One of the (important, IMO) jobs of setting up a protein system for
simulation is deciding on the protonation state and most likely tautomers
(HIE or HID) of the HIS residues.
HIE is more common in proteins, I believe, BUT you should check for EACH
histidine which state is most likely.
There are numerous tools that can help you with this.
A non-exhaustive list of some of them:
pdb2pqr (just google)
reduce (part of AmberTools)
H++ server (see
http://biophysics.cs.vt.edu/)
WHAT-IF optimum hydrogen bond network tool (see
http://swift.cmbi.ru.nl/servers/html/index.html)
If a HIS is in an important place for what you want to study and the
protonation/tautomer isn't clear from the structure, you may want to
consider trying HID, HIE (and if applicable HIP).
Hope this helps,
Marc
On 8 September 2014 14:34, <sunita.tifrh.res.in> wrote:
> Dear users,
>
> AMBER by default makes HIS to HIE which is neutral and hydrogen is on the
> epsilon nitrogen. But if we look at the stability among the three forms at
> pH=7 (close to physiological pH) HID > HIE > HIP.
>
> HID is also neutral and hydrogen is on the delta nitrogen. Most of the
> literature use HIE.
>
> Which one is more accurate to take for the simulation, HID or HIE?
>
> With regards,
> Sunita
>
>
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>
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Received on Mon Sep 08 2014 - 07:00:05 PDT
