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Berkeley scientists create first 3-D map of protein universe

The universe has been mapped! Not the universe of stars, planets, and black holes, but the protein universe, the vast assemblage of biological molecules that are the building blocks of living cells and control the chemical processes which make those cells work. Researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California at Berkeley have created the first three-dimensional global map of the protein structure universe. This map provides important insight into the evolution and demographics of protein structures and may help scientists identify the functions of newly discovered proteins.

Sung-Hou Kim, a chemist who holds a joint appointment with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Chemistry Department, led the development of this map. An internationally recognized authority on protein structures, he expressed surprise at how closely the map, which is based solely on empirical data and a mathematical formula, mirrored the widely used Structural Classification System of Proteins (SCOP), which is based on the visual observations of scientists who have been solving protein structures.

"Our map shows that protein folds are broadly grouped into four different classes that correspond to the four classes of protein structures defined by SCOP," Kim says. "Some have argued that there are really only three classes of protein fold structures but now we can mathematically prove there are four."

Protein folds are recurring structural motifs or "domains" that underlie all protein architecture. Since architecture and function go hand-in-hand for proteins, solving what a protein's structure looks like is a big step towards knowing what that protein does.

The 3-D map created by Kim and his colleagues is described in the February 17, 2003 edition of the Proceedings of the National Academy of Sciences. It shows the distribution in space of the 500 most common protein folds as
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Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
19-Feb-2003


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