Re:BIOCHEMISTRY/PHYSICS
ard (rbrown@smb.sams.ch)
Fri, 18 Apr 1997 08:32:01 +0200
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.
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.
The next level of question to this, what are(is) the most dominating
forces in the formation of the unique structure. In the 60's an oil drop
in water was suggested and said as the oil in water collapses to a globule
so does a stretched sequence of protein collapses into a globular-like
structure. This force was/is called hydrophobicity. Later on it was found
that water around oil/apolar groups in proteins forms very organized
structures known as clathartes/ice-like structures etc. These "ice-like"
structures have small entropy (high structure) Until recently the
understanding was up to this point: formation of highly organized
structures around apolar groups. Recently it has been found that the low
entropy phenomena is not restricted to apolar groups but is found for water
around polar groups as well. So what do we do? What is so unique about
water around polar groups (oily matter)? It has been found it the past few
years that the heat capacity (tendency to absorb heat) around apolar groups
increases while the heat capacity of water around polar groups decreases.
Can this last observation be reproduced by computer simulations? Can this
be explained by a reasonable theory?
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. Hence the
design of a drug from a computer for a diseased protein.
We would appreciate any discussion of this problem.
ard