIIVal], \[IndentingNewLine]\[IndentingNewLine]KmIRaAHB \ = 780; KmIRNADPH = 15; kcat$IR$aAHB = 4700; \[IndentingNewLine]kfIRaAHB \[Rule] Kf2S[KmIRaAHB, KmIRNADPH, kcat$IR$aAHB, Lamda], \[IndentingNewLine]krIRaAHB \[Rule] Kr[kcat$IR$aAHB, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmDADaDMV = 750; kcat$DAD$aDMV = 24000; \[IndentingNewLine]kfDADaDMV \[Rule] Kf[KmDADaDMV, kcat$DAD$aDMV, Lamda], \[IndentingNewLine]krDADaDMV \[Rule] Kr[kcat$DAD$aDMV, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBGlu = 1000; fkcat$TB$Glu = 2000; \[IndentingNewLine]fkfTBGlu \[Rule] Kf[KmTBGlu, fkcat$TB$Glu, Lamda], \[IndentingNewLine]fkrTBGlu \[Rule] Kr[fkcat$TB$Glu, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBaKMV = 200; \ fkcat$TB$aKMV = 1500; \[IndentingNewLine]fkfTBaKMV \[Rule] Kf[KmTBaKMV, fkcat$TB$aKMV, Lamda], \[IndentingNewLine]fkrTBaKMV \[Rule] Kr[fkcat$TB$aKMV, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBIle = 600; \ rkcat$TB$Ile = 3000; \[IndentingNewLine]rkfTBIle \[Rule] Kf[KmTBIle, rkcat$TB$Ile, Lamda], \[IndentingNewLine]rkrTBIle \[Rule] Kr[rkcat$TB$Ile, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBaKG = 2500; \ rkcat$TB$aKG = 2100; \[IndentingNewLine]rkfTBaKG \[Rule] Kf[KmTBaKG, rkcat$TB$aKG, Lamda], \[IndentingNewLine]rkrTBaKG \[Rule] Kr[rkcat$TB$aKG, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLIVIexIle = 7; \ kcat$LIVI$exIle = 200; \[IndentingNewLine]kfLIVIexIle \[Rule] Kf[KmLIVIexIle, kcat$LIVI$exIle, Lamda], \[IndentingNewLine]krLIVIexIle \[Rule] Kr[kcat$LIVI$exIle, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLIVIIexIle = 1; kcat$LIVII$exIle = 1; \[IndentingNewLine]kfLIVIIexIle \[Rule] Kf[KmLIVIIexIle, kcat$LIVII$exIle, Lamda], \[IndentingNewLine]krLIVIIexIle \[Rule] Kr[kcat$LIVII$exIle, Lamda], \[IndentingNewLine]\[IndentingNewLine]kcat$aKMV \ \[Rule] 5, \[IndentingNewLine]kcat$Ile \[Rule] 0.2, \[IndentingNewLine]\[IndentingNewLine]KmAHASIPyr = 10; kcat$AHASI$Pyr = 7000; \[IndentingNewLine]kfAHASIPyr \[Rule] Kf[KmAHASIPyr, kcat$AHASI$Pyr, Lamda], \[IndentingNewLine]krAHASIPyr \[Rule] Kr[kcat$AHASI$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIPyr2 = 1000; kcat$AHASI$Pyr2 = 7000; \[IndentingNewLine]kfAHASIPyr2 \[Rule] Kf[KmAHASIPyr2, kcat$AHASI$Pyr2, Lamda], \[IndentingNewLine]krAHASIPyr2 \[Rule] Kr[kcat$AHASI$Pyr2, Lamda], \[IndentingNewLine]residualRateAHASIValPyr2 \[Rule] 0, \[IndentingNewLine]\[IndentingNewLine]KiAHASIVal = 200; \[IndentingNewLine]kfiAHASIPyrVal \[Rule] Kfi[KmAHASIPyr, kcat$AHASI$Pyr, Lamda, Omega], \[IndentingNewLine]kriAHASIPyrVal \[Rule] Kri[KmAHASIPyr, kcat$AHASI$Pyr, Lamda, Omega, KiAHASIVal], \[IndentingNewLine]kfiAHASIPyr2Val \[Rule] Kfi[KmAHASIPyr2, kcat$AHASI$Pyr2, Lamda, Omega], \[IndentingNewLine]kriAHASIPyr2Val \[Rule] Kri[KmAHASIPyr2, kcat$AHASI$Pyr2, Lamda, Omega, KiAHASIVal], \ \[IndentingNewLine]\[IndentingNewLine]KmAHASIIPyr = 10; kcat$AHASII$Pyr = 7000; \[IndentingNewLine]kfAHASIIPyr \[Rule] Kf[KmAHASIIPyr, kcat$AHASII$Pyr, Lamda], \[IndentingNewLine]krAHASIIPyr \[Rule] Kr[kcat$AHASII$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIIPyr2 = 10000; kcat$AHASII$Pyr2 = 7000; \[IndentingNewLine]kfAHASIIPyr2 \[Rule] Kf[KmAHASIIPyr2, kcat$AHASII$Pyr2, Lamda], krAHASIIPyr2 \[Rule] Kr[kcat$AHASII$Pyr2, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIIIPyr = 10; kcat$AHASIII$Pyr = 7000; \[IndentingNewLine]kfAHASIIIPyr \[Rule] Kf[KmAHASIIIPyr, kcat$AHASIII$Pyr, Lamda], krAHASIIIPyr \[Rule] Kr[kcat$AHASIII$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmAHASIIIPyr2 = 7000; kcat$AHASIII$Pyr2 = 7000; \[IndentingNewLine]kfAHASIIIPyr2 \[Rule] Kf[KmAHASIIIPyr2, kcat$AHASIII$Pyr2, Lamda], krAHASIIIPyr2 \[Rule] Kr[kcat$AHASIII$Pyr2, Lamda], \[IndentingNewLine]residualRateAHASIIIValPyr2 \[Rule] 0.15, \[IndentingNewLine]\[IndentingNewLine]KiAHASIIIVal = 20; \[IndentingNewLine]kfiAHASIIIPyrVal \[Rule] Kfi[KmAHASIIIPyr, kcat$AHASIII$Pyr, Lamda, Omega], \[IndentingNewLine]kriAHASIIIPyrVal \[Rule] Kri[KmAHASIIIPyr, kcat$AHASIII$Pyr, Lamda, Omega, KiAHASIIIVal], \[IndentingNewLine]kfiAHASIIIPyr2Val \[Rule] Kfi[KmAHASIIIPyr2, kcat$AHASIII$Pyr2, Lamda, Omega], \[IndentingNewLine]kriAHASIIIPyr2Val \[Rule] Kri[KmAHASIIIPyr2, kcat$AHASIII$Pyr2, Lamda, Omega, KiAHASIIIVal], \[IndentingNewLine]\[IndentingNewLine]KmIRaAL \ = 290; KmIRNADPH = 15; kcat$IR$aAL = 1100; \[IndentingNewLine]kfIRaAL \[Rule] Kf2S[KmIRaAL, KmIRNADPH, kcat$IR$aAL, Lamda], \[IndentingNewLine]krIRaAL \[Rule] Kr[kcat$IR$aAL, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmDADaDHIV = 2800; kcat$DAD$aDHIV = 24000; \[IndentingNewLine]kfDADaDHIV \[Rule] Kf[KmDADaDHIV, kcat$DAD$aDHIV, Lamda], \[IndentingNewLine]krDADaDHIV \[Rule] Kr[kcat$DAD$aDHIV, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBGlu = 1000; fkcat$TB$Glu = 2000; \[IndentingNewLine]fkfTBGlu \[Rule] Kf[KmTBGlu, fkcat$TB$Glu, Lamda], \[IndentingNewLine]fkrTBGlu \[Rule] Kr[fkcat$TB$Glu, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBaKIV = 300; fkcat$TB$aKIV = 930; \[IndentingNewLine]fkfTBaKIV \[Rule] Kf[KmTBaKIV, fkcat$TB$aKIV, Lamda], \[IndentingNewLine]fkrTBaKIV \[Rule] Kr[fkcat$TB$aKIV, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBVal = 2700; rkcat$TB$Val = 2000; \[IndentingNewLine]rkfTBVal \[Rule] Kf[KmTBVal, rkcat$TB$Val, Lamda], \[IndentingNewLine]rkrTBVal \[Rule] Kr[rkcat$TB$Val, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBaKG = 2500; rkcat$TB$aKG = 2100; \[IndentingNewLine]rkfTBaKG \[Rule] Kf[KmTBaKG, rkcat$TB$aKG, Lamda], \[IndentingNewLine]rkrTBaKG \[Rule] Kr[rkcat$TB$aKG, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTCAla = 100; fkcat$TC$Ala = 2000; \[IndentingNewLine]fkfTCAla \[Rule] Kf[KmTCAla, fkcat$TC$Ala, Lamda], \[IndentingNewLine]fkrTCAla \[Rule] Kr[fkcat$TC$Ala, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTCaKIV = 100; fkcat$TC$aKIV = 1500; \[IndentingNewLine]fkfTCaKIV \[Rule] Kf[KmTCaKIV, fkcat$TC$aKIV, Lamda], \[IndentingNewLine]fkrTCaKIV \[Rule] Kr[fkcat$TC$aKIV, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTCVal = 3000; \ \ rkcat$TC$Val = 3000; \[IndentingNewLine]rkfTCVal \[Rule] Kf[KmTCVal, rkcat$TC$Val, Lamda], \[IndentingNewLine]rkrTCVal \[Rule] Kr[rkcat$TC$Val, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTCPyr = 2000; \ rkcat$TC$Pyr = 3000; \[IndentingNewLine]rkfTCPyr \[Rule] Kf[KmTCPyr, rkcat$TC$Pyr, Lamda], \[IndentingNewLine]rkrTCPyr \[Rule] Kr[rkcat$TC$Pyr, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLIVIexVal = 2; kcat$LIVI$exVal = 500; \[IndentingNewLine]kfLIVIexVal \[Rule] Kf[KmLIVIexVal, kcat$LIVI$exVal, Lamda], \[IndentingNewLine]krLIVIexVal \[Rule] Kr[kcat$LIVI$exVal, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLIVIIexVal = 1; kcat$LIVII$exVal = 1; \[IndentingNewLine]kfLIVIIexVal \[Rule] Kf[KmLIVIIexVal, kcat$LIVII$exVal, Lamda], \[IndentingNewLine]krLIVIIexVal \[Rule] Kr[kcat$LIVII$exVal, Lamda], \[IndentingNewLine]\[IndentingNewLine]kcat$aKIV \ \[Rule] 70, \[IndentingNewLine]kcat$Val \[Rule] 0.2, \[IndentingNewLine]\[IndentingNewLine]KmIPMSacetylCoA = 200\ ; kcat$IPMS$acetylCoA = 1000; \[IndentingNewLine]kfIPMSacetylCoA \[Rule] Kf[KmIPMSacetylCoA, kcat$IPMS$acetylCoA, Lamda], \[IndentingNewLine]krIPMSacetylCoA \[Rule] Kr[kcat$IPMS$acetylCoA, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmIPMSaKIV = 60; kcat$IPMS$aKIV = 1000; \[IndentingNewLine]kfIPMSaKIV \[Rule] Kf[KmIPMSaKIV, kcat$IPMS$aKIV, Lamda], \[IndentingNewLine]krIPMSaKIV \[Rule] Kr[kcat$IPMS$aKIV, Lamda], \[IndentingNewLine]\[IndentingNewLine]KiIPMSLeu = 200; \[IndentingNewLine]kfiIPMSLeu \[Rule] Kfi[KmIPMSacetylCoA, kcat$IPMS$acetylCoA, Lamda, Omega], \[IndentingNewLine]kriIPMSLeu \[Rule] Kri[KmIPMSacetylCoA, kcat$IPMS$acetylCoA, Lamda, Omega, KiIPMSLeu], \ \[IndentingNewLine]\[IndentingNewLine]KiIPMSacetylLeu = 500; \[IndentingNewLine]kfiIPMSacetylLeu \[Rule] Kfi[KmIPMSaKIV, kcat$IPMS$aKIV, Lamda, Omega], \[IndentingNewLine]kriIPMSacetylLeu \[Rule] Kri[KmIPMSaKIV, kcat$IPMS$aKIV, Lamda, Omega, KiIPMSacetylLeu], \ \[IndentingNewLine]\[IndentingNewLine]KmIPMIaIPM = 100; kcat$IPMI$aIPM = 1000; \[IndentingNewLine]kfIPMIaIPM \[Rule] Kf[KmIPMIaIPM, kcat$IPMI$aIPM, Lamda], \[IndentingNewLine]krIPMIaIPM \[Rule] Kr[kcat$IPMI$aIPM, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmIPMIbIPM = 100; kcat$IPMI$bIPM = 1000; \[IndentingNewLine]kfIPMIbIPM \[Rule] Kf[KmIPMIbIPM, kcat$IPMI$bIPM, Lamda], \[IndentingNewLine]krIPMIbIPM \[Rule] Kr[kcat$IPMI$bIPM, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmIPMDHbIPM = 105; KmIPMDHNAD = 320; kcat$IPMDH$bIPM = 4000; \[IndentingNewLine]kfIPMDHbIPM \[Rule] Kf2S[KmIPMDHbIPM, KmIPMDHNAD, kcat$IPMDH$bIPM, Lamda], \[IndentingNewLine]krIPMDHbIPM \[Rule] Kr[kcat$IPMDH$bIPM, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBGlu = 1000; fkcat$TB$Glu = 2000; \[IndentingNewLine]fkfTBGlu \[Rule] Kf[KmTBGlu, fkcat$TB$Glu, Lamda], \[IndentingNewLine]fkrTBGlu \[Rule] Kr[fkcat$TB$Glu, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBaKIC = 200; fkcat$TB$aKIC = 3600; \[IndentingNewLine]fkfTBaKIC \[Rule] Kf[KmTBaKIC, fkcat$TB$aKIC, Lamda], \[IndentingNewLine]fkrTBaKIC \[Rule] Kr[fkcat$TB$aKIC, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBLeu = 4400; rkcat$TB$Leu = 2800; \[IndentingNewLine]rkfTBLeu \[Rule] Kf[KmTBLeu, rkcat$TB$Leu, Lamda], \[IndentingNewLine]rkrTBLeu \[Rule] Kr[rkcat$TB$Leu, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmTBaKG = 2500; rkcat$TB$aKG = 2100; \[IndentingNewLine]rkfTBaKG \[Rule] Kf[KmTBaKG, rkcat$TB$aKG, Lamda], \[IndentingNewLine]rkrTBaKG \[Rule] Kr[rkcat$TB$aKG, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLIVIexLeu = 4; kcat$LIVI$exLeu = 100; \[IndentingNewLine]kfLIVIexLeu \[Rule] Kf[KmLIVIexLeu, kcat$LIVI$exLeu, Lamda], \[IndentingNewLine]krLIVIexLeu \[Rule] Kr[kcat$LIVI$exLeu, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLIVIIexLeu = 1; kcat$LIVII$exLeu = 1; \[IndentingNewLine]kfLIVIIexLeu \[Rule] Kf[KmLIVIIexLeu, kcat$LIVII$exLeu, Lamda], \[IndentingNewLine]krLIVIIexLeu \[Rule] Kr[kcat$LIVII$exLeu, Lamda], \[IndentingNewLine]\[IndentingNewLine]KmLSexLeu = 0.5; kcat$LS$exLeu = 100; \[IndentingNewLine]kfLSexLeu \[Rule] Kf[KmLSexLeu, kcat$LS$exLeu, Lamda], \[IndentingNewLine]krLSexLeu \[Rule] Kr[kcat$LS$exLeu, Lamda], \[IndentingNewLine]\[IndentingNewLine]kcat$aKIC \ \[Rule] \ 25, \[IndentingNewLine]kcat$Leu \[Rule] 0.01\[IndentingNewLine]};\)\)}]], "Input"], Cell[BoxData[ RowBox[{ RowBox[{ StyleBox["(*", FontSize->14], StyleBox["\n", FontSize->14], StyleBox[" ", FontSize->14], RowBox[{ StyleBox["Inputs", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["for", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["Values", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["of", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["Substrate", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["and", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["Enzyme", FontSize->14], StyleBox[" ", FontSize->14], StyleBox["Concentrations", FontSize->14], StyleBox[" ", FontSize->14], RowBox[{ StyleBox["(", FontSize->14], StyleBox[ RowBox[{ StyleBox["m", FontFamily->"Symbol", FontSize->14], StyleBox["M", FontSize->14]}]], StyleBox[")", FontSize->14]}]}], StyleBox["\n", FontSize->14], StyleBox["*)", FontSize->14]}], StyleBox["\[IndentingNewLine]", FontSize->14], StyleBox["\[IndentingNewLine]", FontSize-> 14], \(myICs = {\[IndentingNewLine]Thr[0] \[Equal] 520, \[IndentingNewLine]Pyr[0] \[Equal] 1000, \[IndentingNewLine]Leu[0] \[Equal] 0, \[IndentingNewLine]Ala[0] \[Equal] 2000, \[IndentingNewLine]Glu[0] \[Equal] 2000, \[IndentingNewLine]Ile[0] \[Equal] 0, \[IndentingNewLine]Val[0] \[Equal] 0, \[IndentingNewLine]aKB[0] \[Equal] 0, \[IndentingNewLine]NH3[0] \[Equal] 0, \[IndentingNewLine]aAHB[0] \[Equal] 0, \[IndentingNewLine]aDMV[0] \[Equal] 0, \[IndentingNewLine]aKMV[0] \[Equal] 0, \[IndentingNewLine]aKG[0] \[Equal] 0, \[IndentingNewLine]aAL[0] \[Equal] 0, \[IndentingNewLine]aDHIV[0] \[Equal] 0, \[IndentingNewLine]aKIV[0] \[Equal] 0, \[IndentingNewLine]aIPM[0] \[Equal] 0, \[IndentingNewLine]bIPM[0] \[Equal] 0, \[IndentingNewLine]aKIC[0] \[Equal] 0, \[IndentingNewLine]\[IndentingNewLine]propionylCoA[ 0] \[Equal] 0, \[IndentingNewLine]glutarylCoA[0] \[Equal] 0, \[IndentingNewLine]pantothenate[0] \[Equal] 0, \[IndentingNewLine]acetylCoA[0] \[Equal] 1000, \[IndentingNewLine]CoA[0] \[Equal] 0, \[IndentingNewLine]NADP[0] \[Equal] 0, \[IndentingNewLine]NADPH[0] \[Equal] 1000, \[IndentingNewLine]NAD[0] \[Equal] 1000, \[IndentingNewLine]NADH[0] \[Equal] 0, \[IndentingNewLine]CO2[0] \[Equal] 0, \[IndentingNewLine]protein[0] \[Equal] 0, \[IndentingNewLine]\[IndentingNewLine]TDA[0] \[Equal] 3, \[IndentingNewLine]KDC[0] \[Equal] 2, \[IndentingNewLine]\[IndentingNewLine]AHASI[0] \[Equal] 10, \[IndentingNewLine]AHASICH3CO[0] \[Equal] 0, \[IndentingNewLine]AHASII[0] \[Equal] 0, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (*\ E . \ coli\ K12\ has\ no\ active\ AHASII\ \ *) \[IndentingNewLine]AHASIICH3CO[0] \[Equal] 0, \[IndentingNewLine]AHASIII[0] \[Equal] 2, \[IndentingNewLine]AHASIIICH3CO[0] \[Equal] 0, \[IndentingNewLine]\[IndentingNewLine]IR[0] \[Equal] 13.5, \[IndentingNewLine]DAD[0] \[Equal] 7, \[IndentingNewLine]\[IndentingNewLine]TB[0] \[Equal] 2.5, \[IndentingNewLine]TBNH2[0] \[Equal] 0, \[IndentingNewLine]TC[0] \[Equal] 2, \[IndentingNewLine]TCNH2[0] \[Equal] 0, \[IndentingNewLine]\[IndentingNewLine]IPMS[0] \[Equal] 5, \[IndentingNewLine]IPMSacetyl[0] \[Equal] 0, \[IndentingNewLine]IPMI[0] \[Equal] 6, \[IndentingNewLine]IPMDH[0] \[Equal] 5, \[IndentingNewLine]\[IndentingNewLine]LIVI[0] \[Equal] 10, \[IndentingNewLine]LIVII[0] \[Equal] 0, \[IndentingNewLine]LS[0] \[Equal] 8, \[IndentingNewLine]\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (*\ extracellular\ amino\ acid\ treatment\ \ *) \[IndentingNewLine]exVal[0] \[Equal] 0, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (*\ 1000\ for\ valine\ growth\ inhibition\ \ *) \[IndentingNewLine]exIle[0] \[Equal] 0, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (*\ 500\ for\ isoleucine\ rescue\ *) \[IndentingNewLine]exLeu[ 0] \[Equal] 0, \[IndentingNewLine]\[IndentingNewLine]\[IndentingNewLine]$\ Complex$aKB$KDC$[0] \[Equal] 0, $Complex$Pyr$AHASI$[0] \[Equal] 0, \[IndentingNewLine]$Complex$AHASI$Val$[0] \[Equal] 0, $Complex$Pyr$AHASI$Val$[0] \[Equal] 0, \[IndentingNewLine]$Complex$AHASICH3CO$Val$[0] \[Equal] 0, $Complex$aKB$AHASICH3CO$[0] \[Equal] 0, $Complex$aKB$AHASICH3CO$Val$[0] \[Equal] 0, $Complex$Pyr$AHASICH3CO$[0] \[Equal] 0, $Complex$Pyr$AHASICH3CO$Val$[0] \[Equal] 0, $Complex$Pyr$AHASII$[0] \[Equal] 0, $Complex$aKB$AHASIICH3CO$[0] \[Equal] 0, $Complex$Pyr$AHASIICH3CO$[0] \[Equal] 0, \[IndentingNewLine]$Complex$Pyr$AHASIII$[0] \[Equal] 0, $Complex$AHASIII$Val$[0] \[Equal] 0, \[IndentingNewLine]$Complex$Pyr$AHASIII$Val$[0] \[Equal] 0, $Complex$AHASIIICH3CO$Val$[0] \[Equal] 0, $Complex$aKB$AHASIIICH3CO$[0] \[Equal] 0, $Complex$aKB$AHASIIICH3CO$Val$[0] \[Equal] 0, $Complex$Pyr$AHASIIICH3CO$[0] \[Equal] 0, $Complex$Pyr$AHASIIICH3CO$Val$[0] \[Equal] 0, $Complex$IR$aAHB$NADPH$[0] \[Equal] 0, $Complex$IR$aAL$NADPH$[0] \[Equal] 0, \[IndentingNewLine]$Complex$aDHIV$DAD$[0] \[Equal] 0, $Complex$aDMV$DAD$[0] \[Equal] 0, \[IndentingNewLine]$Complex$Glu$TB$[0] \[Equal] 0, $Complex$aKMV$TBNH2$[0] \[Equal] 0, \[IndentingNewLine]$Complex$aKIV$TBNH2$[0] \[Equal] 0, $Complex$Ile$TB$[0] \[Equal] 0, \[IndentingNewLine]$Complex$Val$TB$[0] \[Equal] 0, $Complex$aKG$TBNH2$[0] \[Equal] 0, \[IndentingNewLine]$Complex$Ala$TC$[0] \[Equal] 0, $Complex$aKIV$TCNH2$[0] \[Equal] 0, \[IndentingNewLine]$Complex$Val$TC$[0] \[Equal] 0, $Complex$Pyr$TCNH2$[0] 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