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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 9 23:39:34 CET 2011

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.


> Many thanks,
> Jo


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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