> We have some questions which we would love to get some feedback on if
>there is anyone on the list who is familiar with the problem.
Who's this royal we?
> The overall question is how a protein with a certain sequence of amino
>acids takes the form of a unique three dimensional structure in water/body.
Very simple. The atoms in the protein and the water attract and repel each
other based on well-known calculations based on their distances, charges, and
orbital arrangements from quantum mechanics. Their movements are constrained
by their covalent bonds, which are also well-understood. The protein
rearranges itself so the energy stored in all the various bonds and
interactions is minimized.
> If it is understood how water behaves around apolar groups and polar
>groups in proteins, it will be easy to understand and predict the formation
>of a unique 3-dimensional structure from a sequence of protein.
No, it won't. The devil is in the details. To simulate a protein in water,
you need to simulate thousands of atoms in the protein and thousands more in
the water. The difficulty of the simulation goes up exponentially with the
number of atoms. The simulations could be programmed today, but the
execution is still in our dreams.