Analysis of  U-R-L model

 

Binding coupled with intramolecular isomerization of both receptor and a ligand into unbinding conformations

 

 

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Contents

 

Goals

 

1. Load equations

 

2. 2D plotting

 

 

 

Conclusions

 

 

 

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Goals

 

In this notebook I will analyze U-R-L model using derivations performed in 

Equilibria/U_R_L_model/U_R_L_derivation.mn

 

 

 

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1. Load equations

 

clean up workspace

reset()

 

 

Set path to save results into:

ProjectName:="U_R_L";

CurrentPath:="/Users/kovrigin/Documents/Workspace/Data/Data.XV/EKM16.Analysis_of_multistep_kinetic_mechanisms/Equilibria/U_R_L_model/";

math

math

 

 

 

Read results of derivations

filename:=CurrentPath.ProjectName.".mb";

fread(filename,Quiet):

 

math

 

anames(All,User);

 

math

 

 

 

 

 

 

 

 

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2. 2D plotting

 

 

 

Plot all on one graph

Total_R:=1e-3:

Total_L:=0.5e-3:

Ka1:=1e6:

Kb1:=10:

Kb2:=10:

 

// display parameters

LRratio_max:=1.2:

LW:=1.5:

 

pReq:=  plot::Function2d(

          Function=(fReq_U_R_L(Total_R, Total_R*LRratio, Ka1, Kb1, Kb2)),

          LegendText="[R]",

          Color = RGB::Black,

          XMin=(0),

          XMax=(LRratio_max),

          XName=(LRratio),

          TitlePositionX=(0),

          LineWidth=LW):

 

 

pLeq:=  plot::Function2d(

          Function=(fLeq_U_R_L(Total_R, Total_R*LRratio, Ka1, Kb1, Kb2)),

          LegendText="[L]",

          Color = RGB::Green,

          XMin=(0),

          XMax=(LRratio_max),

          XName=(LRratio),

          TitlePositionX=(0),

          LineWidth=LW):

 

 

 

pRstareq:=  plot::Function2d(

          Function=(fRstareq_U_R_L(Total_R, Total_R*LRratio, Ka1, Kb1, Kb2)),

          LegendText="[R*]",

          Color = RGB::Blue,

          XMin=(0),

          XMax=(LRratio_max),

          XName=(LRratio),

          TitlePositionX=(0),

          LineWidth=LW):

 

 

 

pLstareq:=  plot::Function2d(

          Function=(fLstareq_U_R_L(Total_R, Total_R*LRratio, Ka1, Kb1, Kb2)),

          LegendText="[L*]",

          Color = RGB::Orange,

          XMin=(0),

          XMax=(LRratio_max),

          XName=(LRratio),

          TitlePositionX=(0),

          LineWidth=LW):

 

 

pRLeq:=  plot::Function2d(

          Function=(fRLeq_U_R_L(Total_R, Total_R*LRratio, Ka1, Kb1, Kb2)),

          LegendText="[RL]",

          Color = RGB::Red,

          XMin=(0),

          XMax=(LRratio_max),

          XName=(LRratio),

          TitlePositionX=(0),

          LineWidth=LW):

 

 

// Report constants

print(Unquoted,ProjectName);

print(Unquoted,"Total_R:=".Total_R.":");

print(Unquoted,"Ka1:=".Ka1.":");

print(Unquoted,"Kb1:=".Kb1.":");

print(Unquoted,"Kb2:=".Kb2.":");

 

 

plot(pReq, pLeq, pRstareq, pLstareq, pRLeq,

   YAxisTitle="M", Header=ProjectName,

   Height=160, Width=120,TicksLabelFont=["Helvetica",12,[0,0,0],Left],

  AxesTitleFont=["Helvetica",14,[0,0,0],Left],

  XGridVisible=TRUE, YGridVisible=TRUE,

  LegendVisible=TRUE, LegendFont=["Helvetica",14,[0,0,0],Left]);

 

U_R_L

Total_R:=0.001:

Ka1:=1000000.0:

Kb1:=10:

Kb2:=10:

MuPAD graphics

 

Jump back to 2D plotting header

 

 

 

 

 

Window

 

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4. Summary of some results

 

Simple test results

 

 

 

 

 

No R* nor L*

No  L*

No R* 

Both R* and L* are populated

 

U_R_L

Total_R:=0.001:

Ka1:=1000000.0:

Kb1:=0:

Kb2:=0:

MuPAD graphics

U_R_L

Total_R:=0.001:

Ka1:=1000000.0:

Kb1:=10:

Kb2:=0:

MuPAD graphics

U_R_L

Total_R:=0.001:

Ka1:=1000000.0:

Kb1:=0:

Kb2:=10:

MuPAD graphics

U_R_L

Total_R:=0.001:

Ka1:=1000000.0:

Kb1:=10:

Kb2:=10:

MuPAD graphics

 

 

 

 

 

 

 

 

 

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Conclusions

 

 

1. The equations work as expected.

 

2. Increasing equilibrium constants of isomerization for either binding partner leads to a decrease in apparent binding affinity as prescribed by

Kapp_U_R_L

math

 

 

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