On Fri, Sep 01, 2017, jacky zhao wrote:
>
> Therefore, I am wondering the role of ACE and NME capping protein in the
> protein simulation.
At the risk of telling you what you already know:
Chemists who synthesize peptides often add capping groups, for various reasons.
The ACE and NME/NHE caps are provided in the Amber libraries so that
simulations can be made on such artificial systems.
Cells (at least in the vast majority of cases) don't cap anything; if there
is something other than an ordinary (charged) amino acid at the N- or
C-terminus, it would be considered a post-translational modification (and would
probably have a different chemistry than ACE or NME.)
Generally, to simulate an "ordinary" protein, one would not use capping groups.
(There are, of course, exceptions to every rule, and others on the list might
want to chime in.) In standard usage, ACE and NME capping groups would
only be called for when dealing with synthetic peptides.
....dac
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Received on Fri Sep 01 2017 - 06:00:08 PDT
