Research Description
The major goal of my research is to understand how complex biological molecules adopt their functional, 3-dimensional conformations: The Protein and RNA Folding Problems. In our protein folding studies, we demonstrated the existence of a kinetic amide isotope effect and applied this unique method to measure when H-bonds form to study the folding of multiple protein types. We learned that different categories of pathways exist depending upon the secondary structure composition. The issue of single versus multiple pathways is one of the most discussed in protein folding and we provided the first demonstration of multiple pathways in a small protein (independent of adventitious effects such as disulfide bonds or proline isomerization).

Highlights of our ribozyme folding studies, conducted in collaboration with T. Pan (BMB), include the development of a thermodynamic and kinetic formalism for ribozyme folding and the proposal of a novel mechanism for the origin of the stability of a thermophilic ribozyme. Our mechanism of using a less structured intermediate and increased cooperativity to achieve higher functional stability for tertiary RNAs is fundamentally different than that commonly proposed to explain the increased stability of thermophilic proteins and has implications to the design of functional ribozymes. Lastly, we presented the first detailed study on RNA folding during transcription. We found that the transcription process alters the folding pathway of ribozymes. Furthermore, the presence of an elongation factor, NusA, significantly accelerates folding through pausing at specific sites. These findings should have implications on macromolecular folding in general and on the functional aspects of transcriptional elongation factors.