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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Received on Wed Sep 10 2014 - 00:00:03 PDT
