Perhaps neither, perhaps both. This is not a trivial question to answer.
Depending on the nature of the interaction, the answer could be "it doesn't
matter", since all that's happening is some kind of H-bond bridge that
modulates protein structure, in which case it may not matter exactly which
residue is given the proton.
On the other hand, you can do constant pH MD to properly sample protonation
states which should allow you to calculate the pKa of each residue (and
determine which one is more often protonated).
However, note that the pKa of a free aspartate is about 4 and a free lysine
is about 10, so something very interesting would have to be happening to
observe LYN-ASH over LYS-ASP I imagine.
Good luck!
Jason
On Fri, Nov 27, 2009 at 4:47 PM, s. Bill <s_bill36.yahoo.co.uk> wrote:
> Dear AMBER
> I have one LYS residue close to ASP residue. According to QM calculation,
> it seems to be LYN and ASH, i.e. the proton prefers to be transefered to the
> carboxylate group rather than to stay on the amine group. So, which form the
> correct one for my simulation, LYS-ASP or LYN-ASH?
> thanks in advance
> S. Bill
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Nov 27 2009 - 17:30:02 PST
