Professional Education

  • Ph.D, Tsinghua University, Biology (2019)
  • Bachelor of Science, Huazhong University of Science and Technology, Biotechnology (2014)

Stanford Advisors

All Publications

  • Author Correction: Stepwise activation of a metabotropic glutamate receptor. Nature Krishna Kumar, K., Wang, H., Habrian, C., Latorraca, N. R., Xu, J., O'Brien, E. S., Zhang, C., Montabana, E., Koehl, A., Marqusee, S., Isacoff, E. Y., Kobilka, B. K. 2024

    View details for DOI 10.1038/s41586-024-07470-5

    View details for PubMedID 38702522

  • Stepwise activation of a metabotropic glutamate receptor. Nature Krishna Kumar, K., Wang, H., Habrian, C., Latorraca, N. R., Xu, J., O'Brien, E. S., Zhang, C., Montabana, E., Koehl, A., Marqusee, S., Isacoff, E. Y., Kobilka, B. K. 2024


    Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich domain to their 7-transmembrane domain1. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the extracellular ligand-binding domain to the G protein-coupling 7-transmembrane domain2. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging, we reveal distinct receptor conformations upon allosteric modulator and G protein binding.

    View details for DOI 10.1038/s41586-024-07327-x

    View details for PubMedID 38632403

    View details for PubMedCentralID 6709600

  • Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq. Communications biology Ham, D., Inoue, A., Xu, J., Du, Y., Chung, K. Y. 2024; 7 (1): 362


    Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.

    View details for DOI 10.1038/s42003-024-06056-1

    View details for PubMedID 38521872

    View details for PubMedCentralID PMC10960872

  • Structural and functional characterization of the endogenous agonist for orphan receptor GPR3. Cell research Chen, G., Staffen, N., Wu, Z., Xu, X., Pan, J., Inoue, A., Shi, T., Gmeiner, P., Du, Y., Xu, J. 2024

    View details for DOI 10.1038/s41422-023-00919-8

    View details for PubMedID 38287118

    View details for PubMedCentralID 6093286

  • Step-wise activation of a Family C GPCR. bioRxiv : the preprint server for biology Kumar, K. K., Wang, H., Habrian, C., Latorraca, N. R., Xu, J., O'Brien, E. S., Zhang, C., Montabana, E., Koehl, A., Marqusee, S., Isacoff, E. Y., Kobilka, B. K. 2023


    Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain (ECD) that is linked via a cysteine-rich domain (CRDs) to their 7-transmembrane (TM) domain. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the ECD to the G protein-coupling TM. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging we reveal distinct receptor conformations upon allosteric modulator and G protein binding.

    View details for DOI 10.1101/2023.08.29.555158

    View details for PubMedID 37693614

    View details for PubMedCentralID PMC10491200

  • Galphas slow conformational transition upon GTP binding and a novel Galphas regulator. iScience Ahn, D., Provasi, D., Duc, N. M., Xu, J., Salas-Estrada, L., Spasic, A., Yun, M. W., Kang, J., Gim, D., Lee, J., Du, Y., Filizola, M., Chung, K. Y. 2023; 26 (5): 106603


    G proteins are major signaling partners for G protein-coupled receptors (GPCRs). Although stepwise structural changes during GPCR-G protein complex formation and guanosine diphosphate (GDP) release have been reported, no information is available with regard to guanosine triphosphate (GTP) binding. Here, we used a novel Bayesian integrative modeling framework that combines data from hydrogen-deuterium exchange mass spectrometry, tryptophan-induced fluorescence quenching, and metadynamics simulations to derive a kinetic model and atomic-level characterization of stepwise conformational changes incurred by the beta2-adrenergic receptor (beta2AR)-Gs complex after GDP release and GTP binding. Our data suggest rapid GTP binding and GTP-induced dissociation of Galphas from beta2AR and Gbetagamma, as opposed to a slow closing of the Galphas alpha-helical domain (AHD). Yeast-two-hybrid screening using Galphas AHD as bait identified melanoma-associated antigen D2 (MAGE D2) as a novel AHD-binding protein, which was also shown to accelerate the GTP-induced closing of the Galphas AHD.

    View details for DOI 10.1016/j.isci.2023.106603

    View details for PubMedID 37128611

  • Structural and dynamic insights into supra-physiological activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature communications Xu, J., Wang, Q., Hübner, H., Hu, Y., Niu, X., Wang, H., Maeda, S., Inoue, A., Tao, Y., Gmeiner, P., Du, Y., Jin, C., Kobilka, B. K. 2023; 14 (1): 376


    The M2 muscarinic receptor (M2R) is a prototypical G-protein-coupled receptor (GPCR) that serves as a model system for understanding GPCR regulation by both orthosteric and allosteric ligands. Here, we investigate the mechanisms governing M2R signaling versatility using cryo-electron microscopy (cryo-EM) and NMR spectroscopy, focusing on the physiological agonist acetylcholine and a supra-physiological agonist iperoxo, as well as a positive allosteric modulator LY2119620. These studies reveal that acetylcholine stabilizes a more heterogeneous M2R-G-protein complex than iperoxo, where two conformers with distinctive G-protein orientations were determined. We find that LY2119620 increases the affinity for both agonists, but differentially modulates agonists efficacy in G-protein and β-arrestin pathways. Structural and spectroscopic analysis suggest that LY211620 stabilizes distinct intracellular conformational ensembles from agonist-bound M2R, which may enhance β-arrestin recruitment while impairing G-protein activation. These results highlight the role of conformational dynamics in the complex signaling behavior of GPCRs, and could facilitate design of better drugs.

    View details for DOI 10.1038/s41467-022-35726-z

    View details for PubMedID 36690613

    View details for PubMedCentralID PMC9870890

  • Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor. Science (New York, N.Y.) Fink, E. A., Xu, J., Hübner, H., Braz, J. M., Seemann, P., Avet, C., Craik, V., Weikert, D., Schmidt, M. F., Webb, C. M., Tolmachova, N. A., Moroz, Y. S., Huang, X. P., Kalyanaraman, C., Gahbauer, S., Chen, G., Liu, Z., Jacobson, M. P., Irwin, J. J., Bouvier, M., Du, Y., Shoichet, B. K., Basbaum, A. I., Gmeiner, P. 2022; 377 (6614): eabn7065


    Because nonopioid analgesics are much sought after, we computationally docked more than 301 million virtual molecules against a validated pain target, the α2A-adrenergic receptor (α2AAR), seeking new α2AAR agonists chemotypes that lack the sedation conferred by known α2AAR drugs, such as dexmedetomidine. We identified 17 ligands with potencies as low as 12 nanomolar, many with partial agonism and preferential Gi and Go signaling. Experimental structures of α2AAR complexed with two of these agonists confirmed the docking predictions and templated further optimization. Several compounds, including the initial docking hit '9087 [mean effective concentration (EC50) of 52 nanomolar] and two analogs, '7075 and PS75 (EC50 4.1 and 4.8 nanomolar), exerted on-target analgesic activity in multiple in vivo pain models without sedation. These newly discovered agonists are interesting as therapeutic leads that lack the liabilities of opioids and the sedation of dexmedetomidine.

    View details for DOI 10.1126/science.abn7065

    View details for PubMedID 36173843

  • Activation and allosteric regulation of the orphan GPR88-Gi1 signaling complex. Nature communications Chen, G., Xu, J., Inoue, A., Schmidt, M. F., Bai, C., Lu, Q., Gmeiner, P., Liu, Z., Du, Y. 2022; 13 (1): 2375


    GPR88 is an orphan class A G-protein-coupled receptor that is highly expressed in the striatum and regulates diverse brain and behavioral functions. Here we present cryo-EM structures of the human GPR88-Gi1 signaling complex with or without a synthetic agonist (1R, 2R)-2-PCCA. We show that (1R, 2R)-2-PCCA is an allosteric modulator binding to a herein identified pocket formed by the cytoplasmic ends of transmembrane segments 5, 6, and the extreme C terminus of the alpha5 helix of Gi1. We also identify an electron density in the extracellular orthosteric site that may represent a putative endogenous ligand of GPR88. These structures, together with mutagenesis studies and an inactive state model obtained from metadynamics simulations, reveal a unique activation mechanism for GPR88 with a set of distinctive structure features and a water-mediated polar network. Overall, our results provide a structural framework for understanding the ligand binding, activation and signaling mechanism of GPR88, and will facilitate the innovative drug discovery for neuropsychiatric disorders and for deorphanization of this receptor.

    View details for DOI 10.1038/s41467-022-30081-5

    View details for PubMedID 35501348

  • Structural insights into ligand recognition, activation, and signaling of the α2A adrenergic receptor. Science advances Xu, J., Cao, S., Hübner, H., Weikert, D., Chen, G., Lu, Q., Yuan, D., Gmeiner, P., Liu, Z., Du, Y. 2022; 8 (9): eabj5347


    The α2A adrenergic receptor (α2AAR) is a G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptor that mediates important physiological functions in response to the endogenous neurotransmitters norepinephrine and epinephrine, as well as numerous chemically distinct drugs. However, the molecular mechanisms of drug actions remain poorly understood. Here, we report the cryo-electron microscopy structures of the human α2AAR-GoA complex bound to norepinephrine and three imidazoline derivatives (brimonidine, dexmedetomidine, and oxymetazoline). Together with mutagenesis and functional data, these structures provide important insights into the molecular basis of ligand recognition, activation, and signaling at the α2AAR. Further structural analyses uncover different molecular determinants between α2AAR and βARs for recognition of norepinephrine and key regions that determine the G protein coupling selectivity. Overall, our studies provide a framework for understanding the signal transduction of the adrenergic system at the atomic level, which will facilitate rational structure-based discovery of safer and more effective medications for α2AAR.

    View details for DOI 10.1126/sciadv.abj5347

    View details for PubMedID 35245122

    View details for PubMedCentralID PMC8896805

  • Long-lived conformational changes in active Gsa revealed in atomistic detail by integrating HDX-MS with enhanced molecular dynamics simulations Provasi, D., Spasic, A., Nguyen Minh Duc, Du, Y., Ahn, D., Xu, J., Chung, K., Filizola, M. CELL PRESS. 2022: 145
  • Cryo-EM structure of the AVP-vasopressin receptor 2-G(s) signaling complex CELL RESEARCH Wang, L., Xu, J., Cao, S., Sun, D., Liu, H., Lu, Q., Liu, Z., Du, Y., Zhang, C. 2021

    View details for DOI 10.1038/s41422-021-00483-z

    View details for Web of Science ID 000626104700001

    View details for PubMedID 33664408

  • Analysis of beta2AR-Gs and beta2AR-Gi complex formation by NMR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America Ma, X., Hu, Y., Batebi, H., Heng, J., Xu, J., Liu, X., Niu, X., Li, H., Hildebrand, P. W., Jin, C., Kobilka, B. K. 2020


    The beta2-adrenergic receptor (beta2AR) is a prototypical G protein-coupled receptor (GPCR) that preferentially couples to the stimulatory G protein Gs and stimulates cAMP formation. Functional studies have shown that the beta2AR also couples to inhibitory G protein Gi, activation of which inhibits cAMP formation [R. P. Xiao, Sci. STKE 2001, re15 (2001)]. A crystal structure of the beta2AR-Gs complex revealed the interaction interface of beta2AR-Gs and structural changes upon complex formation [S. G. Rasmussen et al., Nature 477, 549-555 (2011)], yet, the dynamic process of the beta2AR signaling through Gs and its preferential coupling to Gs over Gi is still not fully understood. Here, we utilize solution nuclear magnetic resonance (NMR) spectroscopy and supporting molecular dynamics (MD) simulations to monitor the conformational changes in the G protein coupling interface of the beta2AR in response to the full agonist BI-167107 and Gs and Gi1 These results show that BI-167107 stabilizes conformational changes in four transmembrane segments (TM4, TM5, TM6, and TM7) prior to coupling to a G protein, and that the agonist-bound receptor conformation is different from the G protein coupled state. While most of the conformational changes observed in the beta2AR are qualitatively the same for Gs and Gi1, we detected distinct differences between the beta2AR-Gs and the beta2AR-Gi1 complex in intracellular loop 2 (ICL2). Interactions with ICL2 are essential for activation of Gs These differences between the beta2AR-Gs and beta2AR-Gi1 complexes in ICL2 may be key determinants for G protein coupling selectivity.

    View details for DOI 10.1073/pnas.2009786117

    View details for PubMedID 32868434

  • Structural mechanism underlying primary and secondary coupling between GPCRs and the Gi/o family. Nature communications Kim, H. R., Xu, J., Maeda, S., Duc, N. M., Ahn, D., Du, Y., Chung, K. Y. 2020; 11 (1): 3160


    Heterotrimeric G proteins are categorized into four main families based on their function and sequence, Gs, Gi/o, Gq/11, and G12/13. One receptor can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. However, the precise mechanism underlying different coupling efficiencies is unknown. Here, we study the structural mechanism underlying primary and secondary Gi/o coupling, using the muscarinic acetylcholine receptor type 2 (M2R) as the primary Gi/o-coupling receptor and the beta2-adrenergic receptor (beta2AR, which primarily couples to Gs) as the secondary Gi/o-coupling receptor. Hydrogen/deuterium exchange mass spectrometry and mutagenesis studies reveal that the engagement of the distal C-terminus of Galphai/o with the receptor differentiates primary and secondary Gi/o couplings. This study suggests that the conserved hydrophobic residue within the intracellular loop 2 of the receptor (residue 34.51) is not critical for primary Gi/o-coupling; however, it might be important for secondary Gi/o-coupling.

    View details for DOI 10.1038/s41467-020-16975-2

    View details for PubMedID 32572026

  • Activation of the alpha2B adrenoceptor by the sedative sympatholytic dexmedetomidine. Nature chemical biology Yuan, D., Liu, Z., Kaindl, J., Maeda, S., Zhao, J., Sun, X., Xu, J., Gmeiner, P., Wang, H., Kobilka, B. K. 2020


    The alpha2 adrenergic receptors (alpha2ARs) are G protein-coupled receptors (GPCRs) that respond to adrenaline and noradrenaline and couple to the Gi/o family of G proteins. alpha2ARs play important roles in regulating the sympathetic nervous system. Dexmedetomidine is a highly selective alpha2AR agonist used in post-operative patients as an anxiety-reducing, sedative medicine that decreases the requirement for opioids. As is typical for selective alphaAR agonists, dexmedetomidine consists of an imidazole ring and a substituted benzene moiety lacking polar groups, which is in contrast to betaAR-selective agonists, which share an ethanolamine group and an aromatic system with polar, hydrogen-bonding substituents. To better understand the structural basis for the selectivity and efficacy of adrenergic agonists, we determined the structure of the alpha2BAR in complex with dexmedetomidine and Go at a resolution of 2.9A by single-particle cryo-EM. The structure reveals the mechanism of alpha2AR-selective activation and provides insights into Gi/o coupling specificity.

    View details for DOI 10.1038/s41589-020-0492-2

    View details for PubMedID 32152538

  • Structure and selectivity engineering of the M1 muscarinic receptor toxin complex. Science (New York, N.Y.) Maeda, S. n., Xu, J. n., N Kadji, F. M., Clark, M. J., Zhao, J. n., Tsutsumi, N. n., Aoki, J. n., Sunahara, R. K., Inoue, A. n., Garcia, K. C., Kobilka, B. K. 2020; 369 (6500): 161–67


    Muscarinic toxins (MTs) are natural toxins produced by mamba snakes that primarily bind to muscarinic acetylcholine receptors (MAChRs) and modulate their function. Despite their similar primary and tertiary structures, MTs show distinct binding selectivity toward different MAChRs. The molecular details of how MTs distinguish MAChRs are not well understood. Here, we present the crystal structure of M1AChR in complex with MT7, a subtype-selective anti-M1AChR snake venom toxin. The structure reveals the molecular basis of the extreme subtype specificity of MT7 for M1AChR and the mechanism by which it regulates receptor function. Through in vitro engineering of MT7 finger regions that was guided by the structure, we have converted the selectivity from M1AChR toward M2AChR, suggesting that the three-finger fold is a promising scaffold for developing G protein-coupled receptor modulators.

    View details for DOI 10.1126/science.aax2517

    View details for PubMedID 32646996

  • Conformational Complexity and Dynamics in a Muscarinic Receptor Revealed by NMR Spectroscopy. Molecular cell Xu, J. n., Hu, Y. n., Kaindl, J. n., Risel, P. n., Hübner, H. n., Maeda, S. n., Niu, X. n., Li, H. n., Gmeiner, P. n., Jin, C. n., Kobilka, B. K. 2019


    The M2 muscarinic acetylcholine receptor (M2R) is a prototypical GPCR that plays important roles in regulating heart rate and CNS functions. Crystal structures provide snapshots of the M2R in inactive and active states, but the allosteric link between the ligand binding pocket and cytoplasmic surface remains poorly understood. Here we used solution NMR to examine the structure and dynamics of the M2R labeled with 13CH3-ε-methionine upon binding to various orthosteric and allosteric ligands having a range of efficacy for both G protein activation and arrestin recruitment. We observed ligand-specific changes in the NMR spectra of 13CH3-ε-methionine probes in the M2R extracellular domain, transmembrane core, and cytoplasmic surface, allowing us to correlate ligand structure with changes in receptor structure and dynamics. We show that the M2R has a complex energy landscape in which ligands with different efficacy profiles stabilize distinct receptor conformations.

    View details for DOI 10.1016/j.molcel.2019.04.028

    View details for PubMedID 31103421

  • Structure-based discovery of selective positive allosteric modulators of antagonists for the M-2 muscarinic acetylcholine receptor PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Korczynska, M., Clark, M. J., Valant, C., Xu, J., Von Moo, E., Albold, S., Weiss, D. R., Torosyan, H., Huang, W., Kruse, A. C., Lyda, B. R., May, L. T., Baltos, J., Sexton, P. M., Kobilka, B. K., Christopoulos, A., Shoichet, B. K., Sunahara, R. K. 2018; 115 (10): E2419–E2428


    Subtype-selective antagonists for muscarinic acetylcholine receptors (mAChRs) have long been elusive, owing to the highly conserved orthosteric binding site. However, allosteric sites of these receptors are less conserved, motivating the search for allosteric ligands that modulate agonists or antagonists to confer subtype selectivity. Accordingly, a 4.6 million-molecule library was docked against the structure of the prototypical M2 mAChR, seeking molecules that specifically stabilized antagonist binding. This led us to identify a positive allosteric modulator (PAM) that potentiated the antagonist N-methyl scopolamine (NMS). Structure-based optimization led to compound '628, which enhanced binding of NMS, and the drug scopolamine itself, with a cooperativity factor (α) of 5.5 and a KB of 1.1 μM, while sparing the endogenous agonist acetylcholine. NMR spectral changes determined for methionine residues reflected changes in the allosteric network. Moreover, '628 slowed the dissociation rate of NMS from the M2 mAChR by 50-fold, an effect not observed at the other four mAChR subtypes. The specific PAM effect of '628 on NMS antagonism was conserved in functional assays, including agonist stimulation of [35S]GTPγS binding and ERK 1/2 phosphorylation. Importantly, the selective allostery between '628 and NMS was retained in membranes from adult rat hypothalamus and in neonatal rat cardiomyocytes, supporting the physiological relevance of this PAM/antagonist approach. This study supports the feasibility of discovering PAMs that confer subtype selectivity to antagonists; molecules like '628 can convert an armamentarium of potent but nonselective GPCR antagonist drugs into subtype-selective reagents, thus reducing their off-target effects.

    View details for PubMedID 29453275