Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Epitope Mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2024

Assessing nanobody interaction with SARS-CoV-2 Nsp9.

The interaction between SARS-CoV-2 non-structural protein Nsp9 and the nanobody 2NSP90 was investigated by NMR spectroscopy using the paramagnetic perturbation methodology PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation). The Nsp9 monomer is an essential component of the replication and transcription complex (RTC) that reproduces the viral gRNA for subsequent propagation. Therefore preventing Nsp9 recruitment in RTC would represent an efficient antiviral strategy that could be applied to different coronaviruses, given the Nsp9 relative invariance. The NMR results were consistent with a previous characterization suggesting a 4:4 Nsp9-to-nanobody stoichiometry with the occurrence of two epitope pairs on each of the Nsp9 units that establish the inter-dimer contacts of Nsp9 tetramer. The oligomerization state of Nsp9 was also analyzed by molecular dynamics simulations and both dimers and tetramers resulted plausible. A different distribution of the mapped epitopes on the tetramer surface with respect to the former 4:4 complex could also be possible, as well as different stoichiometries of the Nsp9-nanobody assemblies such as the 2:2 stoichiometry suggested by the recent crystal structure of the Nsp9 complex with 2NSP23 (PDB ID: 8dqu), a nanobody exhibiting essentially the same affinity as 2NSP90. The experimental NMR evidence, however, ruled out the occurrence in liquid state of the relevant Nsp9 conformational change observed in the same crystal structure.

Viral Nonstructural Proteins↗
PubMed2026

Resurgence and molecular epidemiology of dengue virus serotype 4 amid the COVID-19 pandemic in Thailand.

INTRODUCTION: Dengue virus serotype 4 (DENV4) co-circulates with other serotypes in Thailand, a hyperendemic setting characterized by cyclical shifts in serotype predominance. During the COVID-19 pandemic, related public health interventions may have influenced dengue detection, transmission and epidemiological dynamics. MATERIALS AND METHODS: A total of 413 dengue NS1/PCR-positive samples collected from 2018 to 2024 at a tertiary hospital in Bangkok were serotyped using a real-time PCR DENV1-4 subtyping assay. Forty-seven DENV4-positive samples (Ct < 32) underwent whole-genome sequencing using the ATOPlex DENV1-4 panel on the DNBSEQ-G99RS platform. Sequencing reads were processed using CLC Genomics Workbench, followed by phylogenetic, mutation, codon-based selection-pressure, and epitope-mapping analyses. RESULTS: DENV4 was identified in 18.2% (75/413) of samples, with 48% of cases requiring hospitalization. Detection increased markedly from 11.8% (22/186) during 2018-2021-23.3% (53/227) during 2022-2024 (proportion ratio, 1.97; p&#x202f;=&#x202f;0.0025). Among the 47 whole-genome-sequenced samples, most strains clustered within genotype I lineage 4I_A.3 and showed lineage-associated non-synonymous substitutions. NS1-A90T, NS2A-L113F, and NS3-F523Y appeared exclusively during 2022-2024 (p&#x202f;<&#x202f;0.001), whereas NS2A-L113F, NS5-G223S, and NS5-Q631R showed concordant positive-selection signals by FEL and MEME. CONCLUSIONS: This hospital-based study highlights an increase in DENV4 detection in Bangkok during 2022-2024 compared with 2018-2021, accompanied by predominance of lineage 4I_A.3 distinct from Malaysian and Indonesian strains reported during a similar period. These findings support integrated clinical and genomic surveillance to monitor DENV serotype and genotype dynamics and inform public health and vaccine strategies.

COVID-19 pandemic↗
PubMed2025

Emerging protein sequencing technologies: proteomics without mass spectrometry?

INTRODUCTION: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry. AREAS COVERED: We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture. EXPERT OPINION: Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.

Proteomics↗
PubMed2026

Proteome-wide curation of experimentally validated HPV T-cell epitopes identifies key gaps in our understanding of cellular immunity to HPV and informs vaccine design.

BACKGROUND: Human papillomavirus (HPV) drives both malignant and benign tumours. Current prophylactic vaccines are type-restricted, not optimised for T-cell induction, and lack therapeutic efficacy. Although T-cells are critical for both preventing and clearing HPV infection, experimentally validated HPV T-cell epitopes remain fragmented across the literature, limiting systematic evaluation of cellular immune targets. METHODS: We curated experimentally validated HPV T-cell epitopes from the Immune Epitope Database (IEDB). Epitopes were mapped across HPV proteins and genotypes, and analysed for response rate, sequence conservation across 454 representative HPV genomes, and HLA restriction patterns. RESULTS: 485 unique experimentally validated HPV epitopes have been described (133 studies; 1,494 functional assays). Consistent with research focus and viral biology, E6 and E7 proteins account for >60% of known HPV epitopes despite accounting for ~10% of the viral proteome. High-risk HPV types, especially HPV16 and HPV18, were the most studied (p&#xa0;<.001) and were enriched for CD8+ epitopes (p&#xa0;<.001). We identified major knowledge gaps, including: underrepresentation of structural proteins such as L2; limited epitope coverage for low-prevalence HPV genotypes; a bias towards common HLA alleles. In silico analysis indicated greater conservation of epitopes in L1/L2 and across high-risk HPV types. Conserved, commonly detected, and HLA-promiscuous epitopes were highlighted and we provide panels of candidate epitopes for consideration in immune monitoring, broad-spectrum prophylactic vaccines, and high-risk targeted therapeutic vaccines. CONCLUSION: This study provides the first comprehensive atlas of experimentally validated HPV T-cell epitopes and ranked epitope candidates for translational application. We demonstrate that our understanding of HPV T-cell immunity is constrained by biases in antigen, genotype and HLA focus and by incomplete epitope mapping. Addressing these gaps will be essential for a comprehensive assessment of cellular immunity and for utilising T-cells in next-generation vaccines.

Epitopes, T-Lymphocyte↗
PubMed2024

Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice.

Listeria monocytogenes is a foodborne intracellular bacterial model pathogen. Protective immunity against Listeria depends on an effective CD8+ T cell response, but very few T cell epitopes are known in mice as a common animal infection model for listeriosis. To identify epitopes, we screened for Listeria immunopeptides presented in the spleen of infected mice by mass spectrometry-based immunopeptidomics. We mapped more than 6000&#xa0;mouse self-peptides presented on MHC class I molecules, including 12 high confident Listeria peptides from 12 different bacterial proteins. Bacterial immunopeptides with confirmed fragmentation spectra were further tested for their potential to activate CD8+ T cells, revealing VTYNYINI from the putative cell wall surface anchor family protein LMON_0576 as a novel bona fide peptide epitope. The epitope showed high biological potency in a prime boost model and can be used as a research tool to probe CD8+ T cell responses in the mouse models of Listeria infection. Together, our results demonstrate the power of immunopeptidomics for bacterial antigen identification.

Animals↗
PubMed1976

Structural characteristics of the alloantigens determined by the major histocompatibility complex of the guinea pig.

The GPLA B and Ia (I region-associated) antigens are the products of genes found in the guinea pig major histocompatibility complex. Because of their importance in immune response phenomena, a structural study of these antigens was undertaken. [3H]leucine and [3H]fucose were internally incorporated into guinea pig lymph node cells. The GPLA B and Ia antigens were solubilized by the nonionic detergent Nonidet P-40, purified by affinity chromatography using an adsorbent column of lentil lectin, isolated by immunoprecipitation, and examined by discontinuous polyacrylamide-sodium dodecyl sulfate gel electrophoresis. The GPLA antigens B.1, B.2, B.3, and B.4, were shown to be glycoproteins of mol wt 40,000 daltons and to be noncovalently associated with a 12,000 dalton protein. The molecules bearing B.2 and B.3 in a B.2/B.3 heterozygote are shown to be separable, suggesting the antigenic determinant is a primary gene product. In addition, a new GPLA determinant, S, which resembles the B antigen in that it is found on a molecule of approximately 40,000 daltons, was studied. In a B.2/B.3 S+ animal the molecule bearing antigen S was shown to be independent of those bearing B.2 and B.3, providing evidence that the genes determining B and S are at separate loci. The Ia-bearing molecules identified by anti-Ia.2,4 are glycoproteins of mol wt 58,000 daltons which are composed of two subunits of 33,000 and 25,000 daltons, respectively, linked by disulfide bonds. The Ia-bearing molecules are independent of GPLA-bearing molecules, indicating different loci determining these antigens. By all criteria, the guinea pig GPLA B antigens appear homologous to the murine H-2D and H-2K antigens, while the guinea pig Ia antigens appear homologous to the Ia antigens of the mouse.

ABO Blood-Group System↗
PubMed1976

The major histocompatibility complex of rhesus monkeys. VI. Serology and genetics of Ia-like antigens.

The serology and genetics of11 new cell surface alloantigens of rhesus monkeys are described: They are controlled by the mamor histocompatibility complex but are distinct from the conventional serologically defined (SD) antigens ofRhL-A. The new specifications are termed "Ia-like" because ofserological, immunocytological and other characteristics reminiscent of Ia-antigens of the mouse. Population and family analyses led to the postulation of two segregant series controlling eight of the 11 Ia-like specificities of the monkey. Strong linkage disequilibria with SD2 antigens and genetic mapping on the basis of segregation studies in recombinant offspring in the monkey families, places at least one of the two loci in the vicinity of the SD2 locus of RhL-A, not in the region of the major MLC or LD1 locus. For this and other reasons, the new B-cell alloantigens of rhesus monkeys are not believed to be similar to or associated with the stimulator antigens of LD1. The biological function(s) of the Ia-like antigens of primates are as yet unknown.

Alleles↗
PubMed1976

B-cell antibodies, Ia-like determinants, and their relation to MLC determinants in man.

The HLA supergene is located in the 6th chromosome. Its position to the centromere and the position of a number of polymorphic isoenzymes has been elucidated. The HLA supergene codes not only for determinants present on all nucleated cells, but also for determinants present on B cells and absent from T cells and platelets. These determinants can be recognized by serology, and evidence is presented that some of them are coded for by a hither to unrecognized locus Ag, which is very closely linked to the MLC determinants of the D locus can be recognized with the help of the MLC test using unprimed cells, homozygous for the MLC determinants, so-called typing cells primed against one MLC determinant in the PLT test. So far, 8 MLC determinants have been recognized. Significant disease-association studies in different racial groups appear to be especially informative. They already indicate that the association found so far must rest on different mechanisms. Whether some of them could be caused by partial deficiency for one or more of the complement factors remains to be proven.

Animals↗
PubMed1976

Fc receptors and Ia antigens.

Antibody against Ia antigens inhibits the ability of B lymphocytes to bind aggregated immunoglobulin and to form EA rosettes. The explanation suggested for this phenomenon has been that Ia antigens are identical to or closely associated with Fc receptors. But a variety of observations preclude acceptance of this explanation since inhibition is also demonstrable with antibody against a wide variety of B cell surface components, including H-2K, H-2D, beta2 microglobulin, immunoglobulin, Ly 4.2. Furthermore, Fc receptor function can be separated from Ia antigens by capping or by isolation of membrane components. It seems likely that the mechanism of inhibition of Fc receptors by antibody against Ia antigens is part of a broader spectrum of effects induced when antibody binds to cell membrane antigens.

Animals↗
PubMed1976

Evidence for more than one Ia antigenic specificity on molecules determined by the I-A subregion of the mouse major histocompatibility complex.

Ia antigenic specificities determined by the I-A subregion of the mouse major histocompatibility complex have been examined in strain B10.D2 (H-2d), C57BL/10 (H-2b), and in a (C57BL/6xDBA/2) hybrid (BDF1; H-2b/d). Detergent solubilized, 3H-leucine-labeled antigen preparations were mixed with appropriate alloantisera and precipitation was induced either by addition of goat anti-mouse gamma-globulin or by addition of protein A-bearing Staphylococci. Sequential precipitation analysis showed that in strain B10.D2, Ia specificities 8 and 11 were co-precipitable, and that in strain C57BL/10, Ia specificities 8 and 9 were co-precipitable. In contrast, precipitation of specificities 9 and 11 from a BDF1 antigen preparation showed that these two Ia specificities were on separate molecules. The genetic implications of these data are discussed.

Animals↗