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 - 19:30:02 PST
