Hi,
Definitely don't just treat all HIS as HIE.
The H++ suggestions are likely to be good, but it's always a good idea to
confirm this by looking at the structure yourself.
--Marc
On Sep 10, 2014 7:49 AM, <sunita.tifrh.res.in> wrote:
> Hi Marc,
>
> Thank you so much for your suggestion. I checked my structure using H++
> server which assign some of the HIS as HIE and some as HID. Actually, it
> is a DNA binding protein. So I would like to keep HIS state correctly. The
> exact DNA interacting residues are not known.
>
> For MD simulation, is it ok to keep the protonation status as defined by
> H++ server or should I keep the default one where all HIS are made to HIE?
>
> With regards,
> Sunita
>
>
> > 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 Wed Sep 10 2014 - 01:00:03 PDT
