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 > Auf der Morgenstelle 8 > D-72076 Tuebingen > Tel.: 07071 / 29 73047 > Fax.: 07071 / 29 2470 > mailto:christoph.nimptsch@uni-tuebingen.de > ------------------------------------------