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Heng Zhu, Ph.D.
One of the major efforts of the lab is to apply the protein chip technology to identify various posttranslational modifications on the lysine residues in three model systems, including the budding yeast, E. coli, and humans. Currently, the lab is working on identifying downstream targets of the acetylase complexes, SAGA and NuA4, in collaboration with Shelley Berger’s group. We have also established assay protocols to identify downstream targets of Rsp5p, a HECT-domain E3 ubiquitin ligase in yeast, in collaboration with Cecile Pickart’s group. In addition, we are working closely to survey the yeast proteome for proteins that can recognize various poly-ubiquitin chains with various linkages. Phil Cole’s lab has developed several new reagents that can be used to covalently label the catalytic sites of acetylases. We are pushing forward to applying these compounds on our yeast protein chips to discover new acetylases.
Jorge Escalante plays a major role in studying (de)acetylation in E. coli in this project. We are taking step to extend the protein chip approach to the E. coli proteome with the goal of construction of an E. coli proteome chip that contains ~4,000 unique E. coli proteins. Once E. coli protein chips are in hand, we hope to use them to investigate the (de)acetylation events in the bacteria. A similar strategy will be applied to identify downstream targets of SIRT3 in the human mitochondrial proteome in collaboration with Paddy Onyango.
Figure 1. Protein microarray technology entails expression and/or purification of a set of recombinant proteins, followed by their robotic application to appropriately treated glass slides (upper panel). An example of purified yeast GST-fusion proteins and a typical yeast proteome array stained with anti-GST antibody are shown in the lower panel. Protein microarrays can be used to probe PTM networks and pathways through binding and enzyme activity studies.