Berkeley scientists create first 3-D map of protei...( represented by points which are spatial...)

"When the structure of a new protein is first solved, we can place it in the appropriate location on the map and immediately know who its neighbors are and its evolutionary history which can help us predict what its function may be," Kim says. "This map provides us with a conceptual framework to organize all protein structures and functions and have that information readily available in one place." With the completion of a "working draft" of the human genome in which scientists determined the sequences of the three billion DNA bases that make up the human genome, the big push now is to identify coding genes and the molecular and cellular functions of the proteins associated with them. Coding genes are DNA sequences that translate into sequences of amino acids which RNA assembles into proteins.

The prevailing method for predicting the function of a newly discovered protein is to compare the sequence of its amino acids to the amino acid sequences of proteins whose functions have already been identified. A major problem with relying exclusively on this approach is that while proteins in different organisms may have similar structure and function, the sequences of their amino acids may be dramatically different.

"This is because protein structure and function are much more conserved through evolution than genetically based amino acid sequences," Kim says.

Kim has been a leading advocate for grouping proteins into classes on the basis of their fold structures and using these structural similarities to help predict individual protein functions. While the protein universe may encompass as many as a trillion different kin
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Contact: Lynn Yarris
lcyarris@lbl.gov
510-486-5375
DOE/Lawrence Berkeley National Laboratory
19-Feb-2003