Hi Abilash,
Have a look at the article -
http://pubs.acs.org/doi/abs/10.1021/ja304519d.
Some of the analysis in this work may be helpful for you.
All the best,
CNA
On Mon, Dec 29, 2014 at 8:57 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Dec 28, 2014, Abhilash J wrote:
> >
> > The study i undertake involves estimation of
> > effect of concentration of a compound to a protein.
> > I want to inquire if due to higher concentration of this compound there
> is
> > lack of water near the protein surface, which in turn leads to better
> > interaction between polar groups of the protein itself. I have some
> > experimental evidence to suggest this.
> > Hence the requirement of calculation of enthalpy. In fact i have MD
> > trajectories at different concentrations and i plan on studying the
> > variation.
>
> It sounds to me like you might start by counting the number of waters in
> some
> defined volume around the protein (doing this as a function of
> concentration);
> or maybe count the number of hydrogen bonds between the protein and water
> (again as a function of concentration). Or you might examine direct
> contacts
> between the "compound" and the protein surface. There is a lot of
> literature
> on the study of the effect of compounds like urea or guanidinium on protein
> stability. You might try to adapt some of the analysis tools used in those
> studies to your problem.
>
> ....dac
>
>
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Received on Sun Dec 28 2014 - 21:30:02 PST
