Patricia ClarkDepartment of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, USA F1000 Faculty Member (since 17 October 2011)
Rev John Cardinal OHara, CSC Associate Professor of Chemistry and Biochemistry
EDUCATION & TRAINING:
BS Chemistry, Georgia Institute of Technology (USA)
PhD Molecular Biophysics, University of Texas Southwestern Medical Center at Dallas (USA)
NRSA Postdoctoral Fellow, Department of Biology, Massachusetts Institute of Technology (USA)
Member, American Association for the Advancement of Science (USA)
Member, Biophysical Society (USA)
Member, Protein Society (USA)
Research in the Clark laboratory is focused on two related topics. First, how are the rules for protein folding affected by their native environment, the cell? In the cell, proteins are synthesized in a vectorial fashion. The energy landscape for folding during chain synthesis (or secretion across a membrane) is hence quite different from the energy landscape for the folding of a full-length polypeptide chain. As a result, folding intermediates populated during refolding in vitro might be populated quite differently during vectorial folding. A particular interest in the Clark laboratory is the role of co-translational protein folding in suppressing chain misfolding and aggregation in vivo. A related interest is the display of autotransporter virulence factors on the outer surface of pathogenic gram-negative bacteria. Autotransporter proteins must fold only after secretion across two membranes; what prevents them from folding prematurely in the periplasm?
Second, what are the protein folding rules that govern the formation of beta-sheet structure? Beta-sheets represent a type of regular, repeating protein structure, characterized by an extensive hydrogen bonding network between strands of amino acid residues. Contacts between individual amino acid residues in beta-sheets often represent contacts quite distant in sequence. As a result, it has been extremely difficult to define simple rules for beta-sheet formation, and we expect many beta-sheet topologies will be difficult (if not impossible) to form co-translationally. We are using an extremely simple beta-sheet architecture, the parallel beta-helix, as a model system for developing rules for beta-sheet formation.
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