From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jan 29 2015 - 09:21:27 CST
Hi Erica,
Just for funsies, where did you put the proton on the histidine? In
charmm, you have two options, one to put it on the delta nitrogen, and
the other on the epsilon, and I assume that's true for the others as
well. If you haven't already, I'd put the proton on the epsilon nitrogen
and flip the histidine around so it is the one making the hydrogen bond.
In my brief reading of the paper, their mechanism relies on both
nitrogens forming hydrogen bonds with their surroundings, drawing enough
charge away from CE to make the hydrogen polar. Is this what you see
too? Or did the residue flip from the starting structure, indicating
that the other nitrogen should have been protonated?
-Josh Vermaas
On 01/29/2015 09:03 AM, eprates_at_iqm.unicamp.br wrote:
>
> Hi all,
>
> Have anyone noticed on simulations a persistent interaction between
> the hydrogen from epsilon carbon of histidine and a typical acceptor
> in hydrogen bond (like oxygen or nitrogen)? Or, is anyone aware about
> this uncommon hydrogen bonding reported in molecular dynamics literature?
>
> I could find experimental studies involving this subject (e.g
> http://www.pnas.org/content/97/19/10371.full.pdf+html), but not
> computational ones.
>
> I appreciate any help.
> Best,
> Erica
>
>
>
>
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