scholarly journals Deep Mutational Scanning of Viral Glycoproteins and Their Host Receptors

2021 ◽  
Vol 8 ◽  
Author(s):  
Krishna K. Narayanan ◽  
Erik Procko
Keyword(s):  
Protein Interactions ◽  
Neutralizing Antibodies ◽  
Cell Attachment ◽  
Host Protein ◽  
Viral Escape ◽  
Viral Glycoprotein ◽  
Decoy Receptors ◽  
Viral Glycoproteins ◽  
Host Cell Attachment

Deep mutational scanning or deep mutagenesis is a powerful tool for understanding the sequence diversity available to viruses for adaptation in a laboratory setting. It generally involves tracking an in vitro selection of protein sequence variants with deep sequencing to map mutational effects based on changes in sequence abundance. Coupled with any of a number of selection strategies, deep mutagenesis can explore the mutational diversity available to viral glycoproteins, which mediate critical roles in cell entry and are exposed to the humoral arm of the host immune response. Mutational landscapes of viral glycoproteins for host cell attachment and membrane fusion reveal extensive epistasis and potential escape mutations to neutralizing antibodies or other therapeutics, as well as aiding in the design of optimized immunogens for eliciting broadly protective immunity. While less explored, deep mutational scans of host receptors further assist in understanding virus-host protein interactions. Critical residues on the host receptors for engaging with viral spikes are readily identified and may help with structural modeling. Furthermore, mutations may be found for engineering soluble decoy receptors as neutralizing agents that specifically bind viral targets with tight affinity and limited potential for viral escape. By untangling the complexities of how sequence contributes to viral glycoprotein and host receptor interactions, deep mutational scanning is impacting ideas and strategies at multiple levels for combatting circulating and emergent virus strains.

scholarly journals A structure-based rationale for sialic acid independent host-cell entry of Sosuga virus

2019 ◽  
Vol 116 (43) ◽  
pp. 21514-21520 ◽  
Author(s):  
Alice J. Stelfox ◽  
Thomas A. Bowden
Keyword(s):  
Sialic Acid ◽  
Host Cell ◽  
Receptor Binding ◽  
Cell Attachment ◽  
Cell Entry ◽  
Head Region ◽  
Close Proximity ◽  
Host Cell Attachment ◽  
Host Cell Entry

The bat-borne paramyxovirus, Sosuga virus (SosV), is one of many paramyxoviruses recently identified and classified within the newly established genus Pararubulavirus, family Paramyxoviridae. The envelope surface of SosV presents a receptor-binding protein (RBP), SosV-RBP, which facilitates host-cell attachment and entry. Unlike closely related hemagglutinin neuraminidase RBPs from other genera of the Paramyxoviridae, SosV-RBP and other pararubulavirus RBPs lack many of the stringently conserved residues required for sialic acid recognition and hydrolysis. We determined the crystal structure of the globular head region of SosV-RBP, revealing that while the glycoprotein presents a classical paramyxoviral six-bladed β-propeller fold and structurally classifies in close proximity to paramyxoviral RBPs with hemagglutinin-neuraminidase (HN) functionality, it presents a receptor-binding face incongruent with sialic acid recognition. Hemadsorption and neuraminidase activity analysis confirms the limited capacity of SosV-RBP to interact with sialic acid in vitro and indicates that SosV-RBP undergoes a nonclassical route of host-cell entry. The close overall structural conservation of SosV-RBP with other classical HN RBPs supports a model by which pararubulaviruses only recently diverged from sialic acid binding functionality.

scholarly journals Complementation of the fadA Mutation in Fusobacterium nucleatum Demonstrates that the Surface-Exposed Adhesin Promotes Cellular Invasion and Placental Colonization

2009 ◽  
Vol 77 (7) ◽  
pp. 3075-3079 ◽  
Author(s):  
Akihiko Ikegami ◽  
Peter Chung ◽  
Yiping W. Han
Keyword(s):  
Host Cell ◽  
Cell Attachment ◽  
Adverse Pregnancy Outcome ◽  
Fusobacterium Nucleatum ◽  
Host Cells ◽  
Mouse Placenta ◽  
Host Cell Attachment ◽  
Adverse Pregnancy

ABSTRACT Fusobacterium nucleatum is a gram-negative oral anaerobe implicated in periodontal disease and adverse pregnancy outcome. The organism colonizes the mouse placenta, causing localized infection and inflammation. The mechanism of placental colonization has not been elucidated. Previous studies identified a novel adhesin from F. nucleatum, FadA, as being involved in the attachment and invasion of host cells. The fadA deletion mutant F. nucleatum 12230 US1 was defective in host cell attachment and invasion in vitro, but it also exhibited pleiotropic effects with altered cell morphology and growth rate. In this study, a fadA-complementing clone, F. nucleatum 12230 USF81, was constructed. The expression of FadA on USF81 was confirmed by Western blotting and immunofluorescent labeling. USF81 restored host cell attachment and invasion activities. The ability of F. nucleatum 12230, US1, and USF81 to colonize the mouse placenta was examined. US1 was severely defective in placental colonization compared to the wild type and USF81. Thus, FadA plays an important role in F. nucleatum colonization in vivo. These results also represent the first complementation studies for F. nucleatum. FadA may be a therapeutic target for preventing F. nucleatum colonization of the host.

scholarly journals Protection from cytomegalovirus viremia following glycoprotein B vaccination is not dependent on neutralizing antibodies

2018 ◽  
Vol 115 (24) ◽  
pp. 6273-6278 ◽  
Author(s):  
Ilona Baraniak ◽  
Barbara Kropff ◽  
Lyn Ambrose ◽  
Megan McIntosh ◽  
Gary R. McLean ◽  
...  
Keyword(s):  
Antibody Response ◽  
Neutralizing Antibodies ◽  
De Novo ◽  
Natural Infection ◽  
Neutralizing Antibody ◽  
Glycoprotein B ◽  
Solid Organ ◽  
Viral Glycoprotein ◽  
Viral Spread

Human cytomegalovirus (HCMV) is an important pathogen in transplant patients and in congenital infection. Previously, we demonstrated that vaccination with a recombinant viral glycoprotein B (gB)/MF59 adjuvant formulation before solid organ transplant reduced viral load parameters post transplant. Reduced posttransplant viremia was directly correlated with antibody titers against gB consistent with a humoral response against gB being important. Here we show that sera from the vaccinated seronegative patients displayed little evidence of a neutralizing antibody response against cell-free HCMV in vitro. Additionally, sera from seronegative vaccine recipients had minimal effect on the replication of a strain of HCMV engineered to be cell-associated in a viral spread assay. Furthermore, although natural infection can induce antibody-dependent cellular cytotoxicity (ADCC) responses, serological analysis of seronegative vaccinees again presented no evidence of a substantial ADCC-promoting antibody response being generated de novo. Finally, analyses for responses against major antigenic domains of gB following vaccination were variable, and their pattern was distinct compared with natural infection. Taken together, these data argue that the protective effect elicited by the gB vaccine is via a mechanism of action in seronegative vaccinees that cannot be explained by neutralization or the induction of ADCC. More generally, these data, which are derived from a human challenge model that demonstrated that the gB vaccine is protective, highlight the need for more sophisticated analyses of new HCMV vaccines over and above the quantification of an ability to induce potent neutralizing antibody responses in vitro.

scholarly journals Host Protein Interactions with the 3′ End of Bovine Coronavirus RNA and the Requirement of the Poly(A) Tail for Coronavirus Defective Genome Replication

2000 ◽  
Vol 74 (11) ◽  
pp. 5053-5065 ◽  
Author(s):  
Jeannie F. Spagnolo ◽  
Brenda G. Hogue
Keyword(s):  
Protein Interactions ◽  
Helper Virus ◽  
Host Protein ◽  
Genome Replication ◽  
Mobility Shift ◽  
Bovine Coronavirus ◽  
Replication Assay ◽  
Infected Cells ◽  
Gel Mobility Shift

ABSTRACT RNA viruses have 5′ and 3′ untranslated regions (UTRs) that contain specific signals for RNA synthesis. The coronavirus genome is capped at the 5′ end and has a 3′ UTR that consists of 300 to 500 nucleotides (nt) plus a poly(A) tail. To further our understanding of coronavirus replication, we have begun to examine the involvement of host factors in this process for two group II viruses, bovine coronavirus (BCV) and mouse hepatitis coronavirus (MHV). Specific host protein interactions with the BCV 3′ UTR [287 nt plus poly(A) tail] were identified using gel mobility shift assays. Competition with the MHV 3′ UTR [301 nt plus poly(A) tail] suggests that the interactions are conserved for the two viruses. Proteins with molecular masses of 99, 95, and 73 kDa were detected in UV cross-linking experiments. Less heavily labeled proteins were also detected in the ranges of 40 to 50 and 30 kDa. The poly(A) tail was required for binding of the 73-kDa protein. Immunoprecipitation of UV-cross-linked proteins identified the 73-kDa protein as the cytoplasmic poly(A)-binding protein (PABP). Replication of the defective genomes BCV Drep and MHV MIDI-C, along with several mutants, was used to determine the importance of the poly(A) tail. Defective genomes with shortened poly(A) tails consisting of 5 or 10 A residues were replicated after transfection into helper virus-infected cells. BCV Drep RNA that lacked a poly(A) tail did not replicate, whereas replication of MHV MIDI-C RNA with a deleted tail was detected after several virus passages. All mutants exhibited delayed kinetics of replication. Detectable extension or addition of the poly(A) tail to the mutants correlated with the appearance of these RNAs in the replication assay. RNAs with shortened poly(A) tails exhibited less in vitro PABP binding, suggesting that decreased interactions with the protein may affect RNA replication. The data strongly indicate that the poly(A) tail is an important cis-acting signal for coronavirus replication.

scholarly journals Structure-Based Discovery of a Novel Small-Molecule Inhibitor of Methicillin-Resistant S. aureus

2019 ◽  
Author(s):  
Jie Liu ◽  
Lina Kozhaya ◽  
Victor J. Torres ◽  
Derya Unutmaz ◽  
Min Lu
Keyword(s):  
Cell Attachment ◽  
Immune Defense ◽  
Methicillin Resistant ◽  
Molecule Inhibitor ◽  
Membrane Perforation ◽  
Host Cell Attachment ◽  
Mrsa Infection ◽  
Mrsa Strains ◽  
Antivirulence Agents

SummaryThe rapid emergence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) strains represents a major threat to public health. MRSA elaborates an arsenal of secreted host-damaging virulence factors to mediate pathogenicity and blunt immune defense. Panton-Valentine leukocidin (PVL) and α-toxin are pore-forming cytotoxins of recognized importance in the development of invasive MRSA infection and are thus potential targets for antivirulence therapy. We report the X-ray crystal structures of PVL and α-toxin in their soluble, monomeric and oligomeric, membrane-inserted pore states, in complex with n-tetradecylphosphocholine (C14PC). The structures reveal two evolutionarily conserved phosphatidylcholine binding mechanisms and their roles in modulating host cell attachment, oligomer assembly and membrane perforation. Moreover, we demonstrate that the soluble C14PC compound protects primary human immune cells in vitro against cytolysis by PVL and α-toxin and hence may serve as the basis for the development of novel antivirulence agents to combat MRSA.

scholarly journals Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2

Science ◽  
2020 ◽  
Vol 369 (6508) ◽  
pp. 1261-1265 ◽  
Author(s):  
Kui K. Chan ◽  
Danielle Dorosky ◽  
Preeti Sharma ◽  
Shawn A. Abbasi ◽  
John M. Dye ◽  
...  
Keyword(s):  
Host Cells ◽  
Viral Escape ◽  
Spike Protein ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
High Affinity ◽  
Decoy Receptors ◽  
Catalytically Active ◽  
Interaction Surface

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds angiotensin-converting enzyme 2 (ACE2) on host cells to initiate entry, and soluble ACE2 is a therapeutic candidate that neutralizes infection by acting as a decoy. By using deep mutagenesis, mutations in ACE2 that increase S binding are found across the interaction surface, in the asparagine 90–glycosylation motif and at buried sites. The mutational landscape provides a blueprint for understanding the specificity of the interaction between ACE2 and S and for engineering high-affinity decoy receptors. Combining mutations gives ACE2 variants with affinities that rival those of monoclonal antibodies. A stable dimeric variant shows potent SARS-CoV-2 and -1 neutralization in vitro. The engineered receptor is catalytically active, and its close similarity with the native receptor may limit the potential for viral escape.

scholarly journals Structure-based discovery of a small-molecule inhibitor of methicillin-resistant Staphylococcus aureus virulence

2020 ◽  
Vol 295 (18) ◽  
pp. 5944-5959 ◽  
Author(s):  
Jie Liu ◽  
Lina Kozhaya ◽  
Victor J. Torres ◽  
Derya Unutmaz ◽  
Min Lu
Keyword(s):  
Staphylococcus Aureus ◽  
Host Cell ◽  
Cell Attachment ◽  
Host Cell Membrane ◽  
Methicillin Resistant ◽  
Molecule Inhibitor ◽  
Membrane Perforation ◽  
Host Cell Attachment ◽  
Mrsa Strains

The rapid emergence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) strains poses a major threat to public health. MRSA possesses an arsenal of secreted host-damaging virulence factors that mediate pathogenicity and blunt immune defenses. Panton–Valentine leukocidin (PVL) and α-toxin are exotoxins that create lytic pores in the host cell membrane. They are recognized as being important for the development of invasive MRSA infections and are thus potential targets for antivirulence therapies. Here, we report the high-resolution X-ray crystal structures of both PVL and α-toxin in their soluble, monomeric, and oligomeric membrane-inserted pore states in complex with n-tetradecylphosphocholine (C14PC). The structures revealed two evolutionarily conserved phosphatidylcholine-binding mechanisms and their roles in modulating host cell attachment, oligomer assembly, and membrane perforation. Moreover, we demonstrate that the soluble C14PC compound protects primary human immune cells in vitro against cytolysis by PVL and α-toxin and hence may serve as the basis for the development of an antivirulence agent for managing MRSA infections.

scholarly journals Isolation of a panel of ultra-potent human antibodies neutralizing SARS-CoV-2 and viral variants of concern

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Andrey A. Gorchakov ◽  
Sergey V. Kulemzin ◽  
Sergey V. Guselnikov ◽  
Konstantin O. Baranov ◽  
Tatyana N. Belovezhets ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Viral Escape ◽  
Lung Pathology ◽  
Human Monoclonal Antibodies ◽  
Systematic Analysis ◽  
Treatment And Prevention ◽  
Rational Development ◽  
Small Molecule Drugs

AbstractIn the absence of virus-targeting small-molecule drugs approved for the treatment and prevention of COVID-19, broadening the repertoire of potent SARS-CoV-2-neutralizing antibodies represents an important area of research in response to the ongoing pandemic. Systematic analysis of such antibodies and their combinations can be particularly instrumental for identification of candidates that may prove resistant to the emerging viral escape variants. Here, we isolated a panel of 23 RBD-specific human monoclonal antibodies from the B cells of convalescent patients. A surprisingly large proportion of such antibodies displayed potent virus-neutralizing activity both in vitro and in vivo. Four of the isolated nAbs can be categorized as ultrapotent with an apparent IC100 below 16 ng/mL. We show that individual nAbs as well as dual combinations thereof retain activity against currently circulating SARS-CoV-2 variants of concern (such as B.1.1.7, B.1.351, B.1.617, and C.37), as well as against other viral variants. When used as a prophylactics or therapeutics, these nAbs could potently suppress viral replication and prevent lung pathology in SARS-CoV-2-infected hamsters. Our data contribute to the rational development of oligoclonal therapeutic nAb cocktails mitigating the risk of SARS-CoV-2 escape.

scholarly journals Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Reda Rawi ◽  
Raghvendra Mall ◽  
Chen-Hsiang Shen ◽  
S. Katie Farney ◽  
Andrea Shiakolas ◽  
...  
Keyword(s):  
Machine Learning ◽  
Clinical Trials ◽  
Neutralizing Antibodies ◽  
Viral Escape ◽  
Gradient Boosting ◽  
Clinical Settings ◽  
Gradient Boosting Machine ◽  
Antibody Resistance ◽  
Hiv 1

Abstract Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) have promising utility in prevention and treatment of HIV-1 infection, and several are currently undergoing clinical trials. Due to the high sequence diversity and mutation rate of HIV-1, viral isolates are often resistant to specific bNAbs. Currently, resistant isolates are commonly identified by time-consuming and expensive in vitro neutralization assays. Here, we report machine learning classifiers that accurately predict resistance of HIV-1 isolates to 33 bNAbs. Notably, our classifiers achieved an overall prediction accuracy of 96% for 212 clinical isolates from patients enrolled in four different clinical trials. Moreover, use of gradient boosting machine – a tree-based machine learning method – enabled us to identify critical features, which had high accordance with epitope residues that distinguished between antibody resistance and sensitivity. The availability of an in silico antibody resistance predictor should facilitate informed decisions of antibody usage and sequence-based monitoring of viral escape in clinical settings.

scholarly journals Laboratory and clinical Pseudomonas aeruginosa strains do not bind glycosphingolipids in vitro or during type IV pili-mediated initial host cell attachment

Microbiology ◽  
2006 ◽  
Vol 152 (9) ◽  
pp. 2789-2799 ◽  
Author(s):  
Aufaugh Emam ◽  
Analyn R. Yu ◽  
Hyun-Joo Park ◽  
Radhia Mahfoud ◽  
Julianne Kus ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Epithelial Cell ◽  
Cell Attachment ◽  
Positive Control ◽  
Type Iv Pili ◽  
Lung Epithelial Cells ◽  
Target Cells ◽  
Type Iv ◽  
Host Cell Attachment

The glycosphingolipids (GSLs) gangliotriaosylceramide (Gg3) and gangliotetraosylceramide (Gg4) have been implicated as receptors for type IV pili (T4P)-mediated Pseudomonas aeruginosa epithelial cell attachment. Since P. aeruginosa T4P are divided into five groups, the authors determined whether GSLs in general, and Gg3 and Gg4 in particular, are specifically bound and required for host epithelial cell attachment of clinical and laboratory strains within these groups. An enterohaemorrhagic Escherichia coli strain, CL56, known to bind to both Gg3 and Gg4, provided a positive control. TLC overlay showed no binding of more than 12 P. aeruginosa strains to either Gg3 or Gg4 (or other GSLs), while CL56 Gg3/Gg4 binding was readily detectable. GSL ELISA similarly demonstrated no significant P. aeruginosa binding to Gg3 or Gg4, compared with CL56. Using a selective chemical inhibitor, epithelial cell GSL synthesis was abrogated, and Gg3 and Gg4 expression deleted, but P. aeruginosa attachment was not impaired. Target cell attachment was mediated by T4P, since non-piliated, but flagellated, mutants were unable to bind to the target cells. CFTR (cystic fibrosis transmembrane conductance regulator) has also been implicated as a receptor; however, in this work, overexpression of CFTR had no effect on P. aeruginosa binding. It is concluded that neither Gg3 nor Gg4 are specifically recognized by P. aeruginosa, and that endogenous GSLs do not have a role in the attachment of live intact P. aeruginosa to cultured lung epithelial cells. In contrast to whole piliated P. aeruginosa, T4P sheared from such bacteria showed significant Gg3 and Gg4 binding, which may explain the results of other studies.

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