University of Washington biochemist David Baker to receive 2008 Sackler International
Prize in Biophysics for discoveries in protein folding
Leila Gray
leilag@u.washington.edu
Dr. David Baker, University of Washington
(UW) professor of biochemistry and an
investigator at the Howard Hughes Medical
Research Institute, has been selected to receive
the 2008 Raymond & Beverly Sackler
International Prize in Biophysics, along with
Dr. Martin Gruebele of the University of
Illinois, Urbana-Champaign, and Dr. Jonathan
Weissman of the University of California, San
Francisco.
The field for this year's prize was the physics of
structure formation and self-assembly of
proteins and nucleic acids. The award will be
presented to the three scientists Dec. 15 at
Israel's Tel Aviv University.
The prize was established by arts and sciences
philanthropists Dr. Raymond R. Sackler and his
wife, Beverly Sackler. Raymond Sackler is a
psychiatrist and co-founder of a multinational
pharmaceutical company.
Baker is being honored for his seminal
contributions to computer-based studies of the
manner and the speed in which chains of amino Dr. David Baker
acids fold into protein molecules. Anyone who
has tried to put together a cardboard box knows
the importance of proper folding to get a useful product. The same is true when the body
manufactures proteins.
Creating computer models of protein-folding is essential for figuring out how genetic information
directs protein formation, how proteins work, and how misfolded, misshapen, and malfunctioning
proteins might underlie serious degenerative diseases.
Baker has developed computer programs to predict protein structures from amino acid sequences
in DNA. His program, Rosetta, is among the most accurate. He has combined data from nuclear
magnetic resonance imaging and X-ray defraction imaging with his computer modeling to more
quickly delineate protein molecule structures. He also researches the ways that molecular
configurations of proteins determine their functions in biochemical reactions.
In addition, Baker and his team have developed new protein folds and have designed and built
functional enzymes, and engineered protein interactions, that previously did not exist in nature.
His group has also contributed new ways of studying proteins in membranes -- the thin fatty
covering that separates the inside of the cell from the external environment. These
transmembrane proteins include molecular channels that permit the flow of calcium into and out
of the cell, and that are responsible for the passage of neural impulses and communication
between cells. The Baker group was able to apply the Rosetta program to these unusual proteins
by treating the membranes as a series of layers with different protein folding requirements.
Baker has involved people of all ages and backgrounds from around the world in helping with
protein folding research. People donate their idle computer time to a project called
Rosetta@home. The combined computing power of thousands of home computers around the
globe (called "distributed computing") allows for lengthy, complicated analysis of the data
needed to study how proteins are assembled. Baker and his team have also created Fold-It, a
Web-based protein folding and design game for scientists and non-scientists alike to play to study
protein formation. Players compete to be the best in the world at folding and designing proteins.
More than 20,000 players have downloaded the game. In another aspect of his work, Baker
collaborates with scientists at more than 10 universities to continually update and extend the
Rosetta program, thereby creating a scientific commons to freely share research data on protein
folding.
Baker and his community's discoveries have led to many practical applications in efforts to
design new medications and molecular therapies and in other fields that rely on the structural
mechanics of proteins.