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Rotation Projects

Potential Rotation Projects

  1. One of the five most common structural classes of proteins is the (b/a)8 barrel motif. These proteins have eight parallel b strands arranged in a cylindrical fashion in the hydrophobic core and a corresponding number of amphipathic a-helices that dock on the surface of this cylinder. Equilibrium and kinetic studies of the folding reaction of one representative of this class, the subunit of tryptophan synthase, have shown that this single, symmetrical domain is formed by the progressive development of structure and stability in two partially folded forms. We are currently exploring the folding mechanisms of other (b/a)8 barrel proteins. Our goal for comparing the folding mechanisms of different members of the (b/a)8 barrel family is to learn how sequence relates to folding mechanism. The laboratory rotation would involve studying the equilibrium folding properties of another member of this structural class. Experiences that would be gained include expertise in protein expression and purification, and the collection and analysis of data acquired by spectroscopic techniques such as circular dichroism and fluorescence.

  2. Understanding the mechanism of folding and assembly of oligomeric peptides and proteins will provide important insights into a process that is essential for all forms of life. One model system that we have been using to study multimeric folding events is the homodimeric leucine zipper peptide, GCN4-p1. Mutational studies have yielded insights into the roles of helix propensity, salt bridges and buried polar residues in the transition state for folding. We are currently extending these studies to explore the folding and assembly of heterodimeric and heterotrimeric coiled coils. This rotation will provide training in peptide synthesis, HPLC purification, ultracentrifugation, circular dichroism spectroscopy, fluorescence resonance energy transfer experiments, and data analysis.

  3. The mechanism by which natural proteins fold to their functional forms has been evolutionarily selected to be relevant on a biological time scale.  Synthetic proteins, while designed  to achieve stable native forms, have not had evolutionary pressures applied to remove kinetic traps in their folding mechanisms and may have complicated access routes to their native states.  By studying the folding of five synthetic ├ča-repeat proteins, we will test the proposition that the design principles not only achieve the native state but do so via relatively smooth energy landscapes (Baker lab, Nature 2013).  The project will involve the expression and purification of the synthetic proteins and their biophysical characterization, with a focus on the early folding events


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  • Tryptophan Synthase