[gmx-users] PH of system

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 12/27/15 7:53 PM, Sana Saeed wrote:
> thank you SIR
> i just studies this matter and i knew that we need to protonate the sidechains
> of amino acids LYS, ARG, ASP, GLU, GLN and HIS, and the state of disulfide bridge.
> i am searching for their protonation states at PH 2. but i am not getting any
> answer. can you guide me please.
>

The protonation states of most of those amino acids at pH 2 can be looked up in 
the first chapter or two of any undergraduate biochemistry textbook.

The most thorough approach would be to calculate their pKa values in the context 
of the full protein, which may have unique microenvironments that cause pKa 
shifts.  There are numerous free programs and web servers to do this.  Arg, Lys, 
(always +) and Gln (extremely unlikely to ever be charged) are unlikely to 
deviate from their canonical forms at low pH.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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