Department Affiliation: Primary: Pharmacology and Molecular Sciences;
High Throughput Biology Center (HIT Center)
Degree: Ph.D., Clemson University
Rank: Assistant Professor
Telephone Number: 410-502-0878
Fax Number: 410-502-1872
E-mail address: hzhu4@bs.jhmi.edu
Home Page: http://www.jhu.edu/zhuheng/
School of Medicine Address: Room 333, Broadway Research Building, 733 N. Broadway, Baltimore, MD 21205
Protein posttranslational modification, transcription factor regulatory networks, host-pathogen interaction, and biomarker identification using a proteomics approach
Fueled by the ever-growing DNA sequence information, the field of proteomics has become one of the most important disciplines to characterize protein function and activity and provide insight into functional networks on a global scale. Emerging evidences suggest that proteins rarely act as single, isolated species when performing their function in vivo; they normally associate with other proteins and/or molecules as complexes and function in a network mode. The goals of my laboratory are to discover and characterize the activities of large collections of proteins, to build signaling networks for better understanding the mechanisms of biological processes, and to identify biomarkers for important human diseases. More specifically, our group is interested in analyzing protein posttranslational modifications, identifying important components involved in various signaling networks, and host-pathogen interactions on the proteomics level.
To achieve the above goals we developed two key technologies: high-throughput protein purification (>4,000 proteins/day) and high-density protein microarrays/chip (>15,000 protein/slide). So far, we have fabricated proteome chips in the budding yeast, herpesviruses, and E. coli (K12). We are also currently working on building a focused protein chip in humans. Previously, we and others demonstrated that protein chips could be used to characterize various protein binding properties, including protein-protein, protein-DNA, protein-lipid, and protein-drug interactions, and to identify downstream targets of protein kinases. More recently, our group and colleagues have made significant progress in expanding the application of protein chips in the following directions: 1) novel protein binding assays, such as RNA-protein, live cell-protein, and lectin-protein interactions; 2) novel enzymatic reactions including protein ubiquitination and acetylation; 3) human serum profiling; and 4) a novel approach in protein chip fabrication. The above new assays or approaches have been applied to investigate host-pathogen interactions, protein glycosylation, cell surface glycan profiles, a ubiquitin E3 enzyme in yeast, and biomarker identification in human inflammatory bowel diseases. Our recent progress has been highlighted in five publications. We strongly believe that the protein chip technologies are capable of accumulating massive amount of data to allow comprehensive and systematic analyses of complex eukaryotic proteomes.
Representative Publications:
- Evans-Nguyen KM, Tao SC, Zhu H, Cotter RJ. Protein arrays on patterned porous gold substrates interrogated with mass spectrometry: detection of peptides in plasma. Anal Chem 2008; 80:1448-1458. Epub 2008 Feb 7. Pub Med Reference
- Chen C-S, Korobkova E, Chen H, Zhu J, Jian X, Tao S-C, He H, Zhu H*. A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nature Methods 2008; 5:69-74. Epub 2007 Dec 16. Pub Med Reference
- Lu, J.-Y., Lin, Y.-Y., Tao, S.-C., Zhu, J., Pickart, C.M., Qian, J., and Zhu H*. Functional dissection of a HECT ubiquitin E3 ligase, Mol. Cell Proteomics 2008, 7:35-45. Pub Med Reference
- Hu, S., Li, Y., Liu, G., Song, Q., Wang, L., Han, Y., Zhang, Y., Song, Y., Yao, X., Tao, Y., Zeng, H., Wang, J., Zhu, H., Chen, Z.-N., and Wu, L. A protein chip approach for high-throughput antigen identification and characterization, Proteomics 7:2151-2161, 2007. Pub Med Reference
Zhu, J., Gopinath, K., Murali, A., Yi, G., Hayward, S.D., Zhu, H., Kao, C. RNA binding proteins that inhibit RNA virus infection, Proc. Natl. Acad. Sci. USA 104:3129-3134, 2007. Pub Med Reference
Tao, S.-C. and Zhu, H. Protein chip fabrication by capture of nascent polypeptides, Nature Biotech. 24:1253-1254, 2006. Pub Med Reference
Zhu, H., Hu, S., Jona, G., Zhu, X., Kreiswirth, N., Willey, B.M., Mazzulli, T., Liu, G., Song, Q., Chen, P., Cameron, M., Tyler, A., Wang, J., Wen, J., Chen, W., Compton, S., and Snyder, M . Severe acute respiratory syndrome diagnostics using a coronavirus protein chip, Proc. Natl. Acad. Sci. USA 103:4011-4016, 2006. Pub Med Reference
- Ptacek, J., Devgan, G., Michaud, G., Zhu, H., Zhu, X., Fasolo, J., Guo, H., Jona, G., Breitkreutz, A., Sopko, R., McCartney, R.R., Schmidt, M.C., Rachidi, N., Lee, S.J., Mah, A.S., Meng, L., Stark, M.J., Stern, D.F., De Virgilio, C., Tyers, M., Andrews, B., Gerstein, M., Schweitzer, B., Predki, P.F., and Snyder, M. Global analysis of protein phosphorylation in yeast, Nature 438:679-684, 2005. Pub Med Reference
Hall, D.A., Zhu, H., Zhu, X., Royce, T., Gerstein, M., and Snyder, M. Regulation of gene expression by a metabolic enzyme, Science 306:482-484, 2004. Pub Med Reference
- Kafadar, K.A., Zhu, H., Snyder, M., and Cyert, M.S. Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I, Genes Dev. 17:2698-2708, 2003. Pub Med Reference
Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R.A., Gerstein, M., and Snyder, M. Global analysis of protein activities using proteome chips, Science 293:2101-2105, 2001. Pub Med Reference
Zhu, H., Klemic, J.F., Chang, S., Bertone, P., Casamayor, A., Klemic, K.G., Smith, D., Gerstein, M., Reed, M.A., and Snyder, M. Analysis of yeast protein kinases using protein chips. Nature Genet. 26: 283-289, 2000. Pub Med Reference
Other graduate programs in which Dr. Zhu participates:
