[gmx-users] Tyrosine to phosphotyrosine conversion a must in phosphorylation protein ?

[Najamuddin Memon]

Dear Seke

Yes it Is obligatory to phosphorylate the tyrosine. Use 43a1p extended
phosphorylated force field you will get good results after comparing both
non phosphorylated and phosphorylated structures

Regards
Najam



On Wed, Sep 4, 2019 at 7:31 AM Seketoulie Keretsu <sekekeretsu at gmail.com>
wrote:

> Dear expert,
>
> This is not a gromacs problem however I'm wondering if you can give some
> insight and direction to go look further.
>
> I have a protein phosphorylation protein kinase with a phosphotyrosine at a
> position 20 angstrom away from the binding site. I want to perform an MD to
> study the protein ligand interaction and binding energy calculations. I
> wonder if the modeling of the tyrosine to phophotyrosine is imperative for
> such studies. Is there any review or study done comparing such changes? I
> know newer force fields supports phosphorylation residues but wanted to
> know if failing to use phosphorylation structure would make the study
> useless.
>
> Your inputs will be appreciated.
>
> Thank you.
>
> Sincerely,
>
> Seke
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