It may be unusual for deprotonated TYR in a protein when it's not binding a heme, but it happens. I've recently worked with a protein for which PDB2PQR predicts one of the surface TYR deprotonated at pH 8.5, which is the pH of maximal rate for that protein. Irene Newhouse
> Date: Sun, 5 Feb 2012 09:16:17 +0100
> From: mailmd2011.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Deprotonated Tyrosine
>
> I am just curious about in which condition the Tyr would be
> deprotanated? As far I know , from the aspect of pKa, it is very
> difficult for Tyr to be deprotanted.....
>
>
> On 02/05/2012 09:04 AM, FyD wrote:
> > Dear Thomas,
> >
> >> I would like to simulate a heme binding protein. In this protein, the
> >> heme is coordinated by a his and a tyr. From experimental investigations
> >> it is clear that the tyr is deprotonated. But unfortunately, I cannot
> >> find any parameters for the deprotonated tyr. Has anybody out there such
> >> parameters and is willing to share them.
> > You need a molecular fragment for this Tyr(-); three fragments can be
> > built: N-terminal, C-terminal and central. This is likely you only
> > need the central one; See:
> > http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10 using R.E.D.
> > http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15 using R.E.D.Server
> >
> > Now R.E.D. Server can generate the three fragments in a single step; See:
> > http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> > vs
> > http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
> >
> > regards, Francois
> >
> >
> >
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>
>
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Received on Sun Feb 05 2012 - 16:30:03 PST
