From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Thu Jan 29 2015 - 12:53:52 CST
You probably use CHARMM force field for simulation, so it is strongly
advisable to check how protonation states are assigned in your PDB file,
HSE is histidine with protonated epsilon N. HSD is histidine with
protonated delta N. HSP is charged his, both N are protonated. When you
prepare pdb file, majority of GUI that add hydrogens attempt to add H to
his on positions which fulfill good H-bond network. But this assumption
from the very beginning of simulation not necessary holds for the whole
simulation. Good solution is to try to find NMR or neutron diffraction
structure of the protein of your interest in PDB (if exist) - such
structures include 'explicit' Hs. Then ascribe protonation of HIS in
your structure using those data
On 1/29/2015 6:39 PM, eprates_at_iqm.unicamp.br wrote:
> Hi Josh!
> 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
>>> 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.
>> Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica - Unicamp
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:36 CST