Patricia L. Clark

Patricia L. Clark

Protein Biophysics in Living Cells

Biography

2013-present
Rev. John Cardinal O'Hara CSC Professor of Biochemistry, University of Notre Dame
2013-present
Concurrent Professor, Chemical & Biomolecular Engineering, University of Notre Dame
2010-2013
Rev. John Cardinal O'Hara CSC Associate Professor of Biochemistry,University of Notre Dame
2008-2010
Associate Professor, University of Notre Dame
2006-2008
Assistant Professor, University of Notre Dame
2001-2006
Clare Boothe Luce Assistant Professor of Biochemistry, University of Notre Dame
1997-2001
Postdoctoral Fellow, Massachusetts Institute of Technology
1997
Ph.D. in Molecular Biophysics, University of Texas Southwestern Medical Center
1991
B.S. in Chemistry, Georgia Institute of Technology

Selected Awards

2013
Michael and Kate Barany Award for Young Investigators, Biophysical Society
2003-2007
American Heart Association National Scientist Development Award
2003-2008
NSF CAREER Award
1998-2001
NIH NRSA Postdoctoral Fellowship
1994-1997
NIH Biophysics Predoctoral Training Fellowship

Research Interests

Proteins are long flexible polymers of amino acids, yet each must fold into a complex 3D shape in order to carry out a specific catalytic, binding, or structural activity. Experiments with purified proteins have demonstrated that the information needed for a given protein to obtain its final folded structure is contained within the sequence of its amino acid residues. However, the rules that dictate how a given sequence will fold into a given structure are still unclear. Understanding the rules of protein folding is of utmost importance for predicting protein structure from genomic sequence data, designing novel proteins, and understanding how and why protein folding mechanisms can fail. Failure of protein folding mechanisms, often due to genetic mutations or adverse conditions such as thermal or chemical stress, is the cause of numerous human diseases including cystic fibrosis, Alzheimer's disease, juvenile cataracts, and many forms of cancer.

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 virulence factors on the outer surface of pathogenic gram-negative bacteria. For example, these virulence 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 β-sheet structure? β-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 β-sheets often represent contacts quite distant in sequence. As a result, it has been extremely difficult to define simple rules for β-sheet formation, and we expect that high contact order will make many β-sheet topologies difficult (if not impossible) to form co-translationally. We are using an extremely simple β-sheet architecture, the parallel β-helix, as a model system for developing rules for β-sheet formation.

Recent Papers

  • Sander IM, Chaney JL, Clark PL. (2014) Expanding Anfinsen's Principle: Contributions of Synonymous Codon Selection to Rational Protein Design. J Am Chem Soc. 136:858-61. 
  • Besingi RN, Chaney JL, Clark PL. (2013) An alternative outer membrane secretion mechanism for an autotransporter protein lacking a C-terminal stable core. Mol Microbiol.  90:1028-45.  
  •  Braselmann E, Chaney JL, Clark PL. (2013)  Folding the proteome. Trends Biochem Sci. 38:337-44. 
  •  Braselmann E, Clark PL. (2012) Autotransporters: The Cellular Environment Reshapes a Folding Mechanism to Promote Protein Transport. J Phys Chem Lett.  3:1063-1071. 
  • Renn JP, Junker M, Besingi RN, Braselmann E, Clark PL. (2012)  ATP-independent control of autotransporter virulence protein transport via the folding properties of the secreted protein. Chem Biol. 19:287-96. 
  • Bryan AW Jr, Starner-Kreinbrink JL, Hosur R, Clark PL, Berger B. (2011) Structure-based prediction reveals capping motifs that inhibit β-helix aggregation. Proc Natl Acad Sci U S A. 108:11099-104. 

 

Visit Patricia Clark's publications at PubMed

 

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