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Nucleic Acids Research Jul 2020Major histocompatibility complex (MHC) molecules are expressed on the cell surface, where they present peptides to T cells, which gives them a key role in the...
Major histocompatibility complex (MHC) molecules are expressed on the cell surface, where they present peptides to T cells, which gives them a key role in the development of T-cell immune responses. MHC molecules come in two main variants: MHC Class I (MHC-I) and MHC Class II (MHC-II). MHC-I predominantly present peptides derived from intracellular proteins, whereas MHC-II predominantly presents peptides from extracellular proteins. In both cases, the binding between MHC and antigenic peptides is the most selective step in the antigen presentation pathway. Therefore, the prediction of peptide binding to MHC is a powerful utility to predict the possible specificity of a T-cell immune response. Commonly MHC binding prediction tools are trained on binding affinity or mass spectrometry-eluted ligands. Recent studies have however demonstrated how the integration of both data types can boost predictive performances. Inspired by this, we here present NetMHCpan-4.1 and NetMHCIIpan-4.0, two web servers created to predict binding between peptides and MHC-I and MHC-II, respectively. Both methods exploit tailored machine learning strategies to integrate different training data types, resulting in state-of-the-art performance and outperforming their competitors. The servers are available at http://www.cbs.dtu.dk/services/NetMHCpan-4.1/ and http://www.cbs.dtu.dk/services/NetMHCIIpan-4.0/.
Topics: Amino Acid Motifs; Antigen Presentation; Histocompatibility Antigens Class I; Histocompatibility Antigens Class II; Ligands; Machine Learning; Peptides; Software
PubMed: 32406916
DOI: 10.1093/nar/gkaa379 -
Frontiers in Immunology 2022Efficient scanning of tissue that T cells encounter during their migratory life is pivotal to protective adaptive immunity. In fact, T cells can detect even a single... (Review)
Review
Efficient scanning of tissue that T cells encounter during their migratory life is pivotal to protective adaptive immunity. In fact, T cells can detect even a single antigenic peptide/MHC complex (pMHC) among thousands of structurally similar yet non-stimulatory endogenous pMHCs on the surface of antigen-presenting cells (APCs) or target cells. Of note, the glycocalyx of target cells, being composed of proteoglycans and bulky proteins, is bound to affect and even modulate antigen recognition by posing as a physical barrier. T cell-resident microvilli are actin-rich membrane protrusions that puncture through such barriers and thereby actively place the considerably smaller T-cell antigen receptors (TCRs) in close enough proximity to APC-presented pMHCs so that productive interactions may occur efficiently yet under force. We here review our current understanding of how the plasticity of T-cell microvilli and physicochemical properties of the glycocalyx may affect early events in T-cell activation. We assess insights gained from studies on T-cell plasma membrane ultrastructure and provide an update on current efforts to integrate biophysical aspects such as the amplitude and directionality of TCR-imposed mechanical forces and the distribution and lateral mobility of plasma membrane-resident signaling molecules into a more comprehensive view on sensitized T-cell antigen recognition.
Topics: Antigen-Presenting Cells; Antigens; Lymphocyte Activation; Protein Binding; Receptors, Antigen, T-Cell; T-Lymphocytes
PubMed: 35693808
DOI: 10.3389/fimmu.2022.886328 -
Clinical Pharmacokinetics Feb 2019Therapeutic antibodies are increasingly used to treat various diseases, including neoplasms and chronic inflammatory diseases. Antibodies exhibit complex pharmacokinetic... (Review)
Review
Therapeutic antibodies are increasingly used to treat various diseases, including neoplasms and chronic inflammatory diseases. Antibodies exhibit complex pharmacokinetic properties, notably owing to the influence of antigen mass, i.e. the amount of antigenic targets to which the monoclonal antibody binds specifically. This review focuses on the influence of antigen mass on the pharmacokinetics of therapeutic antibodies quantified by pharmacokinetic modelling in humans. Out of 159 pharmacokinetic studies, 85 reported an influence of antigen mass. This influence led to non-linear elimination decay in 50 publications, which was described using target-mediated drug disposition or derived models, as quasi-steady-state, irreversible binding and Michaelis-Menten models. In 35 publications, the pharmacokinetics was apparently linear and the influence of antigen mass was described as a covariate of pharmacokinetic parameters. If some reported covariates, such as the circulating antigen level or tumour size, are likely to be correlated to antigen mass, others, such as disease activity or disease type, may contain little information on the amount of antigenic targets. In some cases, antigen targets exist in different forms, notably in the circulation and expressed at the cell surface. The influence of antigen mass should be soundly described during the early clinical phases of drug development. To maximise therapeutic efficacy, sufficient antibody doses should be administered to ensure the saturation of antigen targets by therapeutic antibodies in all patients. If necessary, antigen mass should be taken into account in routine clinical practice.
Topics: Animals; Antibodies, Monoclonal; Antigens; Dose-Response Relationship, Immunologic; Humans; Models, Biological
PubMed: 29802542
DOI: 10.1007/s40262-018-0680-3 -
FEBS Letters Oct 2022Mtb8.4, a secretory T-cell antigen of Mycobacterium tuberculosis, is important for providing an antigen-specific immune response. In this study, we showed Mtb8.4 to have...
Mtb8.4, a secretory T-cell antigen of Mycobacterium tuberculosis, is important for providing an antigen-specific immune response. In this study, we showed Mtb8.4 to have both heme-binding and fibril-forming properties, using experimental and in silico methods. High absorbance at 410 nm and interaction with hemin-agarose demonstrated its heme-binding nature. Titration of Mtb8.4 with heme resulted in 1 : 1 stoichiometry. The heme-binding pocket in Mtb8.4 was identified by molecular modeling, and binding residues were predicted using molecular docking. The molecular dynamics simulations of apo- and heme-bound Mtb8.4 confirmed that the heme group forms a stable complex. Transmission electron microscopy analyses and dye-binding assays showed that Mtb8.4 forms fibers. Computational studies predicted that the C-terminal sequence ( AAQYIGLVESV ) is important for forming fibers. In silico analyses further anticipated the probable epitope ( AMAAQLQAV ) of Mtb8.4. The fiber-forming properties of Mtb8.4 could be advantageous from a vaccine perspective for aggregate/fibril-based vaccine delivery or it might influence the epitope presentation of Mtb8.4.
Topics: Mycobacterium tuberculosis; Antigens, Bacterial; Molecular Weight; Molecular Docking Simulation; Heme; T-Lymphocytes; Epitopes
PubMed: 35795993
DOI: 10.1002/1873-3468.14446 -
Computers in Biology and Medicine Mar 2021Due to several limitations of the only available BCG vaccine, to generate adequate protective immune responses, it is important to develop potent and cost-effective...
Due to several limitations of the only available BCG vaccine, to generate adequate protective immune responses, it is important to develop potent and cost-effective vaccines against tuberculosis (TB). In this study, we have used an immune-informatics approach to identify potential peptide based vaccine targets against TB. The proteome of Mycobacterium tuberculosis (Mtb), the causative agent of TB, was analyzed for secretory or surface localized antigenic proteins as potential vaccine candidates. The T- and B-cell epitopes as well as MHC molecule binding efficiency were identified and mapped in the modelled structures of the selected proteins. Based on antigenicity score and molecular dynamic simulation (MD) studies two peptides namely Pep-9 and Pep-15 were analyzed, modelled and docked with MHC-I and MHC-II structures. Both peptides exhibited no cytotoxicity and were able to induce proinflammatory cytokine secretion in stimulated macrophages. The molecular docking, MD and in-vitro studies of the predicted B and T-cell epitopes of Pep-9 and Pep-15 peptides with the modelled MHC structures exhibited strong binding affinity and antigenic properties, suggesting that the complex is stable, and that these peptides can be considered as a potential candidates for the development of vaccine against TB.
Topics: Epitopes, T-Lymphocyte; Histocompatibility Antigens Class II; Molecular Docking Simulation; Mycobacterium tuberculosis; Peptides
PubMed: 33450502
DOI: 10.1016/j.compbiomed.2020.104203 -
Molecular Immunology Aug 2016Antigenic domains are defined to contain a limited number of neighboring epitopes recognized by antibodies (Abs) but their molecular relationship remains rather elusive.... (Review)
Review
Antigenic domains are defined to contain a limited number of neighboring epitopes recognized by antibodies (Abs) but their molecular relationship remains rather elusive. We thoroughly analyzed the antigenic surface of the important pregnancy and tumor marker human chorionic gonadotropin (hCG), a cystine knot (ck) growth factor, and set antigenic domains and epitopes in molecular relationships to each other. Antigenic domains on hCG, its free hCGα and hCGβ subunits are dependent on appropriate inherent molecular features such as molecular accessibility and protrusion indices that determine bulging structures accessible to Abs. The banana-shaped intact hCG comprises ∼7500Å(2) of antigenic surface with minimally five antigenic domains that encompass a continuum of overlapping non-linear composite epitopes, not taking into account the C-terminal peptide extension of hCGβ (hCGβCTP). Epitopes within an antigenic domain are defined by specific Abs, that bury nearly 1000Å(2) of surface accessible area on the antigen and recognize a few up to 15 amino acid (aa) residues, whereby between 2 and 5 of these provide the essential binding energy. Variability in Ab binding modes to the contact aa residues are responsible for the variation in affinity and intra- and inter-species specificity, e.g. cross-reactions with luteinizing hormone (LH). Each genetically distinct fragment antigen binding (Fab) defines its own epitope. Consequently, recognition of the same epitope by different Abs is only possible in cases of genetically identical sequences of its binding sites. Due to combinatorial V(D)J gene segment variability of heavy and light chains, Abs defining numerous epitopes within an antigenic domain can be generated by different individuals and species. Far more than hundred Abs against the immuno-dominant antigenic domains of either subunit at both ends of the hCG-molecule, the tips of peptide loops one and three (Ł1+3) protruding from the central ck, encompassing hCGβŁ1+3 (aa 20-25+64+68-81) and hCGαŁ1 (aa 13-22; Pro16, Phe17, Phe18) plus hCGαŁ3 (Met71, Phe74), respectively, have been identified in the two "ISOBM Tissue Differentiation-7 Workshops on hCG and Related Molecules" and in other studies. These Abs recognize distinct but overlapping epitopes with slightly different specificity profiles and affinities. Heterodimeric-specific epitopes involve neighboring αŁ1 plus βŁ2 (hCGβ44/45 and 47/48). Diagnostically important Abs recognize the middle of the molecule, the ck (aa Arg10, Arg60 and possibly Gln89) and the linear hCGβCTP "tail" (aa 135-145; Asp139, Pro144, Gln145), respectively. Identification of antigenic domains and of specific epitopes is essential for harmonization of Abs in methods that are used for reliable and robust hCG measurements for the management of pregnancy, pregnancy-related disease and tumors.
Topics: Antigens; Chorionic Gonadotropin; Crystallography, X-Ray; Epitopes, B-Lymphocyte; Humans; Models, Molecular
PubMed: 27450517
DOI: 10.1016/j.molimm.2016.06.015 -
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 -
Yonsei Medical Journal Sep 2012Since the 1918 influenza A virus (IAV) pandemic, H1N1 viruses have circulated in human populations. The hemagglutinin (HA) of IAV determines viral antigenicity and often... (Review)
Review
Since the 1918 influenza A virus (IAV) pandemic, H1N1 viruses have circulated in human populations. The hemagglutinin (HA) of IAV determines viral antigenicity and often undergoes N-linked glycosylation (NLG) at several sites. Interestingly, structural analysis of the 1918 and 2009 H1N1 pandemic viruses revealed antigenic similarities attributable to the conserved epitopes and the NLG statuses of their HA proteins. NLG of the globular head of HA is known to modulate the antigenicity, fusion activity, virulence, receptor-binding specificity, and immune evasion of IAV. In addition, the HA of IAV often retains additional mutations. These supplemental mutations compensate for the attenuation of viral properties resulting from the introduced NLG. In human H1N1 viruses, the number and location of NLG sites has been regulated in accordance with the antigenic variability of the NLG-targeted antibody-binding site. The relationship between the NLG and the antigenic variance in HA appears to be stably controlled in the viral context.
Topics: Antigens, Viral; Glycosylation; Hemagglutinin Glycoproteins, Influenza Virus; Humans; Influenza A virus; Influenza, Human; Pandemics
PubMed: 22869469
DOI: 10.3349/ymj.2012.53.5.886 -
Biosensors & Bioelectronics Sep 2019The ability of influenza viruses to rapidly evolve has caused significant challenges in viral surveillance, diagnosis, and therapeutic development. Molecular sequencing... (Review)
Review
The ability of influenza viruses to rapidly evolve has caused significant challenges in viral surveillance, diagnosis, and therapeutic development. Molecular sequencing methods, though powerful tools for monitoring influenza evolution at the genetic level, are not able to fully characterize the antigenic properties of influenza viruses. Understanding influenza virus antigenicity is critical to vaccine development and disease prevention. Traditional immunoassays which have been widely used for evaluating influenza antigenicity have limited throughput. To alleviate these problems, new bioanalytical tools to investigate influenza antigenicity by measuring antibody-antigen binding are an active area of research. Herein, we review immunosensor technologies from the aspects of various sensing principles, while highlighting recent developments in multiplex, label-free detection strategies. Highlighted technologies include electrochemical immunosensors relying on impedimetric detection; these demonstrate simple design and cost effectiveness for mass production. Antibody arrays implemented on an optical interferometric sensor system allow systematic characterization of influenza antigenicity. Quartz microbalance immunosensors are highly sensitive but have yet to be explored for multiplex sensing. Immunosensors made on lateral flow strips have shown promise in rapid diagnosis of influenza subtypes. We anticipate that these and other technologies discussed in the review will facilitate advances in the study of influenza, and other viral pathogens.
Topics: Animals; Antigens, Viral; Biosensing Techniques; Equipment Design; Humans; Immunoassay; Influenza, Human; Alphainfluenzavirus; Orthomyxoviridae; Orthomyxoviridae Infections
PubMed: 31272058
DOI: 10.1016/j.bios.2019.111476 -
Cellular and Molecular Life Sciences :... Aug 2014Whereas research on CD1d has emphasized a few glycosyl ceramides, the broader family of four human CD1 antigen-presenting molecules binds hundreds of distinct... (Review)
Review
Whereas research on CD1d has emphasized a few glycosyl ceramides, the broader family of four human CD1 antigen-presenting molecules binds hundreds of distinct self-lipids. Individual lipid types bind within CD1 grooves in different ways, such that they partially fill the groove, match the groove volume, or protrude substantially from the groove. These differing modes of binding can now be connected to differing immunological functions, as individual lipids can act as stimulatory antigens, inhibitory ligands, or space-filling scaffolds. Because each type of CD1 protein folds to produce antigen-binding grooves with differing sizes and shapes, CD1a, CD1b, CD1c, CD1d, and CD1e have distinct mechanisms of capturing self-lipids and exchanging them for foreign lipids. The size discrepancy between endogeneous lipids and groove volume is most pronounced for CD1b. Recent studies show that the large CD1b cavity can simultaneously bind two self-lipids, the antigen, and its scaffold lipid, which can be exchanged for one large bacterial lipid. In this review, we will highlight recent studies showing how cells regulate lipid antigen loading and the roles CD1 groove structures have in control of the presentation of chemically diverse lipids to T cells.
Topics: Animals; Antigen Presentation; Antigens; Antigens, CD1; Humans; Ligands; Lipids; Models, Molecular; Protein Conformation; T-Lymphocytes
PubMed: 24658584
DOI: 10.1007/s00018-014-1603-6