[gmx-users] Treatment of protein termini when there are missing residues

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 10 05:17:54 CET 2011

On 10/03/11, "Justin A. Lemkul"  <jalemkul at vt.edu> wrote:
> jo hanna wrote:
> >Hello,
> >
> >My question concerns the 'best' way to treat the terminal groups for a protein that is missing residues at both termini, e.g. a 530 residue protein where only residues 15-512 are present in the pdb.
> >
> >My thoughts are that assigning charges to the end groups will result in areas of charge in regions where there may not be any in the native protein and could lead
> >to unknown artifacts. Another option would be to 'cap' or add a blocking group
> >on the end of the protein chain, e.g. ACE, which introduces a group that
> >is non-native to this region of the protein. Or treat the end groups
> >neutrally. I have looked through the literature and while I can find
> >examples of MD being carried out with structures with missing residues at the
> >termini, but I cannot find any description of how these groups are treated.
> >
> >I would appreciate some views on this.
> >
> >N.B. The protein I am wishing to study is catalytically active and therefore I have confidence that these missing residues have no effect on the activity of the
> >protein.
> >
> If the termini are unrelated to your goals, you can treat them in almost any way you wish.  Capping is probably the most common.  I would disagree that this is a "non-native" treatment since the capping groups are basically a partial continuation of a normal peptide backbone.

Indeed, and chemically fairly inert by choice. ACE and NME saturate the peptide "valence" and add a boring methyl in space that would have been filled with the secondary alpha-carbon. Not ideal, but quite good.

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