Scientists Create 3-D Protein Map

BERKELEY, Calif., Feb. 19 -- The first 3-D global map of the protein structure universe has been created by researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) at Berkeley. They says the 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 with Berkeley Lab's Physical Biosciences Div. and UC Berkeley's Chemistry Department, led the development of the map. He said he was surprised 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 said. "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 toward knowing what that protein does.

The 3-D map holds promise for a number of areas of biology and biomedical research, including the design of more effective pharmaceutical drugs that have fewer side-effects, the researchers said. The map is described in the Feb. 18 early edition of the Proceedings of the National Academy of Sciences.

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