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.
-Justin
Many thanks,
Jo
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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