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Banerjee C, Dutta M, Liu X, Roux KH, Taylor KA. Segmentation by classification: A novel and reliable approach for semi-automatic selection of HIV/SIV envelope spikes. J Struct Biol 2020; 209:107426. [PMID: 31733279 DOI: 10.1016/j.jsb.2019.107426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/28/2019] [Accepted: 11/12/2019] [Indexed: 11/30/2022]
Abstract
We describe a semiautomated approach to segment Env spikes from the membrane envelope of Simian Immunodeficiency Virus visualized by cryoelectron tomography of frozen-hydrated specimens. Multivariate data analysis is applied to a large set of overlapping subvolumes extracted semiautomatically from the viral envelope and does not utilize a template of the target structure. The major manual step used in the method involves determination of six points that define an ellipsoid approximating the virion shape. The approach is robust to departures of the actual virion from this starting ellipsoid. A point cage of sufficient density is generated to ensure that any spike-like protein is identified multiple times. Subsequently translational alignment of class averages to a cylindrical reference on a curved surface separates subvolumes with spikes from those without. Spike containing subvolumes identified multiple times are removed by proximity analysis. Slightly different procedures segment spikes in the equatorial and the polar regions. Once all spikes are segmented, further alignment of class averages using separately the polar and spin angles produces recognizable spike images. Our approach localized 96% of the equatorial spikes and 85% of all spikes identified manually; it identifies a significant number of additional spikes missed by manual selection. Two types of spike shapes were segmented, one with near 3-fold symmetry resembling the conventional spike, the other had a T-shape resembling the spike structure obtained when antibodies such as PG9 bind to HIV Env. The approach should be applicable to segmentation of any protein spikes extending from a cellular or virion envelope.
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Affiliation(s)
- Chaity Banerjee
- Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530, United States.
| | - Moumita Dutta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, United States.
| | - Xiuwen Liu
- Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530, United States.
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, United States.
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, United States.
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Dutta M. Recent Advances in Single Particle Cryo-electron Microscopy and Cryo-electron Tomography to Determine the Structures of Biological Macromolecules. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Structure of Simian Immunodeficiency Virus Envelope Spikes Bound with CD4 and Monoclonal Antibody 36D5. J Virol 2017; 91:JVI.00134-17. [PMID: 28539445 DOI: 10.1128/jvi.00134-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/14/2017] [Indexed: 01/29/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1)/simian immunodeficiency virus (SIV) envelope spike (Env) mediates viral entry into host cells. The V3 loop of the gp120 component of the Env trimer contributes to the coreceptor binding site and is a target for neutralizing antibodies. We used cryo-electron tomography to visualize the binding of CD4 and the V3 loop monoclonal antibody (MAb) 36D5 to gp120 of the SIV Env trimer. Our results show that 36D5 binds gp120 at the base of the V3 loop and suggest that the antibody exerts its neutralization effect by blocking the coreceptor binding site. The antibody does this without altering the dynamics of the spike motion between closed and open states when CD4 is bound. The interaction between 36D5 and SIV gp120 is similar to the interaction between some broadly neutralizing anti-V3 loop antibodies and HIV-1 gp120. Two conformations of gp120 bound with CD4 are revealed, suggesting an intrinsic dynamic nature of the liganded Env trimer. CD4 binding substantially increases the binding of 36D5 to gp120 in the intact Env trimer, consistent with CD4-induced changes in the conformation of gp120 and the antibody binding site. Binding by MAb 36D5 does not substantially alter the proportions of the two CD4-bound conformations. The position of MAb 36D5 at the V3 base changes little between conformations, indicating that the V3 base serves as a pivot point during the transition between these two states.IMPORTANCE Glycoprotein spikes on the surfaces of SIV and HIV are the sole targets available to the immune system for antibody neutralization. Spikes evade the immune system by a combination of a thick layer of polysaccharide on the surface (the glycan shield) and movement between spike domains that masks the epitope conformation. Using SIV virions whose spikes were "decorated" with the primary cellular receptor (CD4) and an antibody (36D5) at part of the coreceptor binding site, we visualized multiple conformations trapped by the rapid freezing step, which were separated using statistical analysis. Our results show that the CD4-induced conformational dynamics of the spike enhances binding of the antibody.
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Bobyk KD, Mandadapu SR, Lohith K, Guzzo C, Bhargava A, Lusso P, Bewley CA. Design of HIV Coreceptor Derived Peptides That Inhibit Viral Entry at Submicromolar Concentrations. Mol Pharm 2017; 14:2681-2689. [PMID: 28494151 DOI: 10.1021/acs.molpharmaceut.7b00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV/AIDS continues to pose an enormous burden on global health. Current HIV therapeutics include inhibitors that target the enzymes HIV protease, reverse transcriptase, and integrase, along with viral entry inhibitors that block the initial steps of HIV infection by preventing membrane fusion or virus-coreceptor interactions. With regard to the latter, peptides derived from the HIV coreceptor CCR5 were previously shown to modestly inhibit entry of CCR5-tropic HIV strains, with a peptide containing residues 178-191 of the second extracellular loop (peptide 2C) showing the strongest inhibition. Here we use an iterative approach of amino acid scanning at positions shown to be important for binding the HIV envelope, and recombining favorable substitutions to greatly improve the potency of 2C. The most potent candidate peptides gain neutralization breadth and inhibit CXCR4 and CXCR4/CCR5-using viruses, rather than CCR5-tropic strains only. We found that gains in potency in the absence of toxicity were highly dependent on amino acid position and residue type. Using virion capture assays we show that 2C and the new peptides inhibit capture of CD4-bound HIV-1 particles by antibodies whose epitopes are located in or around variable loop 3 (V3) on gp120. Analysis of antibody binding data indicates that interactions between CCR5 ECL2-derived peptides and gp120 are localized around the base and stem of V3 more than the tip. In the absence of a high-resolution structure of gp120 bound to coreceptor CCR5, these findings may facilitate structural studies of CCR5 surrogates, design of peptidomimetics with increased potency, or use as functional probes for further study of HIV-1 gp120-coreceptor interactions.
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Affiliation(s)
- Kostyantyn D Bobyk
- Laboratory of Bioorganic Chemistry, NIDDK, NIH , Bethesda, Maryland 20892, United States
| | | | - Katheryn Lohith
- Laboratory of Bioorganic Chemistry, NIDDK, NIH , Bethesda, Maryland 20892, United States
| | - Christina Guzzo
- Laboratory of Immunoregulation, NIAID, NIH , Bethesda, Maryland 20892, United States
| | - Abhishek Bhargava
- Laboratory of Bioorganic Chemistry, NIDDK, NIH , Bethesda, Maryland 20892, United States
| | - Paolo Lusso
- Laboratory of Immunoregulation, NIAID, NIH , Bethesda, Maryland 20892, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, NIDDK, NIH , Bethesda, Maryland 20892, United States
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Stephenson KE, Neubauer GH, Bricault CA, Shields J, Bayne M, Reimer U, Pawlowski N, Knaute T, Zerweck J, Seaman MS, Rosenberg ES, Barouch DH. Antibody Responses After Analytic Treatment Interruption in Human Immunodeficiency Virus-1-Infected Individuals on Early Initiated Antiretroviral Therapy. Open Forum Infect Dis 2016; 3:ofw100. [PMID: 27419172 PMCID: PMC4943535 DOI: 10.1093/ofid/ofw100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/06/2016] [Indexed: 01/16/2023] Open
Abstract
The examination of antibody responses in human immunodeficiency virus (HIV)-1-infected individuals in the setting of antiretroviral treatment (ART) interruption can provide insight into the evolution of antibody responses during viral rebound. In this study, we assessed antibody responses in 20 subjects in AIDS Clinical Trials Group A5187, wherein subjects were treated with antiretroviral therapy during acute/early HIV-1 infection, underwent analytic treatment interruption, and subsequently demonstrated viral rebound. Our data suggest that early initiation of ART arrests the maturation of HIV-1-specific antibody responses, preventing epitope diversification of antibody binding and the development of functional neutralizing capacity. Antibody responses do not appear permanently blunted, however, because viral rebound triggered the resumption of antibody maturation in our study. We also found that antibody responses measured by these assays did not predict imminent viral rebound. These data have important implications for the HIV-1 vaccine and eradication fields.
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Affiliation(s)
- Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School; Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts
| | - George H Neubauer
- Center for Virology and Vaccine Research , Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Christine A Bricault
- Center for Virology and Vaccine Research , Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Jennifer Shields
- Center for Virology and Vaccine Research , Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Madeleine Bayne
- Center for Virology and Vaccine Research , Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Ulf Reimer
- JPT Peptide Technologies , Berlin , Germany
| | | | | | | | - Michael S Seaman
- Center for Virology and Vaccine Research , Beth Israel Deaconess Medical Center, Harvard Medical School
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School; Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts
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Yi H, Strauss JD, Ke Z, Alonas E, Dillard RS, Hampton CM, Lamb KM, Hammonds JE, Santangelo PJ, Spearman PW, Wright ER. Native immunogold labeling of cell surface proteins and viral glycoproteins for cryo-electron microscopy and cryo-electron tomography applications. J Histochem Cytochem 2015; 63:780-92. [PMID: 26069287 PMCID: PMC4823802 DOI: 10.1369/0022155415593323] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/29/2015] [Indexed: 11/22/2022] Open
Abstract
Numerous methods have been developed for immunogold labeling of thick, cryo-preserved biological specimens. However, most of the methods are permutations of chemical fixation and sample sectioning, which select and isolate the immunolabeled region of interest. We describe a method for combining immunogold labeling with cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) of the surface proteins of intact mammalian cells or the surface glycoproteins of assembling and budding viruses in the context of virus-infected mammalian cells cultured on EM grids. In this method, the cells were maintained in culture media at physiologically relevant temperatures while sequentially incubated with the primary and secondary antibodies. Subsequently, the immunogold-labeled specimens were vitrified and observed under cryo-conditions in the transmission electron microscope. Cryo-EM and cryo-ET examination of the immunogold-labeled cells revealed the association of immunogold particles with the target antigens. Additionally, the cellular structure was unaltered by pre-immunolabeling chemical fixation and retained well-preserved plasma membranes, cytoskeletal elements, and macromolecular complexes. We think this technique will be of interest to cell biologists for cryo-EM and conventional studies of native cells and pathogen-infected cells.
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Affiliation(s)
- Hong Yi
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia (HY, ERW)
| | - Joshua D Strauss
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
| | - Zunlong Ke
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia (ZK)
| | - Eric Alonas
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia (EA, PJS)
| | - Rebecca S Dillard
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
| | - Cheri M Hampton
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
| | - Kristen M Lamb
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
| | - Jason E Hammonds
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia (EA, PJS)
| | - Paul W Spearman
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
| | - Elizabeth R Wright
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, Georgia (HY, ERW)
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia (JDS, RSD, CMH, KML, JEH, PWS, ERW)
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7
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Zhang W, Cao S, Martin JL, Mueller JD, Mansky LM. Morphology and ultrastructure of retrovirus particles. AIMS BIOPHYSICS 2015; 2:343-369. [PMID: 26448965 PMCID: PMC4593330 DOI: 10.3934/biophy.2015.3.343] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Retrovirus morphogenesis entails assembly of Gag proteins and the viral genome on the host plasma membrane, acquisition of the viral membrane and envelope proteins through budding, and formation of the core through the maturation process. Although in both immature and mature retroviruses, Gag and capsid proteins are organized as paracrystalline structures, the curvatures of these protein arrays are evidently not uniform within one or among all virus particles. The heterogeneity of retroviruses poses significant challenges to studying the protein contacts within the Gag and capsid lattices. This review focuses on current understanding of the molecular organization of retroviruses derived from the sub-nanometer structures of immature virus particles, helical capsid protein assemblies and soluble envelope protein complexes. These studies provide insight into the molecular elements that maintain the stability, flexibility and infectivity of virus particles. Also reviewed are morphological studies of retrovirus budding, maturation, infection and cell-cell transmission, which inform the structural transformation of the viruses and the cells during infection and viral transmission, and lead to better understanding of the interplay between the functioning viral proteins and the host cell.
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Affiliation(s)
- Wei Zhang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA ; Characterization Facility, University of Minnesota, Minneapolis, MN, USA
| | - Sheng Cao
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Jessica L Martin
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Joachim D Mueller
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA ; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA ; Pharmacology Graduate Program, University of Minnesota, Minneapolis, MN, USA ; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA
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