Characterization of epitopes on the cationic peanut peroxidase by four monoclonal antibodies

The epitope sites on the cationic peanut peroxidase were characterized by four monoclonal antibodies raised against this isozyme. Evidence is presented showing that the epitope for monoclonal antibody 1B is located on the polypeptide. Sensitivity of the epitopes recognized by 1M and 2F to 0.1M HCl, boiling, 10 mM periodate and trifluoromethane sulfonic acid treatment indicate that they occur at regions where oligosaccharides are linked to the polypeptide backbone. The antigenic specificity of 2A is, in addition, dependent on the conformation of the epitope site which is destroyed after partial proteolysis of the peroxidase.     

A BASIC microcomputer program for prediction of B and T cell epitopes in proteins

A BASIC microcomputer program (EPIPLOT) has been developed forpredicting B and T cell antigenic sites in proteins from theirprimary structures. The program calculates and plots flexibility,hydrophilicity and antigenicity profiles using 13 differentscales, chosen as those yielding the best predictions on proteinswhose antigenic structures are known. T cell epitope predictionis basedon published algorithms focused on amphiphilic structuresand characteristic sequence patterns. The advantages of jointpredictions in locating T cell antigenic sites are also discussed. Received on December 12, 1989; accepted on January 31, 1990     

Anti-sm autoantibodies in systemic lupus target highly basic surface structures of complexed spliceosomal autoantigens

Autoantibodies directed against spliceosomal proteins are a common and specific feature of systemic lupus erythematosus. These autoantibodies target a collection of proteins, including Sm B, B', D1, D2, and D3. We define the common antigenic targets of Sm D2 and D3 and examine their role in spliceosomal autoimmunity. Our results define nine major common epitopes, five on Sm D2 and four on Sm D3. These epitopes have significantly higher (more basic) isoelectric points than do nonantigenic regions. In fact, this association is of sufficient power to make isoelectric point an excellent predictor of spliceosomal antigenicity. The crystallographic structure of Sm D2 and D3 is now partially described. The anti-Sm D2 and D3 antigenic targets are located on the surface of the respective three-dimensional complexed proteins, thereby suggesting that these epitopes are accessible in the native configuration. All but one of these nine epitopes conspicuously avoid the specific regions involved in intermolecular interactions within the spliceosomal complex. One of the D3 epitopes (RGRGRGMGR) has significant sequence homology with a major antigenic region of Sm D1 (containing a carboxyl-terminal glycine-arginine repeat), and anti-D3 Abs cross-react with this epitope of Sm D1. These results demonstrate that spliceosomal targets of autoimmunity are accessible on native structure surfaces and that cross-reactive epitopes, as well as structural associations of various spliceosomal Ags, may be involved in the induction of autoimmunity in systemic lupus.     

Characterization of the antigenic structure of herpes simplex virus type 1 glycoprotein C through DNA sequence analysis of monoclonal antibody-resistant mutants.

Earlier studies of a group of monoclonal antibody-resistant (mar) mutants of herpes simplex virus type 1 glycoprotein C (gC) operationally defined two distinct antigenic sites on this molecule, each consisting of numerous overlapping epitopes. In this report, we further define epitopes of gC by sequence analysis of the mar mutant gC genes. In 18 mar mutants studied, the mar phenotype was associated with a single nucleotide substitution and a single predicted amino acid change. The mutations were localized to two regions within the coding sequence of the external domain of gC and correlated with the two previously defined antigenic sites. The predicted amino acid substitutions of site I mutants resided between residues Gln-307 and Pro-373, whereas those of site II mutants occurred between amino acids Arg-129 and Glu-247. Of the 12 site II mutations, 9 induced amino acid substitutions within an arginine-rich segment of 8 amino acids extending from residues 143 to 151. The clustering of the majority of substituted residues suggests that they contribute to the structure of the affected sites. Moreover, the patterns of substitutions which affected recognition by antibodies with similar epitope specificities provided evidence that epitope structures are physically linked and overlap within antigenic sites. Of the nine epitopes defined on the basis of mutations, three were located within site I and six were located within site II. Substituted residues affecting the site I epitopes did not overlap substituted residues of site II, supporting our earlier conclusion that sites I and II reside in spatially distinct antigenic domains. A computer analysis of the distribution of charged residues and the predicted secondary structural features of wild-type gC revealed that the two antigenic sites reside within the most hydrophilic regions of the molecule and that the antigenic residues are likely to be organized as beta sheets which loop out from the surface of the molecule. Together, these data and our previous studies support the conclusion that the mar mutations identified by sequence analysis very likely occur within or near the epitope structures themselves. Thus, two highly antigenic regions of gC have now been physically and genetically mapped to well-defined domains of the protein molecule.     

Location of antigenic epitopes on antibody molecules

Using X-ray crystallographic co-ordinates of immunoglobulins, surface regions accessible to a large spherical probe, comparable in size to an antibody domain, were computed. Locations of these exposed regions were compared with those of experimentally determined antigenic sites, i.e. idiotypic, allotypic and isotypic serological markers. In all cases, an excellent agreement was found. The most prominent computed epitopes correspond to convex parts of antibody surface made by reverse turn segments of the polypeptide chain. The computed epitopes occur in homologous positions in all the immunoglobulin domains, and most of the beta-sheet surfaces on the domains are poorly antigenic. The CH2 domain (Fc fragment) has many more antigenic sites than the Fab fragments (antigen-binding fragments). Variable domain epitopes (idiotypes) involve both hypervariable and framework residues, and only about 25% of the hypervariable residues are strongly antigenic. The results indicate that, in a vertebrate body, each antibody molecule may be recognized, and its concentration regulated, by at least 40 complementary anti-immunoglobulin antibodies; therefore, a possibility of an "immune network" with much higher connectivity than is generally assumed should be seriously contemplated.     

Antigenic determinants of vesicular stomatitis virus: analysis with antigenic variants

Antigenic variants of vesicular stomatitis virus (VSV) serotypes New Jersey and Indiana (VSV-NJ, VSV-Ind) were selected by using a panel of monoclonal antibodies (MAb) specific for the major surface glycoprotein (G-protein). The reactivity of antigenic variants with the panel of MAb confirmed observations made by competitive binding assays that four distinct antigenic sites (A-D)NJ on the VSV-NJ G-protein and four partially overlapping sites (A, B1, B2, C)Ind on the VSV-Ind G-protein are involved in virus neutralization. Furthermore, subregions within the A epitopes of both serotypes were detected by variant analysis. The frequency of variation at most epitopes was 1 in 10(5) for VSV-NJ and 1 in 10(6) for VSV-Ind. The A3 and C determinants of VSV-Ind, however, defined by MAb that exhibited overlap in binding to other epitopes, appeared to be relatively invariant. Multiple mutations may be necessary to abolish antibody binding at these sites. Overlap of the C group of anti-VSV-Ind MAb with the A epitopes was assigned to the A2 subregion, because variants selected with A2 MAb show reduced binding of C MAb. Heterogeneous antisera from a primary immune response could detect differences in reactivity between variants at the A epitopes and wild-type VSV-NJ or VSV-Ind, suggesting the A epitope is immunodominant. Hyperimmune sera could detect a small difference between ANJ and BNJ variants compared to wild-type VSV-NJ, but could not distinguish between VSV-Ind variants and wild-type VSV-Ind.     

Determination of protein-derived epitopes by mass spectrometry

Mass spectrometry has evolved as a technique suitable for the characterization of peptides and proteins beyond their linear sequence. The advantages of mass spectrometric sample analysis are high sensitivity, high mass accuracy, rapid analysis time and low sample consumption. In epitope mapping, the molecular structure of an antigen (the epitope or antigenic determinant) that interacts with the paratope (recognition surface) of the antibody is identified. To obtain information on linear, conformational and/or discontinuous epitopes, various approaches have been developed in conjunction with mass spectrometry. These methods include limited proteolysis and epitope footprinting, epitope excision and epitope extraction for linear epitopes and probing the surface accessibility of residues by differential chemical modifications of specific amino acid side chains or by differential hydrogen/deuterium exchange of the protein backbone amides for conformational and discontinuous epitopes. Epitope mapping by mass spectrometry is applicable in basic biochemical research and, with increasing robustness, should soon find its implementation in routine clinical diagnosis.     

Determination of protein-derived epitopes by mass spectrometry

Mass spectrometry has evolved as a technique suitable for the characterization of peptides and proteins beyond their linear sequence. The advantages of mass spectrometric sample analysis are high sensitivity, high mass accuracy, rapid analysis time and low sample consumption. In epitope mapping, the molecular structure of an antigen (the epitope or antigenic determinant) that interacts with the paratope (recognition surface) of the antibody is identified. To obtain information on linear, conformational and/or discontinuous epitopes, various approaches have been developed in conjunction with mass spectrometry. These methods include limited proteolysis and epitope footprinting, epitope excision and epitope extraction for linear epitopes and probing the surface accessibility of residues by differential chemical modifications of specific amino acid side chains or by differential hydrogen/deuterium exchange of the protein backbone amides for conformational and discontinuous epitopes. Epitope mapping by mass spectrometry is applicable in basic biochemical research and, with increasing robustness, should soon find its implementation in routine clinical diagnosis.     

Variable expression and geographic distribution of Mycoplasma agalactiae surface epitopes demonstrated with monoclonal antibodies

Abstract Species-speciGc monoclonal antibodies (MAbs) were developed against Mycoplasma agalactiae reference strain PG2 and French isolate P89 to study the in vitro expression of surface epitopes and to probe the antigenic profiles of 245 field isolates originating from 10 different countries. Colony immunostaining with MAbs on clonal lineage showed that 4 out of 9 species-specific epitopes exhibited a high rate of variation, demonstrating that M. agalactiae possesses a capacity for phenotypic diversification of its surface antigenicity. The emphasis was on dot immunobinding screening of the field isolates with MAbs recognizing permanently expressed epitopes. Eight different profiles could be defined. Great differences in epitope conservation were demonstrated with some area-specific strains completely lacking certain specific determinants. These results indicate that the antigenic variability of M. agalactiae relies not only upon surface switching mechanisms but also upon true epitope differences, partially related to the geographic origin of the isolates.     

Crystal structure of a staphylokinase: variant a model for reduced antigenicity.

Staphylokinase (SAK) is a 15.5-kDa protein from Staphylococcus aureus that activates plasminogen by forming a 1 : 1 complex with plasmin. Recombinant SAK has been shown in clinical trials to induce fibrin-specific clot lysis in patients with acute myocardial infarction. However, SAK elicits high titers of neutralizing antibodies. Biochemical and protein engineering studies have demonstrated the feasibility of generating SAK variants with reduced antigenicity yet intact thrombolytic potency. Here, we present X-ray crystallographic evidence that the SAK(S41G) mutant may assume a dimeric structure. This dimer model, at 2.3-A resolution, could explain a major antigenic epitope (residues A72-F76 and residues K135-K136) located in the vicinity of the dimer interface as identified by phage-display. These results suggest that SAK antigenicity may be reduced by eliminating dimer formation. We propose several potential mutation sites at the dimer interface that may further reduce the antigenicity of SAK.     

The cellular location of a foreign B cell epitope expressed by recombinant bacteria determines its T cell-independent or T cell-dependent characteristics.

We have targeted two foreign B cell antigenic determinants to different locations in the Escherichia coli cell to examine what effect this had on antibody responses elicited by the recombinant bacteria. The two epitopes were the 132-145 peptide from the PreS2 region of hepatitis B virus and the C3 neutralization epitope of poliovirus type 1. They were each expressed in two forms either on the surface, as part of the outer-membrane protein LamB, or soluble in the periplasm, as part of the periplasmic protein MalE. When live bacteria expressing the foreign epitope at the cell surface were used for immunization of mice, they induced T cell-independent antibody responses characterized by a rapid induction of IgM and IgG antibodies. In contrast, when the same foreign epitope was inserted into the MalE protein, the antibody response was only detectable after 3 wk, belonged only to the IgG class and was strictly T cell dependent. This study has therefore identified two major pathways by which epitopes expressed by bacterial cells can stimulate specific antibody responses. The first pathway is mediated by direct activation of B cells by bacterial cell-surface Ag and does not require T cell help. The second pathway is T cell dependent and concerns Ag that can be released from the bacteria in a soluble form. We have also studied the effect of the exact position of the B cell antigenic determinant within the LamB protein and with respect to the outer membrane by comparing the immunogenicity of the PreS epitope inserted at three different permissive sites of LamB. The data indicated that to obtain an antibody response with intact bacteria, the epitope must be protruding sufficiently from the outside of the outer membrane. In contrast, when semipurified hybrid proteins were used as immunogen, the exact position of the B cell antigenic determinant within solubilized LamB protein does not influence its immunogenicity.     

Mapping of antigenic domains of Sendai virus nucleocapsid protein expressed in Escherichia coli.

Several nonoverlapping epitopes were mapped on the primary sequence of the Sendai virus NP protein. After a complete cDNA clone of the Sendai virus NP gene was expressed in Escherichia coli, deletion constructs were used to generate a series of overlapping NP fragments deleted at their C termini. Immunoblot analyses with 11 monoclonal antibodies identified four antigenic sites. All of these sites resided in the C-terminal half of NP and were also the only sites detected with a polyclonal serum. These findings confirm and extend the evidence that the C terminus of the NP protein represents the domain exposed on the surface of the nucleocapsid. One of the monoclonal antibodies reacted with a site, comprising only 6 amino acids, lying with a hinge between an alpha-helix and a beta-strand in the predicted secondary structure of NP. Since this antibody is a potent inhibitor of in vitro viral RNA synthesis (K. L. Deshpande and A. Portner, Virology 139:32-42, 1984), the epitope may be critical to the flexibility of the NP molecule that makes the RNA template accessible during RNA synthesis.     

Fine mapping of antigenic site II of herpes simplex virus glycoprotein D.

Glycoprotein D (gD) is a virion envelope component of herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) which plays an important role in viral infection and pathogenesis. Previously, anti-gD monoclonal antibodies (MAbs) were arranged into groups which recognize distinct type-common and type-specific sites on HSV-1 gD (gD-1) and HSV-2 gD (gD-2). Several groups recognize discontinuous epitopes which are dependent on tertiary structure. Three groups, VII, II, and V, recognize continuous epitopes present in both native and denatured gD. Previously, group II consisted of a single MAb, DL6, whose epitope was localized between amino acids 268 and 287. In the study reported here, we extended our analysis of the antigenic structure of gD, concentrating on continuous epitopes. The DL6 epitope was localized with greater precision to residues 272 to 279. Four additional MAbs including BD78 were identified, each of which recognizes an epitope within residues 264 to 275. BD78 and DL6 blocked each other in binding to gD. In addition, a mutant form of gD was constructed in which the proline at 273 was replaced by serine. This change removes a predicted beta turn in gD. Neither antibody reacted with this mutant, indicating that the BD78 and DL6 epitopes overlap and constitute an antigenic site (site II) within residues 264 to 279. A separate antigenic site (site XI) was recognized by MAb BD66 (residues 284 to 301). This site was only six amino acids downstream of site II, but was distinct as demonstrated by blocking studies. Synthetic peptides mimicking these and other regions of gD were screened with polyclonal antisera to native gD-1 or gD-2. The results indicate that sites II, V, VII, and XI, as well as the carboxy terminus, are the major continuous antigenic determinants on gD. In addition, the results show that the region from residues 264 through 369, except the transmembrane anchor, contains a series of continuous epitopes.     

Machine learning approaches for prediction of linear B-cell epitopes on proteins

Identification and characterization of antigenic determinants on proteins has received considerable attention utilizing both, experimental as well as computational methods. For computational routines mostly structural as well as physicochemical parameters have been utilized for predicting the antigenic propensity of protein sites. However, the performance of computational routines has been low when compared to experimental alternatives. Here we describe the construction of machine learning based classifiers to enhance the prediction quality for identifying linear B-cell epitopes on proteins. Our approach combines several parameters previously associated with antigenicity, and includes novel parameters based on frequencies of amino acids and amino acid neighborhood propensities. We utilized machine learning algorithms for deriving antigenicity classification functions assigning antigenic propensities to each amino acid of a given protein sequence. We compared the prediction quality of the novel classifiers with respect to established routines for epitope scoring, and tested prediction accuracy on experimental data available for HIV proteins. The major finding is that machine learning classifiers clearly outperform the reference classification systems on the HIV epitope validation set.     

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale

Identification of antigenic sites on proteins is of vital importance for developing synthetic peptide vaccines, immunodiagnostic tests and antibody production. Currently, most of the prediction algorithms rely on amino acid propensity scales using a sliding window approach. These methods are oversimplified and yield poor predicted results in practice. In this paper, a novel scale, called the amino acid pair (AAP) antigenicity scale, is proposed that is based on the finding that B-cell epitopes favor particular AAPs. It is demonstrated that, using SVM (support vector machine) classifier, the AAP antigenicity scale approach has much better performance than the existing scales based on the single amino acid propensity. The AAP antigenicity scale can reflect some special sequence-coupled feature in the B-cell epitopes, which is the essence why the new approach is superior to the existing ones. It is anticipated that with the continuous increase of the known epitope data, the power of the AAP antigenicity scale approach will be further enhanced.     

Mapping of six epitopes on haemocyanin subunit Aa 6 by immunoelectron microscopy

Monoclonal antibodies directed against the haemocyanin of the scorpion Androctonus australis were raised in order to map antigenic determinants (epitopes). The method of mapping employed in this study is molecular immunoelectron microscopy. It consists of a direct electron microscopic observation of antigenic molecules labelled with monoclonal antibodies. The epitopes are then localized in a small region of the external surface of the antigenic molecule whose architecture and quaternary structure are well known. Six monoclonal antibodies have been selected and epitopes have been circumscribed within a small area of one subunit among the 24 subunits composing the whole antigenic molecule.     

传染性法氏囊病病毒VP3抗原表位的鉴定

利用肽扫描技术对4株IBDV VP3的单克隆抗体(HRB-3F、HRB-7B、HRB-7C和HRB-10E)的抗原表位进行了研究.通过Western blot和ELISA鉴定,将HRB-3F和HRB-7B的抗原表位定位于VP3 109～119 aa(位于IB-DV聚合蛋白的864～874 aa),HRB-7C和HRB-10E的抗原表位定位于VP3 177～190 aa(位于IBDV聚合蛋白的932～945 aa).进一步检测其反应原性及免疫原性,结果表明,这两个表位均能与抗IBDV阳性血清反应.将这两个表位短肽免疫BALB/c小鼠,其血清可以和IBDV反应,具有较好的免疫原性.与D6948、HK46和UK661等多株IBDV相应区域的同源性进行了比较,结果显示,这两个表位在多种毒株中同源性为100%.通过IBDV VP3抗原表位的研究,筛出两个新的保守线性表位并进行精确定位,对进一步分析IBDV结构与功能以及建立以表位为基础的抗原抗体诊断方法具有重要的意义.     

Correlation among sites of limited proteolysis, enzyme accessibility and segmental mobility

The relationship among accessibility to an enzyme, flexibility, and limited proteolysis was explored. Regions accessible to large probes, comparable in size to proteolytic enzymes, were computed in the crystallographic structures of thermolysin, trypsinogen and ribonuclease. Positions of these accessible regions were compared with sites of autolytic/proteolytic attacks, and with locations of flexible backbone segments. All the proteolytic sites were found to be exceptionally accessible. Most of them were also flexible, but at least one prominent site in trypsinogen appeared to be rigid. Thus, surface exposure seems to be more essential to proteolysis than flexibility.     

Mapping apolipoprotein B on the low density lipoprotein surface by immunoelectron microscopy

Apolipoprotein B (apoB) was mapped using electron microscopy to visualize pairs of monoclonal antibodies binding to the low density lipoprotein (LDL) surface. The sites at which these monoclonals bind the apoB polypeptide sequence had already been established. The angular distances between all possible pairs of binding sites except one allowed the relative placement of six epitopes on the LDL sphere. We conclude that apoB extends over at least a hemisphere of the LDL surface since four epitopes are located in the Northern Hemisphere at sites arbitrarily designated as the North Pole, the Aleutian Islands, Bogotá, and in the Atlantic Ocean, while two are found in the Southern Hemisphere at Buenos Aires and at Madagascar. ApoB appears to possess a restricted flexibility, since these relative epitope locations show a substantial standard deviation in latitude and longitude. Mapping of additional epitopes may provide an answer to the question of whether apoB circumnavigates the LDL sphere.