Epitopes, T-Lymphocyte ; immunology ; HLA Antigens ; immunology ; Hepatitis B virus ; immunology ; Humans ; T-Lymphocytes, Cytotoxic ; immunology

HLA-A * 0201, HLA-A * 1101, and HLA-A * 2401 CTL restricted epitopes of platelet membrane glycoprotein II b/III a antibody of human and mice were predicted by use of SYFPEITHI, RANKPEP, BIMAS, SVMHC, PREDEP, MHCPRED, and PROPRED predictive programs. In the results, the peptides (found in HLAPRED) that can lead to autoimmune disease and have been published were removed; and the epitopes of HLA-A * 0201 must cover the epitopes of HLA-A * 1101 and HLA-A * 2401 being combined to predTAP and TAPPred for predicting the binding affinity of peptides toward the TAP transporter and NetChop, MAPPP, PAProc for predicting cleavages; HLA-DR Th restricted epitopes of GPII b/III a antibody were predicted by SYFPEITHI, RANKPEP, MHCPRED, and HLAPRED, after removal of the peptides (found in HLAPRED) that can lead to autoimmune disease and have been published, the Th epitopes must cover the CTL mixed epitopes as being stated above. The secondary structure, hydrophobic regions, flexibility, surface probability and the B cell epitope were predicted by using various methods. Ten mixed peptides of T cell epitopes were selected from more than 1 740 peptides. They were located at the aa9-115, aa24-38, aa50-64, aa65-81, aa109-121 of anti-GP II b/III a-Human and the aal-15, aa26-40, aa46-60, aa68-82, aa93-107 of anti-GP II b/III a-Mice. B cell epitopes of anti-GP II b/III a-Human might locate at aa5-9, aa22-30, aa40-46, aa55-71, aa80-90, aa100-105, aa110-115; and the epitopes of anti-GP II b/III a-Human might locate at aa5-10, aa38-43, aa58-70, aa77-84, and aa99-105.
Animals ; Antibodies ; immunology ; Epitopes, B-Lymphocyte ; immunology ; Epitopes, T-Lymphocyte ; immunology ; Humans ; Mice ; Platelet Glycoprotein GPIIb-IIIa Complex ; immunology ; Purpura, Thrombocytopenic, Idiopathic ; immunology ; Vaccines ; immunology

<b>OBJECTIVEb>To predict and identify B-cell linear epitopes of hepatitis B e antigen (HBeAg).

<b>METHODSb>The B-cell linear epitopes of HBeAg were predicted using the software provided by NCBI Database and Immune Epitope Database (IEDB) and synthesized by a solid-phase method followed by conjugation with keyhole limpet hemocyanin (KLH). The KLH conjugates were used for immunization of New Zealand white rabbits, and the immune response of the rabbits was monitored by direct ELISA using a bovine serum albumin conjugate of the predicted epitopes. RESULTS Four new B-cell linear epitopes of HBeAg were identified, namely (1)MDIDPYKEFG(10), (37)LYREALESPEHCSP(50), (74)SNLEDPAS(81) and (127)RTPPAYRPPNAPIL(140). The rabbits immunized with the KLH conjugate showed an antibody titer over 1:512 000. The antisera of B-cell linear epitopes collected could specifically react with HBeAg as shown by ELISA.

<b>CONCLUSIONb>Four B-cell linear epitopes of HBeAg have been confirmed using bioinformatics methods, which provides new evidence for further functional studies of HBeAg in hepatitis B.

Animals ; Computational Biology ; Epitopes, B-Lymphocyte ; immunology ; Hepatitis B e Antigens ; immunology ; Hepatitis B virus ; immunology ; Rabbits

The study of antigenic epitopes from Toxoplasma gondii has not only enhanced our understanding of the structure and function of antigens, the reactions between antigens and antibodies, and many other aspects of immunology, but it also plays a significant role in the development of new diagnostic reagents and vaccines. In the present study, T. gondii GRA6 epitopes were identified using bioinformatics tools and a synthetic peptide technique. The potential B cell epitopes of GRA6 predicted by bioinformatics tools concentrated upon 3 regions of GRA6, 1-20 aa, 44-103 aa, and 172-221 aa. Ten shorter peptides from the 3 regions were synthesized and assessed by ELISA using pig sera from different time points after infection. Three of the 10 peptides (amino acids 44-63, 172-191, and 192-211) tested were recognized by all sera and determined to be immunodominant B-cell epitopes of GRA6. The results indicated that we precisely and accurately located the T. gondii GRA6 epitopes using pig sera collected at different time points after infection. The identified epitopes may be very useful for further studies of epitope-based vaccines and diagnostic reagents.
Allergy and Immunology ; Antibodies ; Computational Biology ; Enzyme-Linked Immunosorbent Assay ; Epitopes ; Epitopes, B-Lymphocyte* ; Indicators and Reagents ; Peptides ; Toxoplasma* ; Vaccines

To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response, and to investigate an improved in silico method for linear B-cell epitope (LBE) prediction. We present a sequence-based LBE predictor developed using deep maxout network (DMN) with dropout training techniques. A graphics processing unit (GPU) was used to reduce the training time of the model. A 10-fold cross-validation test on a large, non-redundant and experimentally verified dataset (Lbtope_Fixed_ non_redundant) was performed to evaluate the performance. DMN-LBE achieved an accuracy of 68.33% and an area under the receiver operating characteristic curve (AUC) of 0.743, outperforming other prediction methods in the field. A web server, DMN-LBE, of the improved prediction model has been provided for public free use. We anticipate that DMN-LBE will be beneficial to vaccine development, antibody production, disease diagnosis, and therapy.
Amino Acid Sequence ; Computational Biology ; methods ; Epitopes, B-Lymphocyte ; chemistry ; immunology ; ROC Curve

<b>OBJECTIVEb>To identify HLA-A0201 restricted cytotoxic T lymphocyte (CTL) epitopes derived from the hepatitis B virus e (HBe) antigen, for future use in a specific immunotherapy based on the identified epitope(s).

<b>METHODSb>HBe gene sequences from the hepatitis B virus serotypes with the highest frequencies in China were analyzed by bioinformatic web-based interfaces for quantitative motif prediction, extended motif prediction, and peptide super-motif prediction. Four candidate peptides were identified: HBe1, HBe2, HBe3, and HBe4. The affinities of each were tested in vitro with T2 cells, which lack the transporter-associated with antigen transport (TAP) protein but express low levels of the MHC class I surface molecule, and measured by the T2 binding assay and DC50 assay. Flow cytometry was used to detect the fluorescence index of control and experimental groups.

<b>RESULTSb>The peptides HBe1 (LLWFHISCL), HBe2 (YLVSFGVWI), HBe3 (CLTFGRETV), and HBe4 (DLLDTASAL) were identified and tested as candidate targets. HBe2 and HBe3 showed higher HLA-A0201 affinity. HBe1, HBe2, and HBe3 showed better binding stability.

<b>CONCLUSIONb>Two peptides based on HBe antigen, YLVSFGVWI and CLTFGRETV, possess both sufficient binding affinity and stability and may represent useful HLA-A0201-restricted CTL epitopes. Further study is needed to determine the immunogenic properties of these two peptides in vivo.

Amino Acid Sequence ; Epitopes, T-Lymphocyte ; Hepatitis B e Antigens ; Hepatitis B virus ; immunology ; T-Lymphocytes, Cytotoxic ; immunology

Epitopes, T-Lymphocyte ; HLA-A2 Antigen ; immunology ; Hepatitis B Core Antigens ; genetics ; Hepatitis B virus ; genetics ; immunology ; Humans ; Mutation

<b>OBJECTIVEb>To identify immune epitopes existed in the framework region (FR) of the IgHV protein of B-cell malignance, and explore the use of these FR-derived peptides to induce the family specific immune response in vitro, in order to explore the possibility of a new IgHV gene family-specific immunotherapy for B-cell malignance.

<b>METHODSb>Bioinformatics was used for predicting T cell epitopes in IgHV protein. Peptides of interest were synthesized in vitro. T2 cell binding assay was performed to determine the binding ability of the peptides to HLA-A*0201 molecules. Peptide/HLA tetramer staining was used to detect the number of peptide-specific cytotoxic T lymphocytes (CTLs). Cytotoxicity assay was used to determine killing activity.

<b>RESULTSb>Twelve peptides that were common to seven IgHV gene subfamilies were identified, and 10 (83%) of them were located in the FR of IgHV protein. The synthesized peptides up-regulated HLA*0201 molecules fluorescence intensity on cell surfaces of T2. By using an antigen-specific T-cell expansion system in vitro, the peripheral blood mononuclear cells (PBMNC) from a healthy HLA-A0201 donor were stimulated weekly by autologous PBMNC loaded with the peptide as antigen presenting cells (APC), and the peptide-specific CTLs were demonstrated to be generated successfully in the healthy donors. The frequency of CD8 and peptide/HLA tetramer double positive cells in the gated lymphocyte population was 0.38% before stimulation and increased to 49.38 % after four times stimulation. Cytotoxicity assay indicated that these CTLs were capable of killing the HLA-A*0201, IgHV1 (+) lymphoma cells. Furthermore, the generated CTL could not kill the target cell loaded with the IgHV3 peptide, indicating that the cytotoxicity is family-specific.

<b>CONCLUSIONb>Peptides derived from the IgHV protein FR can successfully induce the generation of peptide-specific CTLs in vitro. These CTLs are capable of killing the lymphoma cell belonged to the same subfamily in a peptide-specific and MHC-restricted way. These findings could potentially form the basis of broadening application of immunoglobulin-directed immunotherapy in B-cell malignancies.

Cells, Cultured ; Epitopes, B-Lymphocyte ; immunology ; Humans ; Immunoglobulin Heavy Chains ; immunology ; Immunoglobulin Variable Region ; immunology ; Lymphoma, B-Cell ; immunology ; T-Lymphocytes, Cytotoxic ; immunology

This study bioinformatically analyzed the non-VP1 capsid proteins (VP2-VP4) of Coxasckievirus A6 (CVA6), with an attempt to predict their basic physicochemical properties, structural/functional features and linear B cell eiptopes. The online tools SubLoc, TargetP and the others from ExPASy Bioinformatics Resource Portal, and SWISS-MODEL (an online protein structure modeling server), were utilized to analyze the amino acid (AA) sequences of VP2-VP4 proteins of CVA6. Our results showed that the VP proteins of CVA6 were all of hydrophilic nature, contained phosphorylation and glycosylation sites and harbored no signal peptide sequences and acetylation sites. Except VP3, the other proteins did not have transmembrane helix structure and nuclear localization signal sequences. Random coils were the major conformation of the secondary structure of the capsid proteins. Analysis of the linear B cell epitopes by employing Bepipred showed that the average antigenic indices (AI) of individual VP proteins were all greater than 0 and the average AI of VP4 was substantially higher than that of VP2 and VP3. The VP proteins all contained a number of potential B cell epitopes and some eiptopes were located at the internal side of the viral capsid or were buried. We successfully predicted the fundamental physicochemical properties, structural/functional features and the linear B cell eiptopes and found that different VP proteins share some common features and each has its unique attributes. These findings will help us understand the pathogenicity of CVA6 and develop related vaccines and immunodiagnostic reagents.
Amino Acid Sequence ; Capsid Proteins ; genetics ; immunology ; Computational Biology ; Enterovirus ; genetics ; pathogenicity ; Epitopes, B-Lymphocyte ; genetics ; immunology ; Humans

<b>OBJECTIVEb>To predict and screen the efficient antigenic epitopes in genus-specific envelope protein LipL41 of Leptospira interrogans and to determine the immunoreactive diversity of LipL41s from different genotypes.

<b>METHODSb>Bioinformatic methods were applied to predict the T/B combined epitope candidates in LipL41/1 and LipL41/2 molecules. The nucleotide fragments encoding epitopes were amplified by PCR. Phage display system with SDS-PAGE was performed to obtain the recombinant PIIIs containing different T/B combined epitopes. Western Blot assays were performed to determine the immunoreactivity of recombinant PIIIs to various antisera including antiserum against rLipL41/1, rLipL41/2 and whole cell of L.interrogans strain Lai, and serum from patients with leptospirosis.

<b>RESULTb>Based on the predicting data, eight common or differential combined epitopes in LipL41s were selected. The nucleotide fragments encoding the epitopes were obtained by PCR. All the T/B combined epitope fragments were correctly inserted into the N end of phage PIII protein and then successfully expressed. All the antisera were able to recognize each of the epitopes but the hybridization signal intensity was different. Among these epitopes, the common T/B combined epitopes LipL41/1-30 and LipL41/1-233 showed a stronger and stable hybridization signals.

<b>CONCLUSIONb>All 8 selected T/B combined epitopes in the study are the efficient antigenic epitopes. The common T/B epitopes LipL41/1-30 and LipL41/1-233 can be first used in development of leptospiral MAP vaccine. The cross immunoreaction is between the differential T/B epitopes LipL41s-89,LipL41s-299 and the different antisera.

Amino Acid Sequence ; Antigens, Bacterial ; genetics ; immunology ; Bacterial Vaccines ; genetics ; immunology ; Cloning, Molecular ; Epitopes, B-Lymphocyte ; genetics ; immunology ; Epitopes, T-Lymphocyte ; genetics ; immunology ; Genotype ; Molecular Sequence Data ; Peptide Library