Stanford Advisors


  • Wah Chiu, Postdoctoral Faculty Sponsor

All Publications


  • 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
  • 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

  • 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
  • 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

  • TRPC Channels and Glioma TRANSIENT RECEPTOR POTENTIAL CANONICAL CHANNELS AND BRAIN DISEASES Li, S., Ding, X., Wang, Y. 2017; 976: 157–65

    Abstract

    Glioma is the most common type of brain tumors and malignant glioma is extremely lethal, with patients' 5-year survival rate less than 10%. Treatment of gliomas poses remarkable clinical challenges, not only because of their particular localization but also because glioma cells possess several malignant biological features, including highly proliferative, highly invasive, highly angiogenic, and highly metabolic aberrant. All these features make gliomas highly recurrent and drug resistant. Finding new and effective molecular drug targets for glioma is an urgent and critical task for both basic and clinical research. Recent studies have proposed a type of non-voltage-gated calcium channels, namely, canonical transient receptor potential (TRPC) channels, to be newly emerged potential drug targets for glioma. They are heavily involved in the proliferation, migration, invasion, angiogenesis, and metabolism of glioma cells. Abundant evidence from both cell models and preclinical mouse models has demonstrated that inhibition of TRPC channels shows promising anti-glioma effect. In this chapter, we will give a comprehensive review on the current progress in the studies on TRPC channels and glioma and discuss their potential clinical implication in glioma therapy.

    View details for DOI 10.1007/978-94-024-1088-4_14

    View details for Web of Science ID 000429061700014

    View details for PubMedID 28508321

  • Crucial role of TRPC6 in maintaining the stability of HIF-1 alpha in glioma cells under hypoxia JOURNAL OF CELL SCIENCE Li, S., Wang, J., Wei, Y., Liu, Y., Ding, X., Dong, B., Xu, Y., Wang, Y. 2015; 128 (17): 3317–29

    Abstract

    Hypoxia-inducible factor-1 (HIF-1) is a key transcription factor responsible for the expression of a broad range of genes that facilitate acclimatization to hypoxia. Its stability is predominantly controlled by rapid hydroxylation of two proline residues in its α-subunit. However, how the rapid hydroxylation of HIF-1α is regulated is not fully understood. Here, we report that transient receptor potential canonical (TRPC) 6 channels control hydroxylation and stability of HIF-1α in human glioma cells under hypoxia. TRPC6 was rapidly activated by IGF-1R-PLCγ-IP3R pathway upon hypoxia. Inhibition of TRPC6 enhanced the levels of α-ketoglutarate and promoted hydroxylation of HIF-1α to suppress HIF-1α accumulation without affecting its transcription or translation. Dimethyloxalylglycine N-(methoxyoxoacetyl)-glycine methyl ester (DMOG), an analog of α-ketoglutarate, reversed the inhibition of HIF-1α accumulation. Moreover, TRPC6 regulated GLUT1 (also known as SLC2A1) expression in a manner that was dependent on HIF-1α accumulation to affect glucose uptake during hypoxia. Our results suggest that TRPC6 regulates metabolism to affect HIF-1α stability and consequent glucose metabolism in human glioma cells under hypoxia.

    View details for DOI 10.1242/jcs.173161

    View details for Web of Science ID 000360715800014

    View details for PubMedID 26187851