Zhihua Du | Chemistry and Biochemistry | SIU

Zhihua Du

Associate Professor

We study the structures and functions of biomacromolecules, such as proteins and RNAs, that participate in vital biological processes including RNA interference (RNAi), telomere maintenance, and antiviral innate immunity in mammalian cells. We employ a range of tools, including X-ray crystallography, NMR, and techniques of biochemistry, molecular & cellular biology, in our research. The goals of our research are two-fold: 1) to reveal the structural and mechanistic details of the biological pathways under investigation; 2) to develop therapeutic strategies based on manipulation of these pathways.

Education

Selected Publications

Wang, G., Yang, Y., Huang, X., Du, Z. (2014) Possible Involvement of Coaxially Stacked Double Pseudoknots in the Regulation of −1 Programmed Ribosomal Frameshifting in RNA Viruses. Journal of Biomolecular Structure & Dynamics. In press.

Yang, Y., Wang, G., Huang, X., Du, Z. (2014) Crystallographic and modelling studies suggest that the SKICH domains from different protein families share a common Ig-like fold but harbour substantial structural variations. Journal of Biomolecular Structure & Dynamics. In press.

Yang, Y., Wang, G., Huang, X., Du, Z. (2014) Expression, purification and crystallization of the SKICH domain of human TAX1BP1. Acta Crystallographica Section F: Structural Biology Communications 70 (5), 619-623

Huang, X., Yang, Y., Wang, G., Cheng, Q., Du, Z. (2014).  Highly Conserved RNA Pseudoknots at the Gag-pol Junction of HIV-1 Suggest a Novel Mechanism of -1 Ribosomal Frameshifting.  RNA 20 (5), 587-593

Shang, J., Wang, G., Yang, Y., Huang, X. & Du, Z. (2013). Structure of the FP domain of Fbxo7 reveals a novel mode of protein-protein interaction. Acta crystallographica. Section D, Biological crystallography. In press.

X Huang, Q Cheng, Z Du (2013). A Genome-wide Analysis of RNA Pseudoknots that Stimulate Efficient -1 Ribosomal Frameshifting or Readthrough in Animal Viruses. BioMed Research Int.  In press.

Shang, J., Wang, G., Yang, Y., Huang, X. & Du, Z. (2013). Expression, purification and crystallization of the FP domain of the human F-box protein Fbxo7 . Acta Cryst. Section F 69, doi:10.1107/S1744309113023154.

X. Huang, G. Wang, Y. Wu, Z. Du (2013). The structure of full-length human CTNNBL1 reveals a distinct member of the armadillo-repeat protein family. Acta crystallographica. Section D, Biological crystallography. 69(Pt 8):1598-608. doi: 10.1107/S0907444913011360.

 X. Huang, Q. Cheng, Z. Du (2013).  Possible utilization of -1 ribosomal frame shifting in the expression of a human SEMA6C isoform. Bioinformation. 9(14):736-8. doi: 10.6026/97320630009736

X. Huang, Z. Du, J. Cheng, Q. Cheng (2013). PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length. Bioinformation. 9(9):440-442

Du Z,Lee JK, Tjhen R, Stroud RM, James TL. Structural and Biochemical Insights into the Dicing Mechanism of Mouse Dicer: a Conserved Lysine is Critical for dsRNA Cleavage. Proceedings of the National Academy of Sciences-USA. 105(7):2391-2396 (2008).

Du Z, Fenn S, James TL. Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms. Journal of Biological Chemistry. 283(42):28757-66 (2008).

Du Z, Fenn S, James TL. Resonance assignment of the first and second KH (hnRNP-K homology) domains of human poly(C)-binding protein-2 (PCBP2). Journal of Biomolecular NMR. 38(2):197 (2007).

Fenn S, Du Z, Lee JK, Tjhen R, Stroud RM, James TL. Crystal structures of the Third KH Domain of Human Poly(C)-Binding Protein-2 in Complex with a C-rich strand of human telomeric DNA at 1.6 Å resolution. Nucleic Acids Research. 35(8):2651-60 (2007).

Du Z, Lee JK, Tjhen R, Stroud RM, James TL. X-ray Crystallographic and NMR Studies of Protein-Protein and Protein-Nucleic Acids Interactions involving the KH domains from Human Poly(C)-Binding Protein-2. RNA. 13(7):1043-51 (2007)

Ulyanov NB, Mujeeb A, Du Z, Tonelli M, Parslow TG, James TL. NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site. Journal of Biological Chemistry. 281(23):16168-77 (2006).

Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James TL. Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 Å. Journal of Biological Chemistry. 280(46):38823-30 (2005).

Du Z, Yu J, Chen Y, Andino R, James TL. Specific Recognition of the C-rich Strand of Human Telomeric DNA and the RNA Template of Human Telomerase by the First KH Domain of Human Poly(C)-Binding Protein-2. Journal of Biological Chemistry, 279(46):48126-34 (2004).

Du Z, Yu J, Ulyanov N, Andino R, James TL. Solution Structure of a Consensus Stem-loop D RNA Domain that Plays Important Roles in Regulating Translation and Replication in Enteroviruses and Rhinoviruses.Biochemistry, 43(38):11959-72 (2004).

Du Z, Ulyanov N, Jinghua Yu J, Andino R & James TL. NMR Structures of Loop B RNAs from the Stem-Loop IV domain of the Enterovirus Internal Ribosome Entry Site: A Single C-to-U Substitution Drastically Changes Shape and Flexibility of RNA. Biochemistry. 43(19):5757-71 (2004).

Du Z, Yu J, Andino R & James TL. Extending the Family of UNCG-like Tetraloop Motifs: NMR Structure of a CACG Tetraloop from Coxsackievirus B3. Biochemistry. 42(15):4373-83 (2003).

Du Z, Lind KE, James TL. Structure of TAR RNA Complexed with a Tat-TAR Interaction Nanomolar Inhibitor that Was Identified by Computational Screening. Chemistry and Biology. 9(6):707-12 (2002).

Lind KE, Du Z, Fujinaga K, Peterlin BM, James TL. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chemistry and Biology. 9(2):185-93 (2002).

Complete publications list