Re: NCS

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Wed Feb 16 2011 - 03:18:29 CST

Hi Flavio,

> The Clustaw alignment of the sequency of this enzyme with other enzymes
> from its family, shows that a lot of residues participating in contact
> between the monomers were lost by deletion or by replacement. We
> believe that this could be the reason of the protein instability,
> because it not works as dimers or monomers.

I do not get it. You know on biochemical grounds that the protein is _not_
a stable homo-oligomer, and this biochemical evidence is in good agreement
with your results from the sequence alignment within the protein family.
You, nevertheless, want to impose an intramolecular symmetry. I must be
missing something ...

> I solved the structure by molecular modelling. The model is good as
> checked by procheck software.

It was bound to be good with respect to procheck's checks.

> The proteins of this family are known to have identical monomers and
> identical contacts between them. We call this as non-crystallographic
> symmetry, as inplemented in Modeller, CNS, X-Plor and Refmac
> crystallographyc softwares.

The term 'non-crystallographic symmetry' only makes sense in the context
of a crystal structure. The (formally ?) correct notation for
intramolecular symmetry is the Schonflies notation. Havind said that, the
fact that you do use the term, would imply that in the original
(crystallographic) structure determination the intramolecular symmetry was
non-crystallographic (with a full tetramer in the asymmetric unit ?).
This, in turn, makes it possible that there were significant departures
from exact (intramolecular) symmetry even in your template structure.
This, of course, may be completely irrelevant with respect to your
research project.

> Regarding the model is good, the problem is that some residues are in
> contact at one interface, but not in others.
>
> My question is: What is the correct? The residue made the contact or
> not? Modelling by satisfaction of spatial restraining can not give me
> the answer.
>
> I am trying to solve this problem by MD.
>
> I expect that electrostatic interactions between residues of the
> interface atract them or repells them.
>
> I was wondering if applying any kind of "NCS" at the interface residues
> during MD simulation, could give me a "mean" scenario of the
> interactions, not a real 'non-crystallographic symmetry' model.

Let's wrap it up : Doing non-restrained MD for a homo-tetrameric model
known on biochemical grounds to be non-existent, would only serve the
purpose of strengthening the evidence that this protein in _not_
oligomeric. This assumes that during MD the oligomer dissociates (and that
you had sufficient computational resources to perform a sufficiently long
simulation to observe that in the first place). The trouble with this
approach is that the evidence obtained is highly circumstantial and your
peers may argue that MD teaches you nothing because, for example, you
could have gotten the same results if all your loops and side-chains are
wrongly placed. The probability that you would be so lucky for MD to 'fix'
the model's problems, is small. The probability that MD will 'fix' the
model's problems with the symmetry imposed (and the side chains 'locked'
in their wrong positions) is even less.

My twocents,
Nicholas

-- 
          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

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