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The NOESY spectrum contain also diagonal crosspeaks. These correspond to the (non-equilibrium Z-) magnetisation decay of the of the spin-themselfs: autorelaxation, or in other words, decay with the T1-type (R1-type) relaxation time (rate).
Rii = ρi = b2/dij6 (J(0) + 3J(ω) + 6J(2ω)) #contribution of one neighbor spin "j" in distance "d".
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- 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.
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- In the task4_to_5 directory,
create a text file using a text editor, the ".upl" file (mol.upl).
This name is used in the instruction file for CYANA, the regCALC.cya file in this exercise. - To do that, copy the "Intermolecular NOE" table - the first column contains the 6 columns needed for identification of the atom pair.
- The seventh column has to be the distance calculated above.
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- Navigate to the task4_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> regCALC
In a little while, the calculation is ready.
We have now the structure file: demo.pdb
and the overview file about the calculation: demo.ovw
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- Copy the calc_ligand_structure into a new one.
cp -r task4_to_5 task4_to_5_noSD - Open the mol.upl In the text editor, delete the line with the problematic restraint(s).
- Repeat the structure calculation in CYANA:
cyana> regCALC
Compare the structures, check the .ovw file.
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- In the part2 directory, execute
cyana regCALC.cya
Look at the structures using chimera molecular viewer.
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- calculate the structure:
cyana regCALC.cya - check the resulting structure using chimera
for clarity, select only the first structure (as in Task 5)
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