From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Sat Nov 29 2003 - 04:37:30 CST
Hi,
I just want to add something to the answer Fangqiang Zhu gave you. If you want
a criterion on which histidines are protonated, you might try this : set up a
structure of your protein with only unprotonated histidines and compute the
electrostatic potential (Swiss PDB Viewer does that well with
Poisson-Boltzmann). Then, you can assume that the His residues in the most
negative electrostatic environment are most likely to be protonated. The best
solution would be to have an experimental value for the total charge of the
protein, in which case you just have to decide on which histidines you place
the missing positive charges. This electrostatic criterion is far from
perfect, so it would be a good idea to also consider the qualitative criteria
Zhu talked about in his post. For example, since the pKa of the solvated
amino-acid is 6, an "external" histidine exposed to water will be protonated
only if neighbouring residues have some sort of stabilizing effect.
Regards,
Jerome Henin
>
> yxiong_at_mail.ccnu.edu.cn wrote:
> > Dear sir,
> > In the tutorial of NAMD program, there is the following advice:
> > ----------------------------------------------------------------------
> > Histidine Residues. Of the 20 amino acids, histidine is the only
> > one which ionizes within the physiological pH range ( ˘ 7.4). This
> > effect is characterized by the pKa of the amino acid side chain. For
> > histidine, the value is 6.04. This leads to the possiblilty of different
> > protonation states for histidine residues in a protein, and makes the
> > consideration of the proper state important in MD simulations. The
> > viable states are one in which the nitrogen of histidine is protonated
> > (listed with residue name ¡°HSD¡± in the topology file), one in which
> > the nitrogen of histidine is protonated (¡°HSE¡±), and one in which
> > both nitrogens are protonated (¡°HSP¡±).
> > -----------------------------------------------------------------------
> > Since the H atoms are not available from the original pdb file, how can
> > I know which type HIS belong to?
> > Thanks!
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:11 CST