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Chen Y, Wang J, Zheng C, Liu Z. Cryo-Electron Microscopy in the Study of Antiviral Innate Immunity. Methods Mol Biol 2025; 2854:177-188. [PMID: 39192129 DOI: 10.1007/978-1-0716-4108-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Cryo-electron microscopy is a powerful methodology in structural biology and has been broadly used in high-resolution structure determination for challenging samples, which are not readily available for traditional techniques. In particular, the strength of super macro-complexes and the lack of a need for crystals for cryo-EM make this technique feasible for the structural study of complexes involved in antiviral innate immunity. This chapter presents detailed information and experimental procedures of Cryo-EM for determining the structures of the complexes using STING as an example. The procedures included a sample quality check, high-resolution data acquisition, and image processing for Cryo-EM 3D structure determination.
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Affiliation(s)
- Yan Chen
- School of Medicine, Shaoguan University, Shaoguan, Guangdong, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Jingyu Wang
- Distinct HealthCare Medical Center, Changsha Section, Shenzhen, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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2
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Wu Z, Chen G, Qiu C, Yan X, Xu L, Jiang S, Xu J, Han R, Shi T, Liu Y, Gao W, Wang Q, Li J, Ye F, Pan X, Zhang Z, Ning P, Zhang B, Chen J, Du Y. Structural basis for the ligand recognition and G protein subtype selectivity of kisspeptin receptor. SCIENCE ADVANCES 2024; 10:eadn7771. [PMID: 39151001 PMCID: PMC11328905 DOI: 10.1126/sciadv.adn7771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 07/11/2024] [Indexed: 08/18/2024]
Abstract
Kisspeptin receptor (KISS1R), belonging to the class A peptide-GPCR family, plays a key role in the regulation of reproductive physiology after stimulation by kisspeptin and is regarded as an attractive drug target for reproductive diseases. Here, we demonstrated that KISS1R can couple to the Gi/o pathway besides the well-known Gq/11 pathway. We further resolved the cryo-electron microscopy (cryo-EM) structure of KISS1R-Gq and KISS1R-Gi complexes bound to the synthetic agonist TAK448 and structure of KISS1R-Gq complex bound to the endogenous agonist KP54. The high-resolution structures provided clear insights into mechanism of KISS1R recognition by its ligand and can facilitate the design of targeted drugs with high affinity to improve treatment effects. Moreover, the structural and functional analyses indicated that conformational differences in the extracellular loops (ECLs), intracellular loops (ICLs) of the receptor, and the "wavy hook" of the Gα subunit may account for the specificity of G protein coupling for KISS1R signaling.
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Affiliation(s)
- Zhangsong Wu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Geng Chen
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Chen Qiu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Xiaoyi Yan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Lezhi Xu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Shirui Jiang
- The Huanan Affiliated Hospital of Shenzhen University, Shenzhen University, 518000 Shenzhen, Guangdong, China
| | - Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Runyuan Han
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tingyi Shi
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Yiming Liu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Wei Gao
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Qian Wang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
- The Huanan Affiliated Hospital of Shenzhen University, Shenzhen University, 518000 Shenzhen, Guangdong, China
| | - Jiancheng Li
- Instrumental Analysis Center, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Fang Ye
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Xin Pan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Zhiyi Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Peiruo Ning
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Binghao Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Jing Chen
- Neurobiology Institute, Jining Medical University, 272067 Jining, Shandong, China
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
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3
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Zhu Y, Xing X, Wang F, Chen L, Zhong C, Lu X, Yu Z, Yang Y, Yao Y, Song Q, Han S, Liu Z, Zhang P. The ATP-bound inward-open conformation of ABCC4 reveals asymmetric ATP binding for substrate transport. FEBS Lett 2024; 598:1967-1980. [PMID: 38886124 DOI: 10.1002/1873-3468.14955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
The multidrug resistance-associated protein (MRP) ABCC4 facilitates substrate transport across the cytoplasmic membrane, crucial for normal physiology and mediating multidrug resistance in tumor cells. Despite intensive studies on MRPs, ABCC4's transport mechanism remains incompletely understood. In this study, we unveiled an inward-open conformation with an ATP bound to degenerate NBD1. Additionally, we captured the structure with both ATP and substrate co-bound in the inward-open state. Our findings uncover the asymmetric ATP binding in ABCC4 and provide insights into substrate binding and transport mechanisms. ATP binding to NBD1 is parallel to substrate binding to ABCC4, and is a prerequisite for ATP-bound NBD2-induced global conformational changes. Our findings shed new light on targeting ABCC4 in combination with anticancer therapy.
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Affiliation(s)
- Yue Zhu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, China
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Xiaoke Xing
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Fuxing Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, China
| | - Luojun Chen
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Chunhui Zhong
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, China
| | - Xiting Lu
- School of Applied Biology, Shenzhen Institute of Technology, China
| | - Zhanwang Yu
- School of Applied Biology, Shenzhen Institute of Technology, China
| | - Yongbo Yang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, China
| | - Suxia Han
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, China
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, China
| | - Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, China
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4
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Zhang P, Liu Z. Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation. Nat Commun 2024; 15:3404. [PMID: 38649359 PMCID: PMC11035591 DOI: 10.1038/s41467-024-47783-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic.
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Affiliation(s)
- Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
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5
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Pan X, Ye F, Ning P, Zhang Z, Li X, Zhang B, Wang Q, Chen G, Gao W, Qiu C, Wu Z, Li J, Zhu L, Xia J, Gong K, Du Y. Structural insights into ligand recognition and selectivity of the human hydroxycarboxylic acid receptor HCAR2. Cell Discov 2023; 9:118. [PMID: 38012147 PMCID: PMC10682194 DOI: 10.1038/s41421-023-00610-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
Hydroxycarboxylic acid receptor 2 (HCAR2) belongs to the family of class A G protein-coupled receptors with key roles in regulating lipolysis and free fatty acid formation in humans. It is deeply involved in many pathophysiological processes and serves as an attractive target for the treatment of cardiovascular, neoplastic, autoimmune, neurodegenerative, inflammatory, and metabolic diseases. Here, we report four cryo-EM structures of human HCAR2-Gi1 complexes with or without agonists, including the drugs niacin (2.69 Å) and acipimox (3.23 Å), the highly subtype-specific agonist MK-6892 (3.25 Å), and apo form (3.28 Å). Combined with molecular dynamics simulation and functional analysis, we have revealed the recognition mechanism of HCAR2 for different agonists and summarized the general pharmacophore features of HCAR2 agonists, which are based on three key residues R1113.36, S17945.52, and Y2847.43. Notably, the MK-6892-HCAR2 structure shows an extended binding pocket relative to other agonist-bound HCAR2 complexes. In addition, the key residues that determine the ligand selectivity between the HCAR2 and HCAR3 are also illuminated. Our findings provide structural insights into the ligand recognition, selectivity, activation, and G protein coupling mechanism of HCAR2, which shed light on the design of new HCAR2-targeting drugs for greater efficacy, higher selectivity, and fewer or no side effects.
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Affiliation(s)
- Xin Pan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
| | - Fang Ye
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Peiruo Ning
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zhiyi Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Xinyu Li
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Binghao Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Qian Wang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Geng Chen
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Wei Gao
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Chen Qiu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zhangsong Wu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Jiancheng Li
- Instrumental Analysis Center, Shenzhen University, Shenzhen, Guangdong, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Kaizheng Gong
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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6
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Fink EA, Xu J, Hübner H, Braz JM, Seemann P, Avet C, Craik V, Weikert D, Schmidt MF, Webb CM, Tolmachova NA, Moroz YS, Huang XP, Kalyanaraman C, Gahbauer S, Chen G, Liu Z, Jacobson MP, Irwin JJ, Bouvier M, Du Y, Shoichet BK, Basbaum AI, Gmeiner P. Structure-based discovery of nonopioid analgesics acting through the α 2A-adrenergic receptor. Science 2022; 377:eabn7065. [PMID: 36173843 PMCID: PMC10360211 DOI: 10.1126/science.abn7065] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Elissa A. Fink
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Graduate Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Jun Xu
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Joao M. Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Philipp Seemann
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Charlotte Avet
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Maximilian F. Schmidt
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Chase M. Webb
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
| | - Nataliya A. Tolmachova
- Enamine Ltd., 02094 Kyiv, Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry, National Ukrainian Academy of Science, 02660 Kyiv, Ukraine
| | - Yurii S. Moroz
- National Taras Shevchenko University of Kyiv, 01601 Kyiv, Ukraine
- Chemspace, Riga LV-1082, Latvia
| | - Xi-Ping Huang
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Geng Chen
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Allan I. Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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7
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Chen G, Xu J, Inoue A, Schmidt MF, Bai C, Lu Q, Gmeiner P, Liu Z, Du Y. Activation and allosteric regulation of the orphan GPR88-Gi1 signaling complex. Nat Commun 2022; 13:2375. [PMID: 35501348 PMCID: PMC9061749 DOI: 10.1038/s41467-022-30081-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/12/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractGPR88 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 α5 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.
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8
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Structural basis of the ligand binding and signaling mechanism of melatonin receptors. Nat Commun 2022; 13:454. [PMID: 35075127 PMCID: PMC8786939 DOI: 10.1038/s41467-022-28111-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Melatonin receptors (MT1 and MT2 in humans) are family A G protein-coupled receptors that respond to the neurohormone melatonin to regulate circadian rhythm and sleep. Numerous efforts have been made to develop drugs targeting melatonin receptors for the treatment of insomnia, circadian rhythm disorder, and cancer. However, designing subtype-selective melatonergic drugs remains challenging. Here, we report the cryo-EM structures of the MT1-Gi signaling complex with 2-iodomelatonin and ramelteon and the MT2-Gi signaling complex with ramelteon. These structures, together with the reported functional data, reveal that although MT1 and MT2 possess highly similar orthosteric ligand-binding pockets, they also display distinctive features that could be targeted to design subtype-selective drugs. The unique structural motifs in MT1 and MT2 mediate structural rearrangements with a particularly wide opening on the cytoplasmic side. Gi is engaged in the receptor core shared by MT1 and MT2 and presents a conformation deviating from those in other Gi complexes. Together, our results provide new clues for designing melatonergic drugs and further insights into understanding the G protein coupling mechanism.
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9
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Wang Z, Hardies SC, Fokine A, Klose T, Jiang W, Cho BC, Rossmann MG. Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes. Structure 2017; 26:238-248.e3. [PMID: 29290487 DOI: 10.1016/j.str.2017.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/16/2017] [Accepted: 12/01/2017] [Indexed: 01/08/2023]
Abstract
Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of most of these proteins have been predicted by bioinformatic methods. A 3.6 Å resolution cryoelectron microscopy map of the icosahedrally averaged TW1 head showed the atomic structures of the major capsid protein, gp57∗, and the capsid-stabilizing protein, gp56. The gp57∗ structure is similar to that of the phage HK97 capsid protein. The gp56 protein has two domains, each having folds similar to that of the N-terminal part of phage λ gpD, indicating a common ancestry. The first gp56 domain clamps adjacent capsomers together, whereas the second domain is required for trimerization. A 6-fold-averaged reconstruction of the distal part of the tail showed that TW1 has six tail spikes, which are unusual for siphophages but are similar to the podophages P22 and Sf6, suggesting a common evolutionary origin of these spikes.
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Affiliation(s)
- Zhiqing Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Stephen C Hardies
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 151-742, Korea
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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10
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Structure, Immunogenicity, and Protective Mechanism of an Engineered Enterovirus 71-Like Particle Vaccine Mimicking 80S Empty Capsid. J Virol 2017; 92:JVI.01330-17. [PMID: 29070691 DOI: 10.1128/jvi.01330-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/12/2017] [Indexed: 01/20/2023] Open
Abstract
Enterovirus 71 (EV71) is the major causative agent of severe hand, foot, and mouth disease, which affects millions of young children in the Asia-Pacific region annually. In this study, we engineered a novel EV71 virus-like particle (VLP) that lacks VP4 (therefore designated VLPΔVP4) and investigated its structure, antigenicity, and vaccine potential. The cryo-electron microscopy (cryo-EM) structure of VLPΔVP4 was reconstructed to 3.71-Å resolution. Results from structural and biochemical analyses revealed that VLPΔVP4 resembles the end product of the viral uncoating process, the 80S empty capsid. VLPΔVP4 is able to elicit high-titer neutralizing antibodies and to fully protect mice against lethal viral challenge. Mechanistic studies showed that, at the cellular level, the anti-VLPΔVP4 sera exert neutralization effects at both pre- and postattachment stages by inhibiting both virus attachment and internalization, and at the molecular level, the antisera can block multiple interactions between EV71 and its key receptors. Our study gives a better understanding of EV71 capsid assembly and provides important information for the design and development of new-generation vaccines for EV71, and perhaps for other enteroviruses, as well.IMPORTANCE Enterovirus 71 (EV71) infection may lead to severe hand, foot, and mouth disease, with significant morbidity and mortality. Knowledge regarding EV71 particle assembly remains limited. Here, we report the generation and characterization of a novel EV71 virus-like particle that lacks the VP4 capsid subunit protein. This particle, termed VLPΔVP4, structurally mimics the 80S empty capsid, which is the end stage of EV71 uncoating. We further show that VLPΔVP4 exhibits desirable immunogenicity and protective efficacy in proof-of-concept studies. In addition, the inhibitory mechanisms of the VLPΔVP4-induced antibodies are unraveled at both the cellular and molecular levels. Our work provides the first evidence of picornaviral particle assembly in the complete absence of VP4 and identifies VLPΔVP4 as an improved EV71 vaccine candidate with desirable traits. These findings not only enhance our understanding of particle assembly and uncoating of picornaviruses, but also provide important information for structure-guided vaccine design for EV71 and other enteroviruses.
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11
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Yu G, Li K, Huang P, Jiang X, Jiang W. Antibody-Based Affinity Cryoelectron Microscopy at 2.6-Å Resolution. Structure 2017; 24:1984-1990. [PMID: 27806259 DOI: 10.1016/j.str.2016.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/16/2016] [Accepted: 09/30/2016] [Indexed: 02/02/2023]
Abstract
The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration.
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Affiliation(s)
- Guimei Yu
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Pengwei Huang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Wen Jiang
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.
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12
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Beta-Propiolactone Inactivation of Coxsackievirus A16 Induces Structural Alteration and Surface Modification of Viral Capsids. J Virol 2017; 91:JVI.00038-17. [PMID: 28148783 DOI: 10.1128/jvi.00038-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 11/20/2022] Open
Abstract
Beta-propiolactone (BPL) is an inactivating agent that is widely used in the vaccine industry. However, its effects on vaccine protein antigens and its mechanisms of action remain poorly understood. Here we present cryo-electron microscopy (cryo-EM) structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids at resolutions of 3.9 Å and 6.5 Å, respectively. Notably, both particles were found to adopt an expanded conformation resembling the 135S-like uncoating intermediate, with characteristic features including an opened 2-fold channel, the externalization of the N terminus of VP1 capsid protein, and the absence of pocket factor. However, major neutralizing epitopes are very well preserved on these particles. Further biochemical analyses revealed that BPL treatment impairs the abilities of CVA16 particles to bind to the attachment receptor heparan sulfate and to a conformation-dependent monoclonal antibody in a BPL dose-dependent manner, indicating that BPL is able to modify surface-exposed amino acid residues. Taken together, our results demonstrate that BPL treatment may induce alteration of the overall structure and surface properties of a nonenveloped viral capsid, thus revealing a novel mode of action of BPL.IMPORTANCE Beta-propiolactone (BPL) is commonly used as an inactivating reagent to produce viral vaccines. It is recognized that BPL inactivates viral infectivity through modification of viral nucleic acids. However, its effect on viral proteins remains largely unknown. Here, we present high-resolution cryo-EM structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids, which reveals an expanded overall conformation and characteristic features that are typical for the 135S-like uncoating intermediate. We further show that the BPL concentration affects the binding of inactivated CVA16 particles to their receptor/antibody. Thus, BPL treatment can alter the overall structure and surface properties of viral capsids, which may lead to antigenic and immunogenic variations. Our findings provide important information for future development of BPL-inactivated vaccines.
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13
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Yan R, Li K, Jiang W. Real-time detection and single-pass minimization of TEM objective lens astigmatism. J Struct Biol 2016; 197:210-219. [PMID: 27838367 DOI: 10.1016/j.jsb.2016.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/29/2016] [Accepted: 11/04/2016] [Indexed: 11/28/2022]
Abstract
Minimization of the astigmatism of the objective lens is a critical daily instrument alignment task essential for high resolution TEM imaging. Fast and sensitive detection of astigmatism is needed to provide real-time feedback and adjust the stigmators to efficiently reduce astigmatism. Currently the method used by many microscopists is to visually examine the roundness of a diffractogram (Thon rings) and iteratively adjust the stigmators to make the Thon rings circular. This subjective method is limited by poor sensitivity and potentially biased by the astigmatism of human eyes. In this study, an s2 power spectra based method, s2stigmator, was developed to allow fast and sensitive detection of the astigmatism in TEM live images. The "radar"-style display provides real-time feedback to guide the adjustment of the objective lens stigmators. Such unique capability allowed us to discover the mapping of the two stigmators to the astigmatism amplitude and angle, which led us to develop a single-pass tuning strategy capable of significantly quicker minimization of the objective lens astigmatism.
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Affiliation(s)
- Rui Yan
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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Liu Z, Gutierrez-Vargas C, Wei J, Grassucci RA, Sun M, Espina N, Madison-Antenucci S, Tong L, Frank J. Determination of the ribosome structure to a resolution of 2.5 Å by single-particle cryo-EM. Protein Sci 2016; 26:82-92. [PMID: 27750394 DOI: 10.1002/pro.3068] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/06/2022]
Abstract
With the advance of new instruments and algorithms, and the accumulation of experience over decades, single-particle cryo-EM has become a pivotal part of structural biology. Recently, we determined the structure of a eukaryotic ribosome at 2.5 Å for the large subunit. The ribosome was derived from Trypanosoma cruzi, the protozoan pathogen of Chagas disease. The high-resolution density map allowed us to discern a large number of unprecedented details including rRNA modifications, water molecules, and ions such as Mg2+ and Zn2+ . In this paper, we focus on the procedures for data collection, image processing, and modeling, with particular emphasis on factors that contributed to the attainment of high resolution. The methods described here are readily applicable to other macromolecules for high-resolution reconstruction by single-particle cryo-EM.
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Affiliation(s)
- Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032
| | - Cristina Gutierrez-Vargas
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Jia Wei
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Robert A Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032
| | - Ming Sun
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Noel Espina
- Division of Infectious Diseases, New York State Department of Health, Wadsworth Center, Albany, New York, 12201
| | - Susan Madison-Antenucci
- Division of Infectious Diseases, New York State Department of Health, Wadsworth Center, Albany, New York, 12201
| | - Liang Tong
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032.,Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032.,Department of Biological Sciences, Columbia University, New York, New York, 10027
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15
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Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit. Proc Natl Acad Sci U S A 2016; 113:12174-12179. [PMID: 27791004 DOI: 10.1073/pnas.1614594113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared with other eukaryotic ribosomes. To investigate the architecture of the trypanosomatid ribosomes, we determined the 2.5-Å structure of the Trypanosoma cruzi ribosome large subunit by single-particle cryo-EM. Examination of this structure and comparative analysis of the yeast ribosomal assembly pathway allowed us to develop a stepwise assembly model for the eight pieces of the large subunit rRNAs and a number of ancillary "glue" proteins. This model can be applied to the characterization of Trypanosoma brucei and Leishmania spp. ribosomes as well. Together with other details, our atomic-level structure may provide a foundation for structure-based design of antitrypanosome drugs.
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Structure determination of a human virus by the combination of cryo-EM and X-ray crystallography. BIOPHYSICS REPORTS 2016; 2:55-68. [PMID: 28018964 PMCID: PMC5138254 DOI: 10.1007/s41048-016-0027-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/17/2016] [Indexed: 01/16/2023] Open
Abstract
Virus 3D atomic structures provide insight into our understanding of viral life cycles and the development of antiviral drugs. X-ray crystallography and cryo-EM have been used to determine the atomic structure of viruses. However, limited availability of biological samples, biosafety issues due to virus infection, and sometimes inherent characteristics of viruses, pose difficulties on combining both methods in determining viral structures. These have made solving the high resolution structure of some medically important viruses very challenging. Here, we describe our recently employed protocols for determining the high-resolution structure of the virus-like particle of hepatitis E virus (HEV), a pathogen of viral hepatitis in human. These protocols include utilizing recombinant baculovirus system to generate sufficient amount of virus particles, single-particle cryo-EM to get an intermediate resolution structure as a phasing model, and X-ray crystallography for final atomic structure determination. Our protocols have solved the hepatitis E virus structure to the resolution of 3.5 Å. The combined methodology is generally applicable to other human infectious viruses.
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17
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Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3. J Virol 2016; 90:7628-39. [PMID: 27279624 PMCID: PMC4988150 DOI: 10.1128/jvi.00746-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/31/2016] [Indexed: 12/14/2022] Open
Abstract
In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae. SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an “altered” particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection. IMPORTANCE A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3. Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm.
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18
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Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma. Proc Natl Acad Sci U S A 2016; 113:8997-9002. [PMID: 27511920 DOI: 10.1073/pnas.1606595113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic structures of the full virion and native empty particle (NEP) of RV-C15a. The virus has 60 "fingers" on the virus outer surface that probably function as dominant immunogens. Because the NEPs also display these fingers, they may have utility as vaccine candidates. A sequence-conserved surface depression adjacent to each finger forms a likely binding site for the sialic acid on its receptor. The RV-C, unlike other EVs, are resistant to capsid-binding antiviral compounds because the hydrophobic pocket in VP1 is filled with multiple bulky residues. These results define potential molecular determinants for designing antiviral therapeutics and vaccines.
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19
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Yu G, Li K, Liu Y, Chen Z, Wang Z, Yan R, Klose T, Tang L, Jiang W. An algorithm for estimation and correction of anisotropic magnification distortion of cryo-EM images without need of pre-calibration. J Struct Biol 2016; 195:207-215. [PMID: 27270241 DOI: 10.1016/j.jsb.2016.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 11/17/2022]
Abstract
Anisotropic magnification distortion of TEM images (mainly the elliptic distortion) has been recently found as a potential resolution-limiting factor in single particle 3-D reconstruction. Elliptic distortions of ∼1-3% have been reported for multiple microscopes under low magnification settings (e.g., 18,000×), which significantly limited the achievable resolution of single particle 3-D reconstruction, especially for large particles. Here we report a generic algorithm that formulates the distortion correction problem as a generalized 2-D alignment task and estimates the distortion parameters directly from the particle images. Unlike the present pre-calibration methods, our computational method is applicable to all datasets collected at a broad range of magnifications using any microscope without need of additional experimental measurements. Moreover, the per-micrograph and/or per-particle level elliptic distortion estimation in our method could resolve potential distortion variations within a cryo-EM dataset, and further improve the 3-D reconstructions relative to constant-value correction by the pre-calibration methods. With successful applications to multiple datasets and cross-validation with the pre-calibration method, we have demonstrated the validity and robustness of our algorithm in estimating the distortion; correction of the elliptic distortion significantly improved the achievable resolutions by ∼1-3 folds and enabled 3-D reconstructions of multiple viral structures at 2.4-2.6Å resolutions. The resolution limits with elliptic distortion and the amounts of resolution improvements with distortion correction were found to strongly correlate with the product of the particle size and the amount of distortion, which can help assess if elliptic distortion is a major resolution limiting factor for single particle cryo-EM projects.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Yue Liu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Zhenguo Chen
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Zhiqing Wang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Thomas Klose
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Liang Tang
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA.
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20
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Structural Basis for Recognition of Human Enterovirus 71 by a Bivalent Broadly Neutralizing Monoclonal Antibody. PLoS Pathog 2016; 12:e1005454. [PMID: 26938634 PMCID: PMC4777393 DOI: 10.1371/journal.ppat.1005454] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/23/2016] [Indexed: 02/01/2023] Open
Abstract
Enterovirus 71 (EV71) is the main pathogen responsible for hand, foot and mouth disease with severe neurological complications and even death in young children. We have recently identified a highly potent anti-EV71 neutralizing monoclonal antibody, termed D5. Here we investigated the structural basis for recognition of EV71 by the antibody D5. Four three-dimensional structures of EV71 particles in complex with IgG or Fab of D5 were reconstructed by cryo-electron microscopy (cryo-EM) single particle analysis all at subnanometer resolutions. The most critical EV71 mature virion-Fab structure was resolved to a resolution of 4.8 Å, which is rare in cryo-EM studies of virus-antibody complex so far. The structures reveal a bivalent binding pattern of D5 antibody across the icosahedral 2-fold axis on mature virion, suggesting that D5 binding may rigidify virions to prevent their conformational changes required for subsequent RNA release. Moreover, we also identified that the complementary determining region 3 (CDR3) of D5 heavy chain directly interacts with the extremely conserved VP1 GH-loop of EV71, which was validated by biochemical and virological assays. We further showed that D5 is indeed able to neutralize a variety of EV71 genotypes and strains. Moreover, D5 could potently confer protection in a mouse model of EV71 infection. Since the conserved VP1 GH-loop is involved in EV71 binding with its uncoating receptor, the scavenger receptor class B, member 2 (SCARB2), the broadly neutralizing ability of D5 might attribute to its inhibition of EV71 from binding SCARB2. Altogether, our results elucidate the structural basis for the binding and neutralization of EV71 by the broadly neutralizing antibody D5, thereby enhancing our understanding of antibody-based protection against EV71 infection.
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21
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Liu Z, Guo F, Wang F, Li TC, Jiang W. 2.9 Å Resolution Cryo-EM 3D Reconstruction of Close-Packed Virus Particles. Structure 2016; 24:319-28. [PMID: 26777413 DOI: 10.1016/j.str.2015.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/14/2015] [Accepted: 12/14/2015] [Indexed: 01/15/2023]
Abstract
Single-particle cryoelectron microscopy typically discards close-packed particle images as unusable data. Here, we report an image processing strategy and case study of obtaining near-atomic resolution 3D reconstructions from close-packed particles. Multiple independent de novo initial models were constructed to determine and cross-validate the particle parameters. The particles with consistent views were further refined including not only Euler angles and center positions but also defocus, astigmatism, beam tilt, and overall and anisotropic magnification. We demonstrated this strategy with a 2.9 Å resolution reconstruction of a 1.67 MDa virus-like particle of a circovirus, PCV2, recorded on 86 photographic films. The map resolution was further validated with a phase-randomization test and local resolution assessment, and the atomic model was validated with MolProbity and EMRinger. Close-packed virus particles were thus shown not only to be useful for high-resolution 3D reconstructions but also to allow data collection at significantly improved throughput for near-atomic resolution reconstructions.
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Affiliation(s)
- Zheng Liu
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Fei Guo
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Feng Wang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Tian-Cheng Li
- Department of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.
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Yu G, Yan R, Zhang C, Mao C, Jiang W. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5157-5163. [PMID: 26179326 DOI: 10.1002/smll.201500531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/13/2015] [Indexed: 06/04/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Chuan Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
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23
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Visualization and quality assessment of the contrast transfer function estimation. J Struct Biol 2015; 192:222-34. [PMID: 26080023 DOI: 10.1016/j.jsb.2015.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/20/2015] [Accepted: 06/11/2015] [Indexed: 11/20/2022]
Abstract
The contrast transfer function (CTF) describes an undesirable distortion of image data from a transmission electron microscope. Many users of full-featured processing packages are often new to electron microscopy and are unfamiliar with the CTF concept. Here we present a common graphical output to clearly demonstrate the CTF fit quality independent of estimation software. Separately, many software programs exist to estimate the four CTF parameters, but their results are difficult to compare across multiple runs and it is all but impossible to select the best parameters to use for further processing. A new measurement is presented based on the correlation falloff of the calculated CTF oscillations against the normalized oscillating signal of the data, called the CTF resolution. It was devised to provide a robust numerical quality metric of every CTF estimation for high-throughput screening of micrographs and to select the best parameters for each micrograph. These new CTF visualizations and quantitative measures will help users better assess the quality of their CTF parameters and provide a mechanism to choose the best CTF tool for their data.
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Li W, Liu Z, Koripella RK, Langlois R, Sanyal S, Frank J. Activation of GTP hydrolysis in mRNA-tRNA translocation by elongation factor G. SCIENCE ADVANCES 2015; 1:e1500169. [PMID: 26229983 PMCID: PMC4517844 DOI: 10.1126/sciadv.1500169] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/03/2015] [Indexed: 06/04/2023]
Abstract
During protein synthesis, elongation of the polypeptide chain by each amino acid is followed by a translocation step in which mRNA and transfer RNA (tRNA) are advanced by one codon. This crucial step is catalyzed by elongation factor G (EF-G), a guanosine triphosphatase (GTPase), and accompanied by a rotation between the two ribosomal subunits. A mutant of EF-G, H91A, renders the factor impaired in guanosine triphosphate (GTP) hydrolysis and thereby stabilizes it on the ribosome. We use cryogenic electron microscopy (cryo-EM) at near-atomic resolution to investigate two complexes formed by EF-G H91A in its GTP state with the ribosome, distinguished by the presence or absence of the intersubunit rotation. Comparison of these two structures argues in favor of a direct role of the conserved histidine in the switch II loop of EF-G in GTPase activation, and explains why GTP hydrolysis cannot proceed with EF-G bound to the unrotated form of the ribosome.
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Affiliation(s)
- Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Blackwell, 165 West 168th Street, New York, NY 10032, USA
| | - Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Blackwell, 165 West 168th Street, New York, NY 10032, USA
| | - Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden
| | - Robert Langlois
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Blackwell, 165 West 168th Street, New York, NY 10032, USA
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC, 75124 Uppsala, Sweden
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, 2-221 Blackwell, 165 West 168th Street, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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25
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Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions. Proc Natl Acad Sci U S A 2014; 111:E4606-14. [PMID: 25313071 DOI: 10.1073/pnas.1407020111] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many dsDNA viruses first assemble a DNA-free procapsid, using a scaffolding protein-dependent process. The procapsid, then, undergoes dramatic conformational maturation while packaging DNA. For bacteriophage T7 we report the following four single-particle cryo-EM 3D reconstructions and the derived atomic models: procapsid (4.6-Å resolution), an early-stage DNA packaging intermediate (3.5 Å), a later-stage packaging intermediate (6.6 Å), and the final infectious phage (3.6 Å). In the procapsid, the N terminus of the major capsid protein, gp10, has a six-turn helix at the inner surface of the shell, where each skewed hexamer of gp10 interacts with two scaffolding proteins. With the exit of scaffolding proteins during maturation the gp10 N-terminal helix unfolds and swings through the capsid shell to the outer surface. The refolded N-terminal region has a hairpin that forms a novel noncovalent, joint-like, intercapsomeric interaction with a pocket formed during shell expansion. These large conformational changes also result in a new noncovalent, intracapsomeric topological linking. Both interactions further stabilize the capsids by interlocking all pentameric and hexameric capsomeres in both DNA packaging intermediate and phage. Although the final phage shell has nearly identical structure to the shell of the DNA-free intermediate, surprisingly we found that the icosahedral faces of the phage are slightly (∼4 Å) contracted relative to the faces of the intermediate, despite the internal pressure from the densely packaged DNA genome. These structures provide a basis for understanding the capsid maturation process during DNA packaging that is essential for large numbers of dsDNA viruses.
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26
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Yu G, Vago F, Zhang D, Snyder JE, Yan R, Zhang C, Benjamin C, Jiang X, Kuhn RJ, Serwer P, Thompson DH, Jiang W. Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies. J Struct Biol 2014; 187:1-9. [PMID: 24780590 DOI: 10.1016/j.jsb.2014.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 11/18/2022]
Abstract
Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Frank Vago
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Dongsheng Zhang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jonathan E Snyder
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Ci Zhang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | | | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Richard J Kuhn
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - David H Thompson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA.
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27
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Abstract
With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3-4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced.
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Affiliation(s)
- Fei Guo
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
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Directed evolution of a virus exclusively utilizing human epidermal growth factor receptor as the entry receptor. J Virol 2013; 87:11231-43. [PMID: 23926357 DOI: 10.1128/jvi.01054-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Rational design and directed evolution are powerful tools to generate and improve protein function; however, their uses are mostly limited to enzyme and antibody engineering. Here we describe a directed-evolution strategy, named the tandem selection and enrichment system (TSES), and its use in generating virus with exclusive specificity for a particular cellular receptor. In TSES, evolving viruses are sequentially and iteratively transferred between two different host cells, one for selection of receptor specificity and the other for enrichment of the fittest virus. By combining rational design and TSES, we generated human epidermal growth factor receptor (EGFR)-specific virus 1 (ESV1). ESV1 has the backbone of Sindbis virus (SINV) and displays an EGF domain engrafted onto structural protein E2 after residue Pro192, together with eight amino acid changes stabilizing the E2-EGF chimera. ESV1 uses EGFR to initiate infection and has lost the capacity to interact with all known SINV receptors. A 12.2-Å cryoelectron microscopic (cryoEM) reconstruction of ESV1 reveals that the E2-EGF fusion adopts a fixed conformation, with EGF sitting at the top of the E2 spike; The EGFR binding interface faces outward, and the EGF domain completely masks SINV receptor binding. The cryoEM structure of ESV1 explains the desirable properties of ESV1 and provides insights for its further modification. TSES expands the scope of directed evolution and can be easily extended to other targeting molecules and viral systems.
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Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A 2013; 110:12301-6. [PMID: 23840063 DOI: 10.1073/pnas.1309947110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3-5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit-subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages.
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