AMBER Archive (2002)

Subject: Re: HIS residues

From: Natasja Brooijmans (nbrooij_at_itsa.ucsf.edu)
Date: Thu Oct 24 2002 - 18:09:55 CDT

It depends on the environment the histidines are in. If the epsilon
nitrogen can make a hydrogen bond if the proton is present, that one
should be protonated, and vice versa. If both nitrogens can form hydrogen
bonds with the environment if protonated, the histidine might be doubly
protonated. YOu would have to build structures for each case and analyze
the hydrogen bonding patterns. Depending on the question you're asking, it
might not be of much importance, and you can just use the standard
histidine state.

Natasja Brooijmans
Graduate Program in Chemistry & Chemical Biology
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-0446
phone: 415-476 8291
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

On Thu, 24 Oct 2002, Joel Konkle-Parker wrote:

> I have a pdb of Acetylcholinesterase (1EEA) that has several HIS
> residues. From what I've read, I understand that LEAP doesn't use HIS,
> it changes it to one of HID, HIE, or HIP, by default HID, so it's best
> to change it within the pdb. Is this a critical item to check? If so,
> what's the best way to find out which type I have?
>
> -Joel
>
>