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Use of a neutralizing antibody helps identify structural features critical for binding of toxin TcdA to the host cell surface.
Kroh HK, Chandrasekaran R, Rosenthal K, Woods R, Jin X, Ohi MD, Nyborg AC, Rainey GJ, Warrener P, Spiller BW, Lacy DB
(2017) J Biol Chem 292: 14401-14412
MeSH Terms: Amino Acid Sequence, Anti-Bacterial Agents, Antibodies, Monoclonal, Humanized, Antibodies, Neutralizing, Bacterial Proteins, Bacterial Toxins, Binding Sites, Antibody, Caco-2 Cells, Clostridium difficile, Conserved Sequence, Crystallography, X-Ray, Enterocytes, Enterotoxins, Epitope Mapping, Glucosyltransferases, Humans, Immunoglobulin Fab Fragments, Models, Molecular, Peptide Fragments, Protein Conformation, Protein Interaction Domains and Motifs, Recombinant Proteins, Repetitive Sequences, Amino Acid
Show Abstract · Added March 15, 2018
is a clinically significant pathogen that causes mild-to-severe (and often recurrent) colon infections. Disease symptoms stem from the activities of two large, multidomain toxins known as TcdA and TcdB. The toxins can bind, enter, and perturb host cell function through a multistep mechanism of receptor binding, endocytosis, pore formation, autoproteolysis, and glucosyltransferase-mediated modification of host substrates. Monoclonal antibodies that neutralize toxin activity provide a survival benefit in preclinical animal models and prevent recurrent infections in human clinical trials. However, the molecular mechanisms involved in these neutralizing activities are unclear. To this end, we performed structural studies on a neutralizing monoclonal antibody, PA50, a humanized mAb with both potent and broad-spectrum neutralizing activity, in complex with TcdA. Electron microscopy imaging and multiangle light-scattering analysis revealed that PA50 binds multiple sites on the TcdA C-terminal combined repetitive oligopeptides (CROPs) domain. A crystal structure of two PA50 Fabs bound to a segment of the TcdA CROPs helped define a conserved epitope that is distinct from previously identified carbohydrate-binding sites. Binding of TcdA to the host cell surface was directly blocked by either PA50 mAb or Fab and suggested that receptor blockade is the mechanism by which PA50 neutralizes TcdA. These findings highlight the importance of the CROPs C terminus in cell-surface binding and a role for neutralizing antibodies in defining structural features critical to a pathogen's mechanism of action. We conclude that PA50 protects host cells by blocking the binding of TcdA to cell surfaces.
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23 MeSH Terms
Structural Insights into Reovirus σ1 Interactions with Two Neutralizing Antibodies.
Dietrich MH, Ogden KM, Katen SP, Reiss K, Sutherland DM, Carnahan RH, Goff M, Cooper T, Dermody TS, Stehle T
(2017) J Virol 91:
MeSH Terms: Amino Acid Sequence, Animals, Antibodies, Neutralizing, Antibodies, Viral, Binding Sites, CHO Cells, Cell Line, Cricetulus, Hemagglutinin Glycoproteins, Influenza Virus, Immunoglobulin Fab Fragments, Mice, Molecular Docking Simulation, Molecular Dynamics Simulation, Neutralization Tests, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, Reoviridae, Structure-Activity Relationship, Viral Proteins, Virus Replication
Show Abstract · Added April 26, 2017
Reovirus attachment protein σ1 engages glycan receptors and junctional adhesion molecule-A (JAM-A) and is thought to undergo a conformational change during the proteolytic disassembly of virions to infectious subvirion particles (ISVPs) that accompanies cell entry. The σ1 protein is also the primary target of neutralizing antibodies. Here, we present a structural and functional characterization of two neutralizing antibodies that target σ1 of serotype 1 (T1) and serotype 3 (T3) reoviruses. The crystal structures revealed that each antibody engages its cognate σ1 protein within the head domain via epitopes distinct from the JAM-A-binding site. Surface plasmon resonance and cell-binding assays indicated that both antibodies likely interfere with JAM-A engagement by steric hindrance. To define the interplay between the carbohydrate receptor and antibody binding, we conducted hemagglutination inhibition assays using virions and ISVPs. The glycan-binding site of T1 σ1 is located in the head domain and is partly occluded by the bound Fab in the crystal structure. The T1-specific antibody inhibited hemagglutination by virions and ISVPs, probably via direct interference with glycan engagement. In contrast to T1 σ1, the carbohydrate-binding site of T3 σ1 is located in the tail domain, distal to the antibody epitope. The T3-specific antibody inhibited hemagglutination by T3 virions but not ISVPs, indicating that the antibody- and glycan-binding sites in σ1 are in closer spatial proximity on virions than on ISVPs. Our results provide direct evidence for a structural rearrangement of σ1 during virion-to-ISVP conversion and contribute new information about the mechanisms of antibody-mediated neutralization of reovirus.
IMPORTANCE - Virus attachment proteins mediate binding to host cell receptors, serve critical functions in cell and tissue tropism, and are often targeted by the neutralizing antibody response. The structural investigation of antibody-antigen complexes can provide valuable information for understanding the molecular basis of virus neutralization. Studies with enveloped viruses, such as HIV and influenza virus, have helped to define sites of vulnerability and guide vaccination strategies. By comparison, less is known about antibody binding to nonenveloped viruses. Here, we structurally investigated two neutralizing antibodies that bind the attachment protein σ1 of reovirus. Furthermore, we characterized the neutralization efficiency, the binding affinity for σ1, and the effect of the antibodies on reovirus receptor engagement. Our analysis defines reovirus interactions with two neutralizing antibodies, allows us to propose a mechanism by which they block virus infection, and provides evidence for a conformational change in the σ1 protein during viral cell entry.
Copyright © 2017 American Society for Microbiology.
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21 MeSH Terms
Structural basis for norovirus neutralization by an HBGA blocking human IgA antibody.
Shanker S, Czakó R, Sapparapu G, Alvarado G, Viskovska M, Sankaran B, Atmar RL, Crowe JE, Estes MK, Prasad BV
(2016) Proc Natl Acad Sci U S A 113: E5830-E5837
MeSH Terms: Amino Acid Sequence, Antibodies, Blocking, Antigens, Blood Group Antigens, Crystallography, X-Ray, Epitopes, Genotype, Humans, Immunoglobulin A, Immunoglobulin Fab Fragments, Models, Molecular, Neutralization Tests, Norovirus, Protein Domains, Viral Proteins
Show Abstract · Added April 13, 2017
Human noroviruses (HuNoVs) cause sporadic and epidemic gastroenteritis worldwide. They are classified into two major genogroups (GI and GII), with each genogroup further divided into multiple genotypes. Susceptibility to these viruses is influenced by genetically determined histo-blood group antigen (HBGA) expression. HBGAs function as cell attachment factors by binding to a surface-exposed region in the protruding (P) domain of the capsid protein. Sequence variations in this region that result in differential HBGA binding patterns and antigenicity are suggested to form a basis for strain diversification. Recent studies show that serum antibodies that block HBGA binding correlate with protection against illness. Although genogroup-dependent variation in HBGA binding specificity is structurally well characterized, an understanding of how antibodies block HBGA binding and how genotypic variations affect such blockade is lacking. Our crystallographic studies of the GI.1 P domain in complex with the Fab fragment of a human IgA monoclonal antibody (IgA 5I2) with HBGA blocking activity show that the antibody recognizes a conformational epitope formed by two surface-exposed loop clusters in the P domain. The antibody engulfs the HBGA binding site but does not affect its structural integrity. An unusual feature of the antigen recognition by IgA 5I2 is the predominant involvement of the CDR light chain 1 in contrast to the commonly observed CDR heavy chain 3, providing a unique perspective into antibody diversity in antigen recognition. Identification of the antigenic site in the P domain shows how genotypic variations might allow escape from antibody neutralization and exemplifies the interplay between antigenicity and HBGA specificity in HuNoV evolution.
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15 MeSH Terms
Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress.
Fox JM, Long F, Edeling MA, Lin H, van Duijl-Richter MKS, Fong RH, Kahle KM, Smit JM, Jin J, Simmons G, Doranz BJ, Crowe JE, Fremont DH, Rossmann MG, Diamond MS
(2015) Cell 163: 1095-1107
MeSH Terms: Alphavirus, Alphavirus Infections, Amino Acid Sequence, Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Chikungunya virus, Cryoelectron Microscopy, Epitopes, Glycoproteins, Humans, Immunoglobulin Fab Fragments, Mice, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Viral Envelope Proteins, Viral Vaccines, Virus Internalization
Show Abstract · Added January 26, 2016
We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O'nyong'nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern.
Copyright © 2015 Elsevier Inc. All rights reserved.
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21 MeSH Terms
Structural basis for Marburg virus neutralization by a cross-reactive human antibody.
Hashiguchi T, Fusco ML, Bornholdt ZA, Lee JE, Flyak AI, Matsuoka R, Kohda D, Yanagi Y, Hammel M, Crowe JE, Saphire EO
(2015) Cell 160: 904-912
MeSH Terms: Amino Acid Sequence, Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Antigen-Antibody Complex, Cell Line, Cross Reactions, Crystallography, X-Ray, Drosophila, Ebolavirus, Humans, Immunoglobulin Fab Fragments, Marburg Virus Disease, Marburgvirus, Models, Molecular, Molecular Sequence Data, Mucins, Sequence Alignment, Viral Envelope Proteins
Show Abstract · Added January 26, 2016
The filoviruses, including Marburg and Ebola, express a single glycoprotein on their surface, termed GP, which is responsible for attachment and entry of target cells. Filovirus GPs differ by up to 70% in protein sequence, and no antibodies are yet described that cross-react among them. Here, we present the 3.6 Å crystal structure of Marburg virus GP in complex with a cross-reactive antibody from a human survivor, and a lower resolution structure of the antibody bound to Ebola virus GP. The antibody, MR78, recognizes a GP1 epitope conserved across the filovirus family, which likely represents the binding site of their NPC1 receptor. Indeed, MR78 blocks binding of the essential NPC1 domain C. These structures and additional small-angle X-ray scattering of mucin-containing MARV and EBOV GPs suggest why such antibodies were not previously elicited in studies of Ebola virus, and provide critical templates for development of immunotherapeutics and inhibitors of entry.
Copyright © 2015 Elsevier Inc. All rights reserved.
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20 MeSH Terms
Mechanism of human antibody-mediated neutralization of Marburg virus.
Flyak AI, Ilinykh PA, Murin CD, Garron T, Shen X, Fusco ML, Hashiguchi T, Bornholdt ZA, Slaughter JC, Sapparapu G, Klages C, Ksiazek TG, Ward AB, Saphire EO, Bukreyev A, Crowe JE
(2015) Cell 160: 893-903
MeSH Terms: Adult, Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Antigen-Antibody Complex, B-Lymphocytes, Female, Humans, Immunoglobulin Fab Fragments, Marburg Virus Disease, Marburgvirus, Models, Molecular, Mutation, Protein Structure, Tertiary, Viral Envelope Proteins
Show Abstract · Added January 26, 2016
The mechanisms by which neutralizing antibodies inhibit Marburg virus (MARV) are not known. We isolated a panel of neutralizing antibodies from a human MARV survivor that bind to MARV glycoprotein (GP) and compete for binding to a single major antigenic site. Remarkably, several of the antibodies also bind to Ebola virus (EBOV) GP. Single-particle EM structures of antibody-GP complexes reveal that all of the neutralizing antibodies bind to MARV GP at or near the predicted region of the receptor-binding site. The presence of the glycan cap or mucin-like domain blocks binding of neutralizing antibodies to EBOV GP, but not to MARV GP. The data suggest that MARV-neutralizing antibodies inhibit virus by binding to infectious virions at the exposed MARV receptor-binding site, revealing a mechanism of filovirus inhibition.
Copyright © 2015 Elsevier Inc. All rights reserved.
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16 MeSH Terms
A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins.
Fibriansah G, Tan JL, Smith SA, de Alwis R, Ng TS, Kostyuchenko VA, Jadi RS, Kukkaro P, de Silva AM, Crowe JE, Lok SM
(2015) Nat Commun 6: 6341
MeSH Terms: Amino Acid Sequence, Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Cell Membrane, Cercopithecus aethiops, Cryoelectron Microscopy, Dengue, Dengue Virus, Enzyme-Linked Immunosorbent Assay, Epitopes, Genotype, Humans, Immunoglobulin Fab Fragments, Membrane Proteins, Mice, Molecular Sequence Data, Neutralization Tests, Protein Binding, Protein Structure, Quaternary, Sequence Homology, Amino Acid, Serogroup, Vero Cells
Show Abstract · Added January 26, 2016
Dengue virus (DENV) infects ~400 million people annually. There is no licensed vaccine or therapeutic drug. Only a small fraction of the total DENV-specific antibodies in a naturally occurring dengue infection consists of highly neutralizing antibodies. Here we show that the DENV-specific human monoclonal antibody 5J7 is exceptionally potent, neutralizing 50% of virus at nanogram-range antibody concentration. The 9 Å resolution cryo-electron microscopy structure of the Fab 5J7-DENV complex shows that a single Fab molecule binds across three envelope proteins and engages three functionally important domains, each from a different envelope protein. These domains are critical for receptor binding and fusion to the endosomal membrane. The ability to bind to multiple domains allows the antibody to fully coat the virus surface with only 60 copies of Fab, that is, half the amount compared with other potent antibodies. Our study reveals a highly efficient and unusual mechanism of molecular recognition by an antibody.
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24 MeSH Terms
A monoclonal antibody against hinge-cleaved IgG restores effector function to proteolytically-inactivated IgGs in vitro and in vivo.
Brezski RJ, Kinder M, Grugan KD, Soring KL, Carton J, Greenplate AR, Petley T, Capaldi D, Brosnan K, Emmell E, Watson S, Jordan RE
(2014) MAbs 6: 1265-73
MeSH Terms: Animals, Antibodies, Monoclonal, Antibodies, Monoclonal, Murine-Derived, Antibody-Dependent Cell Cytotoxicity, Bacterial Proteins, Blood Platelets, Cell Line, Cell Line, Tumor, Cysteine Endopeptidases, Dogs, Enzyme-Linked Immunosorbent Assay, Epitopes, Humans, Immunoglobulin Fab Fragments, Immunoglobulin G, Matrix Metalloproteinase 3, Platelet Count, Proteolysis, Rats, Rituximab
Show Abstract · Added April 22, 2016
We report a chimeric monoclonal antibody (mAb) directed to a neo-epitope that is exposed in the IgG lower hinge following proteolytic cleavage. The mAb, designated 2095-2, displays specificity for IdeS-generated F(ab')₂ fragments, but not for full-length IgG or for closely-related F(ab')₂ fragments generated with other proteases. A critical component of the specificity is provided by the C-terminal amino acid of the epitope corresponding to gly-236 in the IgG1 (also IgG4) hinge. By its ability to bind to IdeS-cleaved anti-CD20 mAb, mAb 2095-2 fully restored antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) against WIL2-S cells to the otherwise inactive anti-CD20 IgG1 F(ab')₂ fragment. Similarly, 2095-2 reinstated ADCC against MDA-MB-231 cells to an anti-CD142 IgG1 F(ab')₂ fragment. mAb 2095-2 was also capable of eliciting both CDC and ADCC to IgG4 F(ab')₂ fragments, an IgG subclass that has weaker ADCC and CDC when intact relative to intact IgG1. The in vitro cell-based efficacy of 2095-2 was extended to the in vivo setting using platelets as a cell clearance surrogate. In a canine model, the co-administration of 2095-2 together with IdeS-generated, platelet-targeting anti-CD41/61 F(ab')₂ fragment not only restored platelet clearance, but did so at a rate and extent of clearance that exceeded that of intact anti-CD41/61 IgG at comparable concentrations. To further explore this unexpected amplification effect, we conducted a rat study in which 2095-2 was administered at a series of doses in combination with a fixed dose of anti-CD41/61 F(ab')₂ fragments. Again, the combination, at ratios as low as 1:10 (w/w) 2095-2 to F(ab')₂, proved more effective than the anti-CD41/61 IgG1 alone. These findings suggest a novel mechanism for enhancing antibody-mediated cell-killing effector functions with potential applications in pathologic settings such as tumors and acute infections where protease activity is abundant.
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20 MeSH Terms
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface.
Fibriansah G, Tan JL, Smith SA, de Alwis AR, Ng TS, Kostyuchenko VA, Ibarra KD, Wang J, Harris E, de Silva A, Crowe JE, Lok SM
(2014) EMBO Mol Med 6: 358-71
MeSH Terms: Amino Acid Sequence, Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Cell Line, Dengue, Dengue Virus, Epitopes, Humans, Immunoglobulin Fab Fragments, Mice, Molecular Dynamics Simulation, Molecular Sequence Data, Protein Structure, Tertiary, Viral Envelope Proteins, Virus Internalization
Show Abstract · Added January 26, 2016
Dengue virus (DENV), which consists of four serotypes (DENV1-4), infects over 400 million people annually. Previous studies have indicated most human monoclonal antibodies (HMAbs) from dengue patients are cross-reactive and poorly neutralizing. Rare neutralizing HMAbs are usually serotype-specific and bind to quaternary structure-dependent epitopes. We determined the structure of DENV1 complexed with Fab fragments of a highly potent HMAb 1F4 to 6 Å resolution by cryo-EM. Although HMAb 1F4 appeared to bind to virus and not E proteins in ELISAs in the previous study, our structure showed that the epitope is located within an envelope (E) protein monomer, and not across neighboring E proteins. The Fab molecules bind to domain I (DI), and DI-DII hinge of the E protein. We also showed that HMAb 1F4 can neutralize DENV at different stages of viral entry in a cell type and receptor dependent manner. The structure reveals the mechanism by which this potent and specific antibody blocks viral infection.
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17 MeSH Terms
Reversion of somatic mutations of the respiratory syncytial virus-specific human monoclonal antibody Fab19 reveal a direct relationship between association rate and neutralizing potency.
Bates JT, Keefer CJ, Utley TJ, Correia BE, Schief WR, Crowe JE
(2013) J Immunol 190: 3732-9
MeSH Terms: Amino Acid Sequence, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Antibody Affinity, Antibody Specificity, Humans, Immunoglobulin Fab Fragments, Immunoglobulin Variable Region, Kinetics, Models, Molecular, Molecular Docking Simulation, Mutation, Neutralization Tests, Protein Binding, Protein Conformation, Recombinant Proteins, Respiratory Syncytial Virus, Human, Viral Fusion Proteins
Show Abstract · Added March 7, 2014
The role of affinity in determining neutralizing potency of mAbs directed against viruses is not well understood. We investigated the kinetic, structural, and functional advantage conferred by individual naturally occurring somatic mutations in the Ab H chain V region of Fab19, a well-described neutralizing human mAb directed to respiratory syncytial virus. Comparison of the affinity-matured Ab Fab19 with recombinant Fab19 Abs that were variants containing reverted amino acids from the inferred unmutated ancestor sequence revealed the molecular basis for affinity maturation of this Ab. Enhanced binding was achieved through mutations in the third H chain CDR (HCDR3) that conferred a markedly faster on-rate and a desirable increase in antiviral neutralizing activity. In contrast, most somatic mutations in the HCDR1 and HCDR2 regions did not significantly enhance Ag binding or antiviral activity. We observed a direct relationship between the measured association rate (Kon) for F protein and antiviral activity. Modeling studies of the structure of the Ag-Ab complex suggested the HCDR3 loop interacts with the antigenic site A surface loop of the respiratory syncytial virus F protein, previously shown to contain the epitope for this Ab by experimentation. These studies define a direct relationship of affinity and neutralizing activity for a viral glycoprotein-specific human mAb.
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19 MeSH Terms