Phone: 301-594-2375
Fax: 301-402-3095
Biography:
Dr. Yawen Bai received his Ph.D. in biophysics (advisor: S. Walter Englander) from the medical school, University of Pennsylvania in 1994. Dr. Bai completed post-doctoral training with Dr. Peter E. Wright at the Scripps Research Institute and was offered a tenure track fellowship in the Laboratory of Biochemistry in September 1997.
Research:
To understand proteins' function and to design new proteins with new functions, it is essential to know the physical principles that control the structure, folding, stability, and dynamics of protein molecules. Our research interest is to investigate these principles and use them to solve practicle problems in basic biomedical research. Currently, we are studying the mechanism of protein folding and learning to design proteins by phage display.
Protein folding mechanism: To learn how proteins fold, their folding processes need to be characterized, which includes intermediates and transition states. This is a difficult task because established methods for structural determination of native proteins are not applicable. So far, amide hydrogen exchange (HX) coupled with NMR has been one of the best techniques to study the structure of protein folding intermediates. This technique allows hydrogen bond formation to be detected. Based on this technique, a native-state HX method was developed to detect folding intermediates under native equilibrium conditions a few years ago (Bai et al., Science, 1995), which allows the structure, stability of the folding intermediates to be studied under equilibrium conditions. Since then, the relationship bebtween the native-state HX results and the kinetic folding pathways of proteins has been an interesting topic in the folding field. In the last four years, we have investigated the kinetic folding pathways of several proteins including cytochrome c, barnase, and a stable variant of apocyt b562 designed by a phage-display method (see below). We found that the kinetic folding behavior of these proteins has a simple relationship with their native-state HX results. That is that the intermediates detected by the native-state HX method populate after the major kinetic barrier-"barrier-early" hypothesis. These results are inconsistent with the folding paradigm established by the earlier studies on the folding pathway of barnase (Matoschek et al., Nature, 1990; Bycroft et al., Nature, 1990), which suggests an intermediate populates early in the folding process. In addition, we also proposed a kinetic criterion to test whether folding intermediates are on- (U <=> I <=> N) or off-pathway (I <=> U <=> N). We demonstrated that the folding intermediate of cyt c and lysozyme are on pathway intermediates. More surprising, we found that there is no definable nucleation sites at the rate-limiting transition state of barnase under native conditions, suggesting that barnase may fold by multiple pathways- a "New View" of protein folding. Our future work will also include investigations on the possible role of folding intermediates in protein function.
Protein Design by phage display Up to date, ~10,000 protein structures have been solved. However, we still do not understand the basic principles that control their uniqueness and stability of these structures. In the last several years, we have tried to test whether phage-display coupled with proteolysis can be used to design proteins that fold uniquely. The design procedure involves following steps: (i) rational design of target fold; (ii) generation of multiple mutations in the core of the target protein; (iii) displaying the mutants on the surface of phage; (iv) selection for stably folded proteins by challenging the protein library with protease. We have successfully applied this procedure to convert a partially unfolded four-helix bundle protein to a stably folded four-helix bundle protein. Further work will be to extend this method as an engineering tool for breeding protein molecules.
Citations:
Bai et al. Proein Sciences 2001; 10, 1056-66.
Takei J. et al. Proc Natl Acad Sci USA 2000; 97:10796-801.
Bai Y. Proc Natl Acad Sci USA 1999; 96:477-480.
Chu et al. Biochemistry 1999; 39:14119-24.
Nawrocki JP et al. J Mol Biol 1999; 293:991-5.
This page was updated June 14, 2001 by Zoraida S. Villadiego