Seitenhistorie

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• For the case of 1:10, 1:1 and 1:200 of protein:ligand fractions, in 035, 035...LessOfLigand and 035...MoreOfLigand.
• Check the simulated NOESY spectra (!note that the axes are not chemical shifts but simply atomic indices!)
  • see the file: NOESYZoomLigand.pdf, the right lower corner is the section corresponding to the ligand.
  • cd ~/exercicesexercises/035_genLigandDistancesExact
  • open NOESYZoomLigand.pdf
  • what is the sign and intensity of the NOESY crosspeaks of the ligand - indices around 120 to the end? (compared  the part of the protein)
• Check now with lower concentration of the ligand (1:1 ration with protein)
  • cd ~/exercicesexercises/035_genLigandDistancesExactLessOfLigand
  • open NOESYZoomLigand.pdf
  • what is not the sign and intensity of the NOESY crosspeaks of the ligand?
• Check with a high concentration of the protein:
  • cd ~/
  exercices
  • exercises/035_genLigandDistancesExactMoreOfLigand
  • open NOESYZoomLigand.pdf
  • the same question
• Based on these simulated spectra, how would you determine structure of a ligand in the bound state?

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• Look at the coordinates (3 and 2 atoms extracted from a protein structure)
  • cd ~/exercises/038_toySystemWeightIntermolecularNoes
  • cat triPepMod.pdb
• Print the content of the file on the screen 

  • cat NOESYwhenDifferentExchangeRates.txt

  • (or you can extract these using: grep -A 5 "NOESY intensities s" outputKex5e*t10)

•  Look at the last column, last two rows, corresponding to the ligand NOE signals and note their intensity for different exchange frequencies - between 5 Hz and 5 MHz
• What would be the consequence of "not so fast" exchange?
  1. for ligand structure calculation
  2. protein structure calculation
  3. protein-ligand distance extraction?
• experiment by modifying the parameters in parametersForKinMatrixDict.json (open in some text editor, such as vim)
• run ./proteinLigandCalcNOESY.py triPepMod.pdb

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In this exercise, we will test the consequence of chemically equivalent atoms and hence the incomplete assignment of the NOESY spectrum, when deriving the cross-relaxation rates. This will be tested on a toy system with four atoms, of which, the middle two will be treated as 1) separate 2, pseudoatom containing both.

Image Added

• ./pdbSimNoeFrontEnd.py triPep4H.pdb. (or cat pdbSimNoeFrontEnd.out)
• follow the three tasks to Compare. Answer namely,
• how,  in the NOESY spectrum, is the crosspeak between the first and last atom  affected by merging the middle ones?
• how is the extracted cross-relaxation rate (again between the first and last atom)  affected by this merging?

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