Hi!
Thanks Case sir and Aneesh for your valuable secessions. I will try these
out and mail back if i come across some issue that i cannot resolve.
Thanks again.
Abhilash
On Mon, Dec 29, 2014 at 10:35 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> 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
