Date: Thu Jan 29 2015 - 11:39:57 CST
I have put the proton in the epsilon nitrogen, that is actually closer
to the oxygen available to be the acceptor on a hydrogen bond then the
other nitrogen. Then, I don't see the histidine flipping in order to
set this expected interaction. Instead, the hydrogen from the carbon
stays persistently directed to the oxygen (an average of 2.5 A
distant). Meanwhile, the unprotonated nitrogen stays interacting with
a water molecule.
In the paper I mentioned and in others I have found, it seems they
assume this kind of interaction can be important when the imidazole is
charged.. but not when neutral (like in my case).
Actually this is not really important in my study, but I got curious about it!
Quoting Josh Vermaas <vermaas2_at_illinois.edu>:
> 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.
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