(************** Content-type: application/mathematica ************** CreatedBy='Mathematica 5.0' 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[ 111773, 2717]*) (*NotebookOutlinePosition[ 112416, 2739]*) (* CellTagsIndexPosition[ 112372, 2735]*) (*WindowFrame->Normal*) Notebook[{ Cell[BoxData[ \( (*\ Threonine\ Deaminase\ \((TDA)\)\ in\ E . \ coli . \ K12\ *) \)], "Input", TextAlignment->Left], Cell[BoxData[{ \(\(\(ClearAll;\)\(\n\) \)\), "\n", \(\(n = 4;\)\ \ \ \ \ \ \ \ \ \ \ \ (*\ for\ TDA\ in\ E . \ coli . \ K12\ *) \[IndentingNewLine]\), "\n", \(\(c = 0.013;\)\ \), "\n", \(\(L0TDA\ = \ 1.05;\)\[IndentingNewLine]\n (*\ \(Substrate\ &\)\ \(Activator : \ threonine\ \((THR)\)\)\ *) \), "\[IndentingNewLine]", \(KmThr = 2700; \ \ \ (*\ uM\ *) \n Alpha[THR_] := N[THR\/KmThr];\[IndentingNewLine]\n (*\ Inhibitor : \ isoleucine\ \((ILE)\); \ Activator : \ valine\ \((VAL)\)\ *) \), "\n", \(KiIle = 15; \ \ \ \ \ \ \ (*\ uM\ *) \ \n KaVal = 550;\[IndentingNewLine]\), "\[IndentingNewLine]", \(\(BetaIle[ILE_] := N[ILE\/KiIle];\)\), "\n", \(\(GammaVal[VAL_] := N[VAL\/KaVal];\)\), "\n", \(\(L1TDA[ILE_, VAL_] := \(L0TDA\ \((1 + BetaIle[ILE])\)\^n\)\/\((1 + \ GammaVal[VAL])\)\^n;\)\n\[IndentingNewLine]\[IndentingNewLine] (*\ Yf\ is\ a\ fraction\ of\ active\ enzyme . \ It' s\ a\ function\ of\ substrate, activator, \ and\ inhibitor\ *) \), "\n", \(\(Yf[THR_, ILE_, VAL_] := \((L1TDA[ILE, VAL]\ c\ Alpha[THR]\ \((1 + c\ Alpha[THR])\)\ \^\(n - 1\) + Alpha[THR]\ \((1 + Alpha[THR])\)\^\(n - 1\))\)\/\((\ L1TDA[ILE, \ VAL]\ \((1 + c\ Alpha[THR])\)\^n + \((1 + Alpha[THR])\)\^n)\);\)\)}], "Input",\ TextAlignment->Left], Cell[CellGroupData[{ Cell["\<\ (* plot for publication *) VAL1=0; 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