Simulating protein folding from phy...( ill be the one in which the positive an...)

That final shape determines the biological activity of the protein. Enzymes, for example, do their work because parts of them match the shapes of the molecules whose reactions they control. Being able to predict the shape from the sequence of amino acids would help biologists identify the functions of proteins made by certain genes, such as those associated with Alzheimer's disease, cystic fibrosis and other hereditary disorders. Accurate predictions of protein shape could also lead to the ability to design new drugs from scratch.

Theoretically, a computer could calculate all the possible shapes for a given chain of amino acids and choose the one with the lowest potential energy. In practice, however, there are so many possibilities that it would take longer than the age of the universe to do all the calculations. So, many researchers take shortcuts, by looking for similarities between the chain to be tested and other known proteins or by simulating a partial fold and then comparing the results to known shapes.

Unfortunately, there are not easy matches for all proteins, so it would be desirable to have what's called an ab initio (from the very beginning) approach that simulates the entire folding process. That's the approach used by the Scheraga group, which bases its simulations on the laws of physics, calculating how the forces between atoms affect their arrangement.

In this case, they shortened the computation by starting out with a simplified version of the amino acid chain. Every amino acid has the same "backbone," a string of one nitrogen atom and two carbon atoms. Different side chains attached to the carbon in the middle identify the 20 different amino acids that make up proteins.

The computer program developed by Scheraga's g
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Contact: Bill Steele
ws21@cornell.edu
607-255-7164
Cornell University News Service
29-Jul-1999