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Jack Zhang, PhD

Assistant Professor of Molecular Biophysics and Biochemistry

Contact Information

Jack Zhang, PhD

Mailing Address

  • Molecular Biophysics and Biochemistry

    260 Whitney Avenue, Yale Science Building

    New Haven, CT 06511

    United States

Research Summary

We long to understand why living cells are alive. The dream is to make clear how lifeless biomolecules work together to give birth to the real life of living cells and eventually form a meaningful organism. We believe the secret lies in the fundamental fact that the Life is eternally dynamic, moving hither and thither in a pre-programmed, interactive and highly regulable way. This is true from individual molecules to a whole cell and from the cells to the whole human body. Motor proteins are the ultimate performers that convert chemical energy to the Life's dynamic movement.

Our lab focuses on the structural mechanisms of motor proteins and cryo-electron microscopy (cryo-EM) methods. The long-term aim is to elucidate the molecular mechanisms of motor-mediated high-level cellular activities from the very basic structural perspectives at atomic details. We are particularly interested in dyneins (and the related protein complexes) for their fascinating roles in intracellular/intraflagellar transport, cell division, organelle positioning, cell motility, neurodevelopment, neurodegeneration, viral infection and their elaborate mechanisms of regulation. In addition to dynein mechanisms and currently available techniques, we are also passionate about cryo-EM/ET methods development and interdisciplinary researches in depth in order to break the technical barriers to visualize atomic structures of large protein complexes as dynamic machinery both in vitro and in situ.

Coauthors

Research Interests

Biochemistry; Biophysics; Cilia; Cytoskeleton; Dyneins; Flagella; Image Processing, Computer-Assisted; Microscopy, Electron; Microscopy, Fluorescence; Microtubules; Molecular Biology; Nervous System Diseases; Protein Conformation; Signal Processing, Computer-Assisted; Tomography; Protein Structure, Tertiary; Cryoelectron Microscopy; Imaging, Three-Dimensional; Axoneme; Axonemal Dyneins; Machine Learning

Research Image

A brief view of cryo-EM flow chart

A brief view of cryo-EM flow chart

Selected Publications

  • Towards dynamic structure of biological complexes at atomic resolution by cryo-EMZhang K. "Towards dynamic structure of biological complexes at atomic resolution by cryo-EM." Chin. Phys. B 2018. 27(6): 66801-066801.
  • A brief introduction of cryo-EM revolution-the Nobel Prize in Chemistry 2017.Zhang K, Liu Z. A brief introduction of cryo-EM revolution-the Nobel Prize in Chemistry 2017. Science China. Life Sciences 2018, 61: 368-370. PMID: 29318502, DOI: 10.1007/s11427-017-9215-3.
  • Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.Zhang K, Foster HE, Rondelet A, Lacey SE, Bahi-Buisson N, Bird AW, Carter AP. Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Cell 2017, 169: 1303-1314.e18. PMID: 28602352, PMCID: PMC5473941, DOI: 10.1016/j.cell.2017.05.025.
  • Crystal structure of E. coli apolipoprotein N-acyl transferase.Lu G, Xu Y, Zhang K, Xiong Y, Li H, Cui L, Wang X, Lou J, Zhai Y, Sun F, Zhang XC. Crystal structure of E. coli apolipoprotein N-acyl transferase. Nature Communications 2017, 8: 15948. PMID: 28885614, PMCID: PMC5500890, DOI: 10.1038/ncomms15948.
  • FIRT: Filtered iterative reconstruction technique with information restoration.Chen Y, Zhang Y, Zhang K, Deng Y, Wang S, Zhang F, Sun F. FIRT: Filtered iterative reconstruction technique with information restoration. Journal Of Structural Biology 2016, 195: 49-61. PMID: 27134004, DOI: 10.1016/j.jsb.2016.04.015.
  • Gctf: Real-time CTF determination and correction.Zhang K. Gctf: Real-time CTF determination and correction. Journal Of Structural Biology 2016, 193: 1-12. PMID: 26592709, PMCID: PMC4711343, DOI: 10.1016/j.jsb.2015.11.003.
  • The structure of the dynactin complex and its interaction with dynein.Urnavicius L, Zhang K, Diamant AG, Motz C, Schlager MA, Yu M, Patel NA, Robinson CV, Carter AP. The structure of the dynactin complex and its interaction with dynein. Science (New York, N.Y.) 2015, 347: 1441-1446. PMID: 25814576, PMCID: PMC4413427, DOI: 10.1126/science.aaa4080.
  • Cryo-EM structures of two bovine adenovirus type 3 intermediates.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. Cryo-EM structures of two bovine adenovirus type 3 intermediates. Virology 2014, 450-451: 174-81. PMID: 24503080, DOI: 10.1016/j.virol.2013.12.012.
  • A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature.Pang X, Fan J, Zhang Y, Zhang K, Gao B, Ma J, Li J, Deng Y, Zhou Q, Egelman EH, Hsu VW, Sun F. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature. Developmental Cell 2014, 31: 73-86. PMID: 25284369, PMCID: PMC4198613, DOI: 10.1016/j.devcel.2014.08.020.
  • C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation.Qiu B, Zhang K, Wang S, Sun F. C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation. Biochemical And Biophysical Research Communications 2014, 446: 380-6. PMID: 24613384, DOI: 10.1016/j.bbrc.2014.02.125.
  • Identification of SERPINB1 as a physiological inhibitor of human granzyme H.Wang L, Li Q, Wu L, Liu S, Zhang Y, Yang X, Zhu P, Zhang H, Zhang K, Lou J, Liu P, Tong L, Sun F, Fan Z. Identification of SERPINB1 as a physiological inhibitor of human granzyme H. Journal Of Immunology (Baltimore, Md. : 1950) 2013, 190: 1319-30. PMID: 23269243, DOI: 10.4049/jimmunol.1202542.
  • Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker TS, Schulten K, Zheng D, Pang H, Sun F. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. PLoS Pathogens 2013, 9: e1003132. PMID: 23341770, PMCID: PMC3547835, DOI: 10.1371/journal.ppat.1003132.
  • Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain.Zhang Y, Wang W, Chen J, Zhang K, Gao F, Gao B, Zhang S, Dong M, Besenbacher F, Gong W, Zhang M, Sun F, Feng W. Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain. Structure (London, England : 1993) 2013, 21: 997-1006. PMID: 23643951, DOI: 10.1016/j.str.2013.04.004.
  • Flexible interwoven termini determine the thermal stability of thermosomes.Zhang K, Wang L, Liu Y, Chan KY, Pang X, Schulten K, Dong Z, Sun F. Flexible interwoven termini determine the thermal stability of thermosomes. Protein & Cell 2013, 4: 432-44. PMID: 23709365, PMCID: PMC3740188, DOI: 10.1007/s13238-013-3026-9.
  • Structure reveals regulatory mechanisms of a MaoC-like hydratase from Phytophthora capsici involved in biosynthesis of polyhydroxyalkanoates (PHAs).Wang H, Zhang K, Zhu J, Song W, Zhao L, Zhang X. Structure reveals regulatory mechanisms of a MaoC-like hydratase from Phytophthora capsici involved in biosynthesis of polyhydroxyalkanoates (PHAs). PloS One 2013, 8: e80024. PMID: 24244597, PMCID: PMC3823801, DOI: 10.1371/journal.pone.0080024.
  • Mechanistic insights into regulated cargo binding by ACAP1 protein.Bai M, Pang X, Lou J, Zhou Q, Zhang K, Ma J, Li J, Sun F, Hsu VW. Mechanistic insights into regulated cargo binding by ACAP1 protein. The Journal Of Biological Chemistry 2012, 287: 28675-85. PMID: 22645133, PMCID: PMC3436524, DOI: 10.1074/jbc.M112.378810.
  • Cryo-EM structure of a transcribing cypovirus.Yang C, Ji G, Liu H, Zhang K, Liu G, Sun F, Zhu P, Cheng L. Cryo-EM structure of a transcribing cypovirus. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 6118-23. PMID: 22492979, PMCID: PMC3341035, DOI: 10.1073/pnas.1200206109.
  • Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping.Cheng L, Sun J, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J, Zhu P. Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 1373-8. PMID: 21220303, PMCID: PMC3029759, DOI: 10.1073/pnas.1014995108.
  • Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography.Wan X, Zhang F, Chu Q, Zhang K, Sun F, Yuan B, Liu Z. Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography. Journal Of Structural Biology 2011, 175: 277-87. PMID: 21699984, DOI: 10.1016/j.jsb.2011.06.002.
  • Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the β-domain pore.Zhai Y, Zhang K, Huo Y, Zhu Y, Zhou Q, Lu J, Black I, Pang X, Roszak AW, Zhang X, Isaacs NW, Sun F. Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the β-domain pore. The Biochemical Journal 2011, 435: 577-87. PMID: 21306302, DOI: 10.1042/BJ20101548.
  • ATOM 1.0: A GPU Powered Package for Electron Tomography Reconstruction.Chu Q, Zhang K, Wan X, Zhang C, Zhang G, Shen B, Liu X, Zhao K, Chu X, Zhang F, Sun F. ATOM 1.0: A GPU Powered Package for Electron Tomography Reconstruction. Acta Biophys Sin 2011, 27:231-241.
  • Structural insights into the substrate specificity of human granzyme H: the functional roles of a novel RKR motif.Wang L, Zhang K, Wu L, Liu S, Zhang H, Zhou Q, Tong L, Sun F, Fan Z. Structural insights into the substrate specificity of human granzyme H: the functional roles of a novel RKR motif. Journal Of Immunology (Baltimore, Md. : 1950) 2012, 188: 765-73. PMID: 22156497, DOI: 10.4049/jimmunol.1101381.
  • Crystal structure of a novel esterase Rv0045c from Mycobacterium tuberculosis.Zheng X, Guo J, Xu L, Li H, Zhang D, Zhang K, Sun F, Wen T, Liu S, Pang H. Crystal structure of a novel esterase Rv0045c from Mycobacterium tuberculosis. PloS One 2011, 6: e20506. PMID: 21637775, PMCID: PMC3102732, DOI: 10.1371/journal.pone.0020506.
  • Substrate Binding Properties of Thermosome ATcpn-β from Acidianus TengchongensisWang L, Zhang K, Fan Z, Dong Z, and Sun F. Substrate Binding Properties of Thermosome ATcpnβ from Acidianus Tengchongensis. Progress in Biochemistry and Biophysics 2011, 38:151-158.
  • Cloning, Expression, Purification and Preliminary Crystallographic Analysis of Caenorhabditis elegans Enoyl-CoA Hydratase.Li Z, Zhang K, Zhai Y, Zhou Q, Geng Y, and Sun F. Cloning, Expression, Purification and Preliminary Crystallographic Analysis of Caenorhabditis elegans Enoyl-CoA Hydratase. Acta Biophys Sin 2010, 26:37-48.
  • Five mutations in N-terminus confer thermostability on mesophilic xylanase.Zhang S, Zhang K, Chen X, Chu X, Sun F, Dong Z. Five mutations in N-terminus confer thermostability on mesophilic xylanase. Biochemical And Biophysical Research Communications 2010, 395: 200-6. PMID: 20361933, DOI: 10.1016/j.bbrc.2010.03.159.
  • Crystal structure of group II chaperonin in the open state.Huo Y, Hu Z, Zhang K, Wang L, Zhai Y, Zhou Q, Lander G, Zhu J, He Y, Pang X, Xu W, Bartlam M, Dong Z, Sun F. Crystal structure of group II chaperonin in the open state. Structure (London, England : 1993) 2010, 18: 1270-9. PMID: 20947016, PMCID: PMC3048791, DOI: 10.1016/j.str.2010.07.009.
  • Development and Frontier of Electron Microscopy 3D Reconstruction.Zhang K, Zhang Y, Hu Z, Ji G, and Sun F. Development and Frontier of Electron Microscopy 3D Reconstruction. Acta Biophys Sin 2010, 26:533-559.
  • 3D Structural Investigation of Caveolae From Porcine Aorta Endothelial Cell by Electron Tomography.Sun S, Zhang K, Xu W, Wang G, Chen J, and Sun F. 3D Structural Investigation of Caveolae From Porcine Aorta Endothelial Cell by Electron Tomography. Progress in Biochemistry and Biophysics 2009, 36:729-735.
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