Professional Education

  • BSc, Hong Kong University of Science and Technology, Molecular Biomedical Sciences (2013)
  • PhD, California Institute of Technology, Biochemistry and Molecular Biophysics (2019)

Stanford Advisors

All Publications

  • Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers PLOS ONE Cohen, A. A., Yang, Z., Gnanapragasam, P. P., Ou, S., Dam, K. A., Wang, H., Bjorkman, P. J. 2021; 16 (3): e0247963


    Current influenza vaccines do not elicit broadly protective immune responses against multiple strains. New strategies to focus the humoral immune response to conserved regions on influenza antigens are therefore required for recognition by broadly neutralizing antibodies. It has been suggested that B-cells with receptors that recognize conserved epitopes would be preferentially stimulated through avidity effects by mosaic particles presenting multiple forms of a variable antigen. We adapted SpyCatcher-based platforms, AP205 virus-like particles (VLPs) and mi3 nanoparticles (NPs), to covalently co-display SpyTagged hemagglutinin (HA) trimers from group 1 and group 2 influenza A strains. Here we show successful homotypic and heterotypic conjugation of up to 8 different HA trimers to both VLPs and NPs. We characterized the HA-VLPs and HA-NPs by cryo-electron tomography to derive the average number of conjugated HAs and their separation distances on particles, and compared immunizations of mosaic and homotypic particles in wild-type mice. Both types of HA particles elicited strong antibody responses, but the mosaic particles did not consistently elicit broader immune responses than mixtures of homotypic particles. We conclude that covalent attachment of HAs from currently-circulating influenza strains represents a viable alternative to current annual influenza vaccine strategies, but in the absence of further modifications, is unlikely to represent a method for making a universal influenza vaccine.

    View details for DOI 10.1371/journal.pone.0247963

    View details for Web of Science ID 000626604100046

    View details for PubMedID 33661993

    View details for PubMedCentralID PMC7932532

  • Diastereomeric Cyclopentane-Based Maltosides (CPMs) as Tools for Membrane Protein Study. Journal of the American Chemical Society Das, M., Mahler, F., Hariharan, P., Wang, H., Du, Y., Mortensen, J. S., Patallo, E. P., Ghani, L., Gluck, D., Lee, H. J., Byrne, B., Loland, C. J., Guan, L., Kobilka, B. K., Keller, S., Chae, P. S. 2020


    Amphiphilic agents, called detergents, are invaluable tools for studying membrane proteins. However, membrane proteins encapsulated by conventional head-to-tail detergents tend to denature or aggregate, necessitating the development of structurally distinct molecules with improved efficacy. Here, a novel class of diastereomeric detergents with a cyclopentane core unit, designated cyclopentane-based maltosides (CPMs), were prepared and evaluated for their ability to solubilize and stabilize several model membrane proteins. A couple of CPMs displayed enhanced behavior compared with the benchmark conventional detergent, n-dodecyl-beta-d-maltoside (DDM), for all the tested membrane proteins including two G-protein-coupled receptors (GPCRs). Furthermore, CPM-C12 was notable for its ability to confer enhanced membrane protein stability compared with the previously developed conformationally rigid NBMs [J. Am. Chem. Soc. 2017, 139, 3072] and LMNG. The effect of the individual CPMs on protein stability varied depending on both the detergent configuration (cis/trans) and alkyl chain length, allowing us draw conclusions on the detergent structure-property-efficacy relationship. Thus, this study not only provides novel detergent tools useful for membrane protein research but also reports on structural features of the detergents critical for detergent efficacy in stabilizing membrane proteins.

    View details for DOI 10.1021/jacs.0c09629

    View details for PubMedID 33315387

  • New Malonate-Derived Tetraglucoside Detergents for Membrane Protein Stability. ACS chemical biology Ehsan, M., Katsube, S., Cecchetti, C., Du, Y., Mortensen, J. S., Wang, H., Nygaard, A., Ghani, L., Loland, C. J., Kobilka, B. K., Byrne, B., Guan, L., Chae, P. S. 2020


    Membrane proteins are widely studied in detergent micelles, a membrane-mimetic system formed by amphiphilic compounds. However, classical detergents have serious limitations in their utility, particularly for unstable proteins such as eukaryotic membrane proteins and membrane protein complexes, and thus, there is an unmet need for novel amphiphiles with enhanced ability to stabilize membrane proteins. Here, we developed a new class of malonate-derived detergents with four glucosides, designated malonate-derived tetra-glucosides (MTGs), and compared these new detergents with previously reported octyl glucose neopentyl glycol (OGNG) and n-dodecyl-beta-d-maltoside (DDM). When tested with two G-protein coupled receptors (GPCRs) and three transporters, a couple of MTGs consistently conferred enhanced stability to all tested proteins compared to DDM and OGNG. As a result of favorable behaviors for a range of membrane proteins, these MTGs have substantial potential for membrane protein research. This study additionally provides a new detergent design principle based on the effect of a polar functional group (i.e., ether) on protein stability depending on its position in the detergent scaffold.

    View details for DOI 10.1021/acschembio.0c00316

    View details for PubMedID 32501004

  • Publisher Correction: Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nature structural & molecular biology Yang, Z., Wang, H., Liu, A. Z., Gristick, H. B., Bjorkman, P. J. 2020


    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    View details for DOI 10.1038/s41594-020-0381-0

    View details for PubMedID 31965081

  • Publisher Correction: Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nature structural & molecular biology Yang, Z., Wang, H., Liu, A. Z., Gristick, H. B., Bjorkman, P. J. 2019


    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    View details for DOI 10.1038/s41594-019-0362-3

    View details for PubMedID 31844248

  • Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nature structural & molecular biology Yang, Z., Wang, H., Liu, A. Z., Gristick, H. B., Bjorkman, P. J. 2019


    The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein, a (gp120-gp41)3 trimer, mediates fusion of viral and host cell membranes after gp120 binding to host receptor CD4. Receptor binding triggers conformational changes allowing coreceptor (CCR5) recognition through CCR5's tyrosine-sulfated amino (N) terminus, release of the gp41 fusion peptide and fusion. We present 3.3A and 3.5A cryo-EM structures of E51, a tyrosine-sulfated coreceptor-mimicking antibody, complexed with a CD4-bound open HIV-1 native-like Env trimer. Two classes of asymmetric Env interact with E51, revealing tyrosine-sulfated interactions with gp120 mimicking CCR5 interactions, and two conformations of gp120-gp41 protomers (A and B protomers in AAB and ABB trimers) that differ in their degree of CD4-induced trimer opening and induction of changes to the fusion peptide. By integrating the new structural information with previous closed and open envelope trimer structures, we modeled the order of conformational changes on the path to coreceptor binding site exposure and subsequent viral-host cell membrane fusion.

    View details for DOI 10.1038/s41594-019-0344-5

    View details for PubMedID 31792452

  • A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales. Proceedings of the National Academy of Sciences of the United States of America Marcovitz, A., Turakhia, Y., Chen, H. I., Gloudemans, M., Braun, B. A., Wang, H., Bejerano, G. 2019


    Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.

    View details for DOI 10.1073/pnas.1818532116

    View details for PubMedID 31570615