We are plotting fluorescence assay spectra collected according to this lab-protocols protocol. Further details of the specific experiment can be found in the fluorescence assay lab notebook on December 15-18, 2015. This notebook is a deeper analysis of data from the 'Spectra-Assay-Analysis' notebook.
This notebook is meant to make a high quality figure showing the shift in bosutinib isomer affinity as a result of the gatekeeper mutant.
In [1]:
from assaytools import grant
from glob import glob
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
In [2]:
file_set = {'Src': glob("../spectra/2015-12-15/*.xml"),
'SrcGK': glob("../spectra/2015-12-16/*.xml"),
'AblGK': glob("../spectra/2015-12-17/*.xml"),
'Abl': glob("../spectra/2015-12-18/*.xml")}
In [3]:
#Define ligands and ligand concentration
ligands = ['Bosutinib','Bosutinib Isomer','Erlotinib','Gefitinib']
ligand_conc = np.array([20.0e-6,9.15e-6,4.18e-6,1.91e-6,0.875e-6,0.4e-6,0.183e-6,0.0837e-6,0.0383e-6,0.0175e-6,0.008e-6,0.0001e-6], np.float64) # ligand concentration, M
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ligand_conc
Out[4]:
In [5]:
SrcGK_BSI = grant.xml2df(file_set['SrcGK'][1])
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SrcGK_BSI.head()
Out[6]:
In [7]:
SrcGK_BSI.head()
Out[7]:
In [8]:
SrcGK_BSI_480 = SrcGK_BSI.loc[480][:12]
In [9]:
SrcGK_BSI_480.values
Out[9]:
In [10]:
plt.semilogx(ligand_conc,SrcGK_BSI_480.values,linewidth=4,color='k')
plt.xlabel('Ligand Concentration (M)')
plt.ylabel('Relative Fluorescence')
plt.tight_layout();
plt.savefig('binding.png',dpi=1000)
In [11]:
Src_BSI = grant.xml2df(file_set['Src'][1])
Src_BSI_480 = Src_BSI.loc[480][:12]
In [12]:
plt.semilogx(ligand_conc,SrcGK_BSI_480.values,linewidth=4,color='k',linestyle='--',label='T341I')
plt.semilogx(ligand_conc,Src_BSI_480.values,linewidth=4,color='k',label='WT')
plt.legend(loc=0)
plt.title('Src',fontsize=30)
plt.xlabel('Ligand Concentration (M)')
plt.ylabel('Relative Fluorescence')
plt.tight_layout();
plt.savefig('Src_GK.eps',type='eps',dpi=1000)
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AblGK_BSI = grant.xml2df(file_set['AblGK'][1])
AblGK_BSI_480 = AblGK_BSI.loc[480][:12]
Abl_BSI = grant.xml2df(file_set['Abl'][1])
Abl_BSI_480 = Abl_BSI.loc[480][:12]
In [14]:
plt.semilogx(ligand_conc,AblGK_BSI_480.values,linewidth=4,color='k',linestyle='--',label='T315I')
plt.semilogx(ligand_conc,Abl_BSI_480.values,linewidth=4,color='k',label='WT')
plt.legend(loc=2)
plt.title('Abl',fontsize=30)
plt.xlabel('Ligand Concentration (M)')
plt.ylabel('Relative Fluorescence')
plt.tight_layout();
plt.savefig('Abl_GK.eps',type='eps',dpi=1000)
In [15]:
plt.semilogx(ligand_conc,Abl_BSI_480.values,linewidth=4,color='k')
plt.xlabel('Ligand Concentration (M)')
plt.ylabel('Relative Fluorescence')
plt.tight_layout();
plt.savefig('binding.png',dpi=1000)
In [16]:
# Below are new figures
In [17]:
plt.semilogx(ligand_conc,SrcGK_BSI_480.values,linewidth=4,color='k',linestyle='--',label='T341I (gatekeeper)')
plt.semilogx(ligand_conc,Src_BSI_480.values,linewidth=4,color='k',label='WT')
plt.legend(loc=0)
plt.title('Src',fontsize=30)
plt.xlabel('[bosutinib isomer] (M)')
plt.ylabel('relative fluorescence')
plt.yticks([])
plt.tight_layout();
plt.savefig('Src_GK_grant.eps',type='eps',dpi=1000)
In [18]:
plt.semilogx(ligand_conc,AblGK_BSI_480.values,linewidth=4,color='k',linestyle='--',label='T315I (gatekeeper)')
plt.semilogx(ligand_conc,Abl_BSI_480.values,linewidth=4,color='k',label='WT')
plt.legend(loc=2)
plt.title('Abl',fontsize=30)
plt.xlabel('[bosutinib isomer] (M)')
plt.ylabel('relative fluorescence')
plt.yticks([])
plt.tight_layout();
plt.savefig('Abl_GK_grant.eps',type='eps',dpi=1000)
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# below are new normalized figures
In [20]:
plt.semilogx(ligand_conc,SrcGK_BSI_480.values/SrcGK_BSI_480.values.max(),linewidth=4,color='k',linestyle='--',label='T341I (gatekeeper)')
plt.semilogx(ligand_conc,Src_BSI_480.values/Src_BSI_480.values.max(),linewidth=4,color='k',label='WT')
plt.legend(loc=0,fontsize=16)
plt.title('Src',fontsize=30)
plt.xlabel('[bosutinib isomer] (M)',fontsize=18)
plt.ylabel('relative fluorescence',fontsize=18)
plt.xticks(fontsize=15)
plt.yticks([])
plt.tight_layout();
plt.savefig('Src_GK_grant.eps',type='eps',dpi=1000)
In [21]:
plt.semilogx(ligand_conc,AblGK_BSI_480.values/AblGK_BSI_480.values.max(),linewidth=4,color='k',linestyle='--',label='T315I (gatekeeper)')
plt.semilogx(ligand_conc,Abl_BSI_480.values/Abl_BSI_480.values.max(),linewidth=4,color='k',label='WT')
plt.legend(loc=2,fontsize=16)
plt.title('Abl',fontsize=30)
plt.xlabel('[bosutinib isomer] (M)',fontsize=18)
plt.ylabel('relative fluorescence',fontsize=18)
plt.xticks(fontsize=15)
plt.yticks([])
plt.tight_layout();
plt.savefig('Abl_GK_grant.eps',type='eps',dpi=1000)
In [22]:
#This works for a full set of proteins
grant.plot_spectra2singlet(file_set,ligands,480,'Spectra_assay_singlets.png')
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