Dear Christoph ,
that N- or C-terminal residues are missing in PDB files issued from X-ray
crystallography is quite common:
These may be cleaved during the purification and crystallization procedure.
Note that the N- or C-terminals of genes are often modified in order to clone
the gene in some vector and then purify it by using for example six
additional His residues (Gateway) as a tag.
Another reason is that the N- and C-term residues often stick out of the
protein and have therefore a tendancy to be un-ordered in the crystal (thus
not visible).
If you now add these residues without aligning at to a know structural
template, Modeller will use a molecular dynamics approach to determine its
structure (loop modelling). So what you are actually doing with these
residues is some kind of ab-initio folding modelling.
Except if you think that these residues are absolutely essential for the
function of your protein, I would leave them out. One way to determine if
they are is to look at a multiple alignment of a larger set of close
sequential homologues, and to evaluate the conservation of these initial
residues.
You can do this online using T-COFFE on the following server:
http://igs-server.cnrs-mrs.fr/Tcoffee/
(look at the color code of the alignment score)
I hope this helps,
Kind regards, Karsten.
On Tuesday 18 February 2003 13:39, Christoph Nimptsch wrote:
> Hi,
>
> assume, I have a PDB file template with some residues missing, e.g. 5 Amino
> acids at the beginning, 10 in the middle and 2 at the end of the sequence.
>
> Now, I use Modeller to complete the template (I align the PDB to its
> sequence) and use it for homology modelling.
>
> Is this a common procedure? What do you think about it? Will the completed
> template be reliable or should I leave the gaps of the template unfixed in
> homology modelling?
>
> Thanks in advance,
>
> Christoph Nimptsch
>
>
>
>
> ------------------------------------------
> Christoph Nimptsch
> Apotheker
> Pharmazeutisches Institut
> Arbeitskreis Prof. Kovar
> Universität Tübingen
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> D-72076 Tuebingen
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