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- create the .upl files from the intramolecular NOE and for intermolecular NOEs
- combined them with the final_protein.upl as in part4/task1
- redo the calculation in cyana
Part 4
Introduction for task 1
In the previous parts, the protein-ligand complex had a low dissociation constant of 0.1 nM. With the concentrations give, this means, that there is almost no free ligand and no free protein. In this exercise, we assume that the dissociation constant is 500uM, equal to the concentration of the components. The fraction of the free ligand will have much higher mobility, and therefore, the autorelaxation rate will be smaller. The crossrelaxation rate will be also strongly affected, particularly the intermolecular NOE, which will build up only for the fraction staying in the complex. On the other hand, relaxation rate of the protein will remain very similar, with some exceptions near the binding site, but those will not be analyzed here.
Task 1
- In the directory part4/task1,
open the simulation_data_500uM.xlsx - looking at the first columns of the buildup curves and decay curves,
notice their differences as compared to the excel table of the data from the previous excercies. - Repeating the instructions in part3/task2, calculate the calibrated intramolecular and intermolecular distances.
- Comment on how much do they differ.
- Is it possible to determine the conformation of weakly bonding ligand, which is in large excess as compared to the protein?
NMR2
NMR2 runs via the platform SAMSON.
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