Design and engineering of novel protein folds, functions and properties
(with David Baker, UW)

A major focus of our research is the selection and engineering of a variety of enzyme catalysts for altered substrate specificities, and for altered biophysical properties such as enhanced stability and catalytic lifetimes.  In 2002, we carried out what was (for us) a seminal experiment in which we created a fully active, chimeric homing endonuclease capable of recognizing and cleaving a complementary chimeric target site.  As part of that project, we discovered that computational algorithms being developed by the laboratory of David Baker at the UW could be successfully applied to such a problem, by repacking a protein interface and creating a novel domain packing architecture.  Subsequently, we (the Baker lab and ourselves in various collaborative mixtures) have used similar algorithms with great success to design a novel protein fold, a novel protein-protein heterodimer association specificity (article 2) and an enzyme catalyst with enhanced thermostability and wild-type activity levels.




Above: Time-line of published engineering studies resulting from collaborations between the Baker and Stoddard lab.  

2002:  Creation of a fully active, chimeric homing endonuclease, involving protein interface redesign. 
2003:  Creation of a fully artificial protein fold and sequence without significant homologoues from nature.  
2004:  Redesign of protein-protein binding specificity, using the colicin-immunity protein system (an HNH endonuclease related to phage homing endonucleases, also studied in the Stoddard lab).  
2005:  Computational thermostabilization of an enzyme catalyst.
2006:  Cool stuff coming soon! 


Our current and long-term aims include:

· Development and exploitation of computational engineering algorithms to alter nucleic acid binding specificities for homing endonucleases and nucleotide deaminase enzymes.  Both projects involve the repacking and optimization of protein-nucleic acid interfaces, which poses substantial challenges relative to protein cores and interfaces.

· Improved algorithms for the redesign of protein-protein binding specificities.

· Continued work on the thermal stabilization of enzymatic catalysts of importance for molecular biology and biotechnology.

· De novo enzyme functionality design.
Click here to go to the bibliography page for this project, and its dowloadable articles

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