[MMTK] Protein mutation: atomic coordinates of substituting residue

Konrad Hinsen research at khinsen.fastmail.net
Mon Feb 28 11:38:07 UTC 2011


On 22 Feb, 2011, at 22:13 , Talipov, Marat wrote:

> I’d like to replace a cysteine residue in the peptide chain by the non-standard residue (which is S-nitrosated cysteine). There is a special function in MMTK for this purpose, named ReplaceResidue(). However it modifies only logical structure of protein thus leaving positions of ‘new’ atoms undefined.

Indeed.

> In mailing list archive, I found a message (http://starship.python.net/pipermail/mmtk/2005/000920.html) where this problem was overcome. However that scripts seems to be not working on the most recent versions of MMTK (I got 2.7.3).  In any case, it was a manual way of solution.

Thanks for tracking down that problem! I have fixed it in a slightly different way which I consider more readable:

        if n > 0:
            for b in self.bonds.bondsOf(r_old.peptide.N):
                self.bonds.remove(b)
        if n < len(self.groups)-1:
            for b in self.bonds.bondsOf(r_old.peptide.C):
                self.bonds.remove(b)

This should be equivalent to your patch in all practically possible situations.

> Is there some way to automatically place atoms of substituting/mutating residue (whose geometry is defined in Database by a Z-Matrix) in correct positions in a protein?

No. I don't see any obstacle to implementing such a method, but it doesn't exist at the moment.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
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91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
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