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Wang N, Zhao D, Wang J, Zhang Y, Wang M, Gao Y, Li F, Wang J, Bu Z, Rao Z, Wang X. Architecture of African swine fever virus and implications for viral assembly. Science 2019; 366:640-644. [PMID: 31624094 DOI: 10.1126/science.aaz1439] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/09/2019] [Indexed: 01/27/2023]
Abstract
African swine fever virus (ASFV) is a giant and complex DNA virus that causes a highly contagious and often lethal swine disease for which no vaccine is available. Using an optimized image reconstruction strategy, we solved the ASFV capsid structure up to 4.1 angstroms, which is built from 17,280 proteins, including one major (p72) and four minor (M1249L, p17, p49, and H240R) capsid proteins organized into pentasymmetrons and trisymmetrons. The atomic structure of the p72 protein informs putative conformational epitopes, distinguishing ASFV from other nucleocytoplasmic large DNA viruses. The minor capsid proteins form a complicated network below the outer capsid shell, stabilizing the capsid by holding adjacent capsomers together. Acting as core organizers, 100-nanometer-long M1249L proteins run along each edge of the trisymmetrons that bridge two neighboring pentasymmetrons and form extensive intermolecular networks with other capsid proteins, driving the formation of the capsid framework. These structural details unveil the basis of capsid stability and assembly, opening up new avenues for African swine fever vaccine development.
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Zhang Q, Liu H, Liu X, Jiang D, Zhang B, Tian H, Yang C, Guddat LW, Yang H, Mi K, Rao Z. Discovery of the first macrolide antibiotic binding protein in Mycobacterium tuberculosis: a new antibiotic resistance drug target. Protein Cell 2019; 9:971-975. [PMID: 29350349 PMCID: PMC6208485 DOI: 10.1007/s13238-017-0502-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Stuart DI, Ren J, Wang X, Rao Z, Fry EE. Hepatitis A Virus Capsid Structure. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031807. [PMID: 30037986 DOI: 10.1101/cshperspect.a031807] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Hepatitis A virus (HAV) has been enigmatic, evading detailed structural analysis for many years. Its recently determined high-resolution structure revealed an angular surface without the indentations often characteristic of receptor-binding sites. The viral protein 1 (VP1) β-barrel shows no sign of a pocket factor and the amino terminus of VP2 displays a "domain swap" across the pentamer interface, as in a subset of mammalian picornaviruses and insect picorna-like viruses. Structure-based phylogeny confirms this placement. These differences suggest an uncoating mechanism distinct from that of enteroviruses. An empty capsid structure reveals internal differences in VP0 and the VP1 amino terminus connected with particle maturation. An HAV/Fab complex structure, in which the antigen-binding fragment (Fab) appears to act as a receptor-mimic, clarifies some historical epitope mapping data, but some remain difficult to reconcile. We still have little idea of the structural features of enveloped HAV particles.
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Cao L, Liu P, Yang P, Gao Q, Li H, Sun Y, Zhu L, Lin J, Su D, Rao Z, Wang X. Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors. PLoS Biol 2019; 17:e3000229. [PMID: 31039149 PMCID: PMC6493668 DOI: 10.1371/journal.pbio.3000229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/28/2019] [Indexed: 02/05/2023] Open
Abstract
Hepatitis A virus (HAV), an enigmatic and ancient pathogen, is a major causative
agent of acute viral hepatitis worldwide. Although there are effective vaccines,
antivirals against HAV infection are still required, especially during fulminant
hepatitis outbreaks. A more in-depth understanding of the antigenic
characteristics of HAV and the mechanisms of neutralization could aid in the
development of rationally designed antiviral drugs targeting HAV. In this paper,
4 new antibodies—F4, F6, F7, and F9—are reported that potently neutralize HAV at
50% neutralizing concentration values (neut50) ranging from 0.1 nM to
0.85 nM. High-resolution cryo-electron microscopy (cryo-EM) structures of HAV
bound to F4, F6, F7, and F9, together with results of our previous studies on
R10 fragment of antigen binding (Fab)-HAV complex, shed light on the locations
and nature of the epitopes recognized by the 5 neutralizing monoclonal
antibodies (NAbs). All the epitopes locate within the same patch and are highly
conserved. The key structure-activity correlates based on the antigenic sites
have been established. Based on the structural data of the single conserved
antigenic site and key structure-activity correlates, one promising drug
candidate named golvatinib was identified by in silico docking studies.
Cell-based antiviral assays confirmed that golvatinib is capable of blocking HAV
infection effectively with a 50% inhibitory concentration (IC50) of
approximately 1 μM. These results suggest that the single conserved antigenic
site from complete HAV capsid is a good antiviral target and that golvatinib
could function as a lead compound for anti-HAV drug development. Structures of hepatitis A virus in complex with five neutralizing antibodies
reveal a single conserved antigenic site and pinpoint key structure-activity
correlates, allowing in silico screening to identify a potent candidate
inhibitor drug, golvatinib. Hepatitis A virus (HAV) is a unique, hepatotropic human picornavirus that infects
approximately 1.5 million people annually and continues to cause mortality
despite a successful vaccine. There are no licensed therapeutic drugs to date.
Better knowledge of HAV antigenic features and neutralizing mechanisms will
facilitate the development of HAV-targeting antiviral drugs. In this study, we
report 4 potent HAV-specific neutralizing monoclonal antibodies (NAbs), together
with our previous reported R10, that efficiently inhibit HAV infection by
blocking attachment to the host cell. All 5 epitopes are located within the same
patch and are highly conserved across 6 genotypes of human HAV, which suggests a
single antigenic site for HAV, highlighting a prime target for structure-based
drug design. Analysis of complexes with the 5 NAbs with varying neutralizing
activities pinpointed key structure-activity correlates. By using a robust in
silico docking method, one promising inhibitor named golvatinib was successfully
identified from the DrugBank Database. In vitro assays confirmed its ability to
block viral infection and revealed its neutralizing mechanism. Our approach
could be useful in the design of effective drugs for picornavirus
infections.
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80
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Wang H, Chen X, Zhang W, Zhou W, Liu X, Rao Z. Structural analysis of molybdopterin synthases from two mycobacterial pathogens. Biochem Biophys Res Commun 2019; 511:21-27. [PMID: 30765225 DOI: 10.1016/j.bbrc.2019.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 11/25/2022]
Abstract
The molybdenum cofactor, composed of molybdopterin and molybdenum, is a necessary compound for the catalytic activity of molybdenum enzymes. Molybdenum cofactor biosynthesis is a conserved multi-step process involving several enzymes. Molybdopterin synthase, a hetero-tetrameric enzyme composed of a pair of MoaE-MoaD subunits, catalyzes the generation of the cis-dithiolene group of molybdopterin in the second step of the process. The cis-dithiolene group can covalently bind molybdenum. Most mycobacterial species possess several genes encoding the full pathway of molybdenum cofactor biosynthesis. In M. smegmatis, the moaD2 and moaE2 genes encode the functional molybdopterin synthase. However, M. tuberculosis has genes encoding several molybdopterin synthase subunit homologs, including moaD1, moaD2, moaE1, moaE2, and moaX, which encodes a MoaD-MoaE fusion protein. Previous studies have shown that moaD2 and moaE2 encode functional molybdopterin synthase. Here, we report the crystal structures of two substrate-free molybdopterin synthases from two different mycobacterial pathogens, M. tuberculosis and M. smegmatis, at 2.1 Å and 2.6 Å resolutions, respectively. The overall structure of both molybdopterin synthases was hetero-tetrameric, consisting of a MoaE2 dimer flanked on either side by single MoaD2 subunits. The carboxyl-terminal domain of MoaD2 inserted into MoaE2, forming the active pocket. A comparison with previously reported molybdopterin synthase structures showed that substrate-binding and catalytic residues were conserved, despite low sequence similarity among these enzymes. The low sequence identity at the MoaE-MoaD heterodimer interface may provide the structural basis to explore mycobacterial inhibitors.
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Li Y, Han X, Xu W, Rao Z, Li X. Purification and characterization of the extracellular region of human receptor tyrosine kinase like orphan receptor 2 (ROR2). Protein Expr Purif 2019; 158:74-80. [PMID: 30826310 DOI: 10.1016/j.pep.2019.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 11/25/2022]
Abstract
Receptor tyrosine kinase like orphan receptor 2 (ROR2) is a co-receptor for some Wnt proteins including Wnt5a that activate the noncanonical Wnt/planar cell polarity (PCP) signaling pathway. Upregulation of ROR2 is associated with several cancer forms. The extracellular region of ROR2, which contains an immunoglobulin (Ig)-like domain, a Frizzled like cysteine-rich domain (CRD) and a Kringle domain, is a potential anticancer drug target. The structural and biochemical properties of the ROR2 extracellular region remain largely unexplored. Here we describe the mapping and purification, using a baculovirus - insect cell system, of a near-full-length ROR2 extracellular fragment (residues 53-402), which is well-behaved and suitable for future structural and biochemical analysis. We show that the extracellular region of ROR2 per se is monomeric in solution. Different monoclonal antibodies raised against the purified ROR2 protein can specifically recognize the protein and can either inhibit or activate the PCP activity in a cell-based assay, and are thus potentially useful for future mechanistic and therapeutic/diagnostic studies. The biological relevance of these antibodies further demonstrates that the purified recombinant ROR2 protein is properly folded and biochemically active.
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82
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Zhou D, Zhao Y, Kotecha A, Fry EE, Kelly JT, Wang X, Rao Z, Rowlands DJ, Ren J, Stuart DI. Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2. Nat Microbiol 2019; 4:414-419. [PMID: 30531980 DOI: 10.1038/s41564-018-0319-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022]
Abstract
Enterovirus 71 (EV71) is a common cause of hand, foot and mouth disease-a disease endemic especially in the Asia-Pacific region1. Scavenger receptor class B member 2 (SCARB2) is the major receptor of EV71, as well as several other enteroviruses responsible for hand, foot and mouth disease, and plays a key role in cell entry2. The isolated structures of EV71 and SCARB2 are known3-6, but how they interact to initiate infection is not. Here, we report the EV71-SCARB2 complex structure determined at 3.4 Å resolution using cryo-electron microscopy. This reveals that SCARB2 binds EV71 on the southern rim of the canyon, rather than across the canyon, as predicted3,7,8. Helices 152-163 (α5) and 183-193 (α7) of SCARB2 and the viral protein 1 (VP1) GH and VP2 EF loops of EV71 dominate the interaction, suggesting an allosteric mechanism by which receptor binding might facilitate the low-pH uncoating of the virus in the endosome/lysosome. Remarkably, many residues within the binding footprint are not conserved across SCARB2-dependent enteroviruses; however, a conserved proline and glycine seem to be key residues. Thus, although the virus maintains antigenic variability even within the receptor-binding footprint, the identification of binding 'hot spots' may facilitate the design of receptor mimic therapeutics less likely to quickly generate resistance.
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83
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Chen X, Chen J, Zhang W, Wang H, Liu X, Zhou W, Yang H, Rao Z. Crystal structure and biochemical study on argininosuccinate lyase from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2019; 510:116-121. [PMID: 30665717 DOI: 10.1016/j.bbrc.2019.01.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 01/12/2019] [Indexed: 11/24/2022]
Abstract
Argininosuccinate lyase (ASL) participates in arginine synthesis through catalysing a reversible reaction in which argininosuccinate (AS) converts into arginine and fumarate. ASL from Mycobacterium tuberculosis is essential for its growth. In this work, the crystal structure of the apo form of MtbASL was determined and reveals a tetrameric structure that is essential for its activity since the active sites are formed by residues from three different monomers. Subsequently, we determined the crystal structure of MtbASL-sulfate complex, and the ligand mimics the negatively charged intermediate. The complex structure and mutagenesis studies indicate that residues S282 and H161 might act as a catalytic dyad. A major conformational change in the MtbASL-SO4 complex structure could be observed upon sulfate binding, and this movement facilitates the interaction between substrate and the residues involved in catalysis. A different conformational change in the C-terminal domain could be observed in the MtbASL-SO4 complex compared with that in other homologues. This difference may be responsible for the lower activity of MtbASL, which is related to the slow growth rate of M. tuberculosis. The C-terminal domain is a potential allosteric site upon inhibitor binding. The various conformational changes and the diversity of the sequence of the potential allosteric site across the homologues might provide clues for designing selective inhibitors against M. tuberculosis.
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84
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Liu W, Liu A, Gao H, Wang Q, Wang L, Warkentin E, Rao Z, Michel H, Peng G. Structural properties of the peroxiredoxin AhpC2 from the hyperthermophilic eubacterium Aquifex aeolicus. Biochim Biophys Acta Gen Subj 2018; 1862:2797-2805. [DOI: 10.1016/j.bbagen.2018.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 11/25/2022]
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85
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Zhu L, Sun Y, Fan J, Zhu B, Cao L, Gao Q, Zhang Y, Liu H, Rao Z, Wang X. Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating. Nat Commun 2018; 9:4985. [PMID: 30478256 PMCID: PMC6255764 DOI: 10.1038/s41467-018-07531-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/31/2018] [Indexed: 12/15/2022] Open
Abstract
Coxsackievirus A10 (CVA10), a human type-A Enterovirus (HEV-A), can cause diseases ranging from hand-foot-and-mouth disease to polio-myelitis-like disease. CVA10, together with some other HEV-As, utilizing the molecule KREMEN1 as an entry receptor, constitutes a KREMEN1-dependent subgroup within HEV-As. Currently, there is no vaccine or antiviral therapy available for treating diseases caused by CVA10. The atomic-resolution structure of the CVA10 virion, which is within the KREMEN1-dependent subgroup, shows significant conformational differences in the putative receptor binding sites and serotype-specific epitopes, when compared to the SCARB2-dependent subgroup of HEV-A, such as EV71, highlighting specific differences between the sub-groups. We also report two expanded structures of CVA10, an empty particle and uncoating intermediate at atomic resolution, as well as a medium-resolution genome structure reconstructed using a symmetry-mismatch method. Structural comparisons coupled with previous results, reveal an ordered signal transmission process for enterovirus uncoating, converting exo-genetic receptor-attachment inputs into a generic RNA release mechanism. The disease-causing pathogen Coxsackievirus A10 (CVA10) is a human type-A Enterovirus. Here the authors present the cryo-EM structures of the mature CVA10 virion and the empty- and A-particles of CVA10, which is of interest for CVA10 vaccine development.
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86
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Gong H, Li J, Xu A, Tang Y, Ji W, Gao R, Wang S, Yu L, Tian C, Li J, Yen HY, Man Lam S, Shui G, Yang X, Sun Y, Li X, Jia M, Yang C, Jiang B, Lou Z, Robinson CV, Wong LL, Guddat LW, Sun F, Wang Q, Rao Z. An electron transfer path connects subunits of a mycobacterial respiratory supercomplex. Science 2018; 362:science.aat8923. [PMID: 30361386 DOI: 10.1126/science.aat8923] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/10/2018] [Indexed: 11/02/2022]
Abstract
We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from Mycobacterium smegmatis. It comprises a complex III dimer flanked on either side by individual complex IV subunits. Complex III and IV associate so that electrons can be transferred from quinol in complex III to the oxygen reduction center in complex IV by way of a bridging cytochrome subunit. We observed a superoxide dismutase-like subunit at the periplasmic face, which may be responsible for detoxification of superoxide formed by complex III. The structure reveals features of an established drug target and provides a foundation for the development of treatments for human tuberculosis.
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87
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Yuan S, Wang J, Zhu D, Wang N, Gao Q, Chen W, Tang H, Wang J, Zhang X, Liu H, Rao Z, Wang X. Cryo-EM structure of a herpesvirus capsid at 3.1 Å. Science 2018; 360:360/6384/eaao7283. [DOI: 10.1126/science.aao7283] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/23/2018] [Indexed: 12/21/2022]
Abstract
Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo–electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C. Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly. Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV.
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88
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Qiu Y, Wang X, Song T, Rao Z, Liu J, Huang Z, Lin T. Comparison of Both Sides for Retroperitoneal Laparoscopic Donor Nephrectomy: Experience From a Single Center in China. Transplant Proc 2018; 49:1244-1248. [PMID: 28735988 DOI: 10.1016/j.transproceed.2017.02.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/14/2016] [Accepted: 02/07/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Laparoscopic donor nephrectomy (LDN) has gradually become the main approach to obtain live donor kidneys. However, the shorter right renal vein limits its wider application. The aim of this study was to compare the outcomes of left- and right-side retroperitoneal LDN. METHODS We reviewed the perioperative data of 527 consecutive donors receiving retroperitoneal pure LDN with a new method at our center between April 2009 and April 2014. The patients were divided into group A (the first 100 patients) and group B (the remaining 427 patients). A total of 423 cases of left donor surgery and 104 cases of right donor surgery were compared. The comparison of the laterality of LDN was also performed between group A and group B. RESULTS This is currently the largest case series of LDN in our country. Although right-side LDN patients had longer operation time and a slightly higher incidence of intraoperative complications compared with left-side LDN patients, the operation time was shorter in both the groups compared with previous reports. In group B, patients undergoing right-side LDN had longer operation time and more frequent complications. Once the learning curve of 100 cases was completed, the incidence of complications and operation time were greatly reduced in both sides for LDN. There was no significant difference in the serum creatinine levels in recipients at 6 months of follow-up. CONCLUSIONS Despite a slightly higher incidence of complications and longer operation time, right-side LDN can achieve equally safe and effective transplantation outcomes. This expands the source of potential donor kidneys.
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Yan L, Qi Y, Huang X, Yu C, Lan L, Guo X, Rao Z, Hu J, Lou Z. Structural basis for GTP hydrolysis and conformational change of MFN1 in mediating membrane fusion. Nat Struct Mol Biol 2018; 25:233-243. [PMID: 29483649 DOI: 10.1038/s41594-018-0034-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/24/2018] [Indexed: 01/05/2023]
Abstract
Fusion of the outer mitochondrial membrane is mediated by the dynamin-like GTPase mitofusin (MFN). Here, we determined the structure of the minimal GTPase domain (MGD) of human MFN1 in complex with GDP-BeF3-. The MGD folds into a canonical GTPase fold with an associating four-helix bundle, HB1, and forms a dimer. A potassium ion in the catalytic core engages GDP and BeF3- (GDP-BeF3-). Enzymatic analysis has confirmed that efficient GTP hydrolysis by MFN1 requires potassium. Compared to previously reported MGD structures, the HB1 structure undergoes a major conformational change relative to the GTPase domains, as they move from pointing in opposite directions to point in the same direction, suggesting that a swing of the four-helix bundle can pull tethered membranes closer to achieve fusion. The proposed model is supported by results from in vitro biochemical assays and mitochondria morphology rescue assays in MFN1-deleted cells. These findings offer an explanation for how Charcot-Marie-Tooth neuropathy type 2 A (CMT2A)-causing mutations compromise MFN-mediated fusion.
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90
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Zhang W, Zheng Q, Yan M, Chen X, Yang H, Zhou W, Rao Z. Structural characterization of the HCoV-229E fusion core. Biochem Biophys Res Commun 2018; 497:705-712. [PMID: 29458023 PMCID: PMC7092869 DOI: 10.1016/j.bbrc.2018.02.136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 02/15/2018] [Indexed: 01/10/2023]
Abstract
HCoV-229E spike (S) protein mediates virion attachment to cells and subsequent fusion of the viral and cellular membranes. This protein is composed of an N-terminal receptor-binding domain (S1) and a C-terminal trans-membrane fusion domain (S2). S2 contains a highly conserved heptad repeat 1 and 2 (HR1 and HR2). In this study, the HRs sequences were designed and connected with a flexible linker. The recombinant fusion core protein was crystallized and its structure was solved at a resolution of 2.45 Å. Then we characterized the binding of HR1s and HR2s via both sequence alignment and structural analysis. The overall structures, especially the residues in some positions of HR2 are highly conserved. Fourteen hydrophobic and three polar residues from each HR1 peptide are packed in layers at the coiled-coil interface. These core amino acids can be grouped into seven heptad repeats. Analysis of hydrophobic and hydrophilic interactions between HR2 helix and HR1 helices, shows that the HR1 and HR2 polypeptides are highly complementary in both shape and chemical properties. Furthermore, the available knowledge concerning HCoV-229E fusion core may make it possible to design small molecule or polypeptide drugs targeting membrane fusion, a crucial step of HCoV-229E infection.
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91
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Qiu X, Lei Y, Yang P, Gao Q, Wang N, Cao L, Yuan S, Huang X, Deng Y, Ma W, Ding T, Zhang F, Wu X, Hu J, Liu SL, Qin C, Wang X, Xu Z, Rao Z. Structural basis for neutralization of Japanese encephalitis virus by two potent therapeutic antibodies. Nat Microbiol 2018; 3:287-294. [PMID: 29379207 DOI: 10.1038/s41564-017-0099-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023]
Abstract
Japanese encephalitis virus (JEV), closely related to dengue, Zika, yellow fever and West Nile viruses, remains neglected and not well characterized 1 . JEV is the leading causative agent of encephalitis, and is responsible for thousands of deaths each year in Asia. Humoral immunity is essential for protecting against flavivirus infections and passive immunization has been demonstrated to be effective in curing disease2,3. Here, we demonstrate that JEV-specific monoclonal antibodies, 2F2 and 2H4, block attachment of the virus to its receptor and also prevent fusion of the virus. Neutralization of JEV by these antibodies is exceptionally potent and confers clear therapeutic benefit in mouse models. A single 20 μg dose of these antibodies resulted in 100% survival and complete clearance of JEV from the brains of mice. The 4.7 Å and 4.6 Å resolution cryo-electron microscopy structures of JEV-2F2-Fab and JEV-2H4-Fab complexes, together with the crystal structure of 2H4 Fab and our recent near-atomic structure of JEV 4 , unveil the nature and location of epitopes targeted by the antibodies. Both 2F2 and 2H4 Fabs bind quaternary epitopes that span across three adjacent envelope proteins. Our results provide a structural and molecular basis for the application of 2F2 and 2H4 to treat JEV infection.
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92
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Zhang X, Yang P, Wang N, Zhang J, Li J, Guo H, Yin X, Rao Z, Wang X, Zhang L. The binding of a monoclonal antibody to the apical region of SCARB2 blocks EV71 infection. Protein Cell 2017; 8:590-600. [PMID: 28447294 PMCID: PMC5546930 DOI: 10.1007/s13238-017-0405-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/16/2017] [Indexed: 12/02/2022] Open
Abstract
Entero virus 71 (EV71) causes hand, foot, and mouth disease (HFMD) and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 (SCARB2) is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody (mAb) that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the region containing residues 77-113 of human SCARB2 contributes significantly to JL2 binding. The structure of the SCARB2-JL2 complex revealed that JL2 binds to the apical region of SCARB2 involving α-helices 2, 5, and 14. Our results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/metabolism
- Binding Sites
- Cell Line
- Crystallography, X-Ray
- Enterovirus A, Human/drug effects
- Enterovirus A, Human/genetics
- Enterovirus A, Human/growth & development
- Enterovirus A, Human/immunology
- Fibroblasts/drug effects
- Fibroblasts/virology
- Gene Expression
- HEK293 Cells
- Humans
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/metabolism
- Lysosomal Membrane Proteins/chemistry
- Lysosomal Membrane Proteins/genetics
- Lysosomal Membrane Proteins/immunology
- Mice
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Scavenger/chemistry
- Receptors, Scavenger/genetics
- Receptors, Scavenger/immunology
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sf9 Cells
- Spodoptera
- Thermodynamics
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93
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Yan Q, Jiang D, Qian L, Zhang Q, Zhang W, Zhou W, Mi K, Guddat L, Yang H, Rao Z. Structural Insight into the Activation of PknI Kinase from M. tuberculosis via Dimerization of the Extracellular Sensor Domain. Structure 2017; 25:1286-1294.e4. [PMID: 28712808 DOI: 10.1016/j.str.2017.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/27/2017] [Accepted: 06/16/2017] [Indexed: 10/19/2022]
Abstract
Protein kinases play central roles in the survival of Mycobacterium tuberculosis within host. Here we report the individual high-resolution crystal structures of the sensor domain (in both monomer and dimer forms) and the kinase domain of PknI, a transmembrane protein member of the serine/threonine protein kinases (STPKs) family. PknI is the first STPK identified whose sensor domain exists in a monomer-dimer equilibrium. Inspection of the two structures of the sensor domain (PknI_SD) revealed conformational changes upon dimerization, with an arm region of critical importance for dimer formation identified. Rapamycin-induced dimerization of unphosphorylated fusions of PknI juxtamembrane and the kinase domain, intended to mimic the dimerization effect presumably imposed by PknI_SD, was observed to be able to activate auto-phosphorylation activity of the kinase domain. In vivo experiments using an M. bovis model suggested PknI functions as a dimer in the regulation of M. tuberculosis growth.
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94
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Qi Y, Yan L, Yu C, Guo X, Zhou X, Hu X, Huang X, Rao Z, Lou Z, Hu J. Structures of human mitofusin 1 provide insight into mitochondrial tethering. J Cell Biol 2017; 215:621-629. [PMID: 27920125 PMCID: PMC5147005 DOI: 10.1083/jcb.201609019] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/02/2016] [Accepted: 10/18/2016] [Indexed: 11/26/2022] Open
Abstract
Mitofusin 1 (MFN1) mediates mitochondrial fusion, but the mechanisms involved are unclear. Qi et al. present the crystal structures of a minimal GTPase domain of human MFN1, which suggest that MFN1 tethers apposing membranes through nucleotide-dependent dimerization. Mitochondria undergo fusion and fission. The merging of outer mitochondrial membranes requires mitofusin (MFN), a dynamin-like GTPase. How exactly MFN mediates membrane fusion is poorly understood. Here, we determined crystal structures of a minimal GTPase domain (MGD) of human MFN1, including the predicted GTPase and the distal part of the C-terminal tail (CT). The structures revealed that a helix bundle (HB) formed by three helices extending from the GTPase and one extending from the CT closely attaches to the GTPase domain, resembling the configuration of bacterial dynamin-like protein. We show that the nucleotide-binding pocket is shallow and narrow, rendering weak hydrolysis and less dependence on magnesium ion, and that association of HB affects GTPase activity. MFN1 forms a dimer when GTP or GDP/BeF3−, but not GDP or other analogs, is added. In addition, clustering of vesicles containing membrane-anchored MGD requires continuous GTP hydrolysis. These results suggest that MFN tethers apposing membranes, likely through nucleotide-dependent dimerization.
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95
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Shao M, Sha Z, Zhang X, Rao Z, Xu M, Yang T, Xu Z, Yang S. Efficient androst-1,4-diene-3,17-dione production by co-expressing 3-ketosteroid-Δ 1 -dehydrogenase and catalase in Bacillus subtilis. J Appl Microbiol 2017; 122:119-128. [PMID: 27797429 DOI: 10.1111/jam.13336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/11/2016] [Accepted: 10/17/2016] [Indexed: 01/02/2023]
Abstract
AIMS 3-ketosteroid-Δ1 -dehydrogenase (KSDD), a flavin adenine dinucleotide (FAD)-dependent enzyme involved in sterol metabolism, specifically catalyses the conversion of androst-4-ene-3,17-dione (AD) to androst-1,4-diene-3,17-dione (ADD). However, the low KSDD activity and the toxic effects of hydrogen peroxide (H2 O2 ) generated during the biotransformation of AD to ADD with FAD regeneration hinder its application on AD conversion. The aim of this work was to improve KSDD activity and eliminate the toxic effects of the generated H2 O2 to enhance ADD production. METHODS AND RESULTS The ksdd gene obtained from Mycobacterium neoaurum JC-12 was codon-optimized to increase its expression level in Bacillus subtilis, and the KSDD activity reached 12·3 U mg-1 , which was sevenfold of that of codon-unoptimized gene. To improve AD conversion, catalase was co-expressed with KSDD in B. subtilis 168/pMA5-ksddopt -katA to eliminate the toxic effects of H2 O2 generated during AD conversion. Finally, under optimized bioconversion conditions, fed-batch strategy was carried out and the ADD yield improved to 8·76 g l-1 . CONCLUSIONS This work demonstrates the potential to improve enzyme activity by codon-optimization and eliminate the toxic effects of H2 O2 by co-expressing catalase. SIGNIFICANCE AND IMPACT OF THE STUDY This study showed the highest ADD productivity ever reported and provides a promising strain for efficient ADD production in the pharmaceutical industry.
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96
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Wang J, Okkeri J, Pavic K, Wang Z, Kauko O, Halonen T, Sarek G, Ojala PM, Rao Z, Xu W, Westermarck J. Oncoprotein CIP2A is stabilized via interaction with tumor suppressor PP2A/B56. EMBO Rep 2017; 18:437-450. [PMID: 28174209 DOI: 10.15252/embr.201642788] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 12/20/2016] [Accepted: 01/09/2017] [Indexed: 01/20/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is a critical human tumor suppressor. Cancerous inhibitor of PP2A (CIP2A) supports the activity of several critical cancer drivers (Akt, MYC, E2F1) and promotes malignancy in most cancer types via PP2A inhibition. However, the 3D structure of CIP2A has not been solved, and it remains enigmatic how it interacts with PP2A. Here, we show by yeast two-hybrid assays, and subsequent validation experiments, that CIP2A forms homodimers. The homodimerization of CIP2A is confirmed by solving the crystal structure of an N-terminal CIP2A fragment (amino acids 1-560) at 3.0 Å resolution, and by subsequent structure-based mutational analyses of the dimerization interface. We further describe that the CIP2A dimer interacts with the PP2A subunits B56α and B56γ. CIP2A binds to the B56 proteins via a conserved N-terminal region, and dimerization promotes B56 binding. Intriguingly, inhibition of either CIP2A dimerization or B56α/γ expression destabilizes CIP2A, indicating opportunities for controlled degradation. These results provide the first structure-function analysis of the interaction of CIP2A with PP2A/B56 and have direct implications for its targeting in cancer therapy.
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97
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Yuan S, Cao L, Ling H, Dang M, Sun Y, Zhang X, Chen Y, Zhang L, Su D, Wang X, Rao Z. TIM-1 acts a dual-attachment receptor for Ebolavirus by interacting directly with viral GP and the PS on the viral envelope. Protein Cell 2016; 6:814-24. [PMID: 26487564 PMCID: PMC4624681 DOI: 10.1007/s13238-015-0220-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/30/2015] [Indexed: 11/09/2022] Open
Abstract
Ebolavirus can cause hemorrhagic fever in humans with a mortality rate of 50%–90%. Currently, no approved vaccines and antiviral therapies are available. Human TIM1 is considered as an attachment factor for EBOV, enhancing viral infection through interaction with PS located on the viral envelope. However, reasons underlying the preferable usage of hTIM-1, but not other PS binding receptors by filovirus, remain unknown. We firstly demonstrated a direct interaction between hTIM-1 and EBOV GP in vitro and determined the crystal structures of the Ig V domains of hTIM-1 and hTIM-4. The binding region in hTIM-1 to EBOV GP was mapped by chimeras and mutation assays, which were designed based on structural analysis. Pseudovirion infection assays performed using hTIM-1 and its homologs as well as point mutants verified the location of the GP binding site and the importance of EBOV GP-hTIM-1 interaction in EBOV cellular entry.
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98
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Shan S, Min H, Liu T, Jiang D, Rao Z. Structural insight into dephosphorylation by trehalose 6‐phosphate phosphatase (OtsB2) from
Mycobacterium tuberculosis. FASEB J 2016; 30:3989-3996. [DOI: 10.1096/fj.201600463r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/08/2016] [Indexed: 11/11/2022]
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99
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Qiu Y, Wang X, Fan J, Rao Z, Lu Y, Lin T. Conversion From Calcineurin Inhibitors to Mammalian Target-of-Rapamycin Inhibitors in Heart Transplant Recipients: A Meta-Analysis of Randomized Controlled Trials. Transplant Proc 2016; 47:2952-6. [PMID: 26707320 DOI: 10.1016/j.transproceed.2015.09.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/17/2015] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Conversion from calcineurin inhibitors (CNIs) to mammalian target-of-rapamycin inhibitors (mTORi) was systematically evaluated in heart transplant recipients (HTRs) for the first time. METHODS MEDLINE (PUBMED), EMBASE, Cochrane Library, and clinical trial registries were searched comprehensively. After screening for eligibility, the randomized controlled trials (RCTs) comparing continuation of CNI with conversion to mTORi therapy underwent review, quality assessment, and data extraction. Outcomes analyzed including creatinine clearance, serum creatinine level, rejection, adverse effects, and triglyceride levels were expressed as mean differences (MDs) or as risk ratios (RRs) with 95% confidence intervals (CIs). RESULTS This is the first systematic review evaluating converting from CNI to mTORi therapy in HTRs. A total of 4 RCTs (231 HTRs, 117 vs 114) were included in our analysis. Patients converted to mTORi had a higher creatinine clearance (MD, 19.31; 95% CI [11.16, 27.46]; P < .00001) and lower serum creatinine levels (MD, -0.15; 95% CI [-0.25, -0.05]; P = .002). Patients converted to mTORi had a significantly higher occurrence of adverse effects, which included skin diseases, gastrointestinal side effects, bone marrow suppression, and infections. There was no significant difference between the 2 groups regarding graft rejection and triglyceride levels (RR, 2.61; 95% CI [0.08, 81.25]; P = .58; MD, 22.89; 95% CI [-21.86, 67.63]; P = .32). CONCLUSIONS Conversion from CNI to mTORi therapy may improve the renal function in HTRs, but the patients may suffer from a high incidence of mTORi-associated adverse events. Therefore, conversion to mTORi must be carefully assessed for the benefits and risks.
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100
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Yao R, Ming Z, Yan L, Li S, Wang F, Ma S, Yu C, Yang M, Chen L, Chen L, Li Y, Yan C, Miao D, Sun Z, Yan J, Sun Y, Wang L, Chu J, Fan S, He W, Deng H, Nan F, Li J, Rao Z, Lou Z, Xie D. DWARF14 is a non-canonical hormone receptor for strigolactone. Nature 2016; 536:469-73. [PMID: 27479325 DOI: 10.1038/nature19073] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022]
Abstract
Classical hormone receptors reversibly and non-covalently bind active hormone molecules, which are generated by biosynthetic enzymes, to trigger signal transduction. The α/β hydrolase DWARF14 (D14), which hydrolyses the plant branching hormone strigolactone and interacts with the F-box protein D3/MAX2, is probably involved in strigolactone detection. However, the active form of strigolactone has yet to be identified and it is unclear which protein directly binds the active form of strigolactone, and in which manner, to act as the genuine strigolactone receptor. Here we report the crystal structure of the strigolactone-induced AtD14-D3-ASK1 complex, reveal that Arabidopsis thaliana (At)D14 undergoes an open-to-closed state transition to trigger strigolactone signalling, and demonstrate that strigolactone is hydrolysed into a covalently linked intermediate molecule (CLIM) to initiate a conformational change of AtD14 to facilitate interaction with D3. Notably, analyses of a highly branched Arabidopsis mutant d14-5 show that the AtD14(G158E) mutant maintains enzyme activity to hydrolyse strigolactone, but fails to efficiently interact with D3/MAX2 and loses the ability to act as a receptor that triggers strigolactone signalling in planta. These findings uncover a mechanism underlying the allosteric activation of AtD14 by strigolactone hydrolysis into CLIM, and define AtD14 as a non-canonical hormone receptor with dual functions to generate and sense the active form of strigolactone.
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