scholarly journals A Dataset of Experimental HLA-B*2705 Peptide Binding Affinities

2014 ◽  
Vol 2014 ◽  
pp. 1-4 ◽  
Author(s):  
Valerie A. Walshe ◽  
Channa K. Hattotuwagama ◽  
Irini A. Doytchinova ◽  
Darren R. Flower
Keyword(s):  
T Cell ◽  
Peptide Binding ◽  
Data Driven ◽  
Quantitative Prediction ◽  
Binding Affinities ◽  
T Cell Epitopes ◽  
Histocompatibility Complex ◽  
Binding Peptides ◽  
Using Data ◽  
Binding Level

T-cell epitopes form the basis of many vaccines, diagnostics, and reagents. Current methods for the in silico identification of T-cell epitopes rely, in the main, on the accurate quantitative prediction of peptide-Major Histocompatibility Complex (pMHC) affinity using data-driven computational approaches. Here, we describe a dataset of experimentally determined pMHC binding affinities for the problematic human class I allele HLA-B*2705. Using an in-house, FACS-based, MHC stabilization assay, we measured binding of 223 peptides. This dataset includes both nonbinding and binding peptides, with measured affinities (expressed as −log10 of the half-maximal binding level) ranging from 1.2 to 7.4. This dataset should provide a useful independent benchmark for new and existing methods for predicting peptide binding to HLA-B*2705.

scholarly journals A Peptide-binding Motif for I-Ag7, the Class II Major Histocompatibility Complex (MHC) Molecule of NOD and Biozzi AB/H Mice

1997 ◽  
Vol 185 (6) ◽  
pp. 1013-1022 ◽  
Author(s):  
Leonard C. Harrison ◽  
Margo C. Honeyman ◽  
Sylvie Trembleau ◽  
Silvia Gregori ◽  
Fabio Gallazzi ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
T Cell ◽  
Critical Role ◽  
Peptide Binding ◽  
Class Ii ◽  
Binding Motif ◽  
T Cell Epitopes ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
Hla Dq

The class II major histocompatibility complex molecule I-Ag7 is strongly linked to the development of spontaneous insulin-dependent diabetes mellitus (IDDM) in non obese diabetic mice and to the induction of experimental allergic encephalomyelitis in Biozzi AB/H mice. Structurally, it resembles the HLA-DQ molecules associated with human IDDM, in having a non-Asp residue at position 57 in its β chain. To identify the requirements for peptide binding to I-Ag7 and thereby potentially pathogenic T cell epitopes, we analyzed a known I-Ag7-restricted T cell epitope, hen egg white lysozyme (HEL) amino acids 9–27. NH2- and COOH-terminal truncations demonstrated that the minimal epitope for activation of the T cell hybridoma 2D12.1 was M12-R21 and the minimum sequence for direct binding to purified I-Ag7 M12-Y20/ K13-R21. Alanine (A) scanning revealed two primary anchors for binding at relative positions (p) 6 (L) and 9 (Y) in the HEL epitope. The critical role of both anchors was demonstrated by incorporating L and Y in poly(A) backbones at the same relative positions as in the HEL epitope. Well-tolerated, weakly tolerated, and nontolerated residues were identified by analyzing the binding of peptides containing multiple substitutions at individual positions. Optimally, p6 was a large, hydrophobic residue (L, I, V, M), whereas p9 was aromatic and hydrophobic (Y or F) or positively charged (K, R). Specific residues were not tolerated at these and some other positions. A motif for binding to I-Ag7 deduced from analysis of the model HEL epitope was present in 27/30 (90%) of peptides reported to be I-Ag7–restricted T cell epitopes or eluted from I-Ag7. Scanning a set of overlapping peptides encompassing human proinsulin revealed the motif in 6/6 good binders (sensitivity = 100%) and 4/13 weak or non-binders (specificity = 70%). This motif should facilitate identification of autoantigenic epitopes relevant to the pathogenesis and immunotherapy of IDDM.

scholarly journals Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning.

1994 ◽  
Vol 180 (6) ◽  
pp. 2353-2358 ◽  
Author(s):  
J Hammer ◽  
E Bono ◽  
F Gallazzi ◽  
C Belunis ◽  
Z Nagy ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
Peptide Binding ◽  
Class Ii ◽  
Side Chain ◽  
T Cell Epitopes ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
Precise Prediction ◽  
Binding Peptides ◽  
Peptide Interaction

We describe here a new method for predicting class II major histocompatibility complex-binding peptides, based on the preferences observed in a systematic series of peptide binding experiments where each position in a "minimal" peptide was replaced individually by every amino acid. The DRB1*0401 peptide binding preferences were determined and incorporated into a computer program that looks through sequences for potential epitopes and assigns each a score. These scores correlate well with previously determined T cell epitopes of foreign antigens and endogenous peptides from self proteins. Our findings hold implications for the design of subunit vaccines and in the identification of autoantigenic peptide regions within self proteins.

Immuno-informatics-based identification of novel potential B cell and T cell epitopes to fight Zika virus infections

2020 ◽  
Vol 20 ◽  
Author(s):  
Wahiba Ezzemani ◽  
Marc P. Windisch ◽  
Anass Kettani ◽  
Haya Altawalah ◽  
Jalal Nourlil ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
T Cell ◽  
Major Histocompatibility Complex Class ◽  
B Cell ◽  
Zika Virus ◽  
T Cell Epitopes ◽  
Complex Class ◽  
Major Histocompatibility ◽  
Virus Infections ◽  
Histocompatibility Complex

Background: Globally, the recent outbreak of Zika virus (ZIKV) in Brazil, Asia Pacific, and other countries highlighted the unmet medical needs. Currently, there are neither effective vaccines nor therapeutics available to prevent or treat ZIKV infection. Objective: In this study, we aimed to design an epitope-based vaccine for ZIKV using an in silico approach to predict and analyze B- and T-cell epitopes. Methods: The prediction of the most antigenic epitopes has targeted the capsid and the envelope proteins as well as nonstructural proteins NS5 and NS3 using immune-informatics tools PROTPARAM, CFSSP, PSIPRED, and Vaxijen v2.0. B and T-cell epitopes were predicted using ABCpred, IEDB, TepiTool, and their toxicity were evaluated using ToxinPred. The 3-dimensional epitope structures were generated by PEP-FOLD. Energy minimization was performed using Swiss-Pdb Viewer, and molecular docking was conducted using PatchDock and FireDock server. Results: As a result, we predicted 307 epitopes of MHCI (major histocompatibility complex class I) and 102 epitopes of MHCII (major histocompatibility complex class II). Based on immunogenicity and antigenicity scores, we identified the four most antigenic MHC I epitopes: MVLAILAFLR (HLA-A*68 :01), ETLHGTVTV (HLA-A*68 :02), DENHPYRTW (HLA-B*44 :02),QEGVFHTMW (HLA-B*44 :03) and TASGRVIEEW (HLA-B*58:01), and MHC II epitopes: IIKKFKKDLAAMLRI (HLA-DRB3*02 :02), ENSKMMLELDPPFGD (HLA-DRB3*01:01), HAETWFFDENHPYRT (HLA-DRB3*01:01), TDGVYRVMTRRLLGS (HLA-DRB1*11 :01), and DGCWYGMEIRPRKEP (HLA-DRB5*01:01). Conclusion : This study provides novel potential B cell and T cell epitopes to fight Zika virus infections and may prompt further development of vaccines against ZIKV and other emerging infectious diseases. However, further investigations for protective immune response by in vitro and in vivo studies to ratify the immunogenicity, safety of the predicted structure, and ultimately the vaccine properties to prevent ZIKV infections are warranted.

Synthetic peptide libraries in the determination of T cell epitopes and peptide binding specificity of class I molecules

1992 ◽  
Vol 22 (6) ◽  
pp. 1405-1412 ◽  
Author(s):  
Ton N. M. Schumacher ◽  
Grada M. Van Bleek ◽  
Marie-ThéRèSe Heemels ◽  
Karl Deres ◽  
Ka Wan Li ◽  
...  
Keyword(s):  
T Cell ◽  
Synthetic Peptide ◽  
Peptide Binding ◽  
Binding Specificity ◽  
Peptide Libraries ◽  
Class I ◽  
T Cell Epitopes ◽  
Peptide Binding Specificity

scholarly journals Human Leukocyte Antigens A*3001 and A*3002 Show Distinct Peptide-Binding Patterns of theMycobacterium tuberculosisProtein TB10.4: Consequences for Immune Recognition

2010 ◽  
Vol 18 (1) ◽  
pp. 125-134 ◽  
Author(s):  
Rebecca Axelsson-Robertson ◽  
Raija K. Ahmed ◽  
Frank F. Weichold ◽  
Marthie M. Ehlers ◽  
Marleen M. Kock ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Recombinant Expression ◽  
Peptide Binding ◽  
Human Leukocyte ◽  
Sub Saharan Africa ◽  
Immune Recognition ◽  
Interleukin 7 ◽  
Binding Peptides ◽  
Sub Saharan

ABSTRACTHigh-tuberculosis (TB)-burden countries are located in sub-Saharan Africa. We examined the frequency of human leukocyte antigen (HLA) alleles, followed by recombinant expression of the most frequent HLA-A alleles, i.e., HLA-A*3001 and HLA-A*3002, to study differences in mycobacterial peptide presentation and CD8+T-cell recognition. We screened a peptide library (9-mer peptides with an 8-amino-acid overlap) for binding, affinity, and off-rate of theMycobacterium tuberculosis-associated antigen TB10.4 and identified only three TB10.4 peptides with considerable binding to HLA-A*3001. In contrast, 22 peptides bound to HLA-A*3002. This reflects a marked difference in the binding preference between the two alleles, with A*3002 tolerating a more promiscuous peptide-binding pattern and A*3001 accommodating only a very selective peptide repertoire. Subsequent analysis of the affinity and off-rate of the binding peptides revealed a strong affinity (8 nM to 7 μM) and moderate off-rate (20 min to 3 h) for both alleles. Construction of HLA-A*3001 and HLA-A*3002 tetramers containing selected binding peptides from TB10.4, including a peptide which was shared among both alleles, QIMYNYPAM (TB10.43-11), allowed us to enumerate epitope-specific T cells in HLA-A*3001- and HLA-A*3002-typed patients with active TB. HLA-A*3001 and HLA-A*3002 major histocompatibility complex-peptide complexes were recognized in individuals with active TB, irrespective of their homozygous HLA-A*3001 or HLA-A*3002 genetic background. The antigen-specific T cells exhibited the CD45RA+CCR7+precursor phenotype and the interleukin-7 receptor (CD127), which were different from the phenotype and receptor exhibited by the parental CD8+T-cell population.

scholarly journals Bordetella pertussis Proteins Dominating the Major Histocompatibility Complex Class II-Presented Epitope Repertoire in Human Monocyte-Derived Dendritic Cells

2014 ◽  
Vol 21 (5) ◽  
pp. 641-650 ◽  
Author(s):  
Rachel M. Stenger ◽  
Hugo D. Meiring ◽  
Betsy Kuipers ◽  
Martien Poelen ◽  
Jacqueline A. M. van Gaans-van den Brink ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Major Histocompatibility Complex ◽  
T Cell ◽  
Bordetella Pertussis ◽  
Human Monocyte ◽  
Class Ii ◽  
T Cell Epitopes ◽  
Major Histocompatibility ◽  
Content Type ◽  
Histocompatibility Complex

ABSTRACTKnowledge of naturally processedBordetella pertussis-specific T cell epitopes may help to increase our understanding of the basis of cell-mediated immune mechanisms to control this reemerging pathogen. Here, we elucidate for the first time the dominant major histocompatibility complex (MHC) class II-presentedB. pertussisCD4+T cell epitopes, expressed on human monocyte-derived dendritic cells (MDDC) after the processing of whole bacterial cells by use of a platform of immunoproteomics technology. Pertussis epitopes identified in the context of HLA-DR molecules were derived from two envelope proteins, i.e., putative periplasmic protein (PPP) and putative peptidoglycan-associated lipoprotein (PAL), and from two cytosolic proteins, i.e., 10-kDa chaperonin groES protein (groES) and adenylosuccinate synthetase (ASS). No epitopes were detectable from known virulence factors. CD4+T cell responsiveness in healthy adults against peptide pools representing epitope regions or full proteins confirmed the immunogenicity of PAL, PPP, groES, and ASS. Elevated lymphoproliferative activity to PPP, groES, and ASS in subjects within a year after the diagnosis of symptomatic pertussis suggested immunogenic exposure to these proteins during clinical infection. The PAL-, PPP-, groES-, and ASS-specific responses were associated with secretion of functional Th1 (tumor necrosis factor alpha [TNF-α] and gamma interferon [IFN-γ]) and Th2 (interleukin 5 [IL-5] and IL-13) cytokines. Relative paucity in the naturalB. pertussisepitope display of MDDC, not dominated by epitopes from known protective antigens, can interfere with the effectiveness of immune recognition ofB. pertussis. A more complete understanding of hallmarks inB. pertussis-specific immunity may advance the design of novel immunological assays and prevention strategies.

scholarly journals Virus-Specific T-Cell Immunity Correlates with Control of GB Virus B Infection in Marmosets

2007 ◽  
Vol 82 (6) ◽  
pp. 3054-3060 ◽  
Author(s):  
David J. Woollard ◽  
Gholamreza Haqshenas ◽  
Xuebin Dong ◽  
Bridget F. Pratt ◽  
Stephen J. Kent ◽  
...  
Keyword(s):  
T Cell ◽  
Epitope Mapping ◽  
Small Animal ◽  
T Cell Responses ◽  
T Cell Epitopes ◽  
Nonstructural Proteins ◽  
Cell Responses ◽  
Histocompatibility Complex ◽  
Cell Immunity ◽  
Ifn Γ

ABSTRACT GB virus B (GBV-B) is a hepatotropic virus that is closely related to hepatitis C virus (HCV). GBV-B causes acute hepatitis in infected marmosets and tamarins and is therefore a useful small-animal model for the study of HCV. We investigated virus-specific T-cell responses in marmosets infected with GBV-B. Gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay responses in the peripheral blood of two marmosets were assessed throughout the course of GBV-B infection. These T-cell responses were directed against the GBV-B nonstructural proteins 3 (NS3), 4A (NS4A), and 5B (NS5B), and their appearance was temporally associated with clearance of viremia. These marmosets were then rechallenged with GBV-B at least 3 months after clearance of the primary infection to determine if the animals were protected from reinfection. There was no detectable viremia following reinfection, although a sharp increase in T-cell responses against GBV-B proteins was observed. Epitope mapping of T-cell responses to GBV-B was performed with liver and blood samples from both marmosets after rechallenge with GBV-B. Three shared, immunodominant T-cell epitopes within NS3 were identified in animals with multiple common major histocompatibility complex class I alleles. IFN-γ ELISPOT responses were also detected in the livers of two marmosets that had resolved a primary GBV-B infection. These responses were high in frequency and were directed against epitopes within GBV-B NS3, NS4A, and NS5B proteins. These results indicate that virus-specific T-cell responses are detectable in the liver and blood of GBV-B-infected marmosets and that the clearance of GBV-B is associated with the appearance of these responses.

scholarly journals Pol-Specific CD8+ T Cells Recognize Simian Immunodeficiency Virus-Infected Cells Prior to Nef-Mediated Major Histocompatibility Complex Class I Downregulation

2007 ◽  
Vol 81 (21) ◽  
pp. 11703-11712 ◽  
Author(s):  
Jonah B. Sacha ◽  
Chungwon Chung ◽  
Jason Reed ◽  
Anna K. Jonas ◽  
Alexander T. Bean ◽  
...  
Keyword(s):  
T Cells ◽  
Major Histocompatibility Complex ◽  
T Cell ◽  
Major Histocompatibility Complex Class ◽  
T Cell Epitopes ◽  
Complex Class ◽  
Mhc I ◽  
Histocompatibility Complex ◽  
Immunodeficiency Virus ◽  
Infected Cells

ABSTRACT Effective, vaccine-induced CD8+ T-cell responses should recognize infected cells early enough to prevent production of progeny virions. We have recently shown that Gag-specific CD8+ T cells recognize simian immunodeficiency virus-infected cells at 2 h postinfection, whereas Env-specific CD8+ T cells do not recognize infected cells until much later in infection. However, it remains unknown when other proteins present in the viral particle are presented to CD8+ T cells after infection. To address this issue, we explored CD8+ T-cell recognition of epitopes derived from two other relatively large virion proteins, Pol and Nef. Surprisingly, infected cells efficiently presented CD8+ T-cell epitopes from virion-derived Pol proteins within 2 h of infection. In contrast, Nef-specific CD8+ T cells did not recognize infected cells until 12 h postinfection. Additionally, we show that SIVmac239 Nef downregulated surface major histocompatibility complex class I (MHC-I) molecules beginning at 12 h postinfection, concomitant with presentation of Nef-derived CD8+ T-cell epitopes. Finally, Pol-specific CD8+ T cells eliminated infected cells as early as 6 h postinfection, well before MHC-I downregulation, suggesting a previously underappreciated antiviral role for Pol-specific CD8+ T cells.

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