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Yawen Bai, Ph.D.
We are interested in understanding the basic principles that control the dynamic folding/unfolding processes of protein and chromatin using biophysical approaches. The failure of proteins to properly fold can impact their activity and/or stability, while the folding and compaction of DNA is critical for the regulation of gene expression and cell function. Defects in either of these processes can contribute to the development of many diseases, including cancer. Thus, an understanding of the fundamental mechanisms involved in protein and chromatin folding processes is critical for the advancement of cancer research, and for the discovery of potential treatment options.
(1) Protein Folding
Protein folding is the final step in the transfer of genetic information from DNA to proteins. In the 1960s, Anfinsen and coworkers at NIH established the thermodynamic principle of protein folding, which states that the native state of a protein has the lowest free energy under physiological conditions. However, the principle that governs the dynamic process of protein folding remains unclear.
We have developed an approach for discovering and characterizing protein folding intermediates, which involves three steps: (i) identifying partially unfolded intermediates by the native-state hydrogen exchange method; (ii) populating the partially unfolded intermediates by a native-state hydrogen exchange-guided protein engineering method; and (iii) determining the high-resolution structures of the populated folding intermediates by the multi-dimensional NMR method.
We have investigated the folding behavior of a number of proteins using the above approach, including cytochrome c, Rd-apocytochrome b562, barnase, PDZ domain, FAT domain, T4 lysozyme, and ribonuclease H. Excitingly, we were the first to determine the structure of a folding intermediate at atomic resolution for three of these proteins: Rd-apocytochrome b562, T4 lysozyme, and ribonuclease H. Our experimental results strongly suggest that the principle that governs the dynamic process of protein folding is the stepwise folding of cooperative structural units (foldons) (see gallery). We have also suggested a possible explanation for the stepwise manner of protein folding in our recent work, in which we discovered that intrinsically disordered proteins can function as histone chaperones and as chromatin factors (see chromatin folding).
(2) Chromatin Folding
The DNA in eukaryotic cells consists of extremely long molecules that must be folded to more compact forms in order to fit within the small cell nucleus. A number of small positively charged proteins called histones help DNA fold. Histones and DNA first form nucleosomes, the structural unit of chromatin. Each nucleosome contains eight histones (H2A-H2B-H3-H4)2 around which ~146 base pairs of DNA are wrapped. With the formation of nucleosomes, chromatin can further fold to form more compact higher-order structures, such as 30-nm fibers.
The dynamic folding/unfolding processes of the nucleosome and chromatin are essential for cell function, and are highly regulated by a number of proteins, including histone chaperones, linker histones, high mobility group proteins, and nucleosome remodeling complexes. They play important roles in the epigenetic regulation of cell function. We use biophysical techniques, in particular the modern NMR method and isothermal titration calorimetry to investigate: (i) interactions between histones and their chaperones (see gallery); and (ii) interactions between nucleosomes and nucleosome-binding proteins (see gallery).
Currently, we are focusing on the histone variants (H2A.Z and CenH3) and their chaperones. In particular, we are investigating the epigenetic targeting of CenH3 to the centromere. We are particularly interested in the structural basis for the binding of CenH3 to the centromere, and for the recognition of the centromeric nucleosome by the kinetochore complex. The kinetochore mediates the connection of the centromere to microtubules, and ensures accurate segregation of chromosomes during mitosis. Lack of such a control can lead to missegregation of chromosomes during mitosis, and can result in aneuploidy, a condition associated with cancer cells. Thus, these studies are of particularly relevance to our understanding of the basic cellular regulatory mechanisms that protect against cancer development.
If you are seeking a postdoctoral position, and prepared for challenging research, please inquire by sending your CV and a short statement of interest.
This page was last updated on 2/19/2013.