Zhihua Du Group Publications | Chemistry and Biochemistry | SIU

Publications

   33. 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.

   32. 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.

   31. 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

   30.  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

   29.  Shang, J., Wang, G., Yang, Y., Huang, X. & Du, Z. (2014). Structure of the FP domain of Fbxo7 reveals a novel mode of protein-protein interaction.Acta Crystallographica Section D: Biological Crystallography, 70 (1):155-164. 

   28.  Huang, X., Cheng, Q., Du, Z. (2013). A Genome-wide Analysis of RNA Pseudoknots that Stimulate Efficient -1 Ribosomal Frameshifting or Readthrough in Animal Viruses. BioMed Research International, vol. 2013, Article ID 984028, 15 pages, 2013. 

   27.  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: Structural Biology and Crystallization Communications, 69(10):1097-1099.

   26. Huang, X., Wang, G., Wu, Y., Du, Z. (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(8):1598-608.

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

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

   23. Du, Z., Fenn, S., Tjhen, R., James, T. L (2008) . 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.

   22. Du, Z., J. K. Lee, et al. (2008). "Structural and biochemical insights into the dicing mechanism of mouse dicer: a conserved lysine is critical for dsRNA cleavage." Proc. Natl. Acad. Sci. U. S. A. 105(7): 2391-2396.

  21. Du, Z., S. Fenn, et al. (2008). "Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms." J. Biol. Chem. 283(42): 28757-28766.

   20. Fenn, S., Z. Du, et al. (2007). "Crystal structure 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 A resolution." Nucleic Acids Res. 35(8): 2651-2660.

   19. Du, Z., K. Lee John, et al. (2007). "X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2." RNA 13(7): 1043-1051.

   18. Ulyanov Nikolai, B., A. Mujeeb, et al. (2006). "NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site." J Biol Chem. 281(23): 16168-16177.

   17. Ulyanov, N. B., Z. Du, et al. (2006). "Refinement of nucleic acid structures with residual dipolar coupling restraints in cartesian coordinate space." Mod. Magn. Reson. 1: 661-666.

   16. Du, Z., K. Lee John, et al. (2005). "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 A." J. Biol. Chem. 280(46): 38823-38830.

   15. Du, Z., J. Yu, et al. (2004). "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): 11959-11972.

   14. Du, Z., J. Yu, et al. (2004). "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." J. Biol. Chem. 279(46): 48126-48134.

   13. Du, Z., B. Ulyanov Nikolai, et al. (2004). "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 the shape and flexibility of RNA." Biochemistry 43(19): 5757-5771.

   12. A. D. Beniaminov, N. B. Ulyanov, A. B. Samokhin, V. I. Ivanov, Z. Du, E. E. Minyat (2003). The Role of Structural Elements in Dimerization of RNA Fragments in Avian Retroviruses. Molecular Biology 37(3):446-455.

   11. Du, Z., J. Yu, et al. (2003). "Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from Coxsackievirus B3." Biochemistry 42(15): 4373-4383.

    10. Wang, Y., M. Wills Norma, et al. (2002). "Comparative studies of frameshifting and nonframeshifting RNA pseudoknots: a mutational and NMR investigation of pseudoknots derived from the bacteriophage T2 gene 32 mRNA and the retroviral gag-pro frameshift site." RNA 8(8): 981-996.

    9. Lind Kenneth, E., Z. Du, et al. (2002). "Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA." Chem. Biol. 9(2): 185-193.

    8. Du, Z., E. Lind Kenneth, et al. (2002). "Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening." Chem. Biol. 9(6): 707-712.

    7. TL James, Z Du, M Mayer (2002), RNA Structures and Structure-Based Drug Discovery. NMR Toronkai Koen Yoshishu. Vol.41;P.42

    6. DW Hoffman, Z Du, JA Holland, MR Hansen, Y Wang, DP Giedroc (2000). Pseudoknot structures in retroviral and bacteriophage messenger RNA: A family of structurally related RNA pseudoknots. MICROSCOPY AND MICROANALYSIS-NEW YORK. Vol. 3. P. 95-96.

    5. Holland, J. A., M. R. Hansen, et al. (1999). "An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2." RNA 5(2): 257-271.

    4. Du, Z., J. A. Holland, et al. (1997). "Base-pairings within the RNA pseudoknot associated with the simian retrovirus-1 gag-pro frameshift site." J. Mol. Biol. 270(3): 464-470.

    3. Du, Z. and D. W. Hoffman (1997). "An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: insights into a family of structurally related RNA pseudoknots." Nucleic Acids Res. 25(6): 1130-1135.

    2. H Qiu, K Kaluarachchi, Z Du, D W Hoffman, D P Giedroc (1996).  Thermodynamics of folding of the RNA pseudoknot of the T4 gene 32 autoregulatory messenger RNA. Biochemistry 35(13):4176-86

    1. Du, Z., D. P. Giedroc, et al. (1996). "Structure of the Autoregulatory Pseudoknot within the Gene 32 Messenger RNA of Bacteriophages T2 and T6: A Model for a Possible Family of Structurally Related RNA Pseudoknots." Biochemistry 35(13): 4187-4198.

Patents:

Thomas L James, Kenneth E Lind, Zhihua Du, B Matija Peterlin, Koh Fujinaga, Rodney Kiplin Guy, Peter Bawden Madrid, Moriz Mayer: Inhibition of RNA function. 2003, US 20030229082