From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sun Apr 02 2006 - 15:11:32 CDT
On Sun, Apr 02, 2006 at 09:05:53PM +0800, xiaojing gong wrote:
> Dear all,
> First, thank those who help me generously.
> When I read something about the topology file, I have two questions:
> 1) There is three types of His residue in topology file: HSE, HSD,HSP.
> for example,
> RESI HSE 0.00 ! neutral His, proton on NE2,
> if this means that the total charge of HSE is zero, even the proton is
> on NE2?
> 2) I am confused in which condition we should use HSE, or HSD or HSP?
> that is to say, corresponding to different real physiological
> condition, which type of His residue shall I choose?
At neutral pH, the His residues should generally be treated as neutral.
In order to decide between HSE and HSD, you should visually inspect the
neighborhood of the residues and try to maximize the hydrogen bond
However, in some cases it might be clear that the His would be involved
in a salt bridge (when it's very close to an Asp or Glu), and then you
should probably consider the His as HSP.
If you have some experimental data on the protonation state of a given
residue, such as from a titration using NMR, you should use it. Besides,
if there's evidence that the protonation state of some residue might be
crucial to the function of your system, you could try to determine the
pKa value theoretically (search the web to see the available programs
that could do that for you) or even run different simulations
considering the different protonation states.
But, as a rule of thumb, your first guess is that the His residues will
be neutral at a neutral pH.
-- Leonardo Giantini Trabuco Ph.D. student Center for Biophysics and Computational Biology University of Illinois at Urbana-Champaign
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