[Chimera-users] Protonating ASP and GLU

[Elaine Meng]

Hi Francesco,
Because the (unshifted) pKa of His is much closer to 7 than the  
(unshifted) pKa of carboxylates; in other words, the alternative  
protonation states of His are much more commonly encountered in  
proteins than those of Asp and Glu.  However, even though there is no  
option in AddH, you can still add the hydrogen in Chimera to form  
neutral Asp/Glu, as described in these previous posts to you:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/002910.html
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/002915.html

In summary, you need to change the atom type of the oxygen you want to  
have the proton, and if it is not already, name that oxygen OD2 in Asp  
(OE2 in Glu) and the other one OD1 in Asp (OE1 in Glu).

Also as mentioned in those posts, instead of using Chimera you could  
do it in Amber, or try some of the many web servers.   You said Reduce  
failed.  I don't recall if it claims to protonate (neutralize) Asp/Glu  
as needed, but if it does, perhaps it concluded that protonation in  
your structure was unfavorable and unlikely.  Maybe one of the other  
servers would do what you want.
> H++
> http://biophysics.cs.vt.edu/H++/
>
> PROPKA/PDB2PQR
> http://propka.ki.ku.dk/~drogers/


Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Sep 18, 2008, at 8:14 AM, Francesco Pietra wrote:

> Is there any special reason why, in the AddH option, side chains are
> only considered for HIS (with full options)? Why similar options are
> not given to protonate GLU and/or ASP at the carboxylate?
>
> The general option to consider H-bonding does not work in my case for
> such residues close to one another in space with Chimera (the two O
> atoms of two ASP residues are at 2.56A from one another). Even Reduce,
> supposed to protonate close lying carboxylates, failed in my case.
> This is why I would consider to add that option in future versions of
> Chimera.
>
> Thanks
> francesco pietra