On Mon, Feb 23, 2015, anu chandra wrote:
>
> I am working with MD simulations of a protein, which get activated by
> divalent ion binding. Many biophysical studies says that the protein I am
> working with has multiple ion binding sites. But, unfortunately, none of
> such ion binding site has been identified through any structural studies.
> The overall objective of my study is to identity such ion binding sites
> through extensive all-atom MD simulation of protein in water box with
> desired concentration of ions.
To my mind, the "overall objective" is to identify the ion binding sites.
Use of MD simulations is one approach you might use. I'd recommend treating
this first as a "docking" problem, and to search for binding sites with that
sort of software. Since this is a simple mono-atomic ion (I think?), you
might just examine the electrostatic potential around the protein to look for
binding sites.
[You need to be clear (both in your own mind, and in using a computer
program) whether you are talking about "outer-sphere" or "inner-sphere"
binding: in the former, the first-shell water molecules are always
present, whereas this is not true in the latter.]
Once you have identified plausible sites, I'd suggest starting some test
MD calculations near some of these to see what happens. But sure you
understand as much as you can about your particular system before embarking
on "extensive" MD simulations with lots ions.
....good luck....dac
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Received on Mon Feb 23 2015 - 07:30:02 PST
