Eunjeong Lee, Jasmina Redzic, Anthony Saviola, Xueni Li, Christopher Ebmeier, Tatiana Kutateladze, Kirk Hansen, Rui Zhao, Natalie Ahn, Nikolai Sluchanko, Elan Eisenmesser (2023). Molecular insight into the specific interactions of the SARS-CoV-2 Nucleocapsid with RNA and host protein. Protein Science. In press. PMID: 36807437.
Sara Espinosa, Francesca De Bortoli, Xueni Li, John Rossi, Marisa E. Wagley, Hei-Yong G. Lo, J. Matthew Taliaferro, Rui Zhao (2022). Human PrpF39 is an alternative splicing factor recruiting U1 snRNP to weak 5’ splice sites. RNA. 29:97-110. PMID: 36316087.
Jothi Anantharajan, Nithya Baburajendran, Grace Lin, Yong Yao Loh, Weijun Xu, Nur Huda Binte Ahmad, Shuang Liu, Anna E. Jasson, John Wee Liang Kuan, Elizabeth Yihui Ng, Yee Khoon Yeo, Alvin W. Hung, Joma Joy, Jeffrey Hill, Heide L Ford, Rui Zhao, Thomas H. Keller, CongBao Kang. Structure-activity relationship studies of allosteric inhibitors of EYA2 tyrosine phosphatase. Protein Science. 31:422-431. PMID 34761455.
Guoxin Zhang, Zhen Dong, Ryan C. Gimple, Arthur Wolin, Qiulian Wu, Zhixin Qiu, Lisa Wood, Jia Z. Shen, Li Jiang, Linjie Zhao, Deguan Lv, Briana C. Prager, Leo J.Y. Kim, Xiuxing Wang, Lingdi Zhang, Ryan L. Anderson, Jeffrey K. Moore, Shideng Bao, Thomas H. Keller, Grace Lin, Congbao Kang, Petra Hamerlik, Rui Zhao, Heide L. Ford, Jeremy N. Rich. Targeting EYA2 Phosphatase Activity in Glioma Stem Cells Induces Mitotic Catastrophe. Journal of Experimental Medicine. 218(11):e20202669. PMID 34617969.
Hong Li, Caiguo Zhang, Bian Li, Hui Deng, Melanie Blevins, Gangwen Han, Bin Fan, Chunxia Yang, Rui Zhao, Whitney High, David Norris, Mayumi Fujita, Xiao-Jing Wang, Mingxia Huang. Inhibition of CtBP-regulated proinflammatory gene transcription attenuates psoriatic skin inflammation. Journal of Investigative Dermatology. 142:390. PMID 34293351.
Shasha Shi, Xueni Li, Rui Zhao (2021). Detecting circRNA in spliceosomal P complex. Methods. 2021 Dec; 196:30-35. PMID: 33577981
Francesca de Bortoli, Sara Espinosa, and Rui Zhao (2020). DEAH-box RNA helicases in pre-mRNA splicing. Trends in Biomedical Sciences. 46:225-238. PMID: 33272784.
Zhou H, Blevins MA, Hsu JY, Kong D, Galbraith MD, Goodspeed A, Culp-Hill R, Oliphant MU, Ramirez D, Zhang L, Pineiro JT, Mathews Griner L, King R, Barnaeva E, Hu X, Southall NT, Ferrer M, Gustafson DL, Regan DP, D'Alessandro A, Costello JC, Patnaik S, Marugan J, Zhao R*, Ford HL* (2020). A SIX1/EYA2 small molecule inhibitor disrupts EMT and metastasis. Cancer Res. 80:2689-2702. PMID: 32341035. *Co-corresponding authors.
Duff MR, Redzic JS, Ryan LP, Paukovich N, Rui Zhao, Nix JC, Pitts TM, Agarwal P, Eisenmesser EZ (2020). Structure, dynamics, and function of the evolutionarily changing biliverdin reductase B family. J Biochem. 168(2):191-202. PMID: 32246827.
Li H, Zhang C, Yang C, Blevins M, Norris D, Rui Zhao, Huang M (2020). C-terminal binding proteins 1 and 2 in traumatic brain injury-induced inflammation and their inhibition as an approach for anti-inflammatory treatment. Int J Biol Sci. 16(7):1107-1120. PMID: 32174788.
Xueni Li, Shiheng Liu, Lingdi Zhang, Aaron Issaian, Ryan C Hill, Sara Espinosa, Yanxiang Cui, Kalli Kappel, Rhiju Das, Kirk C Hansen, Z Hong Zhou*, Rui Zhao* (2019). A unified mechanism for intron and exon definition and back-splicing. Nature. 573:375-380. PMID: 31485080. *Co-corresponding authors.
Jothi Anantharajan, Hengbo Zhou, Lingdi Zhang, Taylor Hotz, Melanie Vincent, Melanie A. Blevins, Anna E. Jansson, John Wee Liang Kuan, Elizabeth Yihui Ng, Yee Khoon Yeo, Nithya Baburajendran, Grace Lin, Alvin W. Hung, Joma Joy, Samarjit Patnaik, Juan Marugan, Pratyaydipta Rudra, Debashis Ghosh, Jeffrey Hill*, Thomas H. Keller*, Rui Zhao*, Heide L. Ford*, CongBao Kang* (2019). Structural and functional analyses of an allosteric Eya2 phosphatase inhibitor that has on target effects in human lung cancer cells. Molecular Cancer Therapeutics. 18:1484-1496. PMID: 31285279. *Co-corresponding authors.
Elan Z Eisenmesser, Adrian Gottschlich, Jasmina S Redzic, Natasia Paukovich, Jay C Nix, Tania Azam, Lingdi Zhang, Rui Zhao, Jeffrey S. Kieft, Erlinkda The, Xianzhong Meng, Charles A Dinarello (2019). The interleukin-37 monomer is the active form for reducing innate immunity. PNAS. 116:5514-5522. PMID: 30819901.
Kalli Kappel, Shiheng Liu, Kevin P. Larsen, Georgios Skiniotis, Elisabetta Viani Puglisi, Joseph D. Puglisi, Z. Hong Zhou, Rui Zhao, Rhiju Das (2018). De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes. Nature Methods. 15:947-954. PMID: 30377372.
Luo J, Bian L, Blevins MA, Wang D, Liang C, Du D, Wu F, Holwerda B, Rui Zhao, Raben D, Zhou H, Young C, Wang XJ. Smad7 promotes healing of radiotherapy-induced oral mucositis without compromising oral cancer therapy in a xenograft mouse model. Clinical Cancer Research. 2018 Sep 5. pii: clincanres.1081.2018. doi: 10.1158/1078-0432.CCR-18-1081. [Epub ahead of print]. PMID: 30185419.
Melanie Blevins, Caiguo Zhang, Lingdi Zhang, Hong Li, Xueni Li, David Norris, Mingxia Huang*, Rui Zhao* (2018). CPP-E1A Fusion Peptides Inhibit CtBP-Mediated Transcriptional Repression. Molecular Oncology. 12:1358-1373. PMID: 29879296. *Co-corresponding authors.
Rebecca L Vartuli, Hengbo Zhou, Lingdi Zhang, Rani K Powers, Jared Klarquist, Pratyaydipta Rudra, Melanie Y Vincent, Debashis Ghosh, James C Costello, Ross M Kedl, Jill E Slansky, Rui Zhao, Heide L Ford (2018). Eya3 Enhances Breast Cancer Progression via Threonine Phosphatase Mediated Upregulation of PD-L1 and Resultant Immune Suppression. J. Clinical Investigation. 128:2535. PMID: 29757193.
Lingdi Zhang, Hengbo Zhou, Xueni Li, Rebecca Vartuli, Rui Zhao*, Heide L. Ford* (2018). Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression. Nature Communications. 9:1047. PMID: 29535359. *Co-corresponding authors.
Shiheng Liu, Xueni Li, Lingdi Zhang, Jiansen Jiang, Ryan C. Hill, Yanxiang Cui, Kirk C. Hansen, Z. Hong Zhou*, Rui Zhao* (2017). Structure of the yeast spliceosomal postcatalytic P complex. Science. 358:1278-1283. PMID: 29146870. * Co-corresponding authors.
Xueni Li, Shiheng Liu, Jiansen Jiang, Lingdi Zhang, Sara Espinosa, Z. Hong Zhou*, Rui Zhao* (2017). CryoEM structure of S. cerevisiae U1 snRNP offers insight into alternative splicing. Nature Communications. 8:1035. PMID: 29051543. * Co-corresponding authors.
Lingdi Zhang, Xueni Li, Ryan C. Hill, Yan Qiu, Wenzheng Zhang, Kirk C. Hansen, Rui Zhao (2015). Brr2 plays a role in spliceosomal activation in addition to U4/U6 unwinding. Nucleic Acids Research. 43:3286-97. PMID: 2560679.
M. A. Blevins, J. Kouznetsova, A. B. Krueger, R. King, L. M. Griner, X. Hu, N. Southall, J. J. Marugan, Q. Zhang*, M. Ferrer*, and Rui Zhao* (2015). Small molecule, NSC95397, inhibits the CtBP1-protein partner interaction and CtBP1-mediated transcription repression. J. Biomolecular Screening. 20:663-72. PMID: 25477201. * Co-corresponding authors.
A. B. Krueger, D. J. Drasin, W. A. Lea, A. N. Patrick, S. Patnaik, D. S. Backos, C. J. Materson, X. Hu, E. Barnaeva, M. J. Holliday, M. A. Blevins, T. P. Robin, E. Z. Eisenmesser, M. Ferrer, A. Simeonov, N. Southall, P. Reigan, J. Marugan*, H. L. Ford*, and Rui Zhao* (2014). Allosteric inhibitors of the Eya2 phosphatase are selective and inhibit Eya2-mediated cell migration. J. Biol. Chem. 289:16349-61. PMID: 24755226. *Co-corresponding authors.
C. Wang, Z. Chen, X. Hong, F. Ning, H. Liu, J. Zang, X. Yan, J. Kemp, C.A. Musselman, T.G. Kutateladze, Rui Zhao, C. Jiang, and G. Zhang. The structural basis of urea-induced unfolding in -catenin. (2014) Acta Cryst. D70: 2840-7.
S. M. Garrey, A. Katolik, M. Prekeris, X. Li, K. York, S. Bernards, S. Fields, Rui Zhao, M. J. Damha, and J. Hesselberth. A homolog of lariat debranching enzyme modulates turnover of branched RNA. (2014). RNA. 20:1337-48.
G. Han, L. Bian, F. Li, A. Cotrim, D. Wang, J. B. Liu, Y. Deng, G. Bird, A. Sowers, J. B. Mitchell, J. S. Gutkind, Rui Zhao, D. Raben, P. T. Dijke, Y. Refaeli, Q. Zhang, and X.-J. Wang. (2013). Preventive and therapeutic effects of Smad7 on radiation-induced oral mucositis. Nature Medicine. 19:421-8.
X. Li, W. Zhang, T. Xu, J. Ramsey, L. Zhang, R. Hill, K. C. Hansen, J. R. Hesselberth, and Rui Zhao. (2013). Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly. Nucleic Acids Research. 41:3805-18. PMID: 23393194
A.N. Patrick, J.H. Cabrera, A.L. Smith, X.S. Chen, H.L. Ford*, Rui Zhao*. (2013). Structural and Functional Analyses of the SIX1/EYA Transcriptional Complex Reveals Insights into Branchio-oto-renal Syndrome and Metastasis. Nature Structural and Molecular Biology. 20:447-453. * Co-corresponding authors.
A.B. Krueger, S.J. Dehdashti, N. Southall, J.J. Marugan, M. Ferrer, X. Li, H. L. Ford, W. Zheng, and Rui Zhao. (2013). Identification of a selective small molecule inhibitor series targeting the Eyes Absent 2 (Eya2) phosphatase activity. J. Biomolecular Screening. 18: 85-96 (e-pub ahead of print July 20, 2012). PMID: 22820394
Y. Deng, H. Deng, J. Liu, G. Han, S. Malkoski, B. Liu, Rui Zhao, XJ. Wang, Q. Zhang. (2012). Transcriptional down-regulation of Brca1 and E-cadherin by CtBP in breast cancer. Mol. Carcinog. 51:500-7.
Farabaugh, S.M., Micalizzi, D.S., Jedlicka, P., Rui Zhao, and Ford, H.L. (2012). Eya2 Is Required to Mediate the Pro-Metastatic Functions of Six1 Via the Induction of TGF-β Signaling, Epithelial-Mesenchymal Transition, and Cancer Stem Cell Properties. Oncogene. 31: 552-62.
Weizhi Liu, Marzena Jankowska-Anyszka, Karolina Piecyk, Laura Dickson, Adam Wallace, Anna Niedzwiecka, Janusz Stepinski, Ryszard Stolarski, Edward Darzynkiewicz, Jeffrey Kieft, Rui Zhao, David N. M. Jones and Richard E. Davis (2011). Structural basis for nematode eIF4E binding an m2,2,7G-Cap and its implications for translation initiation. Nucleic Acid Research. 39: 8820-32.
Guarnieri, M. T., B. S. J. Blagg, Rui Zhao (2011). A high throughput TNP-ATP displacement assay for screening inhibitors of ATP-binding in bacterial histidine kinases. Assay and Drug Developement Technologies, 9: 174-183.
Hong, X., J. Zang, J. White, C. Wang, C.H. Pan, Rui Zhao, R.C. Murphy, S. Dai, P. Henson, J.W. Kappler, J. Hagman, G. Zhang. (2010). Interaction of JMJD6 with single-stranded RNA. PNAS, 107: 14568-72.
Pazy, Y., M. A. Motaleb, M. T. Guarnieri, N. W. Charon, Rui Zhao, R. E. Silversmith (2010). Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate. PNAS. 107, 1924-1929. (Track II direct submission)
Liu, W., Rui Zhao, C. McFarland, J. Kieft, J. Stepinski, M. Jankowska-Anyszka, A. Niedzwiecka, E. Darzynkiewicz, D. N. M. Jones, and R. Davis (2009). Structural insights into parasite eIF4E binding specificity for m7G AND m2,2,7G mRNA cap. J. Biol. Chem. 284, 31336-31349.
Zhang, L., T. Xu, C. Maeder, L. Bud, J. Shanks, J. Nix, C. Guthrie, J.A. Pleiss, Rui Zhao (2009). Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2. Nature Structure and Molecular Biology. 16, 731-739.
Patrick, A.N., B.J. Schiemann, K. Yang, Rui Zhao*, and H. Ford* (2009). Biochemical and functional characterization of 6 Six1 Branchio-Oto-Renal Syndrome mutations. J. Biol. Chem. 284, 20781-20790. * Co-corresponding authors
Yang, K., L. Zhang, T. Xu, A. Heroux, Rui Zhao (2008). Crystal structure of the beta-finger domain of Prp8 reveals analogy to ribosomal proteins. PNAS. 105, 13817-22. (Track II direct submission)
Shen, H., X. Zheng, J. Shen, L. Zhang, Rui Zhao, M. R. Green (2008). Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome. Genes & Development. 22, 1796-1803.
Pedro V Peña, Robert A Hom, Tiffany Hung, Hanyang Lin, Alex J Kuo, Ronald P Wong, Oksana M Subach, Karen S Champagne, Rui Zhao, Vladislav V Verkhusha, Gang Li, Or Gozani, Tatiana G. Kutateladze (2008). Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor. J. Mol. Biol. 380, 303-312.
Guarnieri, M., L. Zhang, J. Shen, Rui Zhao (2008). The Hsp90 inhibitor radicicol interacts with the ATP-binding pocket of bacterial sensor kinase PhoQ. J. Mol. Biol. 379, 82-93.
Bourret, T.J., S. Porwollik, M. McClelland, Rui Zhao, T. Greco, H. Ischiropoulos, A. Vazquez-Torres (2008). Nitric Oxide antagonizes the acid tolerance response that protects Salmonella against innate gastric defenses. PLOS One, 3, 1-11
Bishop, B., J. Dasgupta, M. Klein M, R.L. Garcea, N.D. Christensen, Rui Zhao, X.S. Chen (2007). Crystal structures of four types of HPV L1 capsid proteins: Understanding the specificity of neutralizing monoclonal antibodies. J. Biol. Chem. 282, 30803-30811.
Shen, J., L. Zhang, Rui Zhao (2007). Biochemical characterization of UAP56’s ATPase and helicase activity. J. Biol. Chem., 282, 22544-50.
Zhang, L., J. Shen, M. Guarnieri, A. Heroux., K. Yang, Rui Zhao (2007). Crystal structure of the C-terminal domain of splicing factor Prp8 carrying retinitis pigmentosa mutants. Protein Science, 16, 1024-31.
Pena, P. V., F. Davrazou, X. Shi, K. Walter, V. V. Verkhusha, O. Gozani, Rui Zhao, and T. G. Kutateladze (2006). Molecular mechanism of H3K4Me3 recognition by Plant Homeodomain of Inhibitor of Growth 2 tumor suppressor. Nature, 442, 100-103.
Rui Zhao*, J. Shen, M.R. Green, M. MacMorris, T. Blumenthal (2004). Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. Structure, 12, 1373-1381. * Corresponding author
Gai, D., Rui Zhao, D. Li, C.V. Finkielstein, X. S. Chen (2004). Mechanisms of conformational changes for a replicative hexameric helicase of SV40 Large Tumor antigen. Cell, 119, 47-60.
Li, D.*, Rui Zhao*, W. Lilyestrom, D. Gai, R. Zhang, J. A. Decaprio, E. Fanning, A. Jochimiak, G. Szakonyi, and X. S. Chen (2003). Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Nature, 423, 512-518. * These authors contributed equally to the work.
Kruse, S. W., Rui Zhao*, D. P. Smith and D. N. M. Jones* (2003). Structure of a specific alcohol-binding site defined by the odorant binding protein LUSH from Drosophila melanogaster. Nature Structural Biology, 9, 694-700. * These authors co-supervised this research.
Silversmith, R.E., G.P. Guanga, L. Betts, C. Chu, Rui Zhao, and R. B. Bourret. CheZ-mediated dephosphorylation of the Escherichia coli chemotaxis response regulator CheY: role for CheY glutamate 89 (2003). J. Bacteriology, 185, 1495-1502. (A commentary on this article is also published in the same issue.)
Rui Zhao, E. J. Collins, R. B. Bourret, and R. E. Silversmith (2002). Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ. Nature Structural Biology, 9, 570-575. (The structure appeared on the cover and was discussed in the News & Views of this issue of Nature Structural Biology.)
Rui Zhao, E. J. Collins, R. B. Bourret, and R. E. Silversmith (2002). Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ. Nature Structural Biology, 9, 570-575. (The structure appeared on the cover and was discussed in the News & Views of this issue of Nature Structural Biology.)
Buslepp, J.*, Rui Zhao*, D. Donnini, D. J. Loftus, M. Saad, E. Appella, and E. J. Collins (2001). T cell activity correlates with oligomeric peptide-Major Histocompatibility Complex binding on T cell surface. Journal of Biological Chemistry, 276, 47320-47328. * Both authors contributed equally to this work.
Batalia, A. M., T. J. Kirksey, A. Sharma, L. Jiang, J.-P. Abastado, S. Yan, Rui Zhao, and E. J. Collins (2000). Class I MHC is stabilized against thermal denaturation by physiological concentrations of NaCl. Biochemistry, 39, 9030-9038.
Schuster, M., Rui Zhao, R. B. Bourrett, and E. J. Collins (2000). Correlated switch-binding and signaling in bacterial chemotaxis. Journal of Biological Chemistry, 275, 19752-19758.
Rui Zhao, D. J. Loftus, E. Appella, and E. J. Collins (1999). Structural evidence of T cell xeno-reactivity in the absence of molecular mimicry. Journal of Experimental Medicine, 189, 359-370.
Rui Zhao, A. Hadfield, M.J. Kremer and M. G. Rossmann (1997). Cations in human rhinoviruses. Virology, 227, 13-23.
Hadfield, A.T., W. M. Lee, Rui Zhao, M.A. Oliveria, I. Minor, R.R. Rueckert, and M.G. Rossmann (1997). The refined structure of human rhinovirus 16 at 2.15Å resolution: Implications for the viral life cycle. Structure, 5, 427-441.
Rui Zhao, D.C. Pevear, M.J. Kremer, V. Giranda, J. Kofron, R. Kuhn and M. G. Rossmann (1996). Human Rhinovirus 3 at 3.0Å resolution. Structure, 4, 1205-1220.
Oliveira, M. A., Rui Zhao, W. M. Lee, M. J. Kremer, I. Minor, R. R. Rueckert, G. D. Diana, D. C. Pevear, F. J. Dutko, M. A. McKinlay and M. G. Rossmann (1993). The structure of human rhinovirus 16. Structure, 1, 51-68.