Re: Should you cap C and N termini?

From: Gianluca Interlandi (
Date: Thu Feb 18 2016 - 12:57:24 CST

The general rule is that if you are working with exactly the sequence that
was crystallized (or determined by NMR), then you do not need caps.
Sometimes terminal residues are not seen in X-ray structures and thus not
present in the PDB coordinates. By not adding caps in this situation, you
would put charges were there weren't any when the structure was
determined. In order to find this out, you should read the header of the
PDB. There, it says when the coordinates of residues were not determined.
If terminal residues were not seen in the X-ray structure, then you should
add caps. You should also read the methods of the paper that relates to
the structure and find out what sequence exactly was present at the time
of cystallization or NMR determination and compare that sequence with the
sequence in the PDB. If they match, you do not need caps. For example, if
the sequence crystallized was from residue 14 (e.g., the first 13
residues were a signal peptide that was cleaved) to residue 200 and the
PDB file also goes from residue 14 to 200, then caps are not necessary,
otherwise they are at that terminus that is missing from the PDB.

Another situation is when you manually remove parts of a multi-domain
protein, e.g., because you are only interested in one domain, then I would
also add caps. Whether caps make a difference or not, it all depends on
the protein and how far they are from structural elements, e.g., helices.
For example, positive charges at the N-terminus of a helix could slightly
destabilize a helix (according to Fersht studies on barnase). In that
case, a cap should be added if N-terminal residues are missing from the
PDB or were removed. In the end, you want to replicate as close as
possible the experimental conditions under which the structure was
determined, whether X-ray or NMR. Whether this matters, it depends on the
system and on the questions that you are asking.


On Thu, 18 Feb 2016, Vlad Cojocaru wrote:

> We generally use caps because our systems are individual domains within larger
> proteins ... But if you simulate entire proteins, charged termini should be more
> appropriate.
> Whether it makes a difference or not, I cannot say as we never tested this issue in
> particular.
> Best
> Vlad
> On 02/18/2016 02:09 PM, ashika torikora wrote:
> Hello all,
> My question is more of a broad, open-ended question. I would like to get some
> opinions on whether C and N terminal caps should be added to proteins in
> simulations.
> Thanks y'all,
> xoxo
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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