On 30 September 2016 at 19:45, Mahdi, Sam <sam.mahdi....@my.csun.edu> wrote:
> Sorry, I just want to make sure I fully understand this so I can explain it
> to my PI:
No problems, this is by far the most complicated aspect in the field of NMR ;)
> So if there is symmetry, I can upload the same pdb file with the dimer (set
> A and B) but tell it to read only one set.
Load rather than upload, but yes.
> Since S^2 isn't effected too much
> versus a dimer versus a monomer, the only thing that is important is the
> change in co-ordinates of one set of the dimer (i.e. the differnence in
> co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
> or set A in a different version of that dimer's co-ordinates).
S2 is not affected by the reference frame. This only matters for
comparing diffusion tensors. Though you will only ever see one
tensor, as that is what is in your NMR sample (if you have a
monomer-dimer mix, then you're in trouble and will see a lot of
artificial Rex and ns motions).
> I say this
> because I have already run my protein's data with the pdb structure of the
> monomer, and I have 2 different pdb files the docking program gave back for
> the dimer (2 different ways the dimer could form from one interface).
Well, your analysis will always return the same diffusion tensor. If
you want these diffusion tensors to all be in the same frame, use the
relax structure.superimpose user function with the method='fit to
first' argument. Then just pick which will be your reference
structure and superimpose. You can superimpose A and B - separately -
onto the monomer frame.
Let's pick the monomer as the reference frame. Then:
- If you superimpose "dimer 1, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 1, struct B" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct B" to the monomer, you
should find the same tensor.
If the docking program did not optimise the internal monomer
structure, you will get identical results. Otherwise you'll see minor
internal motion changes. If your PI was hoping that you would be able
to tell him that you have a monomer or one of the 2 dimers in your NMR
tube, well then you will need to start to read many, many papers on
diffusion tensor prediction. But know that all prediction methods
underestimate the diffusion tensor (e.g. David Case is working on this
exact problem for MD simulations). In this case, relaxation data is
not the best NMR method for this. It would be better to use RDCs from
a purely steric alignment and to compare that to what PALES prediction
comes up with (though that itself is still a very rough and imperfect
method).
Regards,
Edward
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