Dear Prof. Case,
Thanks for your valuable inputs. If I made it right, all you suggesting is,
1. To do blind docking in order to search for plausible ion binding sites
(ions are mono-atomic)
2. Then, to do MD with ions placed near to the sites, predicted by docking
program.
I just have a quick query here. While carrying out extensive MD
simulations with protein in ionic solution ( box with ions+water), Do I
have to take care of the charge polarizability while carrying out the
simulation?
Does the MD itself ( without any prior information from docking studies)
can identify plausible ion binding site, probably from longer run?
Many thanks in advance
Anu
On Mon, Feb 23, 2015 at 8:59 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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 Tue Feb 24 2015 - 04:30:02 PST
