[gmx-users] Protonation state of phospho-tyrosine in neutral PH

[Zheng Ruan]

Hi Justin,

Thank you! Based on the PKa value, I will go with the double protonated
P-Tyr for my purpose, since the PKa1 and PKa2 for the PO3 in P-Tyr are 2
and 5.8 respectively.

Ruan

On Fri, Dec 23, 2016 at 1:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/22/16 10:52 AM, Zheng Ruan wrote:
>
>> Hi Gromacs Users,
>>
>> I'm trying to run simulation on a protein with phosphorylated tyrosine
>> residues. The amber force field parameters (http://research.bmh.
>> manchester.ac.uk/bryce/amber) provides three different protonation states
>> of the phospho-tyrosine residue. What is the predominant form of
>> phospho-tyrosine residue in neutral PH? Is there a reference about the PKa
>> values associated with each protonation state?
>>
>>
> https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/
> Sigma/Product_Information_Sheet/1/p9405pis.pdf
>
> Note that the pKa values of the isolated amino acid may differ slightly
> from those found in a polypeptide chain.  Google searching turns up tons of
> results that are relevant, and you could always just do a pKa calculation
> with the many available tools.
>
> -Justin
>
> --
> ==================================================
>
> 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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