Academic Appointments


  • Basic Life Science Research Associate, Bioengineering

Professional Education


  • B.Sc., Jilin Univeristy, Biological pharmacy (2010)
  • Ph.D., Peking Univeristy, Biophysics, Cryo-EM, Ion channel (2015)

All Publications


  • 3D RNA nanocage for encapsulation and shielding of hydrophobic biomolecules to improve the in vivo biodistribution NANO RESEARCH Xu, C., Zhang, K., Yin, H., Li, Z., Krasnoslobodtsev, A., Zheng, Z., Ji, Z., Guo, S., Li, S., Chiu, W., Guo, P. 2020
  • Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Molecular cell Partin, A. C., Zhang, K., Jeong, B., Herrell, E., Li, S., Chiu, W., Nam, Y. 2020

    Abstract

    Metazoan microRNAs require specific maturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). Here we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. Two dsRBDs form a molecular ruler to measure the stem length between the two dsRNA-ssRNA junctions. The specific organization of the dsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site.

    View details for DOI 10.1016/j.molcel.2020.02.016

    View details for PubMedID 32220646

  • Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM. Proceedings of the National Academy of Sciences of the United States of America Zhang, K., Wang, S., Li, S., Zhu, Y., Pintilie, G. D., Mou, T., Schmid, M. F., Huang, Z., Chiu, W. 2020

    Abstract

    Prokaryotes and viruses have fought a long battle against each other. Prokaryotes use CRISPR-Cas-mediated adaptive immunity, while conversely, viruses evolve multiple anti-CRISPR (Acr) proteins to defeat these CRISPR-Cas systems. The type I-F CRISPR-Cas system in Pseudomonas aeruginosa requires the crRNA-guided surveillance complex (Csy complex) to recognize the invading DNA. Although some Acr proteins against the Csy complex have been reported, other relevant Acr proteins still need studies to understand their mechanisms. Here, we obtain three structures of previously unresolved Acr proteins (AcrF9, AcrF8, and AcrF6) bound to the Csy complex using electron cryo-microscopy (cryo-EM), with resolution at 2.57 A, 3.42 A, and 3.15 A, respectively. The 2.57-A structure reveals fine details for each molecular component within the Csy complex as well as the direct and water-mediated interactions between proteins and CRISPR RNA (crRNA). Our structures also show unambiguously how these Acr proteins bind differently to the Csy complex. AcrF9 binds to key DNA-binding sites on the Csy spiral backbone. AcrF6 binds at the junction between Cas7.6f and Cas8f, which is critical for DNA duplex splitting. AcrF8 binds to a distinct position on the Csy spiral backbone and forms interactions with crRNA, which has not been seen in other Acr proteins against the Csy complex. Our structure-guided mutagenesis and biochemistry experiments further support the anti-CRISPR mechanisms of these Acr proteins. Our findings support the convergent consequence of inhibiting degradation of invading DNA by these Acr proteins, albeit with different modes of interactions with the type I-F CRISPR-Cas system.

    View details for DOI 10.1073/pnas.1922638117

    View details for PubMedID 32170016

  • Structure of the G protein chaperone and guanine nucleotide exchange factor Ric-8A bound to Galphai1. Nature communications McClelland, L. J., Zhang, K., Mou, T., Johnston, J., Yates-Hansen, C., Li, S., Thomas, C. J., Doukov, T. I., Triest, S., Wohlkonig, A., Tall, G. G., Steyaert, J., Chiu, W., Sprang, S. R. 2020; 11 (1): 1077

    Abstract

    Ric-8A is a cytosolic Guanine Nucleotide exchange Factor (GEF) that activates heterotrimeric G protein alpha subunits (Galpha) and serves as an essential Galpha chaperone. Mechanisms by which Ric-8A catalyzes these activities, which are stimulated by Casein Kinase II phosphorylation, are unknown. We report the structure of the nanobody-stabilized complex of nucleotide-free Galpha bound to phosphorylated Ric-8A at near atomic resolution by cryo-electron microscopy and X-ray crystallography. The mechanism of Ric-8A GEF activity differs considerably from that employed by G protein-coupled receptors at the plasma membrane. Ric-8A engages a specific conformation of Galpha at multiple interfaces to form a complex that is stabilized by phosphorylation within a Ric-8A segment that connects two Galpha binding sites. The C-terminus of Galpha is ejected from its beta sheet core, thereby dismantling the GDP binding site. Ric-8A binds to the exposed Galpha beta sheet and switch II to stabilize the nucleotide-free state of Galpha.

    View details for DOI 10.1038/s41467-020-14943-4

    View details for PubMedID 32103024

  • Ultra-thermostable RNA nanoparticles for solubilizing and high-yield loading of paclitaxel for breast cancer therapy. Nature communications Guo, S., Vieweger, M., Zhang, K., Yin, H., Wang, H., Li, X., Li, S., Hu, S., Sparreboom, A., Evers, B. M., Dong, Y., Chiu, W., Guo, P. 2020; 11 (1): 972

    Abstract

    Paclitaxel is widely used in cancer treatments, but poor water-solubility and toxicity raise serious concerns. Here we report an RNA four-way junction nanoparticle with ultra-thermodynamic stability to solubilize and load paclitaxel for targeted cancer therapy. Each RNA nanoparticle covalently loads twenty-four paclitaxel molecules as aprodrug. The RNA-paclitaxel complex is structurally rigid and stable, demonstrated by the sub-nanometer resolution imaging of cryo-EM. Using RNA nanoparticles as carriers increases the water-solubility of paclitaxel by 32,000-fold. Intravenous injections of RNA-paclitaxel nanoparticles with specific cancer-targeting ligand dramatically inhibit breast cancer growth, with nearly undetectable toxicity and immune responses in mice. No fatalities are observed at a paclitaxel dose equal to the reported LD50. The use of ultra-thermostable RNA nanoparticles to deliver chemical prodrugs addresses issues with RNA unfolding and nanoparticle dissociation after high-density drug loading. This finding provides a stable nano-platform for chemo-drug delivery as well as an efficient method to solubilize hydrophobic drugs.

    View details for DOI 10.1038/s41467-020-14780-5

    View details for PubMedID 32080195

  • Measurement of atom resolvability in cryo-EM maps with Q-scores. Nature methods Pintilie, G., Zhang, K., Su, Z., Li, S., Schmid, M. F., Chiu, W. 2020

    Abstract

    Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. Q-scores can be calculated for atoms in proteins, nucleic acids, water, ligands and other solvent atoms, using models fitted to or derived from cryo-EM maps. Q-scores can also be averaged to represent larger features such as entire residues and nucleotides. Averaged over entire models, Q-scores correlate very well with the estimated resolution of cryo-EM maps for both protein and RNA. Assuming the models they are calculated from are well fitted to the map, Q-scores can be used as a measure of resolvability in cryo-EM maps at various scales, from entire macromolecules down to individual atoms. Q-score analysis of multiple cryo-EM maps of the same proteins derived from different laboratories confirms the reproducibility of structural features from side chains down to water and ion atoms.

    View details for DOI 10.1038/s41592-020-0731-1

    View details for PubMedID 32042190

  • Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nature methods Kappel, K., Zhang, K., Su, Z., Watkins, A. M., Kladwang, W., Li, S., Pintilie, G., Topkar, V. V., Rangan, R., Zheludev, I. N., Yesselman, J. D., Chiu, W., Das, R. 2020; 17 (7): 699–707

    Abstract

    The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. This hybrid 'Ribosolve' pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.

    View details for DOI 10.1038/s41592-020-0878-9

    View details for PubMedID 32616928

  • Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nature structural & molecular biology Li, S., Su, Z., Lehmann, J., Stamatopoulou, V., Giarimoglou, N., Henderson, F. E., Fan, L., Pintilie, G. D., Zhang, K., Chen, M., Ludtke, S. J., Wang, Y., Stathopoulos, C., Chiu, W., Zhang, J. 2019

    Abstract

    Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.

    View details for DOI 10.1038/s41594-019-0326-7

    View details for PubMedID 31740854

  • Rapid RNA structure determination through cryo-EM, high-throughput biochemistry, and computational modeling Kappel, K., Zhang, K., Su, Z., Pintilie, G., Chiu, W., Das, R. AMER CHEMICAL SOC. 2019
  • Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Zhang, K., Zhang, H., Li, S., Pintilie, G. D., Mou, T., Gao, Y., Zhang, Q., van den Bedeme, H., Schmid, M. F., Au, S., Chiu, W. 2019; 116 (14): 6800–6805
  • Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry CELL RESEARCH Guo, M., Zhang, K., Zhu, Y., Pintilie, G. D., Guan, X., Li, S., Schmid, M. F., Ma, Z., Chiu, W., Huang, Z. 2019; 29 (4): 305–12
  • Structure of Calcarisporiella thermophila Hsp104 Disaggregase that Antagonizes Diverse Proteotoxic Misfolding Events STRUCTURE Michalska, K., Zhang, K., March, Z. M., Hatzos-Skintges, C., Pintilie, G., Bigelow, L., Castellano, L. M., Miles, L. J., Jackrel, M. E., Chuang, E., Jedrzejczak, R., Shorter, J., Chiu, W., Joachimiak, A. 2019; 27 (3): 449-+
  • Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges ACS NANO Jun, H., Shepherd, T. R., Zhang, K., Bricker, W. P., Li, S., Chiu, W., Bathe, M. 2019; 13 (2): 2083–93

    Abstract

    3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. In order to test its generality, we apply TALOS to design an  in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.

    View details for PubMedID 30605605

  • Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nature communications Zhang, K., Li, S., Kappel, K., Pintilie, G., Su, Z., Mou, T. C., Schmid, M. F., Das, R., Chiu, W. 2019; 10 (1): 5511

    Abstract

    Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA.

    View details for DOI 10.1038/s41467-019-13494-7

    View details for PubMedID 31796736

  • The structure of the complex of the cytoplasmic guanine nucleotide exchange factor Ric-8A with G alpha i1 Sprang, S., McClelland, L., Johnston, J., Cindee-Yates-Hansen, Mou, T., Zhang, K. INT UNION CRYSTALLOGRAPHY. 2019: A175
  • Photo-controlled release of paclitaxel and model drugs from RNA pyramids. Nano research Xu, C., Li, H., Zhang, K., Binzel, D. W., Yin, H., Chiu, W., Guo, P. 2019; 12 (1): 41–48

    Abstract

    Stimuli-responsive release of drugs from a nanocarrier in spatial-, temporal-, and dosage-controlled fashions is of great interest in the pharmaceutical industry. Paclitaxel is one of the most effective and popular chemotherapeutic drugs against a number of cancers such as metastatic or nonmetastatic breast cancer, non-small cell lung cancer, refractory ovarian cancer, AIDS-related Kaposi's sarcoma, and head and neck cancers. Here, by taking the advantage of RNA nanotechnology in biomedical and material science, we developed a three-dimensional pyramid-shaped RNA nanocage for a photocontrolled release of cargo, using paclitaxel as a model drug. The light-triggered release of paclitaxel or fluorophore Cy5 was achieved by incorporation of photocleavable spacers into the RNA nanoparticles. Upon irradiation with ultraviolet light, cargos were rapidly released (within 5 min). In vitro treatment of breast cancer cells with the RNA nanoparticles harboring photocleavable paclitaxel showed higher cytotoxicity as compared to RNA nanoparticles without the photocleavable spacer. The methodology provides proof of concept for the application of the light-triggered controlled release of drugs from RNA nanocages.

    View details for DOI 10.1007/s12274-018-2174-x

    View details for PubMedID 31258852

    View details for PubMedCentralID PMC6599617

  • Structure of Calcarisporiella thermophila Hsp104 Disaggregase that Antagonizes Diverse Proteotoxic Misfolding Events. Structure (London, England : 1993) Michalska, K., Zhang, K., March, Z. M., Hatzos-Skintges, C., Pintilie, G., Bigelow, L., Castellano, L. M., Miles, L. J., Jackrel, M. E., Chuang, E., Jedrzejczak, R., Shorter, J., Chiu, W., Joachimiak, A. 2018

    Abstract

    Hsp104 is an AAA+ protein disaggregase with powerful amyloid-remodeling activity. All nonmetazoan eukaryotes express Hsp104 while eubacteria express an Hsp104 ortholog, ClpB. However, most studies have focused on Hsp104 from Saccharomyces cerevisiae and ClpB orthologs from two eubacterial species. Thus, the natural spectrum of Hsp104/ClpB molecular architectures and protein-remodeling activities remains largely unexplored. Here, we report two structures of Hsp104 from the thermophilic fungus Calcarisporiella thermophila (CtHsp104), a 2.70A crystal structure and 4.0A cryo-electron microscopystructure. Both structures reveal left-handed, helical assemblies with all domains clearly resolved. We thus provide the highest resolution and most complete view of Hsp104 hexamers to date. We also establish that CtHsp104 antagonizes several toxic protein-misfolding events invivo where S. cerevisiae Hsp104 is ineffective, including rescue of TDP-43, polyglutamine, and alpha-synuclein toxicity. We suggest that natural Hsp104 variation is an invaluable, untapped resource for illuminating therapeutic disaggregases for fatal neurodegenerative diseases.

    View details for PubMedID 30595457

  • Comparison of Crystal and Cryoem Structures of Hsp104 and ClpB Disaggregases Joachimiak, A., Michalska, K., Zhang, K., March, Z., Hatzos-Skintges, C., Pintilie, G., Bigelow, L., Castellano, L., Miles, L., Jackrel, M., Chuang, E., Jedrzejczak, R., Shorter, J., Chiu, W. WILEY. 2018: 32–33
  • Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach Zhang, K., keane, S. C., Su, Z., robalieva, R., Chen, M., Sciandra, C. A., Marchant, J., Heng, X., Schmid, M. F., Case, D. A., Ludtke, S. J., Summers, M. F., Chiu, W. 2018; 26 (3): 490-498

    Abstract

    Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]2; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs.

    View details for DOI 10.1016/j.str.2018.01.001

    View details for PubMedCentralID PMC5842133

  • Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes NATURE COMMUNICATIONS Santos, R., Bai, L., Singh, P. K., Murakami, N., Fan, H., Zhan, W., Zhu, Y., Jiang, X., Zhang, K., Assker, J., Nathan, C. F., Li, H., Azzi, J., Lin, G. 2017; 8: 1692

    Abstract

    Proteasome inhibitors benefit patients with multiple myeloma and B cell-dependent autoimmune disorders but exert toxicity from inhibition of proteasomes in other cells. Toxicity should be minimized by reversible inhibition of the immunoproteasome β5i subunit while sparing the constitutive β5c subunit. Here we report β5i-selective inhibition by asparagine-ethylenediamine (AsnEDA)-based compounds and present the high-resolution cryo-EM structural analysis of the human immunoproteasome. Despite inhibiting noncompetitively, an AsnEDA inhibitor binds the active site. Hydrophobic interactions are accompanied by hydrogen bonding with β5i and β6 subunits. The inhibitors are far more cytotoxic for myeloma and lymphoma cell lines than for hepatocarcinoma or non-activated lymphocytes. They block human B-cell proliferation and promote apoptotic cell death selectively in antibody-secreting B cells, and to a lesser extent in activated human T cells. Reversible, β5i-selective inhibitors may be useful for treatment of diseases involving activated or neoplastic B cells or activated T cells.

    View details for PubMedID 29167449

  • Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs ADVANCED MATERIALS Khisamutdinov, E. F., Jasinski, D. L., Li, H., Zhang, K., Chiu, W., Guo, P. 2016; 28 (45): 10079–87

    Abstract

    Constructing containers with defined shape and size to load and protect therapeutics and subsequently control their release in the human body has long been a dream. The fabrication of 3D RNA prisms, characterized by atomic force microscopy, cryo-electron microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis, is reported for the loading and protection of small molecules, proteins, small RNA molecules, and their controlled release.

    View details for PubMedID 27758001

    View details for PubMedCentralID PMC5224701

  • The Function of Ile-X-Ile Motif in the Oligomerization and Chaperone-Like Activity of Small Heat Shock Protein AgsA at Room Temperature PROTEIN JOURNAL Zhou, Q., Shi, X., Zhang, K., Shi, C., Huang, L., Chang, Z. 2016; 35 (6): 401–6

    Abstract

    Small heat shock proteins assemble as large oligomers in vitro and exhibit ATP-independent chaperone activities. Ile-X-Ile motif is essential in both the function and oligomer formation. AgsA of Salmonella enterica serovar Typhimurium has been demonstrated to adopt large oligomeric structure and possess strong chaperone activity. Size exclusion chromatography, non-denaturing pore gradient PAGE, and negatively stain electron microscopic analysis of the various C-terminal truncated mutants were performed to investigate the role of Ile-X-Ile motif in the oligomer assembly of AgsA. By measuring the ability to prevent insulin from aggregating induced by TCEP, the chaperone-like activity of AgsA and the C-terminal truncated mutants at room temperature were determined. We found that the truncated mutants with Ile-X-Ile motif partially or fully deleted lost the ability to form large oligomers. Contrast to wild type AgsA which displayed weak chaperone-like activity, those mutants shown significantly enhanced activities at room temperature. In summary, biochemical experiment, activity assay and electron microscopic analysis suggested that Ile-X-Ile motif is essential in oligomer assembly of AgsA and might take the role of an inhibitor for its chaperone-like activity at room temperature.

    View details for DOI 10.1007/s10930-016-9681-y

    View details for Web of Science ID 000389918500002

    View details for PubMedID 27812886

  • Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting ADVANCED MATERIALS Li, H., Zhang, K., Pi, F., Guo, S., Shlyakhtenko, L., Chiu, W., Shu, D., Guo, P. 2016; 28 (34): 7501–7

    Abstract

    RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be extended to construct higher-order polyhedral RNA architectures for various applications such as targeted cancer imaging and therapy.

    View details for PubMedID 27322097

    View details for PubMedCentralID PMC5059845

  • DNA NANOTECHNOLOGY Designer nanoscale DNA assemblies programmed from the top down SCIENCE Veneziano, R., Ratanalert, S., Zhang, K., Zhang, F., Yan, H., Chiu, W., Bathe, M. 2016; 352 (6293): 1534

    Abstract

    Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually for any given target structure. Here, we report a general, top-down strategy to design nearly arbitrary DNA architectures autonomously based only on target shape. Objects are represented as closed surfaces rendered as polyhedral networks of parallel DNA duplexes, which enables complete DNA scaffold routing with a spanning tree algorithm. The asymmetric polymerase chain reaction is applied to produce stable, monodisperse assemblies with custom scaffold length and sequence that are verified structurally in three dimensions to be high fidelity by single-particle cryo-electron microscopy. Their long-term stability in serum and low-salt buffer confirms their utility for biological as well as nonbiological applications.

    View details for PubMedID 27229143

    View details for PubMedCentralID PMC5111087

  • Classification using diffraction patterns for single-particle analysis ULTRAMICROSCOPY Hu, H., Zhang, K., Meng, X. 2016; 164: 46–50

    Abstract

    An alternative method has been assessed; diffraction patterns derived from the single particle data set were used to perform the first round of classification in creating the initial averages for proteins data with symmetrical morphology. The test protein set was a collection of Caenorhabditis elegans small heat shock protein 17 obtained by Cryo EM, which has a tetrahedral (12-fold) symmetry. It is demonstrated that the initial classification on diffraction patterns is workable as well as the real-space classification that is based on the phase contrast. The test results show that the information from diffraction patterns has the enough details to make the initial model faithful. The potential advantage using the alternative method is twofold, the ability to handle the sets with poor signal/noise or/and that break the symmetry properties.

    View details for DOI 10.1016/j.ultramic.2016.03.001

    View details for Web of Science ID 000373526200006

    View details for PubMedID 27010412

  • Binding affinity analysis of the interaction between Homer EVH domain and ryanodine receptor with biosensors based on imaging ellipsometry ANALYTICAL METHODS Kang, T., Zhang, K., Yin, C., Niu, Y., Jin, G. 2016; 8 (14): 2936–40

    View details for DOI 10.1039/c6ay00089d

    View details for Web of Science ID 000373440600010

  • A Novel Mechanism for Small Heat Shock Proteins to Function as Molecular Chaperones SCIENTIFIC REPORTS Zhang, K., Ezemaduka, A. N., Wang, Z., Hu, H., Shi, X., Liu, C., Lu, X., Fu, X., Chang, Z., Yin, C. 2015; 5: 8811

    Abstract

    Small heat shock proteins (sHSPs) are molecular chaperones ubiquitously present in all forms of life, but their function mechanisms remain controversial. Here we show by cryo-electron microscopy and single particle 3D reconstruction that, at the low temperatures (4-25°C), CeHSP17 (a sHSP from Caenorhabditis elegans) exists as a 24-subunit spherical oligomer with tetrahedral symmetry. Our studies demonstrate that CeHSP17 forms large sheet-like super-molecular assemblies (SMAs) at the high temperatures (45-60°C), and such SMAs are apparently the form that exhibits chaperone-like activity. Our findings suggest a novel molecular mechanism for sHSPs to function as molecular chaperones.

    View details for DOI 10.1038/srep08811

    View details for Web of Science ID 000350473700005

    View details for PubMedID 25744691

    View details for PubMedCentralID PMC4351549

  • The molecular architecture of dihydropyrindine receptor/L-type Ca2+ channel complex SCIENTIFIC REPORTS Hu, H., Wang, Z., Wei, R., Fan, G., Wang, Q., Zhang, K., Yin, C. 2015; 5: 8370

    Abstract

    Dihydropyridine receptor (DHPR), an L-type Ca(2+) channel complex, plays an essential role in muscle contraction, secretion, integration of synaptic input in neurons and synaptic transmission. The molecular architecture of DHPR complex remains elusive. Here we present a 15-Å resolution cryo-electron microscopy structure of the skeletal DHPR/L-type Ca(2+) channel complex. The DHPR has an asymmetrical main body joined by a hook-like extension. The main body is composed of a "trapezoid" and a "tetrahedroid". Homologous crystal structure docking and site-specific antibody labelling revealed that the α1 and α2 subunits are located in the "trapezoid" and the β subunit is located in the "tetrahedroid". This structure revealed the molecular architecture of a eukaryotic Ca(2+) channel complex. Furthermore, this structure provides structural insights into the key elements of DHPR involved in physical coupling with the RyR/Ca(2+) release channel and shed light onto the mechanism of excitation-contraction coupling.

    View details for DOI 10.1038/srep08370

    View details for Web of Science ID 000349173000002

    View details for PubMedID 25667046

    View details for PubMedCentralID PMC4322351

  • A Small Heat Shock Protein Enables Escherichia coli To Grow at a Lethal Temperature of 50 degrees C Conceivably by Maintaining Cell Envelope Integrity JOURNAL OF BACTERIOLOGY Ezemaduka, A. N., Yu, J., Shi, X., Zhang, K., Yin, C., Fu, X., Chang, Z. 2014; 196 (11): 2004–11

    Abstract

    It is essential for organisms to adapt to fluctuating growth temperatures. Escherichia coli, a model bacterium commonly used in research and industry, has been reported to grow at a temperature lower than 46.5°C. Here we report that the heterologous expression of the 17-kDa small heat shock protein from the nematode Caenorhabditis elegans, CeHSP17, enables E. coli cells to grow at 50°C, which is their highest growth temperature ever reported. Strikingly, CeHSP17 also rescues the thermal lethality of an E. coli mutant deficient in degP, which encodes a protein quality control factor localized in the periplasmic space. Mechanistically, we show that CeHSP17 is partially localized in the periplasmic space and associated with the inner membrane of E. coli, and it helps to maintain the cell envelope integrity of the E. coli cells at the lethal temperatures. Together, our data indicate that maintaining the cell envelope integrity is crucial for the E. coli cells to grow at high temperatures and also shed new light on the development of thermophilic bacteria for industrial application.

    View details for DOI 10.1128/JB.01473-14

    View details for Web of Science ID 000335909500009

    View details for PubMedID 24659772

    View details for PubMedCentralID PMC4010981