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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 viscosityiviscosity, 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
buidup buildup rate (cross-relaxation rate) and the interproton distance usign using a known distance.
FortunatellyFortunately, there are many proton pairs in the molecule with fixed distance, simply due to the covalent structure.
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In order to calculate the structure (conformation) of the molecule, we need to know the interatomic distances.
This is something what we have already. As these distances come with some inaccuracies, we have to input two distances -
a lower and upper bound in which we believe that the true distance resides.
For practical purpose, we just create two new columns, where the distances derived above are multiplied by factors of
0.8 and 1.2 respectively. In fact, just the upper bound will be enough in our exerciesexercises.
Task 3.d Optional
Create the lower and upper interatomic distances as separate columns.
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There is no closed-form formula to calculate the conformation (structure) from a set of distances.
The setup starts with defining an energy penalty for every experimental distance not fulfilled by the molecular conformation. These are also called distance restraints.
Starting from one chosen conformation, and trying to minimize the structure (using steepest descent or other local method) to fulfill
the distances measured by NOE (or any other means) would fail: the structure would end-up in a local minimum. Instead we
have to search for a global minimum. A commonly used algorithm for a global minimum is called simulated annealing, where
the molecule is heated up such that high-energy barriers (due to van-der Waals clashes) can be surpassed. By a
subsequent cooling, the imposed distance restraints will drive the molecule towards the conformation with minimal
violation of the distance restraitsrestraints. Many attempts will nevertheless end up in different local minima, and hence, only a
subset of resulting conformers, the lowest-energy conformers will be likely to represent the global minimum.
In practice, we have to input the knowledge about the covalent (bonding) stucture 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.
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Note! if using VMD as a molecular viewer, it will refuse to recognize large parts of the secondary structure!
Try to explain what can be causing it.
Check the median of the distance restraints placed into .upl
It should be around 4.2 for intramolecular distances, and 4.4 for the intermolecular distances.
What do you get? discuss.
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