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Part 1
Introduction for task 1:
Take Open the "simulation_data.xlsx". These in part1/task1_to_3 directory. These are for us the experimetal data!
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the spin-themselfs: autorelaxation, or in other words, decay with the T1T1-type (R1R1-type) relaxation time (rate).
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Notice the scale and shape.
How would you obtain the R1 R1 relaxation rate?
Introduction for task 3:
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a: Identify a suitable pair of protons (H-atoms) and measure their distance.
- Open the the ligand molecule (nutlin.pdb)
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- .
- Open the command line: Tools→ General Controls → Command Line and type
- distance @H9,H10
This will be the reference distance
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- rRef.
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.
For the reference pair of protons. We have now also the sigmaRef reference sigma sigmaRef.
Use the formula
r_ij = rRef rRef * (sigmaRefsigmaRef/sigma_ij)^(1/6)
. Vogeli 2014 eq. 63b
to calculate the other distance in the molecule other distances between other atoms (in a separate column).
d: Optional Task intro:
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In practice, we have to input the knowledge about the covalent (bonding) structure of the molecule, and the distance
restraints. The bonding structure can be as simple as the chain of aminoacids, as the standard programs would have
libraries of the actual atomic bonding (topology) for those. For an unknown molecule, we have to supply a full topology
ourselves. These would be different for different programs.
We will use a specialized programprogram specialized structure calculation from NMR restraints: CYANA by Prof. Dr. Peter Günter.
CYANA can obtain the bonding topology from a .mol2 molecular structure file, converting it into its own (library)
format, a .lib file. This library file with contain information about one molecule, but since biopolymers - proteins
contain chain (sequence) of building blocks like aminoacid residues of nucleotides, there has to be also information
about the sequence of those building block. In our case it contains only one record: the name of our ligand molecule.
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Task 4: Calculate the structure of the ligand molecule.
- In the
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- task_4_
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- to_
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- 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 reg.cya file in this exercise. - To do that, copy the
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- "Intermolecular NOE" table - the first column contains the 6 columns needed for identification of the
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- atom pair.
- The seventh column has to be the distance calculated above.
Note that the atom numbers and names have to exactly match the MOL.lib file.
Note also, that that the distance has to be in a numerical format using "dot" as a decimal separator and not a "comma"!
Navigate to the calc_ligand_structure in the terminal (command line) and start the CYANA:
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