Stanford Advisors

All Publications

  • AlphaFold2 structures guide prospective ligand discovery. Science (New York, N.Y.) Lyu, J., Kapolka, N., Gumpper, R., Alon, A., Wang, L., Jain, M. K., Barros-Álvarez, X., Sakamoto, K., Kim, Y., DiBerto, J., Kim, K., Glenn, I. S., Tummino, T. A., Huang, S., Irwin, J. J., Tarkhanova, O. O., Moroz, Y., Skiniotis, G., Kruse, A. C., Shoichet, B. K., Roth, B. L. 2024: eadn6354


    AlphaFold2 (AF2) models have had wide impact, but they have had mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ2 and 5-HT2A receptors, testing hundreds of new molecules and comparing results to docking against the experimental structures. Hit rates were high and similar for the experimental and the AF2 structures, as were affinities. The success of docking against the AF2 models was achieved despite differences in orthosteric residue conformations versus the experimental structures. Determination of the cryo-electron microscopy structure for one of the more potent 5HT2A ligands from the AF2 docking revealed residue accommodations that resembled the AF2 prediction. AF2 models may sample conformations that differ from experimental structures but remain low energy and relevant for ligand discovery, extending the domain of structure-based ligand discovery.

    View details for DOI 10.1126/science.adn6354

    View details for PubMedID 38753765

  • Transport mechanism of human bilirubin transporter ABCC2 tuned by the inter-module regulatory domain. Nature communications Mao, Y. X., Chen, Z. P., Wang, L., Wang, J., Zhou, C. Z., Hou, W. T., Chen, Y. 2024; 15 (1): 1061


    Bilirubin is mainly generated from the breakdown of heme when red blood cells reach the end of their lifespan. Accumulation of bilirubin in human body usually leads to various disorders, including jaundice and liver disease. Bilirubin is conjugated in hepatocytes and excreted to bile duct via the ATP-binding cassette transporter ABCC2, dysfunction of which would lead to Dubin-Johnson syndrome. Here we determine the structures of ABCC2 in the apo, substrate-bound and ATP/ADP-bound forms using the cryo-electron microscopy, exhibiting a full transporter with a regulatory (R) domain inserted between the two half modules. Combined with substrate-stimulated ATPase and transport activity assays, structural analysis enables us to figure out transport cycle of ABCC2 with the R domain adopting various conformations. At the rest state, the R domain binding to the translocation cavity functions as an affinity filter that allows the substrates of high affinity to be transported in priority. Upon substrate binding, the R domain is expelled from the cavity and docks to the lateral of transmembrane domain following ATP hydrolysis. Our findings provide structural insights into a transport mechanism of ABC transporters finely tuned by the R domain.

    View details for DOI 10.1038/s41467-024-45337-5

    View details for PubMedID 38316776

    View details for PubMedCentralID PMC10844203

  • AlphaFold2 structures template ligand discovery. bioRxiv : the preprint server for biology Lyu, J., Kapolka, N., Gumpper, R., Alon, A., Wang, L., Jain, M. K., Barros-Álvarez, X., Sakamoto, K., Kim, Y., DiBerto, J., Kim, K., Tummino, T. A., Huang, S., Irwin, J. J., Tarkhanova, O. O., Moroz, Y., Skiniotis, G., Kruse, A. C., Shoichet, B. K., Roth, B. L. 2023


    AlphaFold2 (AF2) and RosettaFold have greatly expanded the number of structures available for structure-based ligand discovery, even though retrospective studies have cast doubt on their direct usefulness for that goal. Here, we tested unrefined AF2 models prospectively, comparing experimental hit-rates and affinities from large library docking against AF2 models vs the same screens targeting experimental structures of the same receptors. In retrospective docking screens against the σ2 and the 5-HT2A receptors, the AF2 structures struggled to recapitulate ligands that we had previously found docking against the receptors' experimental structures, consistent with published results. Prospective large library docking against the AF2 models, however, yielded similar hit rates for both receptors versus docking against experimentally-derived structures; hundreds of molecules were prioritized and tested against each model and each structure of each receptor. The success of the AF2 models was achieved despite differences in orthosteric pocket residue conformations for both targets versus the experimental structures. Intriguingly, against the 5-HT2A receptor the most potent, subtype-selective agonists were discovered via docking against the AF2 model, not the experimental structure. To understand this from a molecular perspective, a cryoEM structure was determined for one of the more potent and selective ligands to emerge from docking against the AF2 model of the 5-HT2A receptor. Our findings suggest that AF2 models may sample conformations that are relevant for ligand discovery, much extending the domain of applicability of structure-based ligand discovery.

    View details for DOI 10.1101/2023.12.20.572662

    View details for PubMedID 38187536

    View details for PubMedCentralID PMC10769324

  • Placing steroid hormones within the human ABCC3 transporter reveals a compatible amphiphilic substrate-binding pocket. The EMBO journal Wang, J., Li, X., Wang, F. F., Cheng, M. T., Mao, Y. X., Fang, S. C., Wang, L., Zhou, C. Z., Hou, W. T., Chen, Y. 2023; 42 (17): e113415


    The human ABC transporter ABCC3 (also known as MRP3) transports a wide spectrum of substrates, including endogenous metabolites and exogenous drugs. Accordingly, it participates in multiple physiological processes and is involved in diverse human diseases such as intrahepatic cholestasis of pregnancy, which is caused by the intracellular accumulation of bile acids and estrogens. Here, we report three cryogenic electron microscopy structures of ABCC3: in the apo-form and in complexed forms bound to either the conjugated sex hormones β-estradiol 17-(β-D-glucuronide) and dehydroepiandrosterone sulfate. For both hormones, the steroid nuclei that superimpose against each other occupy the hydrophobic center of the transport cavity, whereas the two conjugation groups are separated and fixed by the hydrophilic patches in two transmembrane domains. Structural analysis combined with site-directed mutagenesis and ATPase activity assays revealed that ABCC3 possesses an amphiphilic substrate-binding pocket able to hold either conjugated hormone in an asymmetric pattern. These data build on consensus features of the substrate-binding pocket of MRPs and provide a structural platform for the rational design of inhibitors.

    View details for DOI 10.15252/embj.2022113415

    View details for PubMedID 37485728

    View details for PubMedCentralID PMC10476276

  • Structural insights into human ABCC4-mediated transport of platelet agonist and antagonist NATURE CARDIOVASCULAR RESEARCH Chen, Y., Wang, L., Hou, W., Zha, Z., Xu, K., Zhou, C., Li, Q., Chen, Y. 2023; 2 (7): 693-+
  • Plastic structures for diverse substrates: A revisit of human ABC transporters PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Hou, W., Xu, D., Wang, L., Chen, Y., Chen, Z., Zhou, C., Chen, Y. 2022; 90 (10): 1749-1765


    ATP-binding cassette (ABC) superfamily is one of the largest groups of primary active transporters that could be found in all kingdoms of life from bacteria to humans. In humans, ABC transporters can selectively transport a wide spectrum of substrates across membranes, thus playing a pivotal role in multiple physiological processes. In addition, due to the ability of exporting clinic therapeutics, some ABC transporters were originally termed multidrug resistance proteins. Increasing investigations of human ABC transporters in recent years have provided abundant information for elucidating their structural features, based on the structures at distinct states in a transport cycle. This review focuses on the recent progress in human ABC structural analyses, substrate binding specificities, and translocation mechanisms. We dedicate to summarize the common features of human ABC transporters in different subfamilies, and to discuss the possibility to apply the fast-developing techniques, such as cryogenic electron microscopy, and artificial intelligence-assisted structure prediction, for future studies.

    View details for DOI 10.1002/prot.26406

    View details for Web of Science ID 000844709700001

    View details for PubMedID 35924777

  • Structural basis of substrate recognition and translocation by human very long-chain fatty acid transporter ABCD1. Nature communications Chen, Z. P., Xu, D., Wang, L., Mao, Y. X., Li, Y., Cheng, M. T., Zhou, C. Z., Hou, W. T., Chen, Y. 2022; 13 (1): 3299


    Human ABC transporter ABCD1 transports very long-chain fatty acids from cytosol to peroxisome for β-oxidation, dysfunction of which usually causes the X-linked adrenoleukodystrophy (X-ALD). Here, we report three cryogenic electron microscopy structures of ABCD1: the apo-form, substrate- and ATP-bound forms. Distinct from what was seen in the previously reported ABC transporters, the two symmetric molecules of behenoyl coenzyme A (C22:0-CoA) cooperatively bind to the transmembrane domains (TMDs). For each C22:0-CoA, the hydrophilic 3'-phospho-ADP moiety of CoA portion inserts into one TMD, with the succeeding pantothenate and cysteamine moiety crossing the inter-domain cavity, whereas the hydrophobic fatty acyl chain extends to the opposite TMD. Structural analysis combined with biochemical assays illustrates snapshots of ABCD1-mediated substrate transport cycle. It advances our understanding on the selective oxidation of fatty acids and molecular pathology of X-ALD.

    View details for DOI 10.1038/s41467-022-30974-5

    View details for PubMedID 35676282

  • Structure and transport mechanism of the human cholesterol transporter ABCG1 CELL REPORTS Xu, D., Li, Y., Yang, F., Sun, C., Pan, J., Wang, L., Chen, Z., Fang, S., Yao, X., Hou, W., Zhou, C., Chen, Y. 2022; 38 (4): 110298


    The reverse cholesterol transport pathway is responsible for the maintenance of human cholesterol homeostasis, an imbalance of which usually leads to atherosclerosis. As a key component of this pathway, the ATP-binding cassette transporter ABCG1 forwards cellular cholesterol to the extracellular acceptor nascent high-density lipoprotein (HDL). Here, we report a 3.26-Å cryo-electron microscopy structure of cholesterol-bound ABCG1 in an inward-facing conformation, which represents a turnover condition upon ATP binding. Structural analyses combined with functional assays reveals that a cluster of conserved hydrophobic residues, in addition to two sphingomyelins, constitute a well-defined cholesterol-binding cavity. The exit of this cavity is closed by three pairs of conserved Phe residues, which constitute a hydrophobic path for the release of cholesterol in an acceptor concentration-dependent manner. Overall, we propose an ABCG1-driven cholesterol transport cycle initiated by sphingomyelin-assisted cholesterol recruitment and accomplished by the release of cholesterol to HDL.

    View details for DOI 10.1016/j.celrep.2022.110298

    View details for Web of Science ID 000750976000008

    View details for PubMedID 35081353

  • Structures of human bile acid exporter ABCB11 reveal a transport mechanism facilitated by two tandem substrate-binding pockets CELL RESEARCH Wang, L., Hou, W., Wang, J., Xu, D., Guo, C., Sun, L., Ruan, K., Zhou, C., Chen, Y. 2022; 32 (5): 501-504

    View details for DOI 10.1038/s41422-021-00611-9

    View details for Web of Science ID 000743886500001

    View details for PubMedID 35043010

    View details for PubMedCentralID PMC9061823

  • A gain-of-function mutation of the MATE family transporter DTX6 confers paraquat resistance in Arabidopsis MOLECULAR PLANT Xia, J., Nazish, T., Javaid, A., Ali, M., Liu, Q., Wang, L., Zhang, Z., Zhang, Z., Huang, Y., Wu, J., Yang, Z., Sun, L., Chen, Y., Xiang, C. 2021; 14 (12): 2126-2133


    Paraquat is one of the most widely used nonselective herbicides and has elicited the emergence of paraquat-resistant weeds. However, the molecular mechanisms of paraquat resistance are not completely understood. Here we report the Arabidopsis gain-of-function mutant pqt15-D with significantly enhanced resistance to paraquat and the corresponding gene PQT15, which encodes the Multidrug and Toxic Extrusion (MATE) transporter DTX6. A point mutation at +932 bp in DTX6 causes a G311E amino acid substitution, enhancing the paraquat resistance of pqt15-D, and overexpression of DTX6/PQT15 in the wild-type plants also results in strong paraquat resistance. Moreover, heterologous expression of DTX6 and DTX6-D in Escherichia coli significantly enhances bacterial resistance to paraquat. Importantly, overexpression of DTX6-D enables Arabidopsis plants to tolerate 4 mM paraquat, a near-commercial application level. DTX6/PQT15 is localized in the plasma membrane and endomembrane, and functions as a paraquat efflux transporter as demonstrated by paraquat efflux assays with isolated protoplasts and bacterial cells. Taken together, our results demonstrate that DTX6/PQT15 is an efflux transporter that confers paraquat resistance by exporting paraquat out of the cytosol. These findings reveal a molecular mechanism of paraquat resistance in higher plants and provide a promising candidate gene for engineering paraquat-resistant crops.

    View details for DOI 10.1016/j.molp.2021.09.004

    View details for Web of Science ID 000729175700017

    View details for PubMedID 34509638

  • Structures of cyanobacterial bicarbonate transporter SbtA and its complex with PII-like SbtB CELL DISCOVERY Liu, X., Hou, W., Wang, L., Li, B., Chen, Y., Chen, Y., Jiang, Y., Zhou, C. 2021; 7 (1): 63

    View details for DOI 10.1038/s41421-021-00287-w

    View details for Web of Science ID 000685106500003

    View details for PubMedID 34373447

    View details for PubMedCentralID PMC8352866

  • Cryo-EM structure of human bile salts exporter ABCB11 CELL RESEARCH Wang, L., Hou, W., Chen, L., Jiang, Y., Xu, D., Sun, L., Zhou, C., Chen, Y. 2020; 30 (7): 623-625

    View details for DOI 10.1038/s41422-020-0302-0

    View details for Web of Science ID 000520828000001

    View details for PubMedID 32203132

    View details for PubMedCentralID PMC7343855

  • Cryo-EM structure of human lysosomal cobalamin exporter ABCD4 CELL RESEARCH Xu, D., Feng, Z., Hou, W., Jiang, Y., Wang, L., Sun, L., Zhou, C., Chen, Y. 2019; 29 (12): 1039-1041

    View details for DOI 10.1038/s41422-019-0222-z

    View details for Web of Science ID 000500749600010

    View details for PubMedID 31467407

    View details for PubMedCentralID PMC6951267