Subject: Re[2]: CCL:Question about binding energy and deprotonation energy

From: Qiang Lu <qiangl..at..uci.edu>
Date: Sun, 18 Jul 2004 11:31:57 -0700

Dear gilson and Peter,

   Thanks for the detailed explanation. It helps alot.
In fact I am studying the zinc interface in p53. The zinc binds four
ligands, HIS and 3CYS. A is the imidozole-ZN and B is three
thiolate(3S) which bind to ZN. So BH here represent three thiol
groups(3SH). The main function of the zinc interface
is to stabilize the binding domain. Most of the zinc interface is
buried in the protein. In order to get the deprotonation energy of
thiol group in this structure, I calculated the energy of both
structure with and without deprotonation. The ABH is about 600kcal
lower than that of AB. and C-C-SH is about 300kcal lower than C-C-S.
Although people used thiolate usually. I worried about which state
should be in the real world. The crystal structure pH is 6.8. But
the most important thing is the zinc and the around environment.

-- 
Best regards,
 Qiang                            mailto:qiangl..at..uci.edu

=================Original message text===============
Dear Qiang,

The stability of AB-H relative to AB depends upon the pH. Put 
differently, if you want to know which species, AB-H versus AB, is 
preferred energetically, the answer is that this depends upon the 
concentration of protons.  Basically, AB is a base and the relative 
concentrations of AB and AB-H depends upon the concentration of 
protons, by the law of mass action.

Put differently, your statement that "the total energy of AB-H is
lower than AB" is not really very meaningful, because the stability of 
AB-H depends upon the chemical potential of the proton.

Does this help?

Best regards,
Mike

----- Original Message -----
From: Qiang Lu <qiangl..at..uci.edu>
Date: Friday, July 16, 2004 4:11 pm
Subject: CCL:Question about binding energy and deprotonation energy

> Hi CCLERs,
> 
>   Think about the following two reaction:
> 
>   A + B-H = AB-H
>   A + B  =  AB
> 
>   The total energy of AB-H is lower than AB, but the binding energy
>   between A and B of AB is higher than that of AB-H.
> 
>   Then which state is prefer between AB-H and AB? In another words,
>   is it prefer a deprotonated state of AB-H or not in the nature?
>   
> -- 
> Best regards,
> Qiang Lu                         mailto:qiangl..at..uci.edu
> 

==============End of original message text===========