(* Content-type: application/vnd.wolfram.mathematica *) (*** Wolfram Notebook File ***) (* http://www.wolfram.com/nb *) (* CreatedBy='Mathematica 8.0' *) (*CacheID: 234*) (* Internal cache information: NotebookFileLineBreakTest NotebookFileLineBreakTest NotebookDataPosition[ 157, 7] NotebookDataLength[ 156472, 4018] NotebookOptionsPosition[ 150315, 3838] NotebookOutlinePosition[ 150750, 3855] CellTagsIndexPosition[ 150707, 3852] WindowFrame->Normal*) (* Beginning of Notebook Content *) Notebook[{ Cell[CellGroupData[{ Cell[TextData[{ StyleBox["EAM Global Minimization Against Human Glucocorticoid Receptor \ Experimental Data\n", FontFamily->"Nimbus Sans L", FontSize->26, FontColor->RGBColor[ 0.7803921568627451, 0.4235294117647059, 0.1607843137254902]], StyleBox["\n", FontColor->RGBColor[ 0.7803921568627451, 0.4235294117647059, 0.1607843137254902]], StyleBox["Supplementary Material for Li, et al. (2017) \ \[OpenCurlyDoubleQuote]Genetically tunable frustration controls allostery in \ an intrinsically disordered transcription factor\[CloseCurlyDoubleQuote].\n\n\ Hilser Lab, July 2017. Hesam Motlagh, Jordan White, Jamie Wrabl.\n\nThe \ purpose of this ", FontFamily->"Nimbus Sans L", FontSize->16, FontColor->RGBColor[ 0.7803921568627451, 0.4235294117647059, 0.1607843137254902]], StyleBox["Mathematica", FontFamily->"Nimbus Sans L", FontSize->16, FontSlant->"Italic", FontColor->RGBColor[ 0.7803921568627451, 0.4235294117647059, 0.1607843137254902]], StyleBox[" notebook is an implementation of the Ensemble Allosteric Model \ (EAM) to estimate reasonable parameters that reproduce experimental data for \ human glucocorticoid receptor (GR). The EAM is constrained by ten data \ points measured from in vivo transcription assays and in vitro binding \ affinities measured on five GR isoforms A, B, C1, C2, C3 as defined in Figure \ 1 of Li, et al. This implementation also uses the following experimental \ constraints:\n\n(1) The interaction energies between the DNA-binding domain \ (DBD), and either the regulatory region (R) of C2 or the R of C1, are equal \ to zero kcal/mol.\n\n(2) The coupling energy etween the DBD and the R of B is \ 0.7 times the coupling between the DBD and the R of A.\n\n(3) The measured \ TMAO osmolyte refolding free energies (\[CapitalDelta]G) for C3-NTD \ (N-terminal domain), A-NTD, and C3-NTD-DBD, reported in Supplementary Figure \ 2a of Li, et al.\n\nEight thermodynamic parameters are estimated: \ \[CapitalDelta]GDBD, \[CapitalDelta]g-DBD-R, \[CapitalDelta]gGRE, \ \[CapitalDelta]GRB, \[CapitalDelta]GRC1, \[CapitalDelta]GRC2, \ \[CapitalDelta]gR-F, and a scaling parameter A (necessary to convert EAM \ population to the experimental observable of transcription activity).\n\n\ Instructions: There are 16 numbered sections. Each should be separately \ executed, in numerical order, starting with section 1. Output is the set of \ thermodynamic parameters satisfying the EAM, and a plot of the simulated \ transcription activity and binding affinity compared to experiment. (Such \ data were used to make Figure 3b of Li, et al. Error bars in that Figure \ were obtained by running this notebook multiple times, using different values \ of \[CapitalDelta]GF, \[CapitalDelta]GANTD, and \[CapitalDelta]GC3DBD each \ time, sampled according to normal distributions with mean equal to the \ experimentally measured value and standard deviation equal to the \ experimental error value.) 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