Hi Vero,
this is a pretty broad question, so there may be multiple correct answers
depending on the details. Many proteins have disordered tails in their
natural state, so these residues may not have a defined structure, in which
case it is best to leave them out of a simulation, unless you are studying
this disordered part of the protein. It may be that the disordered part is
due to the protein construct that was used in solving the PDB structure you
start with, it is worth checking the corresponding paper if they changed or
truncated the WT sequence somehow. If you really want those residues in
(and know or suspect that they have a defined secondary structure) then you
should probably look at some kind of homology modelling to build them in if
you can identify a good template (maybe look at the alphafold structure of
your protein as a start). My best guess would be, those residues are
probably not really ordered and leaving them out of an MD is the safest
choice. OTOH, de novo predicting a realistic conformational ensemble for a
disordered protein part is going to be really hard to get right (and
equally hard to test if it might be right).
On the technical side of how to build it, if you have access to the
Schrodinger suite, you can built peptides in the GUI quite easily in e.g.
extended or alpha-helical conformations. You could likewise build the
missing sequence in leap and attach it to the protein, but either way is
just a crude and manual first guess at the structure.
Kind Regards,
Thomas
On Wed, Mar 13, 2024 at 9:31 AM VERONICA MARTIN HERNANDEZ via AMBER <
amber.ambermd.org> wrote:
> **Warning** The sender address (VERONICA MARTIN HERNANDEZ via AMBER ) can
> not be verified, sender email address could be spoofed. Please take care to
> proceed.
> Hi
>
> This is not strictly related to AMBER.
> I was trying to make a conformational change in the structure of a
> protein, but the pdb structure isn't complete, the first 40 residues are
> missing. What is the best software to complete the missing residues?
>
> I don't think they affect much the conformational change because they are
> far from the loop I'm studying, but I'm curious how to solve this problem.
>
> Thanks in advance
> Vero
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 13 2024 - 02:30:02 PDT
