RE: about protonation of HIS in membrane protein

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Apr 13 2005 - 19:47:52 CDT

Yes, that's right. You can use the WHAT IF web interface to check the
protonation states of you HIS's. If your starting structure is correct,
it is straightforward to do it.

Cheers,
Michel

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
Behalf Of Aaron Oakley
Sent: Wednesday, April 13, 2005 7:10 PM
To: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: about protonation of HIS in membrane protein

I would not recommend setting all HIS to HSE.

A better judgment can be made by simply examining
the local hydrogen bonding environment. That's
what we do when determining His, Asn and Gln
side-chain conformation when building crystal structures.

a++

On 14/04/2005, at 12:21 AM, Baoqiang Cao wrote:

> Hi there,
>
> Usually we set HIS as HSE for simplicity, I am just wondering, isn't
> it more correct if we set it according to its position, I mean,
> cytoplasmic, inter membrance, periplasmic? If so, could anybody point
> out some references related to settings? If not, any comments, please!

> Anyway, any comments will be welcomed.
> Thanks.
>
> Best,
> Baoqiang Cao
>
>
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