March 7, 2005
by Emily Carlson

You may not be able to judge a book by its cover, but you can judge a protein by its shape. The three-dimensional structure of a protein, which is made of amino acids, enables it to latch onto other molecules, triggering a host of chemical reactions. When these reactions fail to occur properly, scientists search for the protein structure responsible. While they can easily determine a protein's amino acid sequence, scientists cannot reliably predict how this sequence will fold into a protein with a certain shape and function.

Given this problem, some researchers have decided to work backwards. Rather than starting with a sequence, David Baker, Ph.D., of the University of Washington in Seattle started with a structure. In groundbreaking research, he showed that it is possible to design and build a protein with a specific shape. He sketched a protein structure that had never before been observed and then used a computer modeling program he had created to predict the amino acid sequence that would form the new molecule. Baker used that sequence to build an actual protein that was stable and quite similar in structure to the one he had drawn.

With this ability to create a protein made to order, Baker's research offers a promising new route for developing custom proteins that could be used as drugs or molecular machines to interrupt or enhance a particular reaction inside a cell.