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Bioinformatics (Oxford, England) Jul 2023While antibodies have been ground-breaking therapeutic agents, the structural determinants for antibody binding specificity remain to be fully elucidated, which is...
MOTIVATION
While antibodies have been ground-breaking therapeutic agents, the structural determinants for antibody binding specificity remain to be fully elucidated, which is compounded by the virtually unlimited repertoire of antigens they can recognize. Here, we have explored the structural landscapes of antibody-antigen interfaces to identify the structural determinants driving target recognition by assessing concavity and interatomic interactions.
RESULTS
We found that complementarity-determining regions utilized deeper concavity with their longer H3 loops, especially H3 loops of nanobody showing the deepest use of concavity. Of all amino acid residues found in complementarity-determining regions, tryptophan used deeper concavity, especially in nanobodies, making it suitable for leveraging concave antigen surfaces. Similarly, antigens utilized arginine to bind to deeper pockets of the antibody surface. Our findings fill a gap in knowledge about the antibody specificity, binding affinity, and the nature of antibody-antigen interface features, which will lead to a better understanding of how antibodies can be more effective to target druggable sites on antigen surfaces.
AVAILABILITY AND IMPLEMENTATION
The data and scripts are available at: https://github.com/YoochanMyung/scripts.
Topics: Complementarity Determining Regions; Antibodies; Antigens; Antibody Specificity; Binding Sites, Antibody
PubMed: 37382557
DOI: 10.1093/bioinformatics/btad392 -
Current Opinion in Infectious Diseases Dec 2019BK polyomavirus (BKPyV) has emerged as a significant cause of premature graft failure after kidney transplantation. Without effective antiviral drugs, treatment is based... (Review)
Review
PURPOSE OF REVIEW
BK polyomavirus (BKPyV) has emerged as a significant cause of premature graft failure after kidney transplantation. Without effective antiviral drugs, treatment is based on reducing immunosuppression to regain immune control over BKPyV replication. The paradigm of high-level viruria/decoy cells, BKPyV-DNAemia, and proven nephropathy permits early interventions. Here, we review recent findings about BKPyV-specific antibody and T-cell responses and their potential role in risk stratification, immune monitoring, and therapy.
RECENT FINDING
Kidney transplant recipients having low or undetectable BKPyV-specific IgG immunoglobulin G (IgG) are higher risk for developing BKPyV-DNAemia if the donor has high BKPyV-specific IgG. This observation has been extended to neutralizing antibodies. Immunosuppression, impaired activation, proliferation, and exhaustion of BKPyV-specific T cells may increase the risk of developing BKPyV-DNAemia and nephropathy. Clearance of BKPyV-DNAemia was correlated with high CD8 T cell responses to human leukocyte antigen (HLA)-types presenting BKPyV-encoded immunodominant 9mers. For clinical translation, these data need to be assessed in appropriately designed clinical studies, as outlined in recent guidelines on BKPyV in kidney transplantation.
SUMMARY
Evaluation of BKPyV-specific immune responses in recipient and donor may help to stratify the risk of BKPyV-DNAemia, nephropathy, and graft loss. Future efforts need to evaluate clinical translation, vaccines, and immunotherapy to control BKPyV replication.
Topics: Antibodies, Viral; Antibody Specificity; BK Virus; Host-Pathogen Interactions; Humans; Immunocompromised Host; Immunosuppression Therapy; Infection Control; Kidney Transplantation; Polyomavirus Infections; T-Lymphocytes; Transplant Recipients
PubMed: 31567736
DOI: 10.1097/QCO.0000000000000602 -
Advanced Materials (Deerfield Beach,... Dec 2019Epitope imprinting is a promising tool to generate antibody-like specific recognition sites. Recently, because of the ease of obtaining templates, the flexibility in... (Review)
Review
Epitope imprinting is a promising tool to generate antibody-like specific recognition sites. Recently, because of the ease of obtaining templates, the flexibility in selecting monomers, their resistance to harsh environments, and the high specificity toward targets, epitope-imprinted materials have attracted much attention in various fields, such as bioanalysis, clinical therapy, and pharmacy. Here, the discussion is focused on the current representative epitope imprinting technologies, including epitope bulk imprinting and epitope surface imprinting. Moreover, the application of epitope-imprinted materials to the recognition of peptides, proteins, and cells is reviewed. Finally, the remaining challenges arising from the intrinsic properties of epitope imprinting are discussed, and future development in the field is prospected.
Topics: Antibodies; Antibody Specificity; Biomimetic Materials; Epitopes; Humans
PubMed: 31423663
DOI: 10.1002/adma.201902048 -
Science Translational Medicine Jul 2021Although substantial progress has been made with Ebola virus (EBOV) vaccine measures, the immune correlates of vaccine-mediated protection remain uncertain. Here, five...
Although substantial progress has been made with Ebola virus (EBOV) vaccine measures, the immune correlates of vaccine-mediated protection remain uncertain. Here, five mucosal vaccine vectors based on human and avian paramyxoviruses provided nonhuman primates with varying degrees of protection, despite expressing the same EBOV glycoprotein (GP) immunogen. Each vaccine produced antibody responses that differed in Fc-mediated functions and isotype composition, as well as in magnitude and coverage toward GP and its conformational and linear epitopes. Differences in the degree of protection and comprehensive characterization of the response afforded the opportunity to identify which features and functions were elevated in survivors and could therefore serve as vaccine correlates of protection. Pairwise network correlation analysis of 139 immune- and vaccine-related parameters was performed to demonstrate relationships with survival. Total GP-specific antibodies, as measured by biolayer interferometry, but not neutralizing IgG or IgA titers, correlated with survival. Fc-mediated functions and the amount of receptor binding domain antibodies were associated with improved survival outcomes, alluding to the protective mechanisms of these vaccines. Therefore, functional qualities of the antibody response, particularly Fc-mediated effects and GP specificity, rather than simply magnitude of the response, appear central to vaccine-induced protection against EBOV. The heterogeneity of the response profile between the vaccines indicates that each vaccine likely exhibits its own protective signature and the requirements for an efficacious EBOV vaccine are complex.
Topics: Animals; Antibodies, Neutralizing; Antibodies, Viral; Antibody Specificity; Ebola Vaccines; Ebolavirus; Hemorrhagic Fever, Ebola; Humans; Primates
PubMed: 34261800
DOI: 10.1126/scitranslmed.abg6128 -
Infection and Immunity Sep 2020causes grave systemic infections in humans and other animals and provides a paradigm for other diseases in which the bacteria have both intracellular and extracellular... (Review)
Review
causes grave systemic infections in humans and other animals and provides a paradigm for other diseases in which the bacteria have both intracellular and extracellular lifestyles. New generations of vaccines rely on the essential contribution of the antibody responses for their protection. The quality, antigen specificity, and functions associated with antibody responses to this pathogen have been elusive for a long time. Recent approaches that combine studies in humans and genetically manipulated experimental models and that exploit awareness of the location and within-host life cycle of the pathogen are shedding light on how humoral immunity to operates. However, this area of research remains full of controversy and discrepancies. The overall scenario indicates that antibodies are essential for resistance against systemic infections and can express the highest protective function when operating in conjunction with cell-mediated immunity. Antigen specificity, isotype profile, Fc-gamma receptor usage, and complement activation are all intertwined factors that still arcanely influence antibody-mediated protection to .
Topics: Animals; Antibodies, Bacterial; Antibody Specificity; Complement Activation; Humans; Immunity, Cellular; Immunity, Humoral; Immunoglobulin Isotypes; Receptors, IgG; Salmonella; Salmonella Infections
PubMed: 32601109
DOI: 10.1128/IAI.00219-20 -
Cancer Immunology, Immunotherapy : CII Nov 2019Adoptive cell transfer (ACT) using T cell receptor (TCR) gene-modified T cells is an exciting and rapidly evolving field. Numerous preclinical and clinical studies have... (Review)
Review
Adoptive cell transfer (ACT) using T cell receptor (TCR) gene-modified T cells is an exciting and rapidly evolving field. Numerous preclinical and clinical studies have demonstrated various levels of feasibility, safety, and efficacy using TCR-engineered T cells to treat cancer and viral infections. Although evidence suggests their use can be effective, to what extent and how to improve these therapeutics are still matters of investigation. As TCR affinity has been generally accepted as the central role in defining T cell specificity and sensitivity, selection for and generation of high affinity TCRs has remained a fundamental approach to design more potent T cells. However, traditional methods for affinity-enhancement by random mutagenesis can induce undesirable cross-reactivity causing on- and off-target adverse events, generate exhausted effectors by overstimulation, and ignore other kinetic and cellular parameters that have been shown to impact antigen specificity. In this Focussed Research Review, we comment on the preclinical and clinical potential of TCR gene-modified T cells, summarize our contributions challenging the role TCR affinity plays in antigen recognition, and explore how structure-guided design can be used to manipulate antigen specificity and TCR cross-reactivity to improve the safety and efficacy of TCR gene-modified T cells used in ACT.
Topics: Animals; Antibody Specificity; Cross Reactions; Cytotoxicity, Immunologic; Genes, T-Cell Receptor; Humans; Immunotherapy; Neoplasms; T-Cell Antigen Receptor Specificity; T-Lymphocytes
PubMed: 31595324
DOI: 10.1007/s00262-019-02401-0 -
The Journal of Experimental Medicine Apr 2021Landsteiner's definition of human blood groups and the genetic rules that govern blood transfusion represents a milestone in human genetics and a historic event in...
Landsteiner's definition of human blood groups and the genetic rules that govern blood transfusion represents a milestone in human genetics and a historic event in public health. His research into the specificity of serological reactions, although less well known, has had a critical influence on the development of contemporary views on immune recognition, clonal selection, and immunological self-tolerance.
Topics: Animals; Antibody Specificity; Blood Transfusion; Erythrocytes; Hemagglutination; History, 20th Century; Humans; Immunity, Cellular; Isoantibodies; Rh-Hr Blood-Group System; Self Tolerance; T-Lymphocytes
PubMed: 33710256
DOI: 10.1084/jem.20202038 -
Journal of Virology Nov 2022Rabbit hemorrhagic disease virus (RHDV) typically causes a fatal disease in rabbits. In Australia, RHDV was imported to control the feral rabbit population, while it...
Rabbit hemorrhagic disease virus (RHDV) typically causes a fatal disease in rabbits. In Australia, RHDV was imported to control the feral rabbit population, while it poses a severe threat to native rabbits in other countries. RHDV variants are genetically diverse and serological studies using antibodies isolated from infected rabbits or raised against RHDV virus-like particles (VLPs) have found RHDV variants antigenically distinct. In this study, we determined the X-ray crystal structure of an RHDV GI.2 (N11 strain) protruding (P) domain in complex with a diagnostic monoclonal antibody (2D9) Fab. We showed that 2D9 interacted with conserved and variable residues on top of the P domain with nanomolar affinity. To better illustrate 2D9 specificity, we determined the X-ray crystal structure of an RHDV GI.1b (Ast89 strain) that was a 2D9 non-binder. Structural analysis indicated that amino acid substitutions on the GI.1b P domain likely restricted 2D9 binding. Interestingly, a model of the GI.2 P domain-Fab complex superimposed onto a cryo-EM structure of an RHDV VLP revealed that 2D9 Fab molecules clashed with neighboring Fabs and indicated that there was a reduced antibody binding occupancy. Moreover, the RHDV GI.2 histo-blood group antigen (HBGA) co-factor binding site appeared obstructed when 2D9 was modeled on the VLP and suggested that 2D9 might also function by blocking HBGA attachment. Overall, this new data provides the first structural basis of RHDV antibody specificity and explains how amino acid variation at the binding site likely restricts 2D9 cross-reactivity. Isolated RHDV antibodies have been used for decades to distinguish between antigenic variants, monitor temporal capsid evolution, and examine neutralizing capacities. In this study, we provided the structural basis for an RHDV GI.2 specific diagnostic antibody (2D9) binding and reveal that a small number of amino acid substitutions at the binding site could differentiate between RHDV GI.2 and GI.1b. This novel structural information provides a framework for understanding how RHDV displays a specific antigenic epitope and engages an antibody at the atomic level. Importantly, part of the 2D9 binding region was earlier reported to contain a neutralizing epitope and our structural modeling as well as recent human norovirus antibody-mediated neutralization studies, suggest that the 2D9 antibody has the potential to block HBGA attachment. These new findings should aid in characterizing antigenic variants and advance the development of novel monoclonal antibodies for diagnostics and therapeutics.
Topics: Animals; Rabbits; Antibody Specificity; Blood Group Antigens; Caliciviridae Infections; Epitopes; Hemorrhagic Disease Virus, Rabbit
PubMed: 36326275
DOI: 10.1128/jvi.01217-22 -
JCI Insight Jul 2021BACKGROUNDThe role of humoral immunity in COVID-19 is not fully understood, owing, in large part, to the complexity of antibodies produced in response to the SARS-CoV-2...
BACKGROUNDThe role of humoral immunity in COVID-19 is not fully understood, owing, in large part, to the complexity of antibodies produced in response to the SARS-CoV-2 infection. There is a pressing need for serology tests to assess patient-specific antibody response and predict clinical outcome.METHODSUsing SARS-CoV-2 proteome and peptide microarrays, we screened 146 COVID-19 patients' plasma samples to identify antigens and epitopes. This enabled us to develop a master epitope array and an epitope-specific agglutination assay to gauge antibody responses systematically and with high resolution.RESULTSWe identified linear epitopes from the spike (S) and nucleocapsid (N) proteins and showed that the epitopes enabled higher resolution antibody profiling than the S or N protein antigen. Specifically, we found that antibody responses to the S-811-825, S-881-895, and N-156-170 epitopes negatively or positively correlated with clinical severity or patient survival. Moreover, we found that the P681H and S235F mutations associated with the coronavirus variant of concern B.1.1.7 altered the specificity of the corresponding epitopes.CONCLUSIONEpitope-resolved antibody testing not only affords a high-resolution alternative to conventional immunoassays to delineate the complex humoral immunity to SARS-CoV-2 and differentiate between neutralizing and non-neutralizing antibodies, but it also may potentially be used to predict clinical outcome. The epitope peptides can be readily modified to detect antibodies against variants of concern in both the peptide array and latex agglutination formats.FUNDINGOntario Research Fund (ORF) COVID-19 Rapid Research Fund, Toronto COVID-19 Action Fund, Western University, Lawson Health Research Institute, London Health Sciences Foundation, and Academic Medical Organization of Southwestern Ontario (AMOSO) Innovation Fund.
Topics: Agglutination Tests; Amino Acid Sequence; Antibodies, Neutralizing; Antibodies, Viral; Antibody Formation; Antibody Specificity; COVID-19; COVID-19 Serological Testing; Epitopes; Epitopes, B-Lymphocyte; Humans; Immunity, Humoral; Microarray Analysis; Nucleocapsid; Peptides; SARS-CoV-2; Severity of Illness Index; Spike Glycoprotein, Coronavirus
PubMed: 34081630
DOI: 10.1172/jci.insight.148855 -
Frontiers in Immunology 2021The circumsporozoite protein (CSP) forms the basis of leading subunit malaria vaccine candidates. However, the mechanisms and specific targets of immunity are poorly...
The circumsporozoite protein (CSP) forms the basis of leading subunit malaria vaccine candidates. However, the mechanisms and specific targets of immunity are poorly defined. Recent findings suggest that antibody-mediated complement-fixation and activation play an important role in immunity. Here, we investigated the regions of CSP targeted by functional complement-fixing antibodies and the antibody properties associated with this activity. We quantified IgG, IgM, and functional complement-fixing antibody responses to different regions of CSP among Kenyan adults naturally exposed to malaria (n=102) and using a series of rabbit vaccination studies. Individuals who acquired functional complement-fixing antibodies had higher IgG, IgM and IgG1 and IgG3 to CSP. Acquired complement-fixing antibodies targeted the N-terminal, central-repeat, and C-terminal regions of CSP, and positive responders had greater antibody breadth compared to those who were negative for complement-fixing antibodies (p<0.05). Using rabbit vaccinations as a model, we confirmed that IgG specific to the central-repeat and non-repeat regions of CSP could effectively fix complement. However, vaccination with near full length CSP in rabbits poorly induced antibodies to the N-terminal region compared to naturally-acquired immunity in humans. Poor induction of N-terminal antibodies was also observed in a vaccination study performed in mice. IgG and IgM to all three regions of CSP play a role in mediating complement-fixation, which has important implications for malaria vaccine development.
Topics: Adolescent; Adult; Aged; Animals; Antibodies, Protozoan; Antibody Specificity; Complement Fixation Tests; Humans; Malaria; Malaria Vaccines; Middle Aged; Protozoan Proteins; Rabbits; Vaccination; Young Adult
PubMed: 34925347
DOI: 10.3389/fimmu.2021.775659