[gmx-users] pH dependent simulation

[Justin Lemkul]

On 11/27/17 1:02 AM, Tasneem Kausar wrote:
> pKa of amino acid residue is a constant quantity. Depending on the pH you

That's not strictly true. Titratable amino acids can be found in unique 
microenvironments that cause shifts in canonical values. For instance, 
there are some catalytic lysines known in hydrophobic environments that 
have pKa values of ~4 instead of the canonical value of ~10.5.

-Justin

> can protonate and deprotonate amino acid according to the pKa of particular
> residue.
>
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> On Mon, Nov 27, 2017 at 9:39 AM, <zaved at tezu.ernet.in> wrote:
>
>> Hello Everyone
>>
>> I am trying to simulate a protein at two pH (7.4 and 9.0) using
>> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
>> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
>> positively charged residues.
>>
>> However upon predicting the pKa values using H++ server, I am getting the
>> same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
>> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
>> should have different pKa values at pH 7 and 9).
>>
>> Whether I am in the right direction or doing something wrong!!!
>>
>> Can anyone kindly suggest me how to proceed further?
>>
>> Any suggestion is appreciated.
>>
>> Thank You
>> Zaved
>>
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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