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Publication Record


Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity.
Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, Koblan LW, Kim YB, Badran AH, Liu DR
(2017) Sci Adv 3: eaao4774
MeSH Terms: Bacteriophage mu, Base Pairing, Cell Line, DNA Repair, DNA-Binding Proteins, Enzyme Activation, Gene Frequency, Gene Order, Humans, INDEL Mutation, Uracil-DNA Glycosidase, Viral Proteins
Show Abstract · Added March 21, 2018
We recently developed base editing, the programmable conversion of target C:G base pairs to T:A without inducing double-stranded DNA breaks (DSBs) or requiring homology-directed repair using engineered fusions of Cas9 variants and cytidine deaminases. Over the past year, the third-generation base editor (BE3) and related technologies have been successfully used by many researchers in a wide range of organisms. The product distribution of base editing-the frequency with which the target C:G is converted to mixtures of undesired by-products, along with the desired T:A product-varies in a target site-dependent manner. We characterize determinants of base editing outcomes in human cells and establish that the formation of undesired products is dependent on uracil N-glycosylase (UNG) and is more likely to occur at target sites containing only a single C within the base editing activity window. We engineered CDA1-BE3 and AID-BE3, which use cytidine deaminase homologs that increase base editing efficiency for some sequences. On the basis of these observations, we engineered fourth-generation base editors (BE4 and SaBE4) that increase the efficiency of C:G to T:A base editing by approximately 50%, while halving the frequency of undesired by-products compared to BE3. Fusing BE3, BE4, SaBE3, or SaBE4 to Gam, a bacteriophage Mu protein that binds DSBs greatly reduces indel formation during base editing, in most cases to below 1.5%, and further improves product purity. BE4, SaBE4, BE4-Gam, and SaBE4-Gam represent the state of the art in C:G-to-T:A base editing, and we recommend their use in future efforts.
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12 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
Neutralizing human antibodies prevent Zika virus replication and fetal disease in mice.
Sapparapu G, Fernandez E, Kose N, Bin Cao , Fox JM, Bombardi RG, Zhao H, Nelson CA, Bryan AL, Barnes T, Davidson E, Mysorekar IU, Fremont DH, Doranz BJ, Diamond MS, Crowe JE
(2016) Nature 540: 443-447
MeSH Terms: Africa, Americas, Animals, Antibodies, Monoclonal, Antibodies, Neutralizing, Antibodies, Viral, Antibody Specificity, Asia, B-Lymphocytes, Disease Models, Animal, Epitope Mapping, Female, Fetal Diseases, Fetus, Humans, Infectious Disease Transmission, Vertical, Male, Mice, Models, Molecular, Placenta, Pregnancy, Protein Multimerization, Survival Rate, Viral Proteins, Viral Vaccines, Virus Replication, Zika Virus, Zika Virus Infection
Show Abstract · Added April 13, 2017
Zika virus (ZIKV) is an emerging mosquito-transmitted flavivirus that can cause severe disease, including congenital birth defects during pregnancy. To develop candidate therapeutic agents against ZIKV, we isolated a panel of human monoclonal antibodies from subjects that were previously infected with ZIKV. We show that a subset of antibodies recognize diverse epitopes on the envelope (E) protein and exhibit potent neutralizing activity. One of the most inhibitory antibodies, ZIKV-117, broadly neutralized infection of ZIKV strains corresponding to African and Asian-American lineages. Epitope mapping studies revealed that ZIKV-117 recognized a unique quaternary epitope on the E protein dimer-dimer interface. We evaluated the therapeutic efficacy of ZIKV-117 in pregnant and non-pregnant mice. Monoclonal antibody treatment markedly reduced tissue pathology, placental and fetal infection, and mortality in mice. Thus, neutralizing human antibodies can protect against maternal-fetal transmission, infection and disease, and reveal important determinants for structure-based rational vaccine design efforts.
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28 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
Structures of Ebola virus GP and sGP in complex with therapeutic antibodies.
Pallesen J, Murin CD, de Val N, Cottrell CA, Hastie KM, Turner HL, Fusco ML, Flyak AI, Zeitlin L, Crowe JE, Andersen KG, Saphire EO, Ward AB
(2016) Nat Microbiol 1: 16128
MeSH Terms: Amino Acid Sequence, Antibodies, Monoclonal, Antibody Formation, Cross Reactions, Cryoelectron Microscopy, Ebolavirus, Epitopes, Glycoproteins, Hemorrhagic Fever, Ebola, Humans, Membrane Glycoproteins, Models, Structural, Mutation, Protein Multimerization, Sequence Alignment, Viral Proteins
Show Abstract · Added April 13, 2017
The Ebola virus (EBOV) GP gene encodes two glycoproteins. The major product is a soluble, dimeric glycoprotein (sGP) that is secreted abundantly. Despite the abundance of sGP during infection, little is known regarding its structure or functional role. A minor product, resulting from transcriptional editing, is the transmembrane-anchored, trimeric viral surface glycoprotein (GP). GP mediates attachment to and entry into host cells, and is the intended target of antibody therapeutics. Because large portions of sequence are shared between GP and sGP, it has been hypothesized that sGP may potentially subvert the immune response or may contribute to pathogenicity. In this study, we present cryo-electron microscopy structures of GP and sGP in complex with GP-specific and GP/sGP cross-reactive antibodies undergoing human clinical trials. The structure of the sGP dimer presented here, in complex with both an sGP-specific antibody and a GP/sGP cross-reactive antibody, permits us to unambiguously assign the oligomeric arrangement of sGP and compare its structure and epitope presentation to those of GP. We also provide biophysical evaluation of naturally occurring GP/sGP mutations that fall within the footprints identified by our high-resolution structures. Taken together, our data provide a detailed and more complete picture of the accessible Ebolavirus glycoprotein landscape and a structural basis to evaluate patient and vaccine antibody responses towards differently structured products of the GP gene.
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16 MeSH Terms
Structure and mechanism of the phage T4 recombination mediator protein UvsY.
Gajewski S, Waddell MB, Vaithiyalingam S, Nourse A, Li Z, Woetzel N, Alexander N, Meiler J, White SW
(2016) Proc Natl Acad Sci U S A 113: 3275-80
MeSH Terms: Amino Acid Sequence, Membrane Proteins, Models, Molecular, Molecular Sequence Data, Protein Conformation, Structure-Activity Relationship, Viral Proteins
Show Abstract · Added April 8, 2017
The UvsY recombination mediator protein is critical for efficient homologous recombination in bacteriophage T4 and is the functional analog of the eukaryotic Rad52 protein. During T4 homologous recombination, the UvsX recombinase has to compete with the prebound gp32 single-stranded binding protein for DNA-binding sites and UvsY stimulates this filament nucleation event. We report here the crystal structure of UvsY in four similar open-barrel heptameric assemblies and provide structural and biophysical insights into its function. The UvsY heptamer was confirmed in solution by centrifugation and light scattering, and thermodynamic analyses revealed that the UvsY-ssDNA interaction occurs within the assembly via two distinct binding modes. Using surface plasmon resonance, we also examined the binding of UvsY to both ssDNA and the ssDNA-gp32 complex. These analyses confirmed that ssDNA can bind UvsY and gp32 independently and also as a ternary complex. They also showed that residues located on the rim of the heptamer are required for optimal binding to ssDNA, thus identifying the putative ssDNA-binding surface. We propose a model in which UvsY promotes a helical ssDNA conformation that disfavors the binding of gp32 and initiates the assembly of the ssDNA-UvsX filament.
1 Communities
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7 MeSH Terms
Quelling an innate response to dsRNA.
Ogden KM, Prasad BV
(2015) Oncotarget 6: 28535-6
MeSH Terms: 2',5'-Oligoadenylate Synthetase, Animals, Antiviral Agents, Endoribonucleases, Evolution, Molecular, Exoribonucleases, Gene Expression Regulation, Viral, Host-Pathogen Interactions, Humans, Immunity, Innate, Molecular Targeted Therapy, Nucleic Acid Conformation, Phosphodiesterase Inhibitors, RNA, Double-Stranded, RNA, Viral, Signal Transduction, Viral Proteins, Viruses
Added April 26, 2017
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18 MeSH Terms
Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4.
Buth SA, Menin L, Shneider MM, Engel J, Boudko SP, Leiman PG
(2015) Viruses 7: 4676-706
MeSH Terms: Bacteriophage T4, Biophysical Phenomena, Crystallography, X-Ray, Fatty Acids, Mass Spectrometry, Models, Molecular, Protein Binding, Protein Conformation, Protein Folding, Viral Proteins
Show Abstract · Added November 2, 2017
Gene product 5 (gp5) of bacteriophage T4 is a spike-shaped protein that functions to disrupt the membrane of the target cell during phage infection. Its C-terminal domain is a long and slender β-helix that is formed by three polypeptide chains wrapped around a common symmetry axis akin to three interdigitated corkscrews. The folding and biophysical properties of such triple-stranded β-helices, which are topologically related to amyloid fibers, represent an unsolved biophysical problem. Here, we report structural and biophysical characterization of T4 gp5 β-helix and its truncated mutants of different lengths. A soluble fragment that forms a dimer of trimers and that could comprise a minimal self-folding unit has been identified. Surprisingly, the hydrophobic core of the β-helix is small. It is located near the C-terminal end of the β-helix and contains a centrally positioned and hydrated magnesium ion. A large part of the β-helix interior comprises a large elongated cavity that binds palmitic, stearic, and oleic acids in an extended conformation suggesting that these molecules might participate in the folding of the complete β-helix.
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10 MeSH Terms
Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice.
Hooper KA, Crowe JE, Bloom JD
(2015) J Virol 89: 3737-45
MeSH Terms: Animals, Cell Line, Disease Models, Animal, Dogs, Female, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H5N1 Subtype, Mice, Inbred BALB C, Mutant Proteins, Mutation, Missense, Neuraminidase, Orthomyxoviridae Infections, Protein Binding, Receptors, Virus, Reverse Genetics, Viral Proteins, Virus Attachment, Virus Cultivation
Show Abstract · Added February 2, 2015
UNLABELLED - In nearly all characterized influenza viruses, hemagglutinin (HA) is the receptor-binding protein while neuraminidase (NA) is a receptor-cleaving protein that aids in viral release. However, in recent years, several groups have described point mutations that confer receptor-binding activity on NA, albeit in laboratory rather than natural settings. One of these mutations, D151G, appears to arise in the NA of recent human H3N2 viruses upon passage in tissue culture. We inadvertently isolated the second of these mutations, G147R, in the NA of the lab-adapted A/WSN/33 (H1N1) strain while we were passaging a heavily engineered virus in the lab. G147R also occurs at low frequencies in the reported sequences of viruses from three different lineages: human 2009 pandemic H1N1 (pdmH1N1), human seasonal H1N1, and chicken H5N1. Here we reconstructed a representative G147R NA from each of these lineages and found that all of the proteins have acquired the ability to bind an unknown cellular receptor while retaining substantial sialidase activity. We then reconstructed a virus with the HA and NA of a reported G147R pdmH1N1 variant and found no attenuation of viral replication in cell culture or change in pathogenesis in mice. Furthermore, the G147R virus had modestly enhanced resistance to neutralization by the Fab of an antibody against the receptor-binding pocket of HA, although it remained completely sensitive to the full-length IgG. Overall, our results suggest that circulating N1 viruses occasionally may acquire the G147R NA receptor-binding mutation without impairment of replicative capacity.
IMPORTANCE - Influenza viruses have two main proteins on their surface: one (hemagglutinin) binds incoming viruses to cells, while the other (neuraminidase) helps release newly formed viruses from these same cells. Here we characterize unusual mutant neuraminidases that have acquired the ability to bind to cells. We show that the mutation that allows neuraminidase to bind cells has no apparent adverse effect on viral replication but does make the virus modestly more resistant to a fragment of an antibody that blocks the normal hemagglutinin-mediated mode of viral attachment. Our results suggest that viruses with receptor-binding neuraminidases may occur at low levels in circulating influenza virus lineages.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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19 MeSH Terms
An ITAM in a nonenveloped virus regulates activation of NF-κB, induction of beta interferon, and viral spread.
Stebbing RE, Irvin SC, Rivera-Serrano EE, Boehme KW, Ikizler M, Yoder JA, Dermody TS, Sherry B
(2014) J Virol 88: 2572-83
MeSH Terms: Amino Acid Sequence, Animals, Cell Line, Enzyme Activation, Humans, Immunoreceptor Tyrosine-Based Activation Motif, Interferon-beta, Intracellular Signaling Peptides and Proteins, Mice, Molecular Sequence Data, Myocytes, Cardiac, NF-kappa B, Phosphorylation, Protein Binding, Protein-Tyrosine Kinases, Reoviridae, Sequence Alignment, Syk Kinase, Tyrosine, Viral Proteins, Viral Tropism
Show Abstract · Added May 20, 2014
Immunoreceptor tyrosine-based activation motifs (ITAMs) are signaling domains located within the cytoplasmic tails of many transmembrane receptors and associated adaptor proteins that mediate immune cell activation. ITAMs also have been identified in the cytoplasmic tails of some enveloped virus glycoproteins. Here, we identified ITAM sequences in three mammalian reovirus proteins: μ2, σ2, and λ2. We demonstrate for the first time that μ2 is phosphorylated, contains a functional ITAM, and activates NF-κB. Specifically, μ2 and μNS recruit the ITAM-signaling intermediate Syk to cytoplasmic viral factories and this recruitment requires the μ2 ITAM. Moreover, both the μ2 ITAM and Syk are required for maximal μ2 activation of NF-κB. A mutant virus lacking the μ2 ITAM activates NF-κB less efficiently and induces lower levels of the downstream antiviral cytokine beta interferon (IFN-β) than does wild-type virus despite similar replication. Notably, the consequences of these μ2 ITAM effects are cell type specific. In fibroblasts where NF-κB is required for reovirus-induced apoptosis, the μ2 ITAM is advantageous for viral spread and enhances viral fitness. Conversely, in cardiac myocytes where the IFN response is critical for antiviral protection and NF-κB is not required for apoptosis, the μ2 ITAM stimulates cellular defense mechanisms and diminishes viral fitness. Together, these results suggest that the cell type-specific effect of the μ2 ITAM on viral spread reflects the cell type-specific effects of NF-κB and IFN-β. This first demonstration of a functional ITAM in a nonenveloped virus presents a new mechanism for viral ITAM-mediated signaling with likely organ-specific consequences in the host.
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21 MeSH Terms