[MMTK] normal mode in MMTK

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Oct 23 09:43:07 CEST 2003


On Thursday 23 October 2003 04:20, myang wrote:

> I have a tetrameric protein, wich can dissociate into 4 monomers. I thi=
nk
> characterizing the dissociation with MD simulation is unpratical. Can
> normal mode analysis give any meaningful details? If anyone can give so=
me
> references about NMA on multimeric protein, he/she would be my hero.

The major limitation of normal mode techniques is that they are limited t=
o=20
dynamics in the vicinity of a stable conformation. They cannot describe=20
conformational transitions, of which dissociation is a special case.

However, if the dissociation happens spontaneously (i.e. doesn't require =
some=20
strongly interacting external agent), then the initial direction of the=20
dissociation path is usually among the lowest energy modes. Whether or no=
t=20
that is helpful in your case depends on what exactly you want to find out=
 and=20
on what you know already about your protein.

Note that is your protein is not too small, you can use a simplified C-al=
pha=20
model for the normal mode calculations, which makes the computation extre=
mely=20
fast. It may be worth a try just to see what you get out of it. You can t=
ake=20
the example file "deformation_modes.py" as a starting point, changing onl=
y=20
the file name.

Konrad.
--=20
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