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Journal of Virology Jan 2016HIV-1 establishes persistent infection in part due to its ability to evade host immune responses. Occlusion by glycans contributes to masking conserved sites that are...
Conserved Role of an N-Linked Glycan on the Surface Antigen of Human Immunodeficiency Virus Type 1 Modulating Virus Sensitivity to Broadly Neutralizing Antibodies against the Receptor and Coreceptor Binding Sites.
UNLABELLED
HIV-1 establishes persistent infection in part due to its ability to evade host immune responses. Occlusion by glycans contributes to masking conserved sites that are targets for some broadly neutralizing antibodies (bNAbs). Previous work has shown that removal of a highly conserved potential N-linked glycan (PNLG) site at amino acid residue 197 (N7) on the surface antigen gp120 of HIV-1 increases neutralization sensitivity of the mutant virus to CD4 binding site (CD4bs)-directed antibodies compared to its wild-type (WT) counterpart. However, it is not clear if the role of the N7 glycan is conserved among diverse HIV-1 isolates and if other glycans in the conserved regions of HIV-1 Env display similar functions. In this work, we examined the role of PNLGs in the conserved region of HIV-1 Env, particularly the role of the N7 glycan in a panel of HIV-1 strains representing different clades, tissue origins, coreceptor usages, and neutralization sensitivities. We demonstrate that the absence of the N7 glycan increases the sensitivity of diverse HIV-1 isolates to CD4bs- and V3 loop-directed antibodies, indicating that the N7 glycan plays a conserved role masking these conserved epitopes. However, the effect of the N7 glycan on virus sensitivity to neutralizing antibodies directed against the V2 loop epitope is isolate dependent. These findings indicate that the N7 glycan plays an important and conserved role modulating the structure, stability, or accessibility of bNAb epitopes in the CD4bs and coreceptor binding region, thus representing a potential target for the design of immunogens and therapeutics.
IMPORTANCE
N-linked glycans on the HIV-1 envelope protein have been postulated to contribute to viral escape from host immune responses. However, the role of specific glycans in the conserved regions of HIV-1 Env in modulating epitope recognition by broadly neutralizing antibodies has not been well defined. We show here that a single N-linked glycan plays a unique and conserved role among conserved glycans on HIV-1 gp120 in modulating the exposure or the stability of the receptor and coreceptor binding site without affecting the integrity of the Env in mediating viral infection or the ability of the mutant gp120 to bind to CD4. The observation that the antigenicity of the receptor and coreceptor binding sites can be modulated by a single glycan indicates that select glycan modification offers a potential strategy for the design of HIV-1 vaccine candidates.
Topics: Antibodies, Neutralizing; Antigens, Surface; Binding Sites; Epitopes; Glycosylation; HIV Antibodies; HIV Antigens; HIV Envelope Protein gp120; HIV-1; Humans; Polysaccharides
PubMed: 26512079
DOI: 10.1128/JVI.02321-15 -
PloS One 2020Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors...
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with HLA in a common diagonal binding mode, and KIR-HLA interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the human MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.
Topics: Alleles; Amino Acid Sequence; Binding Sites; Conserved Sequence; Genes, MHC Class I; Histocompatibility Antigens Class I; Humans; Models, Molecular; Peptide Fragments; Polymorphism, Genetic; Protein Binding; Protein Conformation; Protein Folding; Protein Interaction Mapping; Receptors, Antigen, T-Cell; Receptors, KIR; Structure-Activity Relationship
PubMed: 32421728
DOI: 10.1371/journal.pone.0232849 -
Frontiers in Immunology 2018Vγ9Vδ2 T cells represent a major unconventional γδ T cell subset located in the peripheral blood of adults in humans and several non-human primates. Lymphocytes that... (Review)
Review
Vγ9Vδ2 T cells represent a major unconventional γδ T cell subset located in the peripheral blood of adults in humans and several non-human primates. Lymphocytes that constitute this transitional subset can sense subtle level changes of intracellular phosphorylated intermediates of the isoprenoid biosynthesis pathway (phosphoantigens, pAg), such as isopentenyl pyrophosphate, during cell stress events. This unique antigenic activation process operates in a rigorous framework that requires the expression of butyrophilin 3A1 (BTN3A1/CD277) molecules, which are type I glycoproteins that belong to the B7 family. Several studies have further shown that pAg specifically bind to the intracellular B30.2 domain of BTN3A1 linked to the antigenic activation of Vγ9Vδ2 T cells. Here, we highlight the recent advances in BTN3A1 dynamics induced upon the binding of pAg and the contribution of the different subunits to this activation process. Recent reports support that conformational modifications of BTN3A1 might represent a key step in the detection of infection or tumorigenesis by Vγ9Vδ2 T cells. A better understanding of this mechanism will help optimize novel immunotherapeutical approaches that target defined functions of this unique γδ T cell subset.
Topics: Amino Acid Sequence; Antigens; Antigens, CD; Butyrophilins; HEK293 Cells; Humans; Lymphocyte Activation; Phosphorylation; Protein Binding; Receptors, Antigen, T-Cell, gamma-delta; T-Lymphocyte Subsets
PubMed: 29731756
DOI: 10.3389/fimmu.2018.00828 -
Scientific Reports Feb 2017During the display of peptide/human leukocyte antigen (HLA) -I complex for further immune recognition, the cleaved and transported antigenic peptides have to bind to...
During the display of peptide/human leukocyte antigen (HLA) -I complex for further immune recognition, the cleaved and transported antigenic peptides have to bind to HLA-I protein and the binding affinity between peptide epitopes and HLA proteins directly influences the immune recognition ability in human beings. Key factors affecting the binding affinity during the generation, selection and presentation processes of HLA-I complex have not yet been fully discovered. In this study, a new method describing the HLA class I-peptide interactions was proposed. Three hundred and forty features of HLA I proteins and peptide sequences were utilized for analysis by four candidate algorithms, screening the optimal classifier. Features derived from the optimal classifier were further selected and systematically analyzed, revealing the core regulators. The results validated the hypothesis that features of HLA I proteins and related peptides simultaneously affect the binding process, though with discrepant redundancy. Besides, the high relative ratio (16/20) of the amino acid composition features suggests the unique role of sequence signatures for the binding processes. Integrating biological, evolutionary and chemical features of both HLA I molecules and peptides, this study may provide a new perspective of the underlying mechanisms of HLA I-mediated immune reactions.
Topics: Algorithms; Antibody Affinity; Epitopes; Histocompatibility Antigens Class I; Humans; Peptides; Protein Binding
PubMed: 28211542
DOI: 10.1038/srep42768 -
Immunobiology Jul 2021Endoplasmic reticulum aminopeptidase 1 (ERAP1) plays a key role in controlling the immunopeptidomes available for presentation by MHC (major histocompatibility complex)...
Endoplasmic reticulum aminopeptidase 1 (ERAP1) plays a key role in controlling the immunopeptidomes available for presentation by MHC (major histocompatibility complex) molecules, thus influences immunodominance and cell-mediated immunity. It carries out this critical function by a unique molecular ruler mechanism that trims antigenic precursors in a peptide-length and sequence dependent manner. Acting as a molecular ruler, ERAP1 is capable of concurrently binding antigen peptide N- and C-termini by its N-terminal catalytic and C-terminal regulatory domains, respectively. As such ERAP1 can not only monitor substrate's lengths, but also exhibit a degree of sequence specificity at substrates' N- and C-termini. On the other hand, it also allows certain sequence and length flexibility in the middle part of peptide substrates that is critical for shaping MHC restricted immunopeptidomes. Here we report structural and biochemical studies to understand the molecular details on how ERAP1 can accommodate side chains of different anchoring residues at the substrate's C-terminus. We also examine how ERAP1 can accommodate antigen peptide precursors with length flexibility. Based on two newly determined complex structures, we find that ERAP1 binds the C-termini of peptides similarly even with different substrate sequences and/or lengths, by utilizing the same hydrophobic specificity pocket to accommodate peptides with either a Phe or Leu as the C-terminal anchor residue. In addition, SPR (surface plasmon resonance) binding analyses in solution further confirm the biological significance of these peptide-ERAP1 interactions. Similar to the binding mode of MHC-I molecules, ERAP1 accommodates for antigenic peptide length difference by allowing the peptide middle part to kink or bulge at the middle of its substrate binding cleft. This explains how SNP coded variants located at the middle of ERAP1 substrate binding cleft would influence the antigen pool and an individual's susceptibility to diseases.
Topics: Amino Acid Sequence; Aminopeptidases; Antigens; Minor Histocompatibility Antigens; Peptides; Protein Domains; Surface Plasmon Resonance
PubMed: 34247019
DOI: 10.1016/j.imbio.2021.152112 -
PloS One 2013Monoclonal antibodies are widely used to target disease-related antigens. However, because conventional antibody binds to the antigen but cannot eliminate the antigen...
Monoclonal antibodies are widely used to target disease-related antigens. However, because conventional antibody binds to the antigen but cannot eliminate the antigen from plasma, and rather increases the plasma antigen concentration by reducing the clearance of the antigen, some clinically important antigens are still difficult to target with monoclonal antibodies because of the huge dosages required. While conventional antibody can only bind to the antigen, some natural endocytic receptors not only bind to the ligands but also continuously eliminate them from plasma by pH-dependent dissociation of the ligands within the acidic endosome and subsequent receptor recycling to the cell surface. Here, we demonstrate that an engineered antibody, named sweeping antibody, having both pH-dependent antigen binding (to mimic the receptor-ligand interaction) and increased binding to cell surface neonatal Fc receptor (FcRn) at neutral pH (to mimic the cell-bound form of the receptor), selectively eliminated the antigen from plasma. With this novel antigen-sweeping activity, antibody without in vitro neutralizing activity exerted in vivo efficacy by directly eliminating the antigen from plasma. Moreover, conversion of conventional antibody with in vitro neutralizing activity into sweeping antibody further potentiated the in vivo efficacy. Depending on the binding affinity to FcRn at neutral pH, sweeping antibody reduced antigen concentration 50- to 1000-fold compared to conventional antibody. Thereby, sweeping antibody antagonized excess amounts of antigen in plasma against which conventional antibody was completely ineffective, and could afford marked reduction of dosage to a level that conventional antibody can never achieve. Thus, the novel mode of action of sweeping antibody provides potential advantages over conventional antibody and may allow access to the target antigens which were previously undruggable by conventional antibody.
Topics: Animals; Antibodies, Monoclonal; Antigens; Histocompatibility Antigens Class I; Humans; Hydrogen-Ion Concentration; Immunoglobulin G; Mice; Mice, Inbred C57BL; Mice, Transgenic; Mutation; Protein Binding; Protein Engineering; Receptors, Fc; Signal Transduction
PubMed: 23667591
DOI: 10.1371/journal.pone.0063236 -
Journal of Virology Feb 2014The structural flexibility found in human immunodeficiency virus (HIV) envelope glycoproteins creates a complex relationship between antigenicity and sensitivity to...
The structural flexibility found in human immunodeficiency virus (HIV) envelope glycoproteins creates a complex relationship between antigenicity and sensitivity to antiviral antibodies. The study of this issue in the context of viral particles is particularly problematic as conventional virus capture approaches can perturb antigenicity profiles. Here, we employed a unique analytical system based on fluorescence correlation spectroscopy (FCS), which measures antibody-virion binding with all reactants continuously in solution. Panels of nine anti-envelope monoclonal antibodies (MAbs) and five virus types were used to connect antibody binding profiles with neutralizing activities. Anti-gp120 MAbs against the 2G12 or b12 epitope, which marks functional envelope structures, neutralized viruses expressing CCR5-tropic envelopes and exhibited efficient virion binding in solution. MAbs against CD4-induced (CD4i) epitopes considered hidden on functional envelope structures poorly bound these viruses and were not neutralizing. Anti-gp41 MAb 2F5 was neutralizing despite limited virion binding. Similar antigenicity patterns occurred on CXCR4-tropic viruses, except that anti-CD4i MAbs 17b and 19e were neutralizing despite little or no virion binding. Notably, anti-gp120 MAb PG9 and anti-gp41 MAb F240 bound to both CCR5-tropic and CXCR4-tropic viruses without exerting neutralizing activity. Differences in the virus production system altered the binding efficiencies of some antibodies but did not enhance antigenicity of aberrant gp120 structures. Of all viruses tested, only JRFL pseudoviruses showed a direct relationship between MAb binding efficiency and neutralizing potency. Collectively, these data indicate that the antigenic profiles of free HIV particles generally favor the exposure of functional over aberrant gp120 structures. However, the efficiency of virion-antibody interactions in solution inconsistently predicts neutralizing activity in vitro.
Topics: Antigens, Viral; Cell Line; Epitope Mapping; HIV Antibodies; HIV Envelope Protein gp120; HIV Envelope Protein gp41; HIV Infections; HIV-1; Humans; Neutralization Tests; Virion
PubMed: 24284318
DOI: 10.1128/JVI.03048-13 -
Methods in Molecular Biology (Clifton,... 2014Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of...
Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of importance for the development of new effective vaccines capable of activating the cellular arm of the immune response. However, the barrier to the development of peptide-based vaccines with maximum population coverage is that the restricting HLA genes are extremely polymorphic resulting in a vast diversity of peptide-binding HLA specificities and a low population coverage for any given peptide-HLA specificity. One way to reduce this complexity is to group thousands of different HLA molecules into several so-called HLA supertypes: a classification that refers to a group of HLA alleles with largely overlapping peptide binding specificities. In this chapter, we focus on the state-of-the-art classification of HLA supertypes including HLA-I supertypes and HLA-II supertypes and their application in development of peptide-based vaccines.
Topics: Histocompatibility Antigens Class I; Histocompatibility Antigens Class II; Humans; Peptides; Vaccines
PubMed: 25048132
DOI: 10.1007/978-1-4939-1115-8_17 -
Journal of Biomolecular Structure &... Oct 2021Carcinoembryonic antigen-related cell adhesion (CEACAM) molecules belong to a family of membrane glycoproteins that mediate intercellular interactions influencing...
Carcinoembryonic antigen-related cell adhesion (CEACAM) molecules belong to a family of membrane glycoproteins that mediate intercellular interactions influencing cellular growth, immune cell activation, apoptosis, and tumor suppression. Several family members (CEACAM1, CEACAM5, and CEACAM6) are highly expressed in cancers, and they share a conserved N-terminal domain that serves as an attractive target for cancer immunotherapy. A multi-epitope vaccine candidate against this conserved domain has been developed using immunoinformatics tools. Specifically, several epitopes predicted to interact with MHC class I and II molecules were linked together with appropriate linkers. The tertiary structure of the vaccine is generated by homology and modeling. Molecular docking of epitopes to MHC structures have revealed that the lowest energy conformations are the epitopes bound to the antigen-binding groove of the MHC molecules. Subsequent molecular dynamics simulation has confirmed the stability of the binding conformations in solution. The predicted vaccine has relatively high antigenicity and low allergenicity, suggesting that it is an ideal candidate for further refinement and development.Communicated by Ramaswamy H. Sarma.
Topics: Carcinoembryonic Antigen; Cell Adhesion Molecules; Epitopes; Epitopes, T-Lymphocyte; Molecular Docking Simulation; Vaccines
PubMed: 32720576
DOI: 10.1080/07391102.2020.1797539 -
Scientific Reports Feb 2021Nervous necrosis virus (NNV) is a pathogenic fish-virus belonging to the genus Betanodavirus (Nodaviridae). Surface protrusions on NNV particles play a crucial role in...
Nervous necrosis virus (NNV) is a pathogenic fish-virus belonging to the genus Betanodavirus (Nodaviridae). Surface protrusions on NNV particles play a crucial role in both antigenicity and infectivity. We exposed purified NNV particles to different physicochemical conditions to investigate the effects on antigenicity and infectivity, in order to reveal information regarding the conformational stability and spatial relationships of NNV neutralizing-antibody binding sites and cell receptor binding sites. Treatment with PBS at 37 °C, drastically reduced NNV antigenicity by 66-79% on day one, whereas its infectivity declined gradually from 10 to 10 TCID/ml over 10 days. When NNV was treated with carbonate/bicarbonate buffers at different pHs, both antigenicity and infectivity of NNV declined due to higher pH. However, the rate of decline with respect to antigenicity was more moderate than for infectivity. NNV antigenicity declined 75-84% after treatment with 2.0 M urea, however, there was no reduction observed in infectivity. The antibodies used in antigenicity experiments have high NNV-neutralizing titers and recognize conformational epitopes on surface protrusions. The maintenance of NNV infectivity means that receptor binding sites are functionally preserved. Therefore, it seems highly likely that NNV neutralizing-antibody binding sites and receptor binding sites are independently located on surface protrusions.
Topics: Animals; Antigens, Viral; Bicarbonates; Buffers; Carbonates; Epitopes; Fish Diseases; Fishes; Molecular Conformation; Nodaviridae
PubMed: 33574489
DOI: 10.1038/s41598-021-83078-3