Patricia C. Babbitt, Ph.D.
Professor of Biopharmaceutical Sciences and Pharmaceutical Chemistry

Contact Information:
babbitt@cgl.ucsf.edu
Tel: (415) 476-3784
Fax: (415) 476-2744
Box 2550, MB, QB3,
Room 5 North 508E


Links:
lab website

Bioinformatic and experimental analysis of protein superfamilies for understanding protein structure-function relationships and developing strategies for protein engineering

Using superfamily analysis to understand how protein sequence and structure determine protein function. Our computational approach begins with identifying the sets of divergently related proteins that comprise enzyme superfamilies and then attempts to correlate their conserved and variable structural features to similarities and differences in their functions.

This work also requires the development of new tools in protein bioinformatics to identify and evaluate distant relationships and to distinguish those elements of structure that provide common function from those that determine specificity. Designed to take advantage of the huge volumes of data coming out of the genome projects, this approach provides a much more contextual picture of the structure-function paradigm than can be achieved by studying a single protein at a time. This work has been successfully applied to such problems as the prediction of function for unknown reading frames and elucidation of enzyme mechanisms.

We have now begun a large-scale project to identify superfamily relationships across the entire protein universe. As this picture fills in, these data will form a basis set for identification of the entire range of chemical reactions that can be supported by a given superfamily scaffold across many organisms.

Another bioinformatics project in the laboratory seeks to bridge the gap between the genomics and proteomics by extending the tools of protein informatics to accommodate the special data types generated by mass spectrometry. The laboratory is also pursuing experimental research on protein superfamilies associated with delivery of ATP energy inside a cell. These experiments focus on identifying how structural divergence evolved to provide specificity in cellular localization while maintaining these enzymes at high levels of catalytic efficiency.