HR job title
- Associate Professor
- Contact Info
- 1 979 458 9882
- Websites
- ORCiD
- 0000-0002-7912-0819
Zhang, Junjie Associate Professor
Positions
- Associate Professor, Biochemistry and Biophysics, College of Agriculture and Life Sciences
The living cell contains a collection of molecular machines to grow and function. These machines include the ribosomes, the chaperons, the proteasomes and other enzymes. Malfunction of these machines, if occurred in human, are related to many diseases. Understanding their three-dimensional (3D) structures is essential to understand how these machines work in the cell and eventually to treat those related diseases.
Here we use an experimental technique called cryo-electron microscopy (cryo-EM) to image these cellular machines in their native environment at liquid nitrogen temperatures. We then use image processing and graphics techniques to visualize their 3D structures, answering the questions such as how they assemble and how they interact with each other.
In addition, we develop computational modeling tools to interpret and animate these obtained 3D structures to further describe their movements and dynamics.
Here we use an experimental technique called cryo-electron microscopy (cryo-EM) to image these cellular machines in their native environment at liquid nitrogen temperatures. We then use image processing and graphics techniques to visualize their 3D structures, answering the questions such as how they assemble and how they interact with each other.
In addition, we develop computational modeling tools to interpret and animate these obtained 3D structures to further describe their movements and dynamics.
- Overview
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- Research
- Teaching
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Overview
Publications
selected publications
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academic article
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Wang, Y., Theodore, M., Xing, Z., Narsaria, U., Yu, Z., Zeng, L., & Zhang, J.
(2024).
Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus. Science Advances.
10(18), eadl4450.
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Thongchol, J., Yu, Z., Harb, L., Lin, Y., Koch, M., Theodore, M., ... Zeng, L.
(2024).
Removal of Pseudomonas type IV pili by a small RNA virus. Science.
384(6691), eadl0635.
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Meng, R., Xing, Z., Chang, J., Yu, Z., Thongchol, J., Xiao, W., ... Zhang, J.
(2024).
Structural basis of Acinetobacter type IV pili targeting by an RNA virus. Nature Communications.
15(1), 2746.
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Zeng, Y. u., Jiang, M., Robinson, S., Peng, Z., Chonira, V., Simeon, R., ... Chen, Z.
(2022).
A Multi-Specific DARPin Potently Neutralizes Shiga Toxin 2 via Simultaneous Modulation of Both Toxin Subunits. Bioengineering.
9(10), 511-511.
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Cui, Z., Li, X., Shin, J., Gamper, H., Hou, Y., Sacchettini, J. C., & Zhang, J.
(2022).
Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis. Nature Communications.
13(1), 432.
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Chang, J., Gorzelnik, K. V., Thongchol, J., & Zhang, J.
(2022).
Structural Assembly of Q Virion and Its Diverse Forms of Virus-like Particles. Viruses.
14(2), 225-225.
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Jiang, M., Shin, J., Simeon, R., Chang, J., Meng, R., Wang, Y., ... Zhang, J.
(2022).
Structural dynamics of receptor recognition and pH-induced dissociation of full-length Clostridioides difficile Toxin B. PLOS Biology.
20(3), e3001589-e3001589.
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Shen, L., Su, Z., Yang, K., Wu, C., Becker, T., Bell-Pedersen, D., Zhang, J., & Sachs, M. S.
(2021).
Structure of the translating Neurospora ribosome arrested by cycloheximide. Proceedings of the National Academy of Sciences of the United States of America.
118(48), e2111862118.
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Gorzelnik, K. V., & Zhang, J.
(2021).
Cryo-EM reveals infection steps of single-stranded RNA bacteriophages. Progress in Biophysics and Molecular Biology.
160, 79-86.
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Dou, T., Li, Z., Zhang, J., Evilevitch, A., & Kurouski, D.
(2020).
Nanoscale Structural Characterization of Individual Viral Particles Using Atomic Force Microscopy Infrared Spectroscopy (AFM-IR) and Tip-Enhanced Raman Spectroscopy (TERS). Analytical Chemistry.
92(16), 11297-11304.
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Chang, J., Cui, Z., Yang, K., Huang, J., Minary, P., & Zhang, J.
(2020).
Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities. RNA.
26(12), 1755-1766.
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Brock, D. J., Kondow-McConaghy, H., Allen, J., Brkljaa, Z., Kustigian, L., Jiang, M., ... Pellois, J.
(2020).
Mechanism of Cell Penetration by Permeabilization of Late Endosomes: Interplay between a Multivalent TAT Peptide and Bis(monoacylglycero)phosphate. Cell Chemical Biology.
27(10), 1296-1307.e5.
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Krieger, I. V., Kuznetsov, V., Chang, J., Zhang, J., Moussa, S. H., Young, R. F., & Sacchettini, J. C.
(2020).
The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition. Journal of Molecular Biology.
432(16), 4623-4636.
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Peng, Z., Simeon, R., Mitchell, S. B., Zhang, J., Feng, H., & Chen, Z.
(2019).
Designed Ankyrin Repeat Protein (DARPin) Neutralizers of TcdB from Clostridium difficile Ribotype 027. Clinical and Vaccine Immunology.
4(5), e00596-e00519.
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Wang, B. o., Zhang, J., & Wu, Y.
(2019).
A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2. Journal of Chemical Information and Modeling.
59(9), 3899-3909.
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Meng, R., Jiang, M., Cui, Z., Chang, J., Yang, K., Jakana, J., ... Zhang, J.
(2019).
Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nature Communications.
10(1), 3130.
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Simeon, R., Jiang, M., Chamoun-Emanuelli, A. M., Yu, H., Zhang, Y., Meng, R., ... Chen, Z.
(2019).
Selection and characterization of ultrahigh potency designed ankyrin repeat protein inhibitors of C. difficile toxin B. PLOS Biology.
17(6), e3000311-e3000311.
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Brock, D. J., Kustigian, L., Jiang, M., Graham, K., Wang, T., Erazo-Oliveras, A., ... Pellois, J.
(2018).
Efficient cell delivery mediated by lipid-specific endosomal escape of supercharged branched peptides. Traffic.
19(6), 421-435.
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Cui, Z., Gorzelnik, K. V., Chang, J., Langlais, C., Jakana, J., Young, R. y., & Zhang, J.
(2017).
Structures of Q virions, virus-like particles, and the Q-MurA complex reveal internal coat proteins and the mechanism of host lysis. Proceedings of the National Academy of Sciences of the United States of America.
114(44), 11697-11702.
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Yang, K., Chang, J., Cui, Z., Li, X., Meng, R., Duan, L., ... Zhang, J.
(2017).
Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis. Nucleic Acids Research (NAR).
45(18), 10884-10894.
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Weaver, J., Jiang, M., Roth, A., Puchalla, J., Zhang, J., & Rye, H. S.
(2017).
GroEL actively stimulates folding of the endogenous substrate protein PepQ. Nature Communications.
8(1), 15934.
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Yang, S., Jiang, M., Grabowska, M. M., Li, J., Connelly, Z. M., Zhang, J., ... Yu, X.
(2016).
Androgen receptor differentially regulates the proliferation of prostatic epithelial cells in vitro and in vivo. Oncotarget.
7(43), 70404-70419.
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Gorzelnik, K. V., Cui, Z., Reed, C. A., Jakana, J., Young, R. y., & Zhang, J.
(2016).
Asymmetric cryo-EM structure of the canonical Allolevivirus Q reveals a single maturation protein and the genomic ssRNA in situ. Proceedings of the National Academy of Sciences of the United States of America.
113(41), 11519-11524.
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Lee, J. R., Xie, X., Yang, K., Zhang, J., Lee, S. Y., & Shippen, D. E.
(2016).
Dynamic Interactions of Arabidopsis TEN1: Stabilizing Telomeres in Response to Heat Stress. The Plant Cell.
28(9), 2212-2224.
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Yang, K., Ren, Z., Raushel, F. M., & Zhang, J.
(2016).
Structures of the Carbon-Phosphorus Lyase Complex Reveal the Binding Mode of the NBD-like PhnK. Structure.
24(1), 37-42.
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Li, X., Sun, Q., Jiang, C., Yang, K., Hung, L., Zhang, J., & Sacchettini, J. C.
(2015).
Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome. Structure.
23(12), 2387-2387.
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Li, X., Sun, Q., Jiang, C., Yang, K., Hung, L., Zhang, J., & Sacchettini, J. C.
(2015).
Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome. Folding & design.
23(10), 1858-1865.
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DiMaio, F., Zhang, J., Chiu, W., & Baker, D.
(2013).
Cryo-EM model validation using independent map reconstructions. Protein Science.
22(6), 865-868.
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Zhang, Q., Dai, X., Cong, Y., Zhang, J., Chen, D., Dougherty, M. T., ... Chiu, W.
(2013).
Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism. Structure.
21(4), 604-613.
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Zhang, J., Minary, P., & Levitt, M.
(2012).
Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images. Proceedings of the National Academy of Sciences of the United States of America.
109(25), 9845-9850.
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Zhang, J., Ma, B., DiMaio, F., Douglas, N. R., Joachimiak, L. A., Baker, D., ... Chiu, W.
(2011).
Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure.
19(5), 633-639.
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Douglas, N. R., Reissmann, S., Zhang, J., Chen, B. o., Jakana, J., Kumar, R., Chiu, W., & Frydman, J.
(2011).
Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber. Cell.
144(2), 240-252.
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Knee, K. M., Goulet, D. R., Zhang, J., Chen, B. o., Chiu, W., & King, J. A.
(2011).
The group II chaperonin Mm-Cpn binds and refolds human D crystallin. Protein Science.
20(1), 30-41.
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Nakamura, N., Shimizu, Y., Shinkawa, T., Nakata, M., Bammes, B., Zhang, J., & Chiu, W.
(2010).
Automated specimen search in cryo-TEM observation with DIFF-defocus imaging. Journal of Electron Microscopy.
59(4), 299-310.
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Baker, M. L., Zhang, J., Ludtke, S. J., & Chiu, W.
(2010).
Cryo-EM of macromolecular assemblies at near-atomic resolution. Nature Protocols.
5(10), 1697-1708.
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Zhang, J., Baker, M. L., Schrder, G. F., Douglas, N. R., Reissmann, S., Jakana, J., ... Chiu, W.
(2010).
Mechanism of folding chamber closure in a group II chaperonin. Nature.
463(7279), 379-383.
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Pintilie, G. D., Zhang, J., Goddard, T. D., Chiu, W., & Gossard, D. C.
(2010).
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Journal of Structural Biology.
170(3), 427-438.
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Zhang, J., Nakamura, N., Shimizu, Y., Liang, N., Liu, X., Jakana, J., ... Chiu, W.
(2009).
JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. Journal of Structural Biology.
165(1), 1-9.
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Chen, D., Luke, K., Zhang, J., Chiu, W., & Wittung-Stafshede, P.
(2008).
Location and flexibility of the unique C-terminal tail of Aquifex aeolicus co-chaperonin protein 10 as derived by cryo-electron microscopy and biophysical techniques. Journal of Molecular Biology.
381(3), 707-717.
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Thongchol, J., Lill, Z., Hoover, Z., & Zhang, J.
Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages. Viruses.
15(10), 1985-1985.
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Wang, Y., Theodore, M., Xing, Z., Narsaria, U., Yu, Z., Zeng, L., & Zhang, J.
(2024).
Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus. Science Advances.
10(18), eadl4450.
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chapter
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Thongchol, J., & Zhang, J.
(2024).
Purification of Single-Stranded RNA Bacteriophages and Host Receptors for Structural Determination Using Cryo-Electron Microscopy. Methods in molecular biology (Clifton, N.J.).
Phage Engineering and Analysis.
(pp. 185-204).
Springer Nature.
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Zhang, J., Gorzelnik, K. V., Schmid, M. F., & Chiu, W.
(2016).
Single-Particle CryoEM of Macromolecular Complexes. Encyclopedia of Cell Biology.
(pp. 5-13).
Elsevier.
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Thongchol, J., & Zhang, J.
(2024).
Purification of Single-Stranded RNA Bacteriophages and Host Receptors for Structural Determination Using Cryo-Electron Microscopy. Methods in molecular biology (Clifton, N.J.).
Phage Engineering and Analysis.
(pp. 185-204).
Springer Nature.
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conference paper
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Pintilie, G., Zhang, J., Chiu, W., & Gossard, D.
(2009).
Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation. 44-47.
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Pintilie, G., Zhang, J., Chiu, W., & Gossard, D.
(2009).
Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation. 44-47.
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institutional repository document
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Brock, D. J., Kondow-McConaghy, H., Allen, J., Brkljaa, Z., Kustigian, L., Jiang, M., ... Pellois, J.
(2020).
Mechanism of Cell Penetration by Permeabilization of Late Endosomes: Interplay between a Multivalent TAT-Like Cell-Penetrating Peptide and the Lipid Bis(Monoacylglycerol)Phosphate
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Brock, D. J., Kondow-McConaghy, H., Allen, J., Brkljaa, Z., Kustigian, L., Jiang, M., ... Pellois, J.
(2020).
Mechanism of Cell Penetration by Permeabilization of Late Endosomes: Interplay between a Multivalent TAT-Like Cell-Penetrating Peptide and the Lipid Bis(Monoacylglycerol)Phosphate
Research
principal investigator on
- Molecular Mechanism for Genomic RNA Delivery in ssRNA Phages awarded by National Science Foundation - (Arlington, Virginia, United States) 2019 - 2022
- Characterize Essential Regions in C. Difficile Toxin B for its Neutralization awarded by National Institutes of Health - (Bethesda, Maryland, United States) 2018 - 2020
co-principal investigator on
- The Molecular Basis of Viral DNA Sensing through the cGAS-STING Pathway awarded by National Institutes of Health - (Bethesda, Maryland, United States) 2019 - 2024
- Reducing Virulence Through the Suppression of Retractile Pili awarded by National Institute of Allergy and Infectious Diseases - (Bethesda, Maryland, United States) 2020 - 2022
investigator on
Teaching
teaching activities
- BICH101 Perspectives In Bich And Gene Instructor
- BICH303 Elements Of Biol Chem Instructor
- BICH404 Biochemical Calculations Instructor
- BICH491 Hnr-research Instructor
- BICH603 Prin Biochemistry & Biophysics Instructor
- BICH685 Directed Studies Instructor
- BICH689 Sptp: Cryo Em Instructor
- BICH689 Sptp: Cryo-em Instructor
- BICH689 Sptp:cryo-em Instructor
- BICH691 Research Instructor
- GENE101 Perspectives In Bich And Gene Instructor
- GENE491 Hnr-research Instructor
Background
education and training
- Ph.D. in Structural Biology, Baylor College of Medicine - (Houston, Texas, United States) 2009
- B.S. in Physics, Fudan University - (Shanghai, Shanghai, China) 2004
- Stanford University - (Stanford, California, United States) , Postdoctoral Training 2013
Contact
first name
- Junjie
has last name
- Zhang
mailing address
-
Texas A&M University
Biochemistry & Biophysics
3474 TAMU
College Station, TX 77843-3474
USA
Other
In the News
- junjiez@tamu.edu