|
|
|
|
Dr. Hu
http://hulab.tamu.edu/ Projects in my lab involve identifying, characterizing and disrupting interactions between proteins and other molecules. Students in my group get interdisciplinary training in methods ranging from genetics to mass spectrometry, to biophysics, bioinformatics and structural biology. We are using a gene fusion system based on bacteriophage lambda repressor to identify self-assembling protein domains on a genomic scale. Libraries of fragments encoded by the yeast, E. coli, P. aeruginosa and M. tuberculosis genomic DNA are fused downstream of the DNA-binding domain of repressor, which dimerizes too weakly in the absence of its dimerization domain to occupy its operator DNA in vivo. Among the resultant fusion proteins, only those that restore self-assembly confer immunity to phage infection. Using this method, we can simultaneously identify and map hundreds of assembly domains from the target organisms. We are characterizing these structures and molecular nature of the interactions involving these assembly domains and working to develop assembly inhibitors based on proteins and peptides and functional genomics assays (P. aeruginosa and M. tuberculosis are important human pathogens). In other projects, we are developing screens for assembly inhibitors that could be used with combinatorial chemistry libraries, and are developing new approaches to biochemical proteomics in E. coli. We are using a combination of biochemical fractionation methods and mass spectrometry to characterize expressed proteins, protein complexes, and protein localization. We are particularly interested in studying how the assembly and localization of the proteins changes as a function of bacterial physiology. The genomic studies of protein interactions and proteomics require bioinformatics tools and databases. We collaborate to build a model organism data resource for E. coli. Finally, we are continuing the genetic and biophysical characterization of a model protein-protein interaction: the assembly of coiled-coils, using leucine zipper of the yeast transcription factor GCN4 as a model system. Our goal is to understand the determinants of coiled-coil assembly specificity to the point where we can reliably predict assembly from sequences alone. |
