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Ping Zhu, Ph.D, Prof.

Principal Investigator
National Laboratory of Biomacromolecules, IBP

Research Interests: Cryo-electron microscopy (cryo-EM); Chromatin and virus structures

Email: zhup@ibp.ac.cn

Tel: 010-64888799 (office), 010-64888813 (lab)

Address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

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1986.09 - 1990.06  B.S., Zhejiang Univ., Hangzhou, China

1990.09 - 1993.06  M.S., Xi’an Jiaotong Univ., Xi’an, China

1993.09 - 1997.06  Ph.D., Tsinghua Univ., Beijing, China

1997.07 - 1998.12  Lecturer, Tsinghua Univ., Beijing, China

1999.03 - 2008.05  Postdoctoral Research Associate; Assist. in Research (NTTF) ; Associate Scholar/Scientist (NTTF); Florida State Univ., Tallahassee, Florida, USA

2008.06 -                Principal Investigator, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

Membership in Academies & Societies
Research Interests

Rapidly developed in the past years, cryo-electron microscopy (cryo-EM) technology provides a unique way to study the 3D structure of macrobiomolecules in their native status. Our lab is interested in the 3D reconstruction and structural analysis of virus, chromatin and other biomacromolecules and their complexes, primarily utilizing cryo electron microscopy (cryo-EM) and electron tomography (ET) technologies.

The main research interests in the laboratory are:

1. Cryo-electron microscopy

We are interested in the structural study of functional important biomacromolecules and complexes, the in-situ structures of molecular machines, and the visualization of significant biological processes. We are also interested in the methodology involved in the cryo-EM 3D reconstruction process.

2. Chromatin structure and epigenetic regulation

We are interested in the higher-order structure of chromatin (including in vitro and in vivo), and how different epigenetic factors, e.g. histone variant, histone modification, chromatin remodeler, etc, may affect and regulate the structure of nucleosome and chromatin fibers.

3. The assembly, infection and replication of viruses

We are interested in the structures of viruses at different states, trying to reveal the molecular mechanisms of viral assembly, infection and replication. We are also interested in the structural characterizations of vaccine candidates, aiming to help the drug and vaccine designs against these pathogens.

Selected Publications

1. Li J#, Zhang HN#, Li D, Liu YJ, Bayer EA, Cui Q, Feng Y*, Zhu P*. (2023) Structure of the transcription open complex of distinct σI factors. Nat. Comm., 14: 6455 (*corresponding author)

2. Li Y#, Zhang HN#, Li X#, Wu W, Zhu P*. (2023) Cryo-ET study from in vitro to in vivo revealed a general folding mode of chromatin with two-start helical architecture. Cell Rep., 42:113134 (*corresponding author)

3. Huang L#, Wang Y#, Long H#*, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P*, Li G*, Zhou Z*. (2023) Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1. Mol. Cell, 83(16):2884-95 (*corresponding author, cover)

4. Zhang HN#, Li Y#, Liu Y, Li D, Wang L, Song K, Bao K, Zhu P*. (2023) A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST. Nat. Comm.,14:2937 (* corresponding author)

5. Zhang H#, Li H#, Zhang F*, Zhu P*. (2023) A strategy combining denoising and cryo-EM single particle analysis. Brief. Bioinform., 24(3):bbad148 (* corresponding author)

6. Bao K#, Zhang X#, Li D#, Sun W, Sun Z, Wang J*, Zhu P*. (2022) In situ structures of polymerase complex of mammalian reovirus illuminate RdRp activation and transcription regulation. Proc. Natl. Acad. Sci. USA, 119(50):e2203054119 (* corresponding author)

7. Li D#, Zhang X#, Wang Y#, Zhang H, Song K, Bao K, Zhu P*. (2022) A new polymorphism of human amylin fibrils with similar protofilaments and a conserved core. iScience, 25(12):105705 (* corresponding author)

8. Huang X#, Wang Y#, Yu C#, Zhang H#, Ru Q#, Li X, Song K, Zhou M, Zhu P*. (2022) Cryo-EM structures reveal the dynamic transformation of human alpha-2-macroglobulin working as a protease inhibitor. SCI. CHINA Life Sci., 65(12):2491–2504 (*corresponding author)

9. Li H#, Zhang H#, Wan X, Yang Z, Li C, Li J, Han R*, Zhu P*, Zhang F*. (2022) Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer. Bioinformatics, 38(7), 2022–29 (*corresponding author)

10. Bao K#, Qi X#, Li Y, Gong M, Wang X*, Zhu P*. (2022) Cryo-EM structures of infectious bursal disease virus with different virulence provide insights on their assembly and invasion. Science Bull., 67(6):646-54 (*corresponding author)

11. Zhu X, Zhang X*, Zhu P*. (2022) Study on the influences of different metal ions on the formation of human islet amyloid polypeptide fibrils. J. Chin. Elec. Micro. Soc., 41(3):265-71 (*corresponding author, in Chinese)

12. Zhou M#, Dai L#, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P*, Zhou Z*. (2021) Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2. EMBO J., 40(1):e105907 (*corresponding author)

13. Zhang X, Li D, Zhu X, Wang Y, Zhu P*. (2020) Structural characterization and cryo-electron tomography analysis of human islet amyloid polypeptide suggest a synchronous process of the hIAPP1-37 amyloid fibrillation. Biochem. Biophys. Res. Comm., 533(1):125-131(*corresponding author)

14. Guan H#, Wang Y#, Perculija V, Saeed AF, Liu Y, Li J, Jan SS, Li Y, Zhu P*, Ouyang S*. (2020) Cryo-electron microscopy structure of the SADS-CoV spike glycoprotein provides insights into an evolution of unique coronavirus spike proteins. J. Virol., 94(22):e01301-20. (*corresponding author)

15. Yang W#, Wang Y#, Guo J#, He L, Zhou Y, Zheng H, Liu Z, Zhu P*, Zhang XC*. (2020) Cryo‐electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans. Protein Sci., 29(8):1803-15 (*corresponding author)

16. Guan H#, Wang Y#, Yu T#, Huang Y#, Li M, Saeed AF, Perculija V, Li D, Xiao J, Wang D, Zhu P*, Ouyang S*. (2020) Cryo-EM structures of the human PA200 and PA200-20S complex reveal regulation of proteasome gate opening and two PA200 apertures. PLoS Biol., 18(3): e3000654 (*corresponding author)

17. Cao J#, Zhang J#, Lu Y, Luo S*, Zhang J*, Zhu P*. (2019) Cryo-EM structure of native spherical subviral particles isolated from HBV carriers. Virus Res., 259:90-96 (*corresponding author)

18. Wang H#, Guo Z#, Feng H, Chen Y, Chen X, Li Z, Hernández-Ascencio W, Dai X, Zhang Z, Zheng X, Mora-López M, FU Y, Zhang C, Zhu P*, Huang L*. (2018) Novel Sulfolobus virus with an exceptional capsid architecture. J. Virol., 92(5): e01727-17 (*corresponding author)

19. Zhu P*, Li G*. (2016) Higher-order structure of the 30-nm chromatin fiber revealed by cryo-EM. IUBMB Life. 68(11):873-78 (*corresponding author, invited review, cover)

20. Xu P#, Li C#, Chen Z, Jiang S, Fan S, Wang J, Dai J, Zhu P*, Chen Z*. (2016) The NuA4 core complex acetylates nucleosomal histone H4 through a double recognition mechanism, Mol. Cell, 63(6):965–75 (*corresponding author)

21. Zhu P*, Li G*. (2016) Structural insights of nucleosome and the 30-nm chromatin fiber. Curr. Opin.Struc. Biol., 36:106-15 (*corresponding author, invited review)

22. Zhu HT, Zhu P*. (2015) No longer ‘blob-ology’: Cryo-EM is getting into molecular details. SCI. China Life Sci, 58(11): 1154-6 (*corresponding author, insight)

23. Li C#, Zhou M#, Li X, Zhu P*. (2015) Application of cryo-electron microscopy on epigenetic studies. Prog. in Biochem. & Biophys., 42(11):1063-72 (*corresponding author, in Chinese, invited review)

24. Li X#, Feng H#, Zhang J, Sun L, Zhu P*. (2015) Analysis of Chromatin Fiber in Hela Cell with Electron Tomography. Biophys. Report, 1(1): 51-60 (*corresponding author, cover story)

25. Li Z, Qi X, Ren X, Cui L, Wang X*, Zhu P*. (2015) Molecular characteristics and evolutionary analysis of a very virulent infectious bursal disease virus. SCI. China Life Sci., 58(8): 731-38 (*corresponding author, cover story)

26. Li G*, Zhu P*. (2015) Structure and organization of chromatin fiber in the nucleus. FEBS Lett., 589(20):2893-2904 (*corresponding author, invited review)

27. Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P*, Shao F*. (2014) A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. elife, 3:e03714 (*corresponding author)

28. Gong M#, Zhu H#, Zhou J, Yang C, Feng J, Huang X, Ji G, Xu H*, Zhu P*. (2014) Cryo-EM study of insect cell-expressed Enterovirus 71 and Coxsackievirus A16 virus-like particles provides a structural basis for vaccine development. J. Virol., 88(11):6444-52 (*corresponding author)

29. Chen P, Zhu P*, Li G*. (2014) New insights into the helical structure of 30-nm chromatin fibers. Protein & Cell, 5(7):489-91 (*corresponding author)

30. Song F#, Chen P#, Sun D, Wang M, Dong L, Liang D, Xu RM, Zhu P*, Li G*. (2014) Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science, 344 (6182): 376-80 (*corresponding author, Research Article)

31. Cheng L#, Huang X#, Li X, Xiong W, Sun W, Yang C, Zhang K, Wang Y, Liu H, Huang X, Ji G, Sun F, Zheng C*, Zhu P*. (2014) Cryo-EM structures of two bovine adenovirus type 3 intermediates. Virology, 450-451:174-81 (*corresponding author)

32. Zhu H#, Zhuang J#, Feng H, Liang R, Wang J, Xie L*, Zhu P*. (2014) Cryo-EM structure of isomeric molluscan hemocyanin triggered by viral infection. PLoS One, 9(6): e98766 (*corresponding author)

33. Liu J, Zhu H, Feng H, Gong M, Zhu P*. (2014) Architecture of Human HDAC1/2-RbAp46/48 Core Protein Complex Revealed by Electron Microscopy. Prog. in Biochem. & Biophys., 2014, 41(6): 591-97 (*corresponding author, in Chinese)

34. Sun D, Song F, Huang L, Zhang K, Ji G, Chen P*, Zhu P*. (2013) In vitro Assembly and Electron Microscopic Analysis of 30 nm Chromatin Fibers. Prog. in Biochem. & Biophys., 2013, 40(7): 739-47 (*corresponding author, in Chinese, cover story)

35. Yang C, Ji G, Liu H, Zhang K, Liu G, Sun F, Zhu P*, Cheng L*. (2012) Cryo-EM Structure of a transcribing cypovirus. Proc. Natl. Acad. Sci. USA, 109(16):6118-23 (*corresponding author)

36. Cheng L#, Sun J#, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J*, Zhu P*. (2011) Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. Proc. Natl. Acad. Sci. USA, 108(4):1373–78 (* corresponding author)

37. Huang X, Song X, Zhu P*. (2010) Cryo Electron Tomography and Its Application to Biological Research. Acta Biophysica Sinica, 26 (7): 570-578 (*corresponding author, invited review, in Chinese)

38. Zhu P, Winkler H, Chertova E, Taylor K, Roux K*. (2008) Cryoelectron tomography of HIV-1 envelope spikes: further evidence for tripod-like legs. PLoS Pathog, 4(11): e1000203.

39. Zhu P, Liu J, Bess J., Chertova E, Lifson J, Grisé H, Ofek G, Taylor K, Roux K*. (2006) Distribution and Three-Dimensional Structure of AIDS Virus Envelope Spikes. Nature, 441:847-852 (Article)

40. Zhu P, Chertova E., Bess J, Lifson J, Arthur L, Liu J, Taylor KA, Roux KH*. (2003) Electron tomography analysis of envelope glycoprotein trimers on HIV and simian immunodeficiency virus virions. Proc. Natl. Acad. Sci. USA, 100(26):15812-15817

41. Zhu P, Olson WC, Roux KH*. (2001) Structural Flexibility and Function Valency of CD4-IgG2 (PRO 542): Potential for Crosslinking HIV-1 Envelope Spikes, J Virol., 75(14):6682-6686.


(From Ping Zhu, October 16, 2023)


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