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Publications

The David Van Andel Advanced Cryo-Electron Microscopy Suite

Publications containing work performed by VARI’s Cryo-EM Suite are asked to follow these guidelines in their acknowledgements:

  • Acknowledge contributions by The David Van Andel Advanced Cryo-Electron Microscopy Suite by name in the manuscript.
  • Consider authorship for more significant intellectual and planning contributions.
  • Notify Suite staff of successful publications and awarded grant applications. This assists in tracking and maintaining institutional records, which help inform the Suite’s quality services.
HIGHLIGHTED PEER-REVIEWED PUBLICATIONS (Gongpu Zhao, Ph.D.)

Yang M, Chan H, Zhao G, Bahng JH, Zhang P, Kral P, Kotov NA. 2016. Self-assembly of nanoparticles into biomimetic capsid-like nanoshells. Nat Chem doi:10.1038/nchem.2641       Article

Liu C, Perilla JP, Ning J, Lu M, Hou G, Ramalho R, Himes BA, Zhao G, Bedwell GJ, Byeon IJ, Ann J, Gronenborn AM, Prevelige PE, Rousso I, Aiken C, Polenova T, Schulten K, Zhang P. 2016. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Nat Commun 7:10714.     PubMed        Article

Zhao G*, Perilla JR*, Yufenyuy EL*, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. 2013. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497:643.    Article
*Featured on Nature cover. This paper was selected as NIGMS Director’s Featured Research Advance in June 2013.

Yeom J, Yeom B, Chan H, Smith KW, Dominguez-Medina S, Bahng JH, Zhao G, Chang W, Chang SJ, Chuvilin A, Melnikau D, Rogach AL, Zhang P, Link S, Král P, Kotov NA 2015. Chiral templating of self-assembling nanostructures by circularly polarized light. Nat Mater 14:66–72.     Article

Meng X*, Zhao G*, Yufenyuy E*, Ke D, Ning J, DeLucia M, Ahn J, Gronenborn AM, Aiken C, Zhang P. 2012. Protease cleavage leads to formation of mature trimer interface in HIV-1 capsid. PLoS Pathog 8(8): e1002886.     Article
*Co-first author

Zhao G, Ke D, Vu T, Ahn J, Shah VB, Yang R, Aiken C, Charlton L, Gronenborn AM, Zhang P. 2011. Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces. PLoS Pathog 7(3): e1002009.     Article

Byeon IJL, Meng X, Jung J, Zhao G, Yang R, Shi J, Ahn J, Concel J, Aiken C, Zhang P, Gronenborn AM. 2009. Structural convergence between Cryo-EM and NMR reveals novel intersubunit interactions critical for HIV-1 capsid assembly and function. Cell 139:780.      PubMed

OTHER PEER-REVIEWED PUBLICATIONS

Ning J, Erdemci-Tandogan G, Yufenyuy EL, Wagner J, Himes BA, Zhao G, Aiken C, Zandi R, Zhang P. 2016. In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway. Nat Commun 7:13689.     Article

Merg AD, Boatz JC, Mandal A, Zhao G, Mokashi-Punekar S, Liu C, Wang X, Zhang P, van der Wel PCA, Rosi NL. 2016. Peptide-directed assembly of single-helical gold nanoparticle superstructures exhibiting intense chiroptical activity. J Am Chem Soc 138(41):13655.     Article

Cassidy C, Himes BA, Alvarez FJ, Ma J, Zhao G, Perilla JR, Schulten K, Zhang P. 2015. CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. eLife 10.7554/eLife.08419.      Article

Rezikyan A, Jibben ZJ, Rock BA, Zhao G, Koeck FA, Nemanich RF, Treacy MM. 2015. Speckle suppression by decoherence in fuctuation electron microscopy. Microsc Microanal 21(6)1455–1474.         PubMed

Park J, Nguyen TD, Silveira GQ, Bahng JH, Srivastava S, Zhao G, Sun K, Zhang P, Sharon C, Glotzer SC, Kotov NA. 2014. Terminal supraparticle assemblies from similarly charged protein molecules and nanoparticles. Nat Commun 5:3593.      Article

Song C, Blaber MG, Zhao G, Zhang P, Fry HC, Schatz GC, Rosi NL. 2013. Tailorable plasmonic circular dichroism properties of helical nanoparticle superstructures. Nano Lett 13(7)3256–3261.        Article

Jun S, Zhao G, Ning J, Zhang P. 2013. Correlative microscopy for 3D structural analysis of dynamic interactions. J Vis Exp (76):e50386.      Article

Yang H, Ji X, Zhao G, Ning J, Zhao Q, Aiken C, Gronenborn AM, Zhang P, Xiong Y. 2012. Structural insight into HIV-1 capsid recognition by rhesus TRIM5α. Proc Natl Acad Sci U S A 109(45):18372–18377.     Article

Wang K, Strunk K, Zhao G, Gray JL, Zhang P. 2012. 3D structure determination of native mammalian cells using cryo-FIB and cryo-electron tomography. J Struct Biol 180(2):318–326.      PubMed

Jun S, Ke D, Debiec K, Zhao G, Meng X, Ambrose Z, Gibson G, Watkins S, Zhang P. 2011. Direct visualization of HIV-1 infection using correlative live-cell microscopy and cryo-EM tomography. Structure 19(11):1573–1581.     PubMed

Meng X, Zhao G, Zhang P. 2011. Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction. JoVE 54:3041.     Article

Hwang L, Zhao G, Zhang P, Rosi N. 2011. Size-controlled peptide-directed synthesis of hollow spherical gold nanoparticle superstructures. Small 7: doi: 10.1002/smll.201100477.     Article

Song C, Zhao G, Zhang P, Rosi N. 2010. Expeditious synthesis and assembly of sub-100 nm hollow spherical gold nanoparticle superstructures. J Am Chem Soc 132(40):14033–14035.     Article

Zhao G, Treacy MMJ, Buseck PR. 2010. Fluctuation electron microscopy of medium range order in ion-irradiated zircon. Philosoph Mag 90, 4661–4677.     Article

Zhao G, Rougée A, Treacy MMJ, Buseck PR. 2009. Medium-range order in molecular materials: Fluctuation electron microscopy for detecting fullerenes in disordered carbons. Ultramicroscopy 109(2):177–188.      Article

Treacy MMJ, Kumar D, Rougée A, Zhao G, Buseck PR, McNulty I, Fan L, Rau C, Gibson JM. 2008. Glimpsing order within the disarray. J Phys Conf Ser 126(1).      Article

Treacy MMJ, Kumar D, Rougée A, Zhao G, Buseck PR, McNulty I, Fan L, Rau C, Gibson JM. 2007. Probing medium-range structural correlations by fluctuation microscopy. J Phys Condens Matter 19(45).      Article

Zhao G, Zhang Q, Zhang H, Yang G, Tang J, Zhou O, Qin LC. 2006. Field emission of single Cs doped carbon nanotube. Appl Phys Lett 89(26).     Article

Zhao G, Zhang J, Zhang Q, Zhang H, Tang J, Zhou O, Qin LC. 2006. Fabrication and characterization of single nanotube emitters as point electron sources. Appl Phys Lett 89 (19).     Article

Zhang H, Tang J, Zhang Q, Zhao G, Yang G, Zhang J, Zhou O, Qin LC. 2005. Field emission of electron from single LaB6 nanowires. Adv Mater 18, 87.     Article

Zhang H, Zhang Q, Zhao G, Tang J, Zhou O, Qin LC. 2005. Single-crystalline GdB6 nanowire field emitters. J Am Chem Soc 127(38):13120–13121.    Article