School of Life Sciences School of Life Sciences School of Life Sciences
Associate Professor
Biochemistry and Biophysics
cheng_zhu@tju.edu.cn
Building 15, Room 212
Dr. Zhu earned his Bachelor`s degree at Nanjing University in 2007 and the PhD degree at Peking University in 2013. As an undergraduate, he joined a research group on membrane chemistry and gained experience on organic synthesis of amphiphilic molecules and IR reflection absorption spectroscopy. At Peking University, he experimentally studied protein folding mechanisms, designed metal binding proteins and protein-protein interactions. He completed the postdoctoral training at Dokholyan lab of UNC Chapel Hill and studied computational protein design. He became the associate professor (tenure-track) at the School of Life Sciences of Tianjin University since 2019. Dr. Zhu`s interdisciplinary research combines biochemistry, biophysics, and computation, for the purpose of designing novel protein structures and functions, including HIV-1 immunogens. His series work of rational protein design was published in Nature Communications, PNAS, Immunity, Structure, Biophysical Journal, Protein Science etc. and highlighted by Science Daily, F1000, and Nature research microbiology community.
Rational protein design provides useful reagents to combat the persistent global threats imposed by rapidly evolving pathogens, such as human immunodeficiency viruse. High accuracy structural design and stabilization of specific conformational states are enabled by advancements in biomolecule modeling, force field development, and sampling methods. As an example of protein design on native conformations, epitope grafting presents the target region on a heterologous protein scaffold with preserved structural or antibody-binding properties. The resulting protein binders and immunogens have the advantages of stability, amenability and selectivity over naturally evolved immunoglobulin or synthesized small molecules.
The goal of Zhu group is to apply computational protein design and biomolecular engineering methods to overcome the barriers to the generation of immunity against foreign antigens (viruses) and mutated self-antigens (cancer antigens). The methods developed in our research enabled atomic-level orchestration of protein conformations and provided valuable reagents for biomedical investigations. We also expand the knowledge of structural design to engineering both native and non-native protein conformers, which are relevant in enzymatic reactions, transformation between active/inactive states, and misfolded proteins in cellular condensates.
- Doctoral degree| Peking University| Physical Chemistry| 2013
- Bachelor’s Degree| Nanjing University| Chemistry| 2007
- Protein Design
- Molecular Simulation
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2019.9-Now
School of Life Sciences | Tianjin University | Associate Professor (Principle Investigator)  -
2018.6-2019.9
Department of Pharmacology | Penn State College of Medicine | PostDoc  -
2013.10-2018.6
Department of Biochemistry and Biophysics | University of North Carolina at Chapel Hill | PostDoc 
- Papers
- [1] Yanru Liu, Ziwei Zhou, Fenghui Guan, Zhen Han, Cheng Zhu*, Sheng Ye*, Xuekui Yu*, Anna Qiao*, "Ligand Recognition and Activation Mechanism of the Alicarboxylic Acid Receptors", Journal of Molecular Biology, 2024 436(22):168795.
- [2] Xiangyu Huang, Zhenchao Zhao, Cheng Zhu, Lvye Chai, Ya Yan, Ye Yuan, Lei Wu, Minjie Li, Xiaohan Jiang, Haiwei Wang, Zheng Liu, Pingwei Li, Xin Li*, "Species-specific IL-1β is an inflammatory sensor of Seneca Valley Virus 3C Protease", Plos Pathogens, 2024 20(7):e1012398
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- [3] Hongyan Yin, Zhenchao Zhao, Ya Yan, Ye Yuan, Weiyu Qu, Haiwei Wang, Cheng Zhu, Pingwei Li, Xin Li*, "Seneca Valley virus circumvents Gasdermin A-mediated inflammation by targeting the pore-formation domain for cleavage", mBio, 2024, e0168024
- [4] Gang Luo, Jingkai Zhang, Tianxu Wang, Hao Cui, Yukun Bai, Jianchen Luo, Jinqiu Zhang, Mao Zhang, Linyan Di, Yuncong Yuan, Kang Xiong, Xiangtai Yu, Yaling Zhang, Chao Shen, Cheng Zhu, Yong Wang, Chang Su, Yang Lu*, "A human commensal-pathogenic fungus suppresses host immunity via targeting TBK1" Cell Host & Microbe, 2024, 32: 1–16
- [5] Jingyu Cui, Jiafang Piao, Houyu Han, Weipan Peng, Mengyao Lin, Dianming Zhou*, Cheng Zhu*, Xiaoqun Gong* "Semiarbitrary qPCR for Sensitive Detection of Circulating miRNA via Terminal Deoxynucleotidyl Transferase-Assisted RNA-Primed DNA Polymerization", Analytical Chemistry, 2024, 96(26):10496-10505.
- [6] Ruihan Dong, Rongrong Liu, Ziyu Liu, Yangang Liu, Gaomei Zhao, Honglei Li, Shiyuan Hou, Xiaohan Ma, Huarui Kang, Jing Liu, Fei Guo, Ping Zhao, Junping Wang, Cheng Wang*, Xingan Wu*, Sheng Ye*, Cheng Zhu*, "Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning", eLife, 2024, https://doi.org/10.7554/eLife.97330.1
- [7] Chen Zhang, Fang Tong, Bin Zhou, Mingdong He, Shuai Liu, Xiaomeng Zhou, Qiang Ma, Tianyu Feng, Wan-Jie Du, Huan Yang, Hao Xu, Lei Xiao, Zhen-Zhong Xu, Cheng Zhu, Ruiqi Wu*, Yan-Qing Wang*, Qingjian Han*, "TMC6 Functions as a GPCR-like Receptor to Sense Noxious Heat Via Gαq Signaling", Cell Discovery, 2024, 10(1): 66
- [8] Xiaoning Gao, WuYan Guo, Peiyuan Liu, Mingyue Yuwen, Zixiang Liu, Ruyang Tan, Kairui Liu, Zhiru Yang, Junli Ba, Xue Bai, Shiti Shama, Cong Tang, Kai Miao, Haozhi Pei, Liren Liu, Cheng Zhu*, Tao Wang*, Bo Zhang*, Jun Kang* "Capsaicin acts as a novel NRF2 agonist to suppress ethanol induced gastric mucosa oxidative damage by directly disrupting the KEAP1-NRF2 interaction", eLife, 2024, https://doi.org/10.7554/eLife.97632.1
- [9] Yuqiong Xia, Keyun Wu, Chang Liu, Xuejuan Zhao, Jun Wang, Jianxia Cao, Zhaoxu Chen, Minchao Fang, Jie Yu, Cheng Zhu, Xianghan Zhang*, Zhongliang Wang* “Filamentous-Actin-Mimicking Nanoplatform for Enhanced Cytosolic Protein Delivery” Advanced Science, 2024 11(10):e2305600
- [10] Rongrong Liu, Yunhua Lv, Wenjie Sun, Min Li, Ningning Ge, Cheng Zhu, Yaxin Ding, Ziyu Liu, Ruixue Ma, Yuxiao Huang, Shiyuan Hou, Qikang Ying, Tianle Gu, Fang Wang, Lingling Nie, Youchun Wang, Weijin Huang*, Jiayi Shu*, Xingan Wu* “Investigation of a subunit protein vaccine for HFRS based on a consensus sequence between envelope glycoproteins of HTNV and SEOV” Virus Research, 2023, 334:199149
- [11] Jun Kang, Mengqian Huang, Jinyu Li, Keke Zhang, Cheng Zhu, Sihua Liu, Zhenwei Zhou, Tao Wang*, Zhiyun Wang* "Enterovirus D68 VP3 Targets the Interferon Regulatory Factor 7 To Inhibit Type I Interferon Response" Microbiology Spectrum, 2023, 11(3): e0413822
- [12] Xun Sun, Jing Yu, Cheng Zhu, Xinreng Mo, Qiangqiang Sun, Dandan Yang, Chang Su*, Yang Lu* "Recognition of galactose by a scaffold protein recruits a transcriptional activator for the GAL regulon induction in Candida albicans" eLife, 2023, 12: e84155
- [13] Yanyan Wu, Qian Wang, Pingan Zhang, Cheng Zhu, Guangyin Xu* "miR-1306-3p directly activates P2X3 receptors in primary sensory neurons to induce visceral pain in rats" PAIN, 2023, 164(7):1555-1565
- [14] Zhuozhi Chen, Rongdi Duan, Yunjie Xiao, Yi Wei, Hanxiao Zhang, Xinzhao Sun, Shen Wang, Yingying Cheng, Xue Wang, Shanwei Tong, Yunxiao Yao, Cheng Zhu, Haitao Yang, Yanyan Wang*, Zefang Wang* "Biodegradation of highly crystallized poly(ethylene terephthalate) through cell surface codisplay of bacterial PETase and hydrophobin" Nature Communications, 2022, 13(1):7138
- [15] Mao Zhang, Cheng Zhu, Yuanyuan Duan, Tongbao Liu, Haoping Liu, Chang Su*, Yang Lu* "The intrinsically disordered region from PP2C phosphatases functions as a conserved CO2 sensor" Nature Cell Biology, 2022, 24(7): 1029–1037
- [16] Rongrong Liu, Ziyu Liu, Haoran Peng, Yunhua Lv, Yunan Feng, Junjun Kang, Naining Lu, Ruixue Ma, Shiyuan Hou, Wenjie Sun, Qikang Ying, Fang Wang, Qikang Gao, Ping Zhao, Cheng Zhu*, Yixing Wang*, Xingan Wu* "Bomidin: An Optimized Antimicrobial Peptide With Broad Antiviral Activity Against Enveloped Viruses" Frontiers in immunology 2022, 13: 851642
- [17] Yaxin Wang, Binghong Xu, Sen Ma, Hao Wang, Luqing Shang, Cheng Zhu*, Sheng Ye*, "Discovery of SARS-CoV-2 3CLPro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions", Int J Mol Sci. 2022, 23(4):2392
- [18] Binghong Xu, Meijun Liu, Sen Ma, Yuying Ma, Si Liu, Luqing Shang, Cheng Zhu*, Sheng Ye*, Yaxin Wang*, "4-Iminooxazolidin-2-One as a Bioisostere of Cyanohydrin Suppresses EV71 Proliferation by Targeting 3C pro" Microbiology Spectrum 2021: e0102521
- [19] C. Zhu, X. Zhou, Z. Liu, H. Chen, H. Wu, X. Yang, X. Zhu, J. Ma*, H. Dong* “The morphology of hydroxyapatite nanoparticles regulates cargo recognition in clathrin-mediated endocytosis” Frontiers in Molecular Bioscience 2021 8:627015
- [20] J.Y Cheng, S. Gao, C. Zhu, S.H. Liu, J.Y. Li, J. Kang, Z. Wang, T. Wang* "Typical Stress Granule Proteins Interact with the 3' Untranslated Region of Enterovirus D68 To Inhibit Viral Replication" Journal of Virology 2020, 94, e02041-19
- [21] C. Zhu, E. Dukhovlinova, O. Council, L.H. Ping, E.M. Fasion, G.W. Yin, E.L. Potter, L. Kincer, S.L. Campbell, S.R. Benhabbour, H.M. Ke, R. Swanstrom, N.V. Dokholyan, " Rationally Designed Carbohydrate-Occluded Epitopes Elicit HIV-1 Env-Specific Antibodies" Nature Communications 2019, 10, 948
- [22] X. Li, M. Deng, A. Petrucelli, C. Zhu, J.Y. Mo, L. Zhang, J.W. Tam, P. Ariel, B.Y. Zhao, S. Zhang, H.M. Ke, N.V. Dokholyan, J.A. Duncan, J.P.Y. Ting, "Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon" Immunity 2019, 50, 591-599
- [23] C. Zhu, Q. Han, A. Samoshkin, M. Convertino, A. Linton, E.M. Fasion, R. Ji, L. Diatchenko and N.V. Dokholyan*, "Stabilization of mu-opioid receptor facilitates its cellular translocation and signaling", Proteins 2019, 87, 878-884
- [24] C. Zhu, M.V. Beck, J.D. Griffith, M. Deshmukh, N.V. Dokholyan, "Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis" Proc. Natl. Acad. Sci. USA 2018, 115, 4661-4665
- [25] F.M. James, C. Zhu, E. Proctor, Y. Z. Tao, W.J. Cui, H.M. Ke, N.V. Dokholyan, "A Phosphomimetic Mutation Stabilizes Cu, Zn Superoxide Dismutase and Rescues Cell Viability in the Context of an ALS-associated Mutation" Structure 2016, 24, 1898-1906
- [26] C. Zhu, C.S. Zhang, T. Zhang, X.L. Zhang, L.H. Lai, "Rational Design of TNFα Binding Proteins Based on the De Novo Designed Protein DS119" Protein Sci. 2016, 25, 2066-2075
- [27] C. Zhu, Z.W. Dai, H.H. Liang, T. Zhang, F. Gai, L.H. Lai, "Slow and bimolecular folding of a de novo designed monomeric protein DS119" Biophys. J. 2013, 105, 2141-2148
- [28] C. Zhu, C.S. Zhang, H.H. Liang, L.H. Lai, "Engineering a zinc binding site into the de novo designed protein DS119 with a beta-alpha-beta structure" Protein & Cell 2011, 2, 1006-1013