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

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

Dengue virus (DENV) envelope [E] protein is the major surface protein of the virions that indued neutralizing antibodies. The domain III of envelope protein (EDIII) is an immunogenic region that holds potential for the development of vaccines; however, the epitopes of DENV EDIII, especially neutralizing B-cell linear epitopes, have not been comprehensively mapped. We mapped neutralizing B-cell linear epitopes on DENV-1 EDIII using 27 monoclonal antibodies against DENV-1 EDIII proteins from mice immunized with the DENV-1 EDIII. Epitope recognition analysis was performed using two set of sequential overlapping peptides (16m and 12m) that spanned the entire EDIII protein from DENV-1, respectively. This strategy identified a DENV-1 type- specific and a group-specific neutralizing epitope, which were highly conserved among isolates of DENV-1 and the four DENV serotypes and located at two regions from DENV-1 E, namely amino acid residues 309-320 and 381-392(aa 309-320 and 381-392), respectively. aa310 -319(310KEVAETQHGT319)was similar among the four DENV serotypes and contact residues on aa 309 -320 from E protein were defined and found that substitution of residues E309 , V312, A313 and V320 in DENV-2, -3, -4 isolates were antigenically silent. We also identified a DENV-1 type-specific strain-restricted neutralizing epitope, which was located at the region from DENV-1 E, namely amino acid residues 329-348 . These novel type- and group-specific B-cell epitopes of DENV EDIII may aid help us elucidate the dengue pathogenesis and accelerate vaccine design.
Amino Acid Sequence ; Animals ; Antibodies, Neutralizing ; immunology ; Dengue ; virology ; Dengue Virus ; chemistry ; genetics ; immunology ; Epitope Mapping ; Epitopes, B-Lymphocyte ; chemistry ; genetics ; immunology ; Humans ; Mice ; Molecular Sequence Data ; Viral Envelope Proteins ; chemistry ; genetics ; immunology

Plasmodium falciparum can invade all stages of red blood cells, while Plasmodium vivax can invade only reticulocytes. Although many P. vivax proteins have been discovered, their functions are largely unknown. Among them, P. vivax reticulocyte binding proteins (PvRBP1 and PvRBP2) recognize and bind to reticulocytes. Both proteins possess a C-terminal hydrophobic transmembrane domain, which drives adhesion to reticulocytes. PvRBP1 and PvRBP2 are large (> 326 kDa), which hinders identification of the functional domains. In this study, the complete genome information of the P. vivax RBP family was thoroughly analyzed using a prediction server with bioinformatics data to predict B-cell epitope domains. Eleven pvrbp family genes that included 2 pseudogenes and 9 full or partial length genes were selected and used to express recombinant proteins in a wheat germ cell-free system. The expressed proteins were used to evaluate the humoral immune response with vivax malaria patients and healthy individual serum samples by protein microarray. The recombinant fragments of 9 PvRBP proteins were successfully expressed; the soluble proteins ranged in molecular weight from 16 to 34 kDa. Evaluation of the humoral immune response to each recombinant PvRBP protein indicated a high antigenicity, with 38-88% sensitivity and 100% specificity. Of them, N-terminal parts of PvRBP2c (PVX_090325-1) and PvRBP2 like partial A (PVX_090330-1) elicited high antigenicity. In addition, the PvRBP2-like homologue B (PVX_116930) fragment was newly identified as high antigenicity and may be exploited as a potential antigenic candidate among the PvRBP family. The functional activity of the PvRBP family on merozoite invasion remains unknown.
Epitopes, B-Lymphocyte/*chemistry/genetics/*immunology ; Female ; Humans ; Immunodominant Epitopes/chemistry/genetics/*immunology ; Malaria, Vivax/immunology/*parasitology ; Middle Aged ; Plasmodium vivax/chemistry/genetics/*immunology ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics/*immunology ; Reticulocytes/*parasitology

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

To study the B cell linear epitopes of rabies virus CVS-11 nucleoprotein, peptides were synthesized according to the amino acid sequences of B cell linear epitopes. Linear epitopes predicted by bioinformatics analysis were evaluated with immunological techniques. Indirect enzyme-linked immunosorbent assay showed that titers of antibodies to peptides (355-369 and 385-400 residues of rabies virus CVS-11 nucleoprotein) were above 1:12 800 in mouse sera. The antibodies recognized denatured rabies virus CVS-11 nucleoprotein in Western blot analysis. Purified anti-peptide antibodies recognized natural rabies virus CVS-11 nucleoprotein in BHK-21 cells in indirect fluorescent antibody test. The 355-369 and 385-400 residues of rabies virus CVS-11 nucleoprotein were validated as B cell linear epitopes.
Amino Acid Sequence ; Animals ; Antibodies, Viral ; immunology ; Epitope Mapping ; Epitopes, B-Lymphocyte ; chemistry ; genetics ; immunology ; Female ; Humans ; Male ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; Nucleoproteins ; chemistry ; genetics ; immunology ; Rabies ; immunology ; virology ; Rabies virus ; chemistry ; genetics ; immunology

<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.

<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.

We predict in this paper B-cell epitopes of Epstein-Barr virus nuclear antigen-1 (EBNA-1) and analyze the results matched with the related autoantigens sequence of human. We selected EBV-1 standard strain NA-1 amino acid sequence as the basis. We predicted B-cell dominant epitopes of EBNA-1 with the methods of SOPMA, GOR and HNN, combined with the multi-parameter analysis of transmembrane domain, hydrophilicity profile, surface probability, antigenicity index, polarity and average flexibility. The blastp method was adopted to analyze the matched results between the predicted B-cell epitopes of EBNA-1 and the related autoantigens sequence of human. The results have shown that the possible B-cell dominant epitopes of EBNA-1 were located in the N terminal regions of 16-23, 35-78, 332-337, 340-357, 398-404, 419-432 and 620-637, in which different regions gained higher scores when matched with small nuclear ribonucleoprotein SmB, SmD, ribonucleoprotein SSA, heterogeneous nuclear ribonucleoprotein hnRNP A1, hnRNP G, respectively. It was available to predict B-cell dominant epitopes of EBNA-1 with multiparameter methods and to analyze the same or similar autoantigens sequences of human, which laid a theory foundation for the study of pathogenesis, diagnosis and treatment of autoimmune diseases.
Amino Acid Sequence ; Autoantigens ; immunology ; Base Sequence ; Epitopes, B-Lymphocyte ; immunology ; Epstein-Barr Virus Nuclear Antigens ; immunology ; Humans ; Molecular Sequence Data ; Sequence Homology, Amino Acid

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