...
- 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?
- for ligand structure calculation
- protein structure calculatioincalculation
- protein-ligand distance extraction?
- experiment by modifying the parameters in parametersForKinMatrixDict.json
- run ./proteinLigandCalcNOESY.py triPepMod.pdb
Assuming the fast exchange, the derive the correct intermolecular distances between the protein and ligand, the extracted cross-relaxation rates have to be scaled by the population of the components (P, L, PL). The formulas are in presentation, whereas the code is used in the end if the python script. You can check it if there is time left.
039 (advanced)
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.
- ./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?
You saw that the NOESY crosspeak can be in principle recovered exactly even if the atoms, mediating the relayed magnetization transfer, are merged.
- See the time-evolution of the cross-peak (first and last atom) as plotted in "relayedThroughHHorQ.pdf". What does it mean?
- In the script, change the "specIndex" from 10 to 50; now the NOESY will be simulated for tauMixing=2.5s
- rerun the script. Notice the changes in the output.
- see also the new "relayedThroughHHorQ.pdf" file.
041
We have exact distances (assume we are able to obtain them), but we ignore the populations, so the intermolecular calibration is wrong.
...
...
Assembled by Dr. Jiří Mareš,shaped by discussion with Prof. Julien Orts, Florian Wolf and other members of the research group (https://bionmr.univie.ac.at/people/)
...