...
Task2: Plot the diagonal peak intensities as function of the mixing time:
- Notice the scale and shape.
- How would you obtain the R1 relaxation rate?
Introduction for task 3:
The initial rate of the NOESY crosspeak, is directly proportional to the distance between the respective spins (protons). The other dependency comes from the rotational correlation time of the molecule, which is dependent on temperature, solvent viscosity, solvation shell of the molecule, shape of the molecule, and in the case of a small molecule partly bound to a larger protein, the effective correlation time is also modulated by this partial bounding - the chemical exchange. Therefore, it is practical to leave these dependencies aside, and calibrate the relation between the NOE buildup rate (cross-relaxation rate) and the interproton distance using a known distance. Fortunately, there are many proton pairs in the molecule with fixed distance, simply due to the covalent structure.
...
b: calculate the cross-relaxation rate.
- In a separate column, assuming a linear buildup in time: chose now the first mixing time to get the initial cross-relaxation rate.
- Note, that this cross-relaxation rate is not normalized (it is not in [s-1]), but since we will do the referencing using a know distance, we do not have to normalize.
c: Calibrate the distances.
...
Note that the atom numbers and names have to exactly match the MOL.lib file.
Note also, that the distance has to be in a numerical format using "dot" as a decimal separator and not a "comma"!
- Navigate to the task_4_to_5 directory in the terminal (command line) and start the CYANA:
$ cyana - In the cyana prompt, call the instruction in req.cya (leaving out the .cya) to perform the structure calculation:
cyana> reg
In less than a minutelittle while, the calculation is ready.
We have now the structure file: demo.pdb
and the overview file about the calculation: demo.ovw
- Close CYANA
cyana> exit
Introduction for task 5:
From the theoretical introduction about NOE, we know that the existence of crosspeak between two spins does not have to be caused by the direct through-space transfer of magnetisation between them. Instead, magnetisation transfer via an third nucleus can occur. This is called spin diffusion.
...