51
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Zhu X, Mannar D, Srivastava SS, Berezuk AM, Demers JP, Saville JW, Leopold K, Li W, Dimitrov DS, Tuttle KS, Zhou S, Chittori S, Subramaniam S. Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. PLoS Biol 2021; 19:e3001237. [PMID: 33914735 PMCID: PMC8112707 DOI: 10.1371/journal.pbio.3001237] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/11/2021] [Accepted: 04/16/2021] [Indexed: 12/15/2022] Open
Abstract
The recently reported "UK variant" (B.1.1.7) of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We present a 2.9-Å resolution cryo-electron microscopy (cryo-EM) structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. This additional interaction provides a structural explanation for the increased ACE2 affinity of the N501Y mutant, and likely contributes to its increased infectivity. However, this mutation does not result in large structural changes, enabling important neutralization epitopes to be retained in the spike receptor binding domain. We confirmed this through biophysical assays and by determining cryo-EM structures of spike protein ectodomains bound to 2 representative potent neutralizing antibody fragments.
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Affiliation(s)
- Xing Zhu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shanti S. Srivastava
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M. Berezuk
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-Philippe Demers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - James W. Saville
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karoline Leopold
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, United States of America
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, United States of America
| | - Katharine S. Tuttle
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven Zhou
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sagar Chittori
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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52
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Structural basis for the shared neutralization mechanism of three classes of human papillomavirus type 58 antibodies with disparate modes of binding. J Virol 2021; 95:JVI.01587-20. [PMID: 33472937 PMCID: PMC8092703 DOI: 10.1128/jvi.01587-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human papillomavirus type 58 (HPV58) is associated with cervical cancer and poses a significant health burden worldwide. Although the commercial 9-valent HPV vaccine covers HPV58, the structural and molecular-level neutralization sites of the HPV58 complete virion are not fully understood. Here, we report the high-resolution (∼3.5 Å) structure of the complete HPV58 pseudovirus (PsV58) using cryo-electron microscopy (cryo-EM). Three representative neutralizing monoclonal antibodies (nAbs 5G9, 2H3 and A4B4) were selected through clustering from a nAb panel against HPV58. Bypassing the steric hindrance and symmetry-mismatch in the HPV Fab-capsid immune-complex, we present three different neutralizing epitopes in the PsV58, and show that, despite differences in binding, these nAbs share a common neutralization mechanism. These results offer insight into HPV58 genotype specificity and broaden our understanding of HPV58 neutralization sites for antiviral research.IMPORTANCE Cervical cancer primarily results from persistent infection with high-risk types of human papillomavirus (HPV). HPV type 58 (HPV58) is an important causative agent, especially within Asia. Despite this, we still have limited data pertaining to the structural and neutralizing epitopes of HPV58, and this encumbers our in-depth understanding of the virus mode of infection. Here, we show that representative nAbs (5G9, 10B11, 2H3, 5H2 and A4B4) from three different groups share a common neutralization mechanism that appears to prohibit the virus from associating with the extracellular matrix and cell surface. Furthermore, we identify that the nAbs engage via three different binding patterns: top-center binding (5G9 and 10B11), top-fringe binding (2H3 and 5H2), and fringe binding (A4B4). Our work shows that, despite differences in the pattern in binding, nAbs against HPV58 share a common neutralization mechanism. These results provide new insight into the understanding of HPV58 infection.
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53
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Gilbert RJC. Electron microscopy as a critical tool in the determination of pore forming mechanisms in proteins. Methods Enzymol 2021; 649:71-102. [PMID: 33712203 DOI: 10.1016/bs.mie.2021.01.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Electron microscopy has consistently played an important role in the description of pore-forming protein systems. The discovery of pore-forming proteins has depended on visualization of the structural pores formed by their oligomeric protein complexes, and as electron microscopy has advanced technologically so has the degree of insight it has been able to give. This review considers a large number of published studies of pore-forming complexes in prepore and pore states determined using single-particle cryo-electron microscopy. Sample isolation and preparation, imaging and image analysis, structure determination and optimization of results are all discussed alongside challenges which pore-forming proteins particularly present. The review also considers the use made of cryo-electron tomography to study pores within their membrane environment and which will prove an increasingly important approach for the future.
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Affiliation(s)
- Robert J C Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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54
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Punjani A, Fleet DJ. 3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM. J Struct Biol 2021; 213:107702. [PMID: 33582281 DOI: 10.1016/j.jsb.2021.107702] [Citation(s) in RCA: 425] [Impact Index Per Article: 141.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Single particle cryo-EM excels in determining static structures of protein molecules, but existing 3D reconstruction methods have been ineffective in modelling flexible proteins. We introduce 3D variability analysis (3DVA), an algorithm that fits a linear subspace model of conformational change to cryo-EM data at high resolution. 3DVA enables the resolution and visualization of detailed molecular motions of both large and small proteins, revealing new biological insight from single particle cryo-EM data. Experimental results demonstrate the ability of 3DVA to resolve multiple flexible motions of α-helices in the sub-50 kDa transmembrane domain of a GPCR complex, bending modes of a sodium ion channel, five types of symmetric and symmetry-breaking flexibility in a proteasome, large motions in a spliceosome complex, and discrete conformational states of a ribosome assembly. 3DVA is implemented in the cryoSPARC software package.
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Affiliation(s)
- Ali Punjani
- Department of Computer Sciences, University of Toronto M5S 3G4, Canada; Vector Institute, 710-661 University Ave., Toronto M5G 1M1, Canada; Structura Biotechnology Inc., 129-100 College Ave., Toronto M5G 1L5, Canada.
| | - David J Fleet
- Department of Computer Sciences, University of Toronto M5S 3G4, Canada; Vector Institute, 710-661 University Ave., Toronto M5G 1M1, Canada.
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55
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A Three-Dimensional Model of the Yeast Transmembrane Sensor Wsc1 Obtained by SMA-Based Detergent-Free Purification and Transmission Electron Microscopy. J Fungi (Basel) 2021; 7:jof7020118. [PMID: 33562593 PMCID: PMC7915640 DOI: 10.3390/jof7020118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022] Open
Abstract
The cell wall sensor Wsc1 belongs to a small family of transmembrane proteins, which are crucial to sustain cell integrity in yeast and other fungi. Wsc1 acts as a mechanosensor of the cell wall integrity (CWI) signal transduction pathway which responds to external stresses. Here we report on the purification of Wsc1 by its trapping in water-soluble polymer-stabilized lipid nanoparticles, obtained with an amphipathic styrene-maleic acid (SMA) copolymer. The latter was employed to transfer tagged sensors from their native yeast membranes into SMA/lipid particles (SMALPs), which allows their purification in a functional state, i.e., avoiding denaturation. The SMALPs composition was characterized by fluorescence correlation spectroscopy, followed by two-dimensional image acquisition from single particle transmission electron microscopy to build a three-dimensional model of the sensor. The latter confirms that Wsc1 consists of a large extracellular domain connected to a smaller intracellular part by a single transmembrane domain, which is embedded within the hydrophobic moiety of the lipid bilayer. The successful extraction of a sensor from the yeast plasma membrane by a detergent-free procedure into a native-like membrane environment provides new prospects for in vitro structural and functional studies of yeast plasma proteins which are likely to be applicable to other fungi, including plant and human pathogens.
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56
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Herrmann T, Torres R, Salgado EN, Berciu C, Stoddard D, Nicastro D, Jenni S, Harrison SC. Functional refolding of the penetration protein on a non-enveloped virus. Nature 2021; 590:666-670. [PMID: 33442061 PMCID: PMC8297411 DOI: 10.1038/s41586-020-03124-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 12/08/2020] [Indexed: 11/09/2022]
Abstract
A non-enveloped virus requires a membrane lesion to deliver its genome into a target cell1. For rotaviruses, membrane perforation is a principal function of the viral outer-layer protein, VP42,3. Here we describe the use of electron cryomicroscopy to determine how VP4 performs this function and show that when activated by cleavage to VP8* and VP5*, VP4 can rearrange on the virion surface from an 'upright' to a 'reversed' conformation. The reversed structure projects a previously buried 'foot' domain outwards into the membrane of the host cell to which the virion has attached. Electron cryotomograms of virus particles entering cells are consistent with this picture. Using a disulfide mutant of VP4, we have also stabilized a probable intermediate in the transition between the two conformations. Our results define molecular mechanisms for the first steps of the penetration of rotaviruses into the membranes of target cells and suggest similarities with mechanisms postulated for other viruses.
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Affiliation(s)
- Tobias Herrmann
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Graduate Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Raúl Torres
- Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Eric N Salgado
- Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Seqirus USA, Cambridge, MA, USA
| | - Cristina Berciu
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, MA, USA.,Microscopy Core Facility, McLean Hospital, Belmont, MA, USA
| | - Daniel Stoddard
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, MA, USA.,Department of Cell Biology, University of Texas Southwestern, Dallas, TX, USA
| | - Daniela Nicastro
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, MA, USA.,Department of Cell Biology, University of Texas Southwestern, Dallas, TX, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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57
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Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections. Nat Commun 2021; 12:264. [PMID: 33431876 PMCID: PMC7801428 DOI: 10.1038/s41467-020-20465-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/03/2020] [Indexed: 01/10/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Neutralizing antibodies against SARS-CoV-2 are an option for drug development for treating COVID-19. Here, we report the identification and characterization of two groups of mouse neutralizing monoclonal antibodies (MAbs) targeting the receptor-binding domain (RBD) on the SARS-CoV-2 spike (S) protein. MAbs 2H2 and 3C1, representing the two antibody groups, respectively, bind distinct epitopes and are compatible in formulating a noncompeting antibody cocktail. A humanized version of the 2H2/3C1 cocktail is found to potently neutralize authentic SARS-CoV-2 infection in vitro with half inhibitory concentration (IC50) of 12 ng/mL and effectively treat SARS-CoV-2-infected mice even when administered at as late as 24 h post-infection. We determine an ensemble of cryo-EM structures of 2H2 or 3C1 Fab in complex with the S trimer up to 3.8 Å resolution, revealing the conformational space of the antigen–antibody complexes and MAb-triggered stepwise allosteric rearrangements of the S trimer, delineating a previously uncharacterized dynamic process of coordinated binding of neutralizing antibodies to the trimeric S protein. Our findings provide important information for the development of MAb-based drugs for preventing and treating SARS-CoV-2 infections. Here, the authors identify and characterize two mouse-derived monoclonal antibodies against SARS-CoV-2 spike protein that target different epitopes in RBD and block the interaction S/ACE2 and show that a formulated humanized version cocktail exhibits prophylaxis and therapeutic antiviral effects in an hACE2-adenovector expressed mouse model.
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58
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Malladi SK, Singh R, Pandey S, Gayathri S, Kanjo K, Ahmed S, Khan MS, Kalita P, Girish N, Upadhyaya A, Reddy P, Pramanick I, Bhasin M, Mani S, Bhattacharyya S, Joseph J, Thankamani K, Raj VS, Dutta S, Singh R, Nadig G, Varadarajan R. Design of a highly thermotolerant, immunogenic SARS-CoV-2 spike fragment. J Biol Chem 2021; 296:100025. [PMID: 33154165 PMCID: PMC7832000 DOI: 10.1074/jbc.ra120.016284] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Virtually all SARS-CoV-2 vaccines currently in clinical testing are stored in a refrigerated or frozen state prior to use. This is a major impediment to deployment in resource-poor settings. Furthermore, several of them use viral vectors or mRNA. In contrast to protein subunit vaccines, there is limited manufacturing expertise for these nucleic-acid-based modalities, especially in the developing world. Neutralizing antibodies, the clearest known correlate of protection against SARS-CoV-2, are primarily directed against the receptor-binding domain (RBD) of the viral spike protein, suggesting that a suitable RBD construct might serve as a more accessible vaccine ingredient. We describe a monomeric, glycan-engineered RBD protein fragment that is expressed at a purified yield of 214 mg/l in unoptimized, mammalian cell culture and, in contrast to a stabilized spike ectodomain, is tolerant of exposure to temperatures as high as 100 °C when lyophilized, up to 70 °C in solution and stable for over 4 weeks at 37 °C. In prime:boost guinea pig immunizations, when formulated with the MF59-like adjuvant AddaVax, the RBD derivative elicited neutralizing antibodies with an endpoint geometric mean titer of ∼415 against replicative virus, comparing favorably with several vaccine formulations currently in the clinic. These features of high yield, extreme thermotolerance, and satisfactory immunogenicity suggest that such RBD subunit vaccine formulations hold great promise to combat COVID-19.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- Binding Sites
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/biosynthesis
- COVID-19 Vaccines/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Female
- Guinea Pigs
- HEK293 Cells
- Hot Temperature
- Humans
- Immunogenicity, Vaccine
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Domains
- Protein Interaction Domains and Motifs
- Protein Stability
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- SARS-CoV-2/chemistry
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccination
- Vaccine Potency
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Affiliation(s)
| | - Randhir Singh
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Suman Pandey
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Savitha Gayathri
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | | | - Parismita Kalita
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Nidhi Girish
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Aditya Upadhyaya
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Poorvi Reddy
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Ishika Pramanick
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Munmun Bhasin
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Jeswin Joseph
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Kerala, India
| | - Karthika Thankamani
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Kerala, India
| | - V Stalin Raj
- Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Kerala, India
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Gautham Nadig
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
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59
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Reboul CF, Heo J, Machello C, Kiesewetter S, Kim BH, Kim S, Elmlund D, Ercius P, Park J, Elmlund H. SINGLE: Atomic-resolution structure identification of nanocrystals by graphene liquid cell EM. SCIENCE ADVANCES 2021; 7:7/5/eabe6679. [PMID: 33514557 PMCID: PMC7846166 DOI: 10.1126/sciadv.abe6679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Analysis of the three-dimensional (3D) structures of nanocrystals with solution-phase transmission electron microscopy is beginning to reveal their unique physiochemical properties. We developed a "one-particle Brownian 3D reconstruction method" based on imaging of ensembles of colloidal nanocrystals using graphene liquid cell electron microscopy. Projection images of differently rotated nanocrystals are acquired using a direct electron detector with high temporal (<2.5 ms) resolution and analyzed to obtain an ensemble of 3D reconstructions. Here, we introduce computational methods required for successful atomic-resolution 3D reconstruction: (i) tracking of the individual particles throughout the time series, (ii) subtraction of the interfering background of the graphene liquid cell, (iii) identification and rejection of low-quality images, and (iv) tailored strategies for 2D/3D alignment and averaging that differ from those used in biological cryo-electron microscopy. Our developments are made available through the open-source software package SINGLE.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Junyoung Heo
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
| | - Chiara Machello
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Byung Hyo Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
- Department of Organic Materials and Fiber Engineering, Soongsil University, Seoul 06978, South Korea
| | - Sungin Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jungwon Park
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul 08826, South Korea.
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, South Korea
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
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60
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Xu C, Wang Y, Liu C, Zhang C, Han W, Hong X, Wang Y, Hong Q, Wang S, Zhao Q, Wang Y, Yang Y, Chen K, Zheng W, Kong L, Wang F, Zuo Q, Huang Z, Cong Y. Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM. SCIENCE ADVANCES 2021; 7:eabe5575. [PMID: 33277323 PMCID: PMC7775788 DOI: 10.1126/sciadv.abe5575] [Citation(s) in RCA: 271] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/04/2020] [Indexed: 05/21/2023]
Abstract
The recent outbreaks of SARS-CoV-2 pose a global health emergency. The SARS-CoV-2 trimeric spike (S) glycoprotein interacts with the human ACE2 receptor to mediate viral entry into host cells. We report the cryo-EM structures of a tightly closed SARS-CoV-2 S trimer with packed fusion peptide and an ACE2-bound S trimer at 2.7- and 3.8-Å resolution, respectively. Accompanying ACE2 binding to the up receptor-binding domain (RBD), the associated ACE2-RBD exhibits continuous swing motions. Notably, the SARS-CoV-2 S trimer appears much more sensitive to the ACE2 receptor than the SARS-CoV S trimer regarding receptor-triggered transformation from the closed prefusion state to the fusion-prone open state, potentially contributing to the superior infectivity of SARS-CoV-2. We defined the RBD T470-T478 loop and Y505 as viral determinants for specific recognition of SARS-CoV-2 RBD by ACE2. Our findings depict the mechanism of ACE2-induced S trimer conformational transitions from the ground prefusion state toward the postfusion state, facilitating development of anti-SARS-CoV-2 vaccines and therapeutics.
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Affiliation(s)
- Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Hong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalei Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Yang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaijian Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zheng
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang Kong
- The National Facility for Protein Science in Shanghai (NFPS), Shanghai 201210, China
| | - Fangfang Wang
- The National Facility for Protein Science in Shanghai (NFPS), Shanghai 201210, China
| | - Qinyu Zuo
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhong Huang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China
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Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 2020; 153:240901. [PMID: 33380110 PMCID: PMC7773420 DOI: 10.1063/5.0026025] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023] Open
Abstract
Knowledge of protein structure is paramount to the understanding of biological function, developing new therapeutics, and making detailed mechanistic hypotheses. Therefore, methods to accurately elucidate three-dimensional structures of proteins are in high demand. While there are a few experimental techniques that can routinely provide high-resolution structures, such as x-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, which have been developed to determine the structures of proteins, these techniques each have shortcomings and thus cannot be used in all cases. However, additionally, a large number of experimental techniques that provide some structural information, but not enough to assign atomic positions with high certainty have been developed. These methods offer sparse experimental data, which can also be noisy and inaccurate in some instances. In cases where it is not possible to determine the structure of a protein experimentally, computational structure prediction methods can be used as an alternative. Although computational methods can be performed without any experimental data in a large number of studies, inclusion of sparse experimental data into these prediction methods has yielded significant improvement. In this Perspective, we cover many of the successes of integrative modeling, computational modeling with experimental data, specifically for protein folding, protein-protein docking, and molecular dynamics simulations. We describe methods that incorporate sparse data from cryo-EM, NMR, mass spectrometry, electron paramagnetic resonance, small-angle x-ray scattering, Förster resonance energy transfer, and genetic sequence covariation. Finally, we highlight some of the major challenges in the field as well as possible future directions.
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Affiliation(s)
- Justin T. Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
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Al-Azzawi A, Ouadou A, Duan Y, Cheng J. Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. BMC Bioinformatics 2020; 21:534. [PMID: 33371884 PMCID: PMC7768659 DOI: 10.1186/s12859-020-03885-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 02/04/2023] Open
Abstract
Background Cryo-EM data generated by electron tomography (ET) contains images for individual protein particles in different orientations and tilted angles. Individual cryo-EM particles can be aligned to reconstruct a 3D density map of a protein structure. However, low contrast and high noise in particle images make it challenging to build 3D density maps at intermediate to high resolution (1–3 Å). To overcome this problem, we propose a fully automated cryo-EM 3D density map reconstruction approach based on deep learning particle picking. Results A perfect 2D particle mask is fully automatically generated for every single particle. Then, it uses a computer vision image alignment algorithm (image registration) to fully automatically align the particle masks. It calculates the difference of the particle image orientation angles to align the original particle image. Finally, it reconstructs a localized 3D density map between every two single-particle images that have the largest number of corresponding features. The localized 3D density maps are then averaged to reconstruct a final 3D density map. The constructed 3D density map results illustrate the potential to determine the structures of the molecules using a few samples of good particles. Also, using the localized particle samples (with no background) to generate the localized 3D density maps can improve the process of the resolution evaluation in experimental maps of cryo-EM. Tested on two widely used datasets, Auto3DCryoMap is able to reconstruct good 3D density maps using only a few thousand protein particle images, which is much smaller than hundreds of thousands of particles required by the existing methods. Conclusions We design a fully automated approach for cryo-EM 3D density maps reconstruction (Auto3DCryoMap). Instead of increasing the signal-to-noise ratio by using 2D class averaging, our approach uses 2D particle masks to produce locally aligned particle images. Auto3DCryoMap is able to accurately align structural particle shapes. Also, it is able to construct a decent 3D density map from only a few thousand aligned particle images while the existing tools require hundreds of thousands of particle images. Finally, by using the pre-processed particle images,
Auto3DCryoMap reconstructs a better 3D density map than using the original particle images.
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Affiliation(s)
- Adil Al-Azzawi
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA
| | - Anes Ouadou
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA
| | - Ye Duan
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO, 65211, USA.
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63
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Barnes CO, Jette CA, Abernathy ME, Dam KMA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP, Bjorkman PJ. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 2020; 588:682-687. [PMID: 33045718 PMCID: PMC8092461 DOI: 10.1038/s41586-020-2852-1] [Citation(s) in RCA: 1102] [Impact Index Per Article: 275.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein1-5 show promise therapeutically and are being evaluated clinically6-8. Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies5 in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs9. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Angiotensin-Converting Enzyme 2/ultrastructure
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Neutralizing/ultrastructure
- Binding Sites/genetics
- Binding Sites/immunology
- COVID-19/immunology
- Cell Line
- Cryoelectron Microscopy
- Humans
- Models, Molecular
- Mutation
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- Receptors, Coronavirus/ultrastructure
- SARS-CoV-2/chemistry
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- SARS-CoV-2/ultrastructure
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/ultrastructure
- COVID-19 Drug Treatment
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Affiliation(s)
- Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Claudia A Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shannon R Esswein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrey G Malyutin
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Punjani A, Zhang H, Fleet DJ. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat Methods 2020; 17:1214-1221. [PMID: 33257830 DOI: 10.1038/s41592-020-00990-8] [Citation(s) in RCA: 660] [Impact Index Per Article: 165.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/06/2020] [Indexed: 11/09/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability negatively impacts computational three-dimensional (3D) reconstruction with existing iterative refinement algorithms that assume rigidity. We introduce non-uniform refinement, an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability. Unlike common shift-invariant regularizers, non-uniform refinement systematically removes noise from disordered regions, while retaining signal useful for aligning particle images, yielding dramatically improved resolution and 3D map quality in many cases. We obtain high-resolution reconstructions for multiple membrane proteins as small as 100 kDa, demonstrating increased effectiveness of cryo-EM for this class of targets critical in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package.
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Affiliation(s)
- Ali Punjani
- Department of Computer Sciences, University of Toronto, Toronto, Ontario, Canada. .,Vector Institute, Toronto, Ontario, Canada. .,Structura Biotechnology Inc., Toronto, Ontario, Canada.
| | - Haowei Zhang
- Department of Computer Sciences, University of Toronto, Toronto, Ontario, Canada
| | - David J Fleet
- Department of Computer Sciences, University of Toronto, Toronto, Ontario, Canada. .,Vector Institute, Toronto, Ontario, Canada.
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Wang Z, Barnes CO, Gautam R, Cetrulo Lorenzi JC, Mayer CT, Oliveira TY, Ramos V, Cipolla M, Gordon KM, Gristick HB, West AP, Nishimura Y, Raina H, Seaman MS, Gazumyan A, Martin M, Bjorkman PJ, Nussenzweig MC, Escolano A. A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch. eLife 2020; 9:e61991. [PMID: 33084569 PMCID: PMC7577740 DOI: 10.7554/elife.61991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
A small fraction of HIV-1- infected humans develop broadly neutralizing antibodies (bNAbs) against HIV-1 that protect macaques from simian immunodeficiency HIV chimeric virus (SHIV). Similarly, a small number of macaques infected with SHIVs develop broadly neutralizing serologic activity, but less is known about the nature of simian antibodies. Here, we report on a monoclonal antibody, Ab1485, isolated from a macaque infected with SHIVAD8 that developed broadly neutralizing serologic activity targeting the V3-glycan region of HIV-1 Env. Ab1485 neutralizes 38.1% of HIV-1 isolates in a 42-pseudovirus panel with a geometric mean IC50 of 0.055 µg/mLl and SHIVAD8 with an IC50 of 0.028 µg/mLl. Ab1485 binds the V3-glycan epitope in a glycan-dependent manner. A 3.5 Å cryo-electron microscopy structure of Ab1485 in complex with a native-like SOSIP Env trimer showed conserved contacts with the N332gp120 glycan and gp120 GDIR peptide motif, but in a distinct Env-binding orientation relative to human V3/N332gp120 glycan-targeting bNAbs. Intravenous infusion of Ab1485 protected macaques from a high dose challenge with SHIVAD8. We conclude that macaques can develop bNAbs against the V3-glycan patch that resemble human V3-glycan bNAbs.
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | | | - Christian T Mayer
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Kristie M Gordon
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Henna Raina
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical CenterBostonUnited States
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Malcolm Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute. The Rockefeller UniversityNew YorkUnited States
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
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66
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Naydenova K, Jia P, Russo CJ. Cryo-EM with sub-1 Å specimen movement. Science 2020; 370:223-226. [PMID: 33033219 PMCID: PMC7116250 DOI: 10.1126/science.abb7927] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
Most information loss in cryogenic electron microscopy (cryo-EM) stems from particle movement during imaging, which remains poorly understood. We show that this movement is caused by buckling and subsequent deformation of the suspended ice, with a threshold that depends directly on the shape of the frozen water layer set by the support foil. We describe a specimen support design that eliminates buckling and reduces electron beam-induced particle movement to less than 1 angstrom. The design allows precise foil tracking during imaging with high-speed detectors, thereby lessening demands on cryostage precision and stability. It includes a maximal density of holes, which increases throughput in automated cryo-EM without degrading data quality. Movement-free imaging allows extrapolation to a three-dimensional map of the specimen at zero electron exposure, before the onset of radiation damage.
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Affiliation(s)
| | - Peipei Jia
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide 5005, Australia
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67
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Barnes CO, Jette CA, Abernathy ME, Dam KMA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP, Bjorkman PJ. Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.30.273920. [PMID: 32869026 PMCID: PMC7457611 DOI: 10.1101/2020.08.30.273920] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic presents an urgent health crisis. Human neutralizing antibodies (hNAbs) that target the host ACE2 receptor-binding domain (RBD) of the SARS-CoV-2 spike1-5 show therapeutic promise and are being evaluated clincally6-8. To determine structural correlates of SARS-CoV-2 neutralization, we solved 8 new structures of distinct COVID-19 hNAbs5 in complex with SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed classification into categories: (1) VH3-53 hNAbs with short CDRH3s that block ACE2 and bind only to "up" RBDs, (2) ACE2-blocking hNAbs that bind both "up" and "down" RBDs and can contact adjacent RBDs, (3) hNAbs that bind outside the ACE2 site and recognize "up" and "down" RBDs, and (4) Previously-described antibodies that do not block ACE2 and bind only "up" RBDs9. Class 2 comprised four hNAbs whose epitopes bridged RBDs, including a VH3-53 hNAb that used a long CDRH3 with a hydrophobic tip to bridge between adjacent "down" RBDs, thereby locking spike into a closed conformation. Epitope/paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, suggesting combinations for clinical use, and providing insight into immune responses against SARS-CoV-2.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Claudia A. Jette
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E. Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shannon R. Esswein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrey G. Malyutin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Naima G. Sharaf
- Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Present address: Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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68
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Barnes CO, West AP, Huey-Tubman KE, Hoffmann MAG, Sharaf NG, Hoffman PR, Koranda N, Gristick HB, Gaebler C, Muecksch F, Lorenzi JCC, Finkin S, Hägglöf T, Hurley A, Millard KG, Weisblum Y, Schmidt F, Hatziioannou T, Bieniasz PD, Caskey M, Robbiani DF, Nussenzweig MC, Bjorkman PJ. Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell 2020; 182:828-842.e16. [PMID: 32645326 PMCID: PMC7311918 DOI: 10.1016/j.cell.2020.06.025] [Citation(s) in RCA: 599] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022]
Abstract
Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
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MESH Headings
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Betacoronavirus/chemistry
- Betacoronavirus/immunology
- COVID-19
- Coronavirus Infections/blood
- Coronavirus Infections/immunology
- Coronavirus Infections/therapy
- Cross Reactions
- Cryoelectron Microscopy
- Epitope Mapping
- Epitopes
- Humans
- Immunization, Passive
- Immunoglobulin Fab Fragments/blood
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/isolation & purification
- Immunoglobulin Fab Fragments/ultrastructure
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/isolation & purification
- Immunoglobulin G/ultrastructure
- Middle East Respiratory Syndrome Coronavirus/chemistry
- Middle East Respiratory Syndrome Coronavirus/immunology
- Models, Molecular
- Pandemics
- Pneumonia, Viral/blood
- Pneumonia, Viral/immunology
- Severe acute respiratory syndrome-related coronavirus/chemistry
- Severe acute respiratory syndrome-related coronavirus/immunology
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- COVID-19 Serotherapy
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Affiliation(s)
- Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Magnus A G Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Naima G Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thomas Hägglöf
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Yu X, Yi P, Hamilton RA, Shen H, Chen M, Foulds CE, Mancini MA, Ludtke SJ, Wang Z, O'Malley BW. Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes. Mol Cell 2020; 79:812-823.e4. [PMID: 32668201 DOI: 10.1016/j.molcel.2020.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 01/15/2023]
Abstract
Steroid receptors activate gene transcription by recruiting coactivators to initiate transcription of their target genes. For most nuclear receptors, the ligand-dependent activation function domain-2 (AF-2) is a primary contributor to the nuclear receptor (NR) transcriptional activity. In contrast to other steroid receptors, such as ERα, the activation function of androgen receptor (AR) is largely dependent on its ligand-independent AF-1 located in its N-terminal domain (NTD). It remains unclear why AR utilizes a different AF domain from other receptors despite that NRs share similar domain organizations. Here, we present cryoelectron microscopy (cryo-EM) structures of DNA-bound full-length AR and its complex structure with key coactivators, SRC-3 and p300. AR dimerization follows a unique head-to-head and tail-to-tail manner. Unlike ERα, AR directly contacts a single SRC-3 and p300. The AR NTD is the primary site for coactivator recruitment. The structures provide a basis for understanding assembly of the AR:coactivator complex and its domain contributions for coactivator assembly and transcriptional regulation.
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Affiliation(s)
- Xinzhe Yu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hong Shen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muyuan Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven J Ludtke
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhao Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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70
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Barnes CO, West AP, Huey-Tubman KE, Hoffmann MA, Sharaf NG, Hoffman PR, Koranda N, Gristick HB, Gaebler C, Muecksch F, Cetrulo Lorenzi JC, Finkin S, Hagglof T, Hurley A, Millard KG, Weisblum Y, Schmidt F, Hatziioannou T, Bieniasz PD, Caskey M, Robbiani DF, Nussenzweig MC, Bjorkman PJ. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.28.121533. [PMID: 32577645 PMCID: PMC7302198 DOI: 10.1101/2020.05.28.121533] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1A and RBD epitopes. A 3.4Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on "up" RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Magnus A.G. Hoffmann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Naima G. Sharaf
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pauline R. Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Harry B. Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Hagglof
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G. Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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71
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Malladi SK, Schreiber D, Pramanick I, Sridevi MA, Goldenzweig A, Dutta S, Fleishman SJ, Varadarajan R. One-step sequence and structure-guided optimization of HIV-1 envelope gp140. Curr Res Struct Biol 2020; 2:45-55. [PMID: 33688632 PMCID: PMC7939140 DOI: 10.1016/j.crstbi.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Stabilization of the metastable envelope glycoprotein (Env) of HIV-1 is hypothesized to improve induction of broadly neutralizing antibodies. We improved the expression yield and stability of the HIV-1 envelope glycoprotein BG505SOSIP.664 gp140 by means of a previously described automated sequence and structure-guided computational thermostabilization approach, PROSS. This combines sequence conservation information with computational assessment of mutant stabilization, thus taking advantage of the extensive natural sequence variation present in HIV-1 Env. PROSS is used to design three gp140 variants with 17–45 mutations relative to the parental construct. One of the designs is experimentally observed to have a fourfold improvement in yield and a 4 °C increment in thermostability. In addition, the designed immunogens have similar antigenicity profiles to the native flexible linker version of wild type, BG505SOSIP.664 gp140 (NFL Wt) to major epitopes targeted by broadly neutralizing antibodies. PROSS eliminates the laborious process of screening many variants for stability and functionality, providing a proof of principle of the method for stabilization and improvement of yield without compromising antigenicity for next generation complex, highly glycosylated vaccine candidates. One-step stabilization of HIV-1 Env gp140. One-step yield improvement of HIV-1 Env gp140. Native-like oligomeric conformation of designed vaccine candidates. Unaltered antigenicity of designed vaccine candidates.
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Affiliation(s)
| | - David Schreiber
- Department of BioMolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ishika Pramanick
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | | | - Adi Goldenzweig
- Department of BioMolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | | | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, India
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72
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Kumar D, Yu X, Crawford SE, Moreno R, Jakana J, Sankaran B, Anish R, Kaundal S, Hu L, Estes MK, Wang Z, Prasad BVV. 2.7 Å cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity. SCIENCE ADVANCES 2020; 6:eaay6410. [PMID: 32494598 PMCID: PMC7159914 DOI: 10.1126/sciadv.aay6410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo-electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.
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Affiliation(s)
- Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinzhe Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rodolfo Moreno
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joanita Jakana
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- CryoEM Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ramakrishnan Anish
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Soni Kaundal
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- CryoEM Core, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author. (B.V.V.P.); (Z.W.)
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author. (B.V.V.P.); (Z.W.)
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73
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Lee S, Roh SH, Lee J, Sung N, Liu J, Tsai FTF. Cryo-EM Structures of the Hsp104 Protein Disaggregase Captured in the ATP Conformation. Cell Rep 2020; 26:29-36.e3. [PMID: 30605683 PMCID: PMC6347426 DOI: 10.1016/j.celrep.2018.12.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/12/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022] Open
Abstract
Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with Clp/Hsp100 protein unfoldases, different and seemingly conflicting 3D structures have been reported. Examining the structure of Hsp104 poses considerable challenges because Hsp104 readily hydrolyzes ATP, whereas ATP analogs can be slowly turned over and are often contaminated with other nucleotide species. Here, we present the single-particle electron cryo-microscopy (cryo-EM) structures of a catalytically inactive Hsp104 variant (Hsp104DWB) in the ATP-bound state determined between 7.7 Å and 9.3 Å resolution. Surprisingly, we observe that the Hsp104DWB hexamer adopts distinct ring conformations (closed, extended, and open) despite being in the same nucleotide state. The latter underscores the structural plasticity of Hsp104 in solution, with different conformations stabilized by nucleotide binding. Our findings suggest that, in addition to ATP hydrolysis-driven conformational changes, Hsp104 uses stochastic motions to translocate unfolded polypeptides. Hsp104 is a ring-forming ATPase that facilitates the disaggregation of amorphous and amyloid-forming protein aggregates. Lee et al. present three distinct cryo-EM structures of a catalytically inactive Hsp104-ATP variant, demonstrating that Hsp104 is a dynamic molecular machine and providing the structural basis for the passive threading of unfolded polypeptides.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Soung Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jungsoon Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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74
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Abstract
Cross-validation is used to determine the validity of a model on unseen data by assessing if the model is overfitted to noise. It is widely used in many fields, from artificial intelligence to structural biology in X-ray crystallography and nuclear magnetic resonance. Although there are concerns of map overfitting in cryo-electron microscopy (cryo-EM), cross-validation is rarely used. The problem is that establishing a performance metric of the maps over unseen data (given by 2D-projection images) is difficult due to the low signal-to-noise ratios in the individual particles. Here, I present recent advances for cryo-EM map reconstruction. I highlight that the gold-standard procedure can fail to detect map overfitting in certain cases, showing the necessity of assessing the map quality on unbiased data. Finally, I describe the challenges and advantages of developing a robust cross-validation methodology for cryo-EM.
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Affiliation(s)
- Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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75
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Xie R, Chen YX, Cai JM, Yang Y, Shen HB. SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment. J Chem Inf Model 2020; 60:2614-2625. [DOI: 10.1021/acs.jcim.9b01099] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rui Xie
- Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Xuan Chen
- Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia-Ming Cai
- Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Yang
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China
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76
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Colbasevici A, Voskoboynikova N, Orekhov PS, Bozdaganyan ME, Karlova MG, Sokolova OS, Klare JP, Mulkidjanian AY, Shaitan KV, Steinhoff HJ. Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183207. [PMID: 31987867 DOI: 10.1016/j.bbamem.2020.183207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Abstract
Amphiphilic maleic acid-containing copolymers account for a recent methodical breakthrough in the study of membrane proteins. Their application enables a detergent-free extraction of membrane proteins from lipid bilayers, yielding stable water-soluble, discoidal lipid bilayer particles with incorporated proteins, which are wrapped with copolymers. Although many studies confirm the potential of this approach for membrane protein research, the interactions between the maleic acid-containing copolymers and extracted lipids, as well as possible effects of the copolymers on lipid-embedded proteins deserve further scrutinization. Here, we combine electron paramagnetic resonance spectroscopy and coarse-grain molecular dynamics simulations to compare the distribution and dynamics of lipids in lipid particles of phospholipid bilayers encased either by an aliphatic diisobutylene/maleic acid copolymer (DIBMALPs) or by an aromatic styrene/maleic acid copolymer (SMALPs). Nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels experience restrictions of their reorientational motion depending on the type of encasing copolymer. The dynamics of the lipids was less constrained in DIBMALPs than in SMALPs with the affinity of spin labeled lipids to the polymeric rim being more pronounced in SMALPs.
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Affiliation(s)
| | | | - Philipp S Orekhov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Sechenov University, Moscow 119146, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marine E Bozdaganyan
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Maria G Karlova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga S Sokolova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Johann P Klare
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Konstantin V Shaitan
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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77
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Jenni S, Bloyet LM, Diaz-Avalos R, Liang B, Whelan SPJ, Grigorieff N, Harrison SC. Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor. Cell Rep 2020; 30:53-60.e5. [PMID: 31914397 PMCID: PMC7049099 DOI: 10.1016/j.celrep.2019.12.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/22/2019] [Accepted: 12/06/2019] [Indexed: 11/15/2022] Open
Abstract
The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0 Å resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5' nucleotide.
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Affiliation(s)
- Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Louis-Marie Bloyet
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ruben Diaz-Avalos
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Bo Liang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sean P J Whelan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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78
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Pye VE, Rosa A, Bertelli C, Struwe WB, Maslen SL, Corey R, Liko I, Hassall M, Mattiuzzo G, Ballandras-Colas A, Nans A, Takeuchi Y, Stansfeld PJ, Skehel JM, Robinson CV, Pizzato M, Cherepanov P. A bipartite structural organization defines the SERINC family of HIV-1 restriction factors. Nat Struct Mol Biol 2020; 27:78-83. [PMID: 31907454 PMCID: PMC6956856 DOI: 10.1038/s41594-019-0357-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022]
Abstract
The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of human SERINC5 and its orthologue from Drosophila melanogaster at subnanometer and near-atomic resolution, respectively. The structures reveal a novel fold comprised of ten transmembrane helices organized into two subdomains and bisected by a long diagonal helix. A lipid binding groove and clusters of conserved residues highlight potential functional sites. A structure-based mutagenesis scan identified surface-exposed regions and the interface between the subdomains of SERINC5 as critical for HIV-1-restriction activity. The same regions are also important for viral sensitization to neutralizing antibodies, directly linking the antiviral activity of SERINC5 with remodeling of the HIV-1 envelope glycoprotein.
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Affiliation(s)
- Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK
| | - Cinzia Bertelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, Italy
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Sarah L Maslen
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Robin Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Mark Hassall
- National Institute for Biological Standards and Control, Hertfordshire, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Hertfordshire, UK
| | | | - Andrea Nans
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Yasuhiro Takeuchi
- National Institute for Biological Standards and Control, Hertfordshire, UK
- UCL Division of Infection and Immunity, The Rayne Building, London, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Warwick, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, Italy.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK.
- Department of Infectious Disease, Imperial College London, St Mary's Campus, Norfolk Place, London, UK.
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79
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Benjin X, Ling L. Developments, applications, and prospects of cryo-electron microscopy. Protein Sci 2019; 29:872-882. [PMID: 31854478 PMCID: PMC7096719 DOI: 10.1002/pro.3805] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022]
Abstract
Cryo‐electron microscopy (cryo‐EM) is a structural biological method that is used to determine the 3D structures of biomacromolecules. After years of development, cryo‐EM has made great achievements, which has led to a revolution in structural biology. In this article, the principle, characteristics, history, current situation, workflow, and common problems of cryo‐EM are systematically reviewed. In addition, the new development direction of cryo‐EM—cryo‐electron tomography (cryo‐ET), is discussed in detail. Also, cryo‐EM is prospected from the following aspects: the structural analysis of small proteins, the improvement of resolution and efficiency, and the relationship between cryo‐EM and drug development. This review is dedicated to giving readers a comprehensive understanding of the development and application of cryo‐EM, and to bringing them new insights.
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Affiliation(s)
- Xu Benjin
- Laboratory Medicine Department in Fenyang College of Shanxi Medical University, Shanxi, Fenyang, China
| | - Liu Ling
- Laboratory Medicine Department in Fenyang College of Shanxi Medical University, Shanxi, Fenyang, China
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80
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Kundu N, Verma P, Kumar A, Dhar V, Dutta S, Chattopadhyay K. N-Terminal Region of Vibrio parahemolyticus Thermostable Direct Hemolysin Regulates the Membrane-Damaging Action of the Toxin. Biochemistry 2019; 59:605-614. [DOI: 10.1021/acs.biochem.9b00937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nidhi Kundu
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Pratima Verma
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
| | - Anil Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Vinica Dhar
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kausik Chattopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali 140306, Punjab, India
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Tegunov D, Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods 2019; 16:1146-1152. [PMID: 31591575 PMCID: PMC6858868 DOI: 10.1038/s41592-019-0580-y] [Citation(s) in RCA: 642] [Impact Index Per Article: 128.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/21/2019] [Indexed: 12/22/2022]
Abstract
The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens must be tightly coupled to data preprocessing to ensure the best data quality and microscope usage. Here we describe Warp, a software that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Warp corrects micrographs for global and local motion, estimates the local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. The software further includes deep-learning-based models for accurate particle picking and image denoising. The output from Warp can be fed into established programs for particle classification and 3D-map refinement. Our benchmarks show improvement in the nominal resolution, which went from 3.9 Å to 3.2 Å, of a published cryo-EM data set for influenza virus hemagglutinin. Warp is easy to install from http://github.com/cramerlab/warp and computationally inexpensive, and has an intuitive, streamlined user interface.
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Affiliation(s)
- Dimitry Tegunov
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
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Reddy HK, Carroni M, Hajdu J, Svenda M. Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture. eLife 2019; 8:48496. [PMID: 31513011 PMCID: PMC6750898 DOI: 10.7554/elife.48496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
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Affiliation(s)
- Hemanth Kn Reddy
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Department of Applied Physics, Biomedical and X-Ray Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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83
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MitCHAP-60 and Hereditary Spastic Paraplegia SPG-13 Arise from an Inactive hsp60 Chaperonin that Fails to Fold the ATP Synthase β-Subunit. Sci Rep 2019; 9:12300. [PMID: 31444388 PMCID: PMC6707239 DOI: 10.1038/s41598-019-48762-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/09/2019] [Indexed: 12/01/2022] Open
Abstract
The human mitochondrial heat shock protein 60 (hsp60) is a tetradecameric chaperonin that folds proteins in the mitochondrial matrix. An hsp60 D3G mutation leads to MitCHAP-60, an early onset neurodegenerative disease while hsp60 V72I has been linked to SPG13, a form of hereditary spastic paraplegia. Previous studies have suggested that these mutations impair the protein folding activity of hsp60 complexes but the detailed mechanism by which these mutations lead the neuromuscular diseases remains unknown. It is known, is that the β-subunit of the human mitochondrial ATP synthase co-immunoprecipitates with hsp60 indicating that the β-subunit is likely a substrate for the chaperonin. Therefore, we hypothesized that hsp60 mutations cause misfolding of proteins that are critical for aerobic respiration. Negative-stain electron microscopy and DLS results suggest that the D3G and V72I complexes fall apart when treated with ATP or ADP and are therefore unable to fold denatured substrates such as α-lactalbumin, malate dehydrogenase (MDH), and the β-subunit of ATP synthase in in-vitro protein-folding assays. These data suggests that hsp60 plays a crucial role in folding important players in aerobic respiration such as the β-subunit of the ATP synthase. The hsp60 mutations D3G and V72I impair its ability to fold mitochondrial substrates leading to abnormal ATP synthesis and the development of the MitCHAP-60 and SPG13 neuromuscular degenerative disorders.
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Kežar A, Kavčič L, Polák M, Nováček J, Gutiérrez-Aguirre I, Žnidarič MT, Coll A, Stare K, Gruden K, Ravnikar M, Pahovnik D, Žagar E, Merzel F, Anderluh G, Podobnik M. Structural basis for the multitasking nature of the potato virus Y coat protein. SCIENCE ADVANCES 2019; 5:eaaw3808. [PMID: 31328164 PMCID: PMC6636993 DOI: 10.1126/sciadv.aaw3808] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/10/2019] [Indexed: 05/02/2023]
Abstract
Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
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Affiliation(s)
- Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Martin Polák
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- University of Nova Gorica, Vipavska cesta, 5000 Nova Gorica, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Corresponding author.
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85
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In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase. J Mol Biol 2019; 431:3124-3138. [PMID: 31233764 DOI: 10.1016/j.jmb.2019.06.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/07/2019] [Accepted: 06/14/2019] [Indexed: 02/03/2023]
Abstract
Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the "double-layer particle," or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions ("triple-layer particles"), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosylmethionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, double-strand RNA genome.
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86
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Schoofs T, Barnes CO, Suh-Toma N, Golijanin J, Schommers P, Gruell H, West AP, Bach F, Lee YE, Nogueira L, Georgiev IS, Bailer RT, Czartoski J, Mascola JR, Seaman MS, McElrath MJ, Doria-Rose NA, Klein F, Nussenzweig MC, Bjorkman PJ. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Immunity 2019; 50:1513-1529.e9. [PMID: 31126879 PMCID: PMC6591006 DOI: 10.1016/j.immuni.2019.04.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/20/2019] [Accepted: 04/26/2019] [Indexed: 12/30/2022]
Abstract
Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env's silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448gp120 glycan. Effective bNAbs can therefore be raised against HIV-1 Env's silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.
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Affiliation(s)
- Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nina Suh-Toma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Westridge High School, 324 Madeline Drive, Pasadena, CA 91105, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Franziska Bach
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Yu Erica Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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87
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Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z. In situ structure and assembly of the multidrug efflux pump AcrAB-TolC. Nat Commun 2019; 10:2635. [PMID: 31201302 PMCID: PMC6570770 DOI: 10.1038/s41467-019-10512-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug efflux pumps actively expel a wide range of toxic substrates from the cell and play a major role in intrinsic and acquired drug resistance. In Gram-negative bacteria, these pumps form tripartite assemblies that span the cell envelope. However, the in situ structure and assembly mechanism of multidrug efflux pumps remain unknown. Here we report the in situ structure of the Escherichia coli AcrAB-TolC multidrug efflux pump obtained by electron cryo-tomography and subtomogram averaging. The fully assembled efflux pump is observed in a closed state under conditions of antibiotic challenge and in an open state in the presence of AcrB inhibitor. We also observe intermediate AcrAB complexes without TolC and discover that AcrA contacts the peptidoglycan layer of the periplasm. Our data point to a sequential assembly process in living bacteria, beginning with formation of the AcrAB subcomplex and suggest domains to target with efflux pump inhibitors.
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Affiliation(s)
- Xiaodong Shi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James M Bell
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hans Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Forrester
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Joanita Jakana
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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88
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Drennan AC, Krishna S, Seeger MA, Andreas MP, Gardner JM, Sether EKR, Jaspersen SL, Rayment I. Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication. Mol Biol Cell 2019; 30:1505-1522. [PMID: 30969903 PMCID: PMC6724696 DOI: 10.1091/mbc.e19-03-0167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/05/2019] [Indexed: 11/12/2022] Open
Abstract
Centrosomes and spindle pole bodies (SPBs) are membraneless organelles whose duplication and assembly is necessary for bipolar mitotic spindle formation. The structural organization and functional roles of major proteins in these organelles can provide critical insights into cell division control. Spc42, a phosphoregulated protein with an N-terminal dimeric coiled-coil (DCC), assembles into a hexameric array at the budding yeast SPB core, where it functions as a scaffold for SPB assembly. Here, we present in vitro and in vivo data to elucidate the structural arrangement and biological roles of Spc42 elements. Crystal structures reveal details of two additional coiled-coils in Spc42: a central trimeric coiled-coil and a C-terminal antiparallel DCC. Contributions of the three Spc42 coiled-coils and adjacent undetermined regions to the formation of an ∼145 Å hexameric lattice in an in vitro lipid monolayer assay and to SPB duplication and assembly in vivo reveal structural and functional redundancy in Spc42 assembly. We propose an updated model that incorporates the inherent symmetry of these Spc42 elements into a lattice, and thereby establishes the observed sixfold symmetry. The implications of this model for the organization of the central SPB core layer are discussed.
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Affiliation(s)
- Amanda C. Drennan
- Department of Biochemistry, University of Wisconsin–Madison, WI 53706
| | | | - Mark A. Seeger
- Department of Biochemistry, University of Wisconsin–Madison, WI 53706
| | | | | | | | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Ivan Rayment
- Department of Biochemistry, University of Wisconsin–Madison, WI 53706
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89
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Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J. The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis. Cell 2019; 177:751-765.e15. [PMID: 30955883 DOI: 10.1016/j.cell.2019.03.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/03/2018] [Accepted: 03/04/2019] [Indexed: 01/02/2023]
Abstract
Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a pivot point for a TRiC-PFD conformational cycle. PFD alternates between an open "latched" conformation and a closed "engaged" conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Soung Hun Roh
- Department of Biological Science, Seoul National University, Seoul, South Korea
| | - Boxue Ma
- Baylor College of Medicine, Houston, TX 77030, USA
| | - Grigore Pintilie
- Department of Biological Science, Seoul National University, Seoul, South Korea
| | - Lukasz A Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, UTSouthwestern, North Campus, Dallas, TX 75390, USA
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Thomas Walzthoeni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program in Molecular Life Sciences, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland; Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
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90
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An HIV-1 Broadly Neutralizing Antibody from a Clade C-Infected Pediatric Elite Neutralizer Potently Neutralizes the Contemporaneous and Autologous Evolving Viruses. J Virol 2019; 93:JVI.01495-18. [PMID: 30429339 DOI: 10.1128/jvi.01495-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/29/2018] [Indexed: 11/20/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) have demonstrated protective effects against HIV-1 in primate studies and recent human clinical trials. Elite neutralizers are potential candidates for isolation of HIV-1 bNAbs. The coexistence of bNAbs such as BG18 with neutralization-susceptible autologous viruses in an HIV-1-infected adult elite controller has been suggested to control viremia. Disease progression is faster in HIV-1-infected children than in adults. Plasma bNAbs with multiple epitope specificities are developed in HIV-1 chronically infected children with more potency and breadth than in adults. Therefore, we evaluated the specificity of plasma neutralizing antibodies of an antiretroviral-naive HIV-1 clade C chronically infected pediatric elite neutralizer, AIIMS_330. The plasma antibodies showed broad and potent HIV-1 neutralizing activity with >87% (29/33) breadth, a median inhibitory dilution (ID50) value of 1,246, and presence of N160 and N332 supersite-dependent HIV-1 bNAbs. The sorting of BG505.SOSIP.664.C2 T332N gp140 HIV-1 antigen-specific single B cells of AIIMS_330 resulted in the isolation of an HIV-1 N332 supersite-dependent bNAb, AIIMS-P01. The AIIMS-P01 neutralized 67% of HIV-1 cross-clade viruses, exhibited substantial indels despite limited somatic hypermutations, interacted with native-like HIV-1 trimer as observed in negative stain electron microscopy, and demonstrated high binding affinity. In addition, AIIMS-P01 neutralized the coexisting and evolving autologous viruses, suggesting the coexistence of vulnerable autologous viruses and HIV-1 bNAbs in the AIIMS_330 pediatric elite neutralizer. Such pediatric elite neutralizers can serve as potential candidates for isolation of novel HIV-1 pediatric bNAbs and for understanding the coevolution of virus and host immune response.IMPORTANCE More than 50% of the HIV-1 infections globally are caused by clade C viruses. To date, there is no effective vaccine to prevent HIV-1 infection. Based on the structural information of the currently available HIV-1 bNAbs, attempts are under way to design immunogens that can elicit correlates of protection upon vaccination. Here, we report the isolation and characterization of an HIV-1 N332 supersite-dependent bNAb, AIIMS-P01, from a clade C chronically infected pediatric elite neutralizer. The N332 supersite is an important epitope and is one of the current HIV-1 vaccine targets. AIIMS-P01 potently neutralized the contemporaneous and autologous evolving viruses and exhibited substantial indels despite low somatic hypermutations. Taken together with the information on infant bNAbs, further isolation and characterization of bNAbs contributing to the plasma breadth in HIV-1 chronically infected children may help provide a better understanding of their role in controlling HIV-1 infection.
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91
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Yin S, Zhang B, Yang Y, Huang Y, Shen HB. Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric. J Chem Inf Model 2019; 59:1658-1667. [DOI: 10.1021/acs.jcim.8b00853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Shuo Yin
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key
Laboratory of System Control and Information Processing, Ministry
of Education of China, Shanghai 200240, China
| | - Biao Zhang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key
Laboratory of System Control and Information Processing, Ministry
of Education of China, Shanghai 200240, China
| | - Yang Yang
- Department of Computer Science, Shanghai Jiao Tong University, and Key Laboratory
of Shanghai Education Commission for Intelligent Interaction and Cognitive
Engineering, Shanghai 200240, China
| | - Yan Huang
- State Key Laboratory of Infrared Physics Shanghai Institute of Technical Physics, Chinese Academy of Sciences, 500 Yutian Road, Shanghai 200083, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key
Laboratory of System Control and Information Processing, Ministry
of Education of China, Shanghai 200240, China
- Department of Computer Science, Shanghai Jiao Tong University, and Key Laboratory
of Shanghai Education Commission for Intelligent Interaction and Cognitive
Engineering, Shanghai 200240, China
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92
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Natesh R. Single-Particle cryo-EM as a Pipeline for Obtaining Atomic Resolution Structures of Druggable Targets in Preclinical Structure-Based Drug Design. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [PMCID: PMC7121590 DOI: 10.1007/978-3-030-05282-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) and three-dimensional (3D) image processing have gained importance in the last few years to obtain atomic structures of drug targets. Obtaining atomic-resolution 3D structure better than ~2.5 Å is a standard approach in pharma companies to design and optimize therapeutic compounds against drug targets like proteins. Protein crystallography is the main technique in solving the structures of drug targets at atomic resolution. However, this technique requires protein crystals which in turn is a major bottleneck. It was not possible to obtain the structure of proteins better than 2.5 Å resolution by any other methods apart from protein crystallography until 2015. Recent advances in single-particle cryo-EM and 3D image processing have led to a resolution revolution in the field of structural biology that has led to high-resolution protein structures, thus breaking the cryo-EM resolution barriers to facilitate drug discovery. There are 24 structures solved by single-particle cryo-EM with resolution 2.5 Å or better in the EMDataBank (EMDB) till date. Among these, five cryo-EM 3D reconstructions of proteins in the EMDB have their associated coordinates deposited in Protein Data Bank (PDB), with bound inhibitor/ ligand. Thus, for the first time, single-particle cryo-EM was included in the structure-based drug design (SBDD) pipeline for solving protein structures independently or where crystallography has failed to crystallize the protein. Further, this technique can be complementary and supplementary to protein crystallography field in solving 3D structures. Thus, single-particle cryo-EM can become a standard approach in pharmaceutical industry in the design, validation, and optimization of therapeutic compounds targeting therapeutically important protein molecules during preclinical drug discovery research. The present chapter will describe briefly the history and the principles of single-particle cryo-EM and 3D image processing to obtain atomic-resolution structure of proteins and their complex with their drug targets/ligands.
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93
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Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Mechanisms of opening and closing of the bacterial replicative helicase. eLife 2018; 7:41140. [PMID: 30582519 PMCID: PMC6391071 DOI: 10.7554/elife.41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
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Affiliation(s)
- Jillian Chase
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States
| | - Andrew Catalano
- Department of Chemistry and Biochemistry, City College of New York, New York, United States
| | - Alex J Noble
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Paul Db Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Kelly Molloy
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Danaya Pakotiprapha
- Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Martin Samuels
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brian Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Amedee des Georges
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States
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94
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Chen M, Baker ML. Automation and assessment of de novo modeling with Pathwalking in near atomic resolution cryoEM density maps. J Struct Biol 2018; 204:555-563. [DOI: 10.1016/j.jsb.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/28/2018] [Accepted: 09/08/2018] [Indexed: 01/30/2023]
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95
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Cryo-EM reveals ligand induced allostery underlying InsP 3R channel gating. Cell Res 2018; 28:1158-1170. [PMID: 30470765 PMCID: PMC6274648 DOI: 10.1038/s41422-018-0108-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/02/2018] [Accepted: 10/22/2018] [Indexed: 01/06/2023] Open
Abstract
Inositol-1,4,5-trisphosphate receptors (InsP3Rs) are cation channels that mobilize Ca2+ from intracellular stores in response to a wide range of cellular stimuli. The paradigm of InsP3R activation is the coupled interplay between binding of InsP3 and Ca2+ that switches the ion conduction pathway between closed and open states to enable the passage of Ca2+ through the channel. However, the molecular mechanism of how the receptor senses and decodes ligand-binding signals into gating motion remains unknown. Here, we present the electron cryo-microscopy structure of InsP3R1 from rat cerebellum determined to 4.1 Å resolution in the presence of activating concentrations of Ca2+ and adenophostin A (AdA), a structural mimetic of InsP3 and the most potent known agonist of the channel. Comparison with the 3.9 Å-resolution structure of InsP3R1 in the Apo-state, also reported herein, reveals the binding arrangement of AdA in the tetrameric channel assembly and striking ligand-induced conformational rearrangements within cytoplasmic domains coupled to the dilation of a hydrophobic constriction at the gate. Together, our results provide critical insights into the mechanistic principles by which ligand-binding allosterically gates InsP3R channel.
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96
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Tharakaraman K, Watanabe S, Chan KR, Huan J, Subramanian V, Chionh YH, Raguram A, Quinlan D, McBee M, Ong EZ, Gan ES, Tan HC, Tyagi A, Bhushan S, Lescar J, Vasudevan SG, Ooi EE, Sasisekharan R. Rational Engineering and Characterization of an mAb that Neutralizes Zika Virus by Targeting a Mutationally Constrained Quaternary Epitope. Cell Host Microbe 2018; 23:618-627.e6. [PMID: 29746833 DOI: 10.1016/j.chom.2018.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/01/2018] [Accepted: 04/10/2018] [Indexed: 11/25/2022]
Abstract
Following the recent emergence of Zika virus (ZIKV), many murine and human neutralizing anti-ZIKV antibodies have been reported. Given the risk of virus escape mutants, engineering antibodies that target mutationally constrained epitopes with therapeutically relevant potencies can be valuable for combating future outbreaks. Here, we applied computational methods to engineer an antibody, ZAb_FLEP, that targets a highly networked and therefore mutationally constrained surface formed by the envelope protein dimer. ZAb_FLEP neutralized a breadth of ZIKV strains and protected mice in distinct in vivo models, including resolving vertical transmission and fetal mortality in infected pregnant mice. Serial passaging of ZIKV in the presence of ZAb_FLEP failed to generate viral escape mutants, suggesting that its epitope is indeed mutationally constrained. A single-particle cryo-EM reconstruction of the Fab-ZIKV complex validated the structural model and revealed insights into ZAb_FLEP's neutralization mechanism. ZAb_FLEP has potential as a therapeutic in future outbreaks.
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Affiliation(s)
- Kannan Tharakaraman
- Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jia Huan
- School of Biological Sciences and Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Vidya Subramanian
- Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yok Hian Chionh
- Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Singapore, Singapore
| | - Aditya Raguram
- Harvard College, Harvard University, Cambridge, MA 02138, USA
| | - Devin Quinlan
- Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Megan McBee
- Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Singapore, Singapore
| | - Eugenia Z Ong
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Esther S Gan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Anu Tyagi
- School of Biological Sciences and Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shashi Bhushan
- School of Biological Sciences and Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences and Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore; Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Singapore, Singapore.
| | - Ram Sasisekharan
- Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Singapore, Singapore.
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97
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Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S. Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA. Sci Rep 2018; 8:13587. [PMID: 30206241 PMCID: PMC6133939 DOI: 10.1038/s41598-018-31850-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/23/2018] [Indexed: 11/09/2022] Open
Abstract
Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.
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MESH Headings
- Binding Sites
- Cryoelectron Microscopy
- Models, Molecular
- Mycobacterium smegmatis/genetics
- Mycobacterium smegmatis/metabolism
- Mycobacterium smegmatis/ultrastructure
- Nucleic Acid Conformation
- Protein Binding
- Protein Biosynthesis
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- Satabdi Mishra
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Tofayel Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anu Tyagi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jian Shi
- Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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98
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Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. New software tools in EMAN2 inspired by EMDatabank map challenge. J Struct Biol 2018; 204:283-290. [PMID: 30189321 DOI: 10.1016/j.jsb.2018.09.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/23/2018] [Accepted: 09/01/2018] [Indexed: 12/01/2022]
Abstract
EMAN2 is an extensible software suite with complete workflows for performing high-resolution single particle analysis, 2-D and 3-D heterogeneity analysis, and subtomogram averaging, among other tasks. Participation in the recent CryoEM Map Challenge sponsored by the EMDatabank led to a number of significant improvements to the single particle analysis process in EMAN2. A new convolutional neural network particle picker was developed, which dramatically improves particle picking accuracy for difficult data sets. A new particle quality metric capable of accurately identifying "bad" particles with a high degree of accuracy, no human input, and a negligible amount of additional computation, has been introduced, and this now serves as a replacement for earlier human-biased methods. The way 3-D single particle reconstructions are filtered has been altered to be more comparable to the filter applied in several other popular software packages, dramatically improving the appearance of sidechains in high-resolution structures. Finally, an option has been added to perform local resolution-based iterative filtration, resulting in local resolution improvements in many maps.
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Affiliation(s)
- James M Bell
- Graduate Program in Quantitative and Computational Biology, Baylor College of Medicine, United States
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, United States
| | - Tunay Durmaz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, United States
| | - Adam C Fluty
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, United States
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, United States.
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99
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Reboul CF, Kiesewetter S, Eager M, Belousoff M, Cui T, De Sterck H, Elmlund D, Elmlund H. Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE. J Struct Biol 2018; 204:172-181. [PMID: 30092280 DOI: 10.1016/j.jsb.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/24/2018] [Accepted: 08/06/2018] [Indexed: 12/23/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE software suite, for determination of the relative 3D orientations of single-particle projection images. PRIME has primarily found use for generation of an initial ab initio 3D reconstruction. Here we show that the strategy behind PRIME, iterative estimation of per-particle orientation distributions with stochastic hill climbing, provides a competitive approach to near-atomic resolution single-particle 3D reconstruction. A number of mathematical techniques for accelerating the convergence rate are introduced, leading to a speedup of nearly two orders of magnitude. We benchmarked our developments on numerous publicly available data sets and conclude that near-atomic resolution ab initio 3D reconstructions can be obtained with SIMPLE in a matter of hours, using standard over-the-counter CPU workstations.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; School of Mathematical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael Eager
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Matthew Belousoff
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Tiangang Cui
- School of Mathematical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Hans De Sterck
- School of Mathematical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia.
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia.
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100
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Jenni S, Harrison SC. Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface. Science 2018; 360:552-558. [PMID: 29724956 DOI: 10.1126/science.aar6436] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Kinetochores connect mitotic-spindle microtubules with chromosomes, allowing microtubule depolymerization to pull chromosomes apart during anaphase while resisting detachment as the microtubule shortens. The heterodecameric DASH/Dam1 complex (DASH/Dam1c), an essential component of yeast kinetochores, assembles into a microtubule-encircling ring. The ring associates with rodlike Ndc80 complexes to organize the kinetochore-microtubule interface. We report the cryo-electron microscopy structure (at ~4.5-angstrom resolution) of a DASH/Dam1c ring and a molecular model of its ordered components, validated by evolutionary direct-coupling analysis. Integrating this structure with that of the Ndc80 complex and with published interaction data yields a molecular picture of kinetochore-microtubule attachment, including how flexible, C-terminal extensions of DASH/Dam1c subunits project and contact widely separated sites on the Ndc80 complex rod and how phosphorylation at previously identified sites might regulate kinetochore assembly.
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Affiliation(s)
- Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard University, 250 Longwood Avenue, Boston, MA 02115, USA
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