Hi David,
Thanks for your suggestion.
I found my pThr2 locates in the N-terminus. Will it also be protonated into T1P with a net charge of -1?
Thanks,
Ming
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, 18 February 2020 11:35 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Force field for terminal phosphorylated residues
On Tue, Feb 18, 2020, Ming Tang wrote:
>
>I found that amber does not treat phosphorylated residues (e.g., pThr)
>differently when they locate in the protein terminal. This results in
>the situation that terminal phosphothreonine (TPO) has a charge of
>negative 3. Is this reliable?
I don't know of any Amber library entries for C-terminal phosphorylated amino acids, so I don't know how you built your protein. The TPO residue in leaprc.phosaa10 is for a pThr in the middle of a chain.
I don't know of any litereature on the pKa of a pThr when it is at the C-terminus, but there may be some. My guess is that the side chain would be more likely to be protonated (i.e. in the -1 charge state), due to the influence of the COO- group.
...dac
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Received on Tue Feb 18 2020 - 22:00:02 PST
