On 10/03/11, "Justin A. Lemkul" <[email protected]> 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. Mark
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