Zhihao Zhuang

TitleAssistant Professor
InstitutionUniversity of Delaware
DepartmentChemistry & Biochemistry
Address160 Academy St.
Newark DE 19716
Phone302-831-8940
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Gui W, Shen S, Zhuang Z. Photocaged Cell-Permeable Ubiquitin Probe for Temporal Profiling of Deubiquitinating Enzymes. J Am Chem Soc. 2020 Nov 18; 142(46):19493-19501. PMID: 33141564.
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    2. Paudel P, Zhang Q, Leung C, Greenberg HC, Guo Y, Chern YH, Dong A, Li Y, Vedadi M, Zhuang Z, Tong Y. Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X. Proc Natl Acad Sci U S A. 2019 Mar 26. PMID: 30914461.
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    3. Gui W, Ott CA, Yang K, Chung JS, Shen S, Zhuang Z. Cell-Permeable Activity-Based Ubiquitin Probes Enable Intracellular Profiling of Human Deubiquitinases. J Am Chem Soc. 2018 Oct 03; 140(39):12424-12433. PMID: 30240200.
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    4. Gong P, Davidson GA, Gui W, Yang K, Bozza WP, Zhuang Z. Activity-based ubiquitin-protein probes reveal target protein specificity of deubiquitinating enzymes. Chem Sci. 2018 Oct 28; 9(40):7859-7865. PMID: 30429995.
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    5. Ott CA, Baljinnyam B, Zakharov AV, Jadhav A, Simeonov A, Zhuang Z. Cell Lysate-Based AlphaLISA Deubiquitinase Assay Platform for Identification of Small Molecule Inhibitors. ACS Chem Biol. 2017 09 15; 12(9):2399-2407. PMID: 28836754.
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    6. Li G, Yuan L, Zhuang Z. Chemical Synthesis of Activity-Based Diubiquitin Probes. Methods Mol Biol. 2017; 1513:223-232. PMID: 27807841.
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    7. Tencer AH, Liang Q, Zhuang Z. Divergence in Ubiquitin Interaction and Catalysis among the Ubiquitin-Specific Protease Family Deubiquitinating Enzymes. Biochemistry. 2016 Aug 23; 55(33):4708-19. PMID: 27501351.
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    8. Yang K, Li G, Gong P, Gui W, Yuan L, Zhuang Z. Chemical Protein Ubiquitylation with Preservation of the Native Cysteine Residues. Chembiochem. 2016 Jun 2; 17(11):995-8. PMID: 27113245.
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    9. Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response. Structure. 2015 Apr 7; 23(4):724-33. PMID: 25773143.
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    10. Dexheimer TS, Rosenthal AS, Luci DK, Liang Q, Villamil MA, Chen J, Sun H, Kerns EH, Simeonov A, Jadhav A, Zhuang Z, Maloney DJ. Synthesis and Structure-Activity Relationship Studies of N-Benzyl-2-phenylpyrimidin-4-amine Derivatives as Potent USP1/UAF1 Deubiquitinase Inhibitors with Anticancer Activity against Nonsmall Cell Lung Cancer. J Med Chem. 2014 Oct 9; 57(19):8099-110. PMID: 25229643.
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    11. Yang K, Gong P, Gokhale P, Zhuang Z. Chemical protein polyubiquitination reveals the role of a noncanonical polyubiquitin chain in DNA damage tolerance. ACS Chem Biol. 2014 Aug 15; 9(8):1685-91. PMID: 24918305.
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    12. Liang Q, Dexheimer TS, Zhang P, Rosenthal AS, Villamil MA, You C, Zhang Q, Chen J, Ott CA, Sun H, Luci DK, Yuan B, Simeonov A, Jadhav A, Xiao H, Wang Y, Maloney DJ, Zhuang Z. A selective USP1-UAF1 inhibitor links deubiquitination to DNA damage responses. Nat Chem Biol. 2014 Apr; 10(4):298-304. PMID: 24531842.
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    13. Li G, Liang Q, Gong P, Tencer AH, Zhuang Z. Activity-based diubiquitin probes for elucidating the linkage specificity of deubiquitinating enzymes. Chem Commun (Camb). 2013 Nov 28; 50(2):216-8. PMID: 24225431.
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    14. Villamil MA, Liang Q, Zhuang Z. The WD40-repeat protein-containing deubiquitinase complex: catalysis, regulation, and potential for therapeutic intervention. Cell Biochem Biophys. 2013 Sep; 67(1):111-26. PMID: 23797609.
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    15. Burkhart RA, Peng Y, Norris ZA, Tholey RM, Talbott VA, Liang Q, Ai Y, Miller K, Lal S, Cozzitorto JA, Witkiewicz AK, Yeo CJ, Gehrmann M, Napper A, Winter JM, Sawicki JA, Zhuang Z, Brody JR. Mitoxantrone Targets Human Ubiquitin-Specific Peptidase 11 (USP11) and Is a Potent Inhibitor of Pancreatic Cancer Cell Survival. Mol Cancer Res. 2013 Aug; 11(8):901-11. PMID: 23696131.
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    16. Yang K, Weinacht CP, Zhuang Z. Regulatory role of ubiquitin in eukaryotic DNA translesion synthesis. Biochemistry. 2013 May 14; 52(19):3217-28. PMID: 23634825.
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    17. Bozza WP, Liang Q, Gong P, Zhuang Z. Transient Kinetic Analysis of USP2-Catalyzed Deubiquitination Reveals a Conformational Rearrangement in the K48-Linked Diubiquitin Substrate. Biochemistry. 2012 Dec 18; 51(50):10075-86. PMID: 23211065.
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    18. Villamil MA, Liang Q, Chen J, Choi YS, Hou S, Lee KH, Zhuang Z. Serine Phosphorylation Is Critical for the Activation of Ubiquitin-Specific Protease 1 and Its Interaction with WD40-Repeat Protein UAF1. Biochemistry. 2012 Nov 13; 51(45):9112-23. PMID: 23116119.
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    19. Juhasz S, Balogh D, Hajdu I, Burkovics P, Villamil MA, Zhuang Z, Haracska L. Characterization of human Spartan/C1orf124, an ubiquitin-PCNA interacting regulator of DNA damage tolerance. Nucleic Acids Res. 2012 Nov 1; 40(21):10795-808. PMID: 22987070.
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    20. Song F, Thoden JB, Zhuang Z, Latham J, Trujillo M, Holden HM, Dunaway-Mariano D. The catalytic mechanism of the hotdog-fold enzyme superfamily 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU. Biochemistry. 2012 Sep 4; 51(35):7000-16. PMID: 22873756.
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    21. Bozza WP, Yang K, Wang J, Zhuang Z. Developing peptide-based multivalent antagonists of proliferating cell nuclear antigen and a fluorescence-based PCNA binding assay. Anal Biochem. 2012 Aug 1; 427(1):69-78. PMID: 22522186.
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    22. Villamil MA, Chen J, Liang Q, Zhuang Z. A noncanonical cysteine protease USP1 is activated through active site modulation by USP1-associated factor 1. Biochemistry. 2012 Apr 3; 51(13):2829-39. PMID: 22439892.
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    23. Chen J, Dexheimer TS, Ai Y, Liang Q, Villamil MA, Inglese J, Maloney DJ, Jadhav A, Simeonov A, Zhuang Z. Selective and cell-active inhibitors of the USP1/ UAF1 deubiquitinase complex reverse cisplatin resistance in non-small cell lung cancer cells. Chem Biol. 2011 Nov 23; 18(11):1390-400. PMID: 22118673.
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    24. Tsutakawa SE, Van Wynsberghe AW, Freudenthal BD, Weinacht CP, Gakhar L, Washington MT, Zhuang Z, Tainer JA, Ivanov I. Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA. Proc Natl Acad Sci U S A. 2011 Oct 25; 108(43):17672-7. PMID: 22006297.
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    25. Bozza WP, Zhuang Z. Biochemical characterization of a multidomain deubiquitinating enzyme Ubp15 and the regulatory role of its terminal domains. Biochemistry. 2011 Jul 26; 50(29):6423-32. PMID: 21710968.
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    26. Chen J, Bozza W, Zhuang Z. Ubiquitination of PCNA and its essential role in eukaryotic translesion synthesis. Cell Biochem Biophys. 2011 Jun; 60(1-2):47-60. PMID: 21461937.
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    27. Ai Y, Wang J, Johnson RE, Haracska L, Prakash L, Zhuang Z. A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase ?. Mol Biosyst. 2011 Jun; 7(6):1874-82. PMID: 21483899.
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    28. Chen J, Ai Y, Wang J, Haracska L, Zhuang Z. Chemically ubiquitylated PCNA as a probe for eukaryotic translesion DNA synthesis. Nat Chem Biol. 2010 Apr; 6(4):270-2. PMID: 20208521.
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    29. Manosas M, Spiering MM, Zhuang Z, Benkovic SJ, Croquette V. Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome. Nat Chem Biol. 2009 Dec; 5(12):904-12. PMID: 19838204.
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    30. Li Z, Song F, Zhuang Z, Dunaway-Mariano D, Anderson KS. Monitoring enzyme catalysis in the multimeric state: direct observation of Arthrobacter 4-hydroxybenzoyl-coenzyme A thioesterase catalytic complexes using time-resolved electrospray ionization mass spectrometry. Anal Biochem. 2009 Nov 15; 394(2):209-16. PMID: 19635449.
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    31. Zhuang Z, Ai Y. Processivity factor of DNA polymerase and its expanding role in normal and translesion DNA synthesis. Biochim Biophys Acta. 2010 May; 1804(5):1081-93. PMID: 19576301.
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    32. Tao GH, Yang LQ, Gong CM, Huang HY, Liu JD, Liu JJ, Yuan JH, Chen W, Zhuang ZX. Effect of PARP-1 deficiency on DNA damage and repair in human bronchial epithelial cells exposed to Benzo(a)pyrene. Mol Biol Rep. 2009 Nov; 36(8):2413-22. PMID: 19247804.
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    33. Hu GH, Zhuang ZX, Huang HY, Yu L, Yang LQ, Ji WD. [Relationship between polymerase eta expression and DNA damage-tolerance in human hepatic cells by hydroquinone]. Zhonghua Yu Fang Yi Xue Za Zhi. 2009 Jan; 43(1):56-60. PMID: 19534882.
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    34. Zhuang Z, Johnson RE, Haracska L, Prakash L, Prakash S, Benkovic SJ. Regulation of polymerase exchange between Poleta and Poldelta by monoubiquitination of PCNA and the movement of DNA polymerase holoenzyme. Proc Natl Acad Sci U S A. 2008 Apr 8; 105(14):5361-6. PMID: 18385374.
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    35. Willis MA, Zhuang Z, Song F, Howard A, Dunaway-Mariano D, Herzberg O. Structure of YciA from Haemophilus influenzae (HI0827), a hexameric broad specificity acyl-coenzyme A thioesterase. Biochemistry. 2008 Mar 4; 47(9):2797-805. PMID: 18260643.
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    36. Hu GH, Zhuang ZX. [Advances of study on human translesion synthesis DNA polymerase eta]. Wei Sheng Yan Jiu. 2006 Nov; 35(6):808-11. PMID: 17290774.
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    37. Song F, Zhuang Z, Dunaway-Mariano D. Structure-activity analysis of base and enzyme-catalyzed 4-hydroxybenzoyl coenzyme A hydrolysis. Bioorg Chem. 2007 Feb; 35(1):1-10. PMID: 16962159.
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    38. Zhuang Z, Berdis AJ, Benkovic SJ. An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex. Biochemistry. 2006 Jul 4; 45(26):7976-89. PMID: 16800623.
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    39. Smiley RD, Zhuang Z, Benkovic SJ, Hammes GG. Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation. Biochemistry. 2006 Jul 4; 45(26):7990-7. PMID: 16800624.
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    40. Zhuang Z, Yoder BL, Burgers PM, Benkovic SJ. The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer. Proc Natl Acad Sci U S A. 2006 Feb 21; 103(8):2546-51. PMID: 16476998.
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    41. Song F, Zhuang Z, Finci L, Dunaway-Mariano D, Kniewel R, Buglino JA, Solorzano V, Wu J, Lima CD. Structure, function, and mechanism of the phenylacetate pathway hot dog-fold thioesterase PaaI. J Biol Chem. 2006 Apr 21; 281(16):11028-38. PMID: 16464851.
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    42. Xi J, Zhang Z, Zhuang Z, Yang J, Spiering MM, Hammes GG, Benkovic SJ. Interaction between the T4 helicase loading protein (gp59) and the DNA polymerase (gp43): unlocking of the gp59-gp43-DNA complex to initiate assembly of a fully functional replisome. Biochemistry. 2005 May 31; 44(21):7747-56. PMID: 15909989.
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    43. Yang J, Xi J, Zhuang Z, Benkovic SJ. The oligomeric T4 primase is the functional form during replication. J Biol Chem. 2005 Jul 8; 280(27):25416-23. PMID: 15897200.
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    44. Xi J, Zhuang Z, Zhang Z, Selzer T, Spiering MM, Hammes GG, Benkovic SJ. Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. Biochemistry. 2005 Feb 22; 44(7):2305-18. PMID: 15709743.
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    45. Zhuang Z, Spiering MM, Berdis AJ, Trakselis MA, Benkovic SJ. 'Screw-cap' clamp loader proteins that thread. Nat Struct Mol Biol. 2004 Jul; 11(7):580-1. PMID: 15221017.
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    46. Yang J, Zhuang Z, Roccasecca RM, Trakselis MA, Benkovic SJ. The dynamic processivity of the T4 DNA polymerase during replication. Proc Natl Acad Sci U S A. 2004 Jun 1; 101(22):8289-94. PMID: 15148377.
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    47. Zhuang Z, Song F, Zhang W, Taylor K, Archambault A, Dunaway-Mariano D, Dong J, Carey PR. Kinetic, Raman, NMR, and site-directed mutagenesis studies of the Pseudomonas sp. strain CBS3 4-hydroxybenzoyl-CoA thioesterase active site. Biochemistry. 2002 Sep 17; 41(37):11152-60. PMID: 12220180.
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