Strategies for epitope analysis using peptide synthesis

Demonstration of evolutionary differences between conserved antigenic epitopes in the minor nucleocapsid protein of human papillomavirus types 6b, 16 and 18

We studied human papillomavirus (HPV) minor nucleocapsid protein (L2) by epitope scanning. Conserved antigenic epitopes identified by rabbit antiserum to bovine papillomavirus (BPV) were revealed in HPV-6b (amino acids, aa, 196-205); HPV-16 (aa:s 376-85) and HPV-18 (aa:s 221-230). L2 proteins. The first two epitopes were situated in hydrophilic regions of the proteins. Aligning the aa-sequences that corresponded to the epitopes with the total L2 sequences of BPV and HPV1a revealed consensus motifs between BPV, HPV1a and the reactive HPV type. In the non-reactive types amino acid alterations were noted. Mismatch between HPV1a sequences and the corresponding HPV-6b and HPV-16, HPV-6b and HPV-18, and HPV-16 and HPV-18 sequences suggests that the alterations may have evolved to facilitate immune surveillance of the genital HPV types.

Multi-pin peptide synthesis strategy for T cell determinant analysis

Techniques to synthesize many peptides simultaneously exist, however their individual cleavage and subsequent purification constitutes a bottleneck to total throughput. Biological screening of peptides is generally carried out at physiological pH in aqueous solutions. However, peptides, unless individually purified are usually contaminated by residual compounds used in their preparation such as trifluoroacetic acid, organic solvents, scavengers etc. In testing with cellular systems, such as T cell determinant analysis, such contaminations must be rigorously excluded. We have extended the pin synthesis technique of synthesizing and screening large number of peptides (Geysen et al., 1984) to the analysis of T cell determinants. Peptides can be synthesized on polyethylene pins, the side chain protective groups removed and the peptides washed free of contaminants. A linker system stable under these conditions can then be triggered to cleave the peptides from the pins in an aqueous solution at neutral pH. This strategy enables the rapid mapping of T cell determinants. It is also applicable to other systems where large numbers of solution phase peptides are required, for example, in the study of hormone analogues.

Major antigenic domain recognized by monoclonal antibodies maps within the carboxy-terminal moiety of a recombinant human immunodeficiency virus-1 p24 protein

Antigenicity in mice of a recombinant polypeptide including the complete amino acid sequence of mature human immunodeficiency virus type 1 p24 protein was studied by induction of monoclonal antibodies (MAbs). A panel of nine recloned hybridomas secreting MAbs with anti-p24 reactivity was isolated and further characterized. Competitive inhibition experiments suggested that the MAbs could be grouped into four epitopic classes corresponding to at least two distinct determinants. Analysis of reactivity to recombinant p24 deletion variants indicated that all the recognized epitopes are localized within a carboxy-terminal domain (amino acids 168-208) which should be largely exposed in recombinant as well as authentic antigen. Lack of response to N-terminal and central portions of p24 suggests that the antigenicity of those regions in the natural polypeptide is strongly conformation-dependent.

A subgroup-specific antigenic site in the G protein of respiratory syncytial virus forms a disulfide-bonded loop

An antigenic site (represented by 15 amino acids, residues 174 to 188, designated peptide 12) of the large glycoprotein G of respiratory syncytial virus was demonstrated to be subgroup specific in peptide enzyme-linked immunosorbent assay tests with murine monoclonal antibodies and human postinfection sera. The role of individual amino acids in this subgroup-specific site was determined by use of single-amino-acid-deletion sets of peptides. When monoclonal antibodies were reacted with the deletion sets, a broad amino acid dependence of 11 or 12 residues, Cys-176 (Ile-175 in subgroup B) to Cys-186, was found. Human postinfection sera exhibited a narrower reaction profile (for subgroup A, Cys-182 to Trp-183; for subgroup B, Cys-176 to Lys-183). Reduction of peptides on microtiter plates by treatment with dithiothreitol completely destroyed their antigenic activity in tests with monoclonal antibodies and human postinfection sera of subgroup B. A variant of peptide 12 containing all four cysteines of the G protein (represented by 16 amino acids, residues 172 to 187, designated peptide 12var) also was subgroup specific. We concluded that the activity of the antigenic site in tests with monoclonal antibodies for subgroups A and B appears to depend on intrapeptide disulfide bonds. Reactions with postinfection sera of subgroup B also may depend on a disulfide bond. In contrast, postinfection sera of subgroup A appeared to have the capacity to identify a subgroup-specific site in a linear form of the selected 15-amino-acid-long peptide. Treatment of peptides with dithiothreitol had no effect on their antigenic activity in tests with human postinfection sera of subgroup A. These findings have relevance for molecular engineering of peptide antigens for use in respiratory syncytial virus subgroup-specific site-directed serology.

Immunoaccessible peptide sequences of the major outer membrane protein from Chlamydia trachomatis serovar C

The antigenicity of the major outer membrane protein of Chlamydia trachomatis serovar C was assessed by using overlapping hexapeptide homologs of serovar C major outer membrane protein and rabbit antisera in a peptide enzyme-linked immunosorbent assay. Five immunogenic sites were found distributed within variable sequences of the protein: four were immunodominant and three were surface exposed on native elementary bodies of serovar C. None was surface exposed on serovars H, I, and J.

Structure of viral B-cell epitopes

Four categories of viral epitopes can be distinguished that have been designated cryptotopes, neotopes, metatopes and neutralization epitopes. Specific examples of each epitope type are presented and the methods used for locating their positions in viral proteins are described. The epitopes of four well-characterized viruses, namely poliovirus, foot-and-mouth disease virus, influenza virus and tobacco mosaic virus are briefly described.

Linear B-cell epitopes of the major core protein of human immunodeficiency virus types 1 and 2

Nine murine monoclonal antibodies directed to the major core protein p24 of human immunodeficiency virus type 1 (HIV-1) were obtained and then tested by using an epitope mapping system (Pepscan) covering the whole p24HIV1 protein to characterize antigenic domains. Four different linear epitopes were identified. Monoclonal antibodies recognizing three of these epitopes also reacted to p26HIV2 in Western blotting (immunoblotting). A monoclonal antibody specific for the fourth epitope, located at position 179 to 188 of the gag polyprotein p55HIV1 (human T-cell lymphotropic virus type 3B strain), did not react with HIV type 2 (HIV-2) core proteins. The corresponding sequence is constant in all known HIV-2 and simian immunodeficiency virus (SIV) isolates, including a very divergent SIV strain from African green monkeys (SIVagm/tyo). This observation may be relevant to the phylogeny of primate lentiviruses. Two of the conserved epitopes might be immunogenic during natural infection and could therefore be used for diagnosis and prognosis purposes. These two epitopes are AAEWDRVHP and EIYKRWII, starting at positions 209 and 260 of the polyprotein p55HIV1, respectively.

Structure of rubella E1 glycoprotein epitopes established by multiple peptide synthesis

Essential parts of epitopes have been identified on rubella virion envelope glycoprotein E1, by scanning with overlapping octapeptides situated between amino acids 243-286 in a previously determined antigenic domain.

Novel cross-reactive epitopes on asexual blood stage antigens of Plasmodium falciparum

An IgM monoclonal antibody that reacts with the merozoite membrane and internal merozoite antigens was shown to recognize several previously characterized asexual blood stage antigens of Plasmodium falciparum as well as new antigens. Among the reactive antigens identified were FIRA, GYMSSA, RESA and the S-antigen. Analysis of the cross-reactions between FIRA and GYMSSA by epitope scanning was performed. The most reactive peptides in GYMSSA had the common sequence STNS. The cross-reactive epitopes in FIRA could, in many cases, be explained by the results of a replacement net analysis performed on the STNS epitope. It is proposed that the cross-reactive epitopes, which in several cases have no obvious linear homology but possess high S, T and N content, may be present as loops or coils on the surface of the molecules.

A general procedure for evaluation of immunological relevance of synthetic peptides: peptides synthesized on paper in enzyme-linked immunosorbent assay

Multiple continuous-flow solid-phase peptide synthesis has been adapted for synthesis of peptides on a cellulose carrier (Whatman 3MM paper). Paper-bound synthetic peptides that represent antigenic determinants of particular proteins detected antibodies against the respective proteins in an enzyme-linked immunosorbent assay. The method is applied to the synthesis, and use in site-directed serology, of four peptides derived from the gp41 glycoprotein of HIV, the Epstein-Barr virus-determined nuclear antigen-1 and VCA proteins of the Epstein-Barr virus, and the early region of human papillomavirus type 11.

Peptides on phage: a vast library of peptides for identifying ligands

We have constructed a vast library of peptides for finding compounds that bind to antibodies and other receptors. Millions of different hexapeptides were expressed at the N terminus of the adsorption protein (pIII) of fd phage. The vector fAFF1, derived from the tetracycline resistance-transducing vector fd-tet, allows cloning of oligonucleotides in a variety of locations in the 5' region of gene III. A library of 3 x 10(8) recombinants was generated by cloning randomly synthesized oligonucleotides. The library was screened for high-avidity binding to a monoclonal antibody (3-E7) that is specific for the N terminus of beta-endorphin (Tyr-Gly-Gly-Phe). Fifty-one clones selected by three rounds of the affinity purification technique called panning were sequenced and found to differ from previously known ligands for this antibody. The striking finding is that all 51 contained tyrosine as the N-terminal residue and that 48 contained glycine as the second residue. The binding affinities of six chemically synthesized hexapeptides from this set range from 0.35 microM (Tyr-Gly-Phe-Trp-Gly-Met) to 8.3 microM (Tyr-Ala-Gly-Phe-Ala-Gln), compared with 7.1 nM for a known high-affinity ligand (Tyr-Gly-Gly-Phe-Leu). These results show that ligands can be identified with no prior information concerning antibody specificity. Peptide libraries are also likely to be useful in finding ligands that bind to other classes of receptors and in discovering pharmacologic agents.

Immunological and structural features of the protein core of human polymorphic epithelial mucin

The protein core of high mol. wt polymorphic epithelial mucin (PEM--approximately 400 kDa glycoprotein) which is associated with breast carcinomas, consists of a repeating 20 amino acid peptide motif [Gendler et al. (1988) J. biol. Chem. 263, 12,820-12,823]. Monoclonal antibodies C595 (anti-urinary mucin) and NCRC-11 (anti-breast carcinoma cells), and other antibodies against human milk fat globule membranes, were found to recognize determinants present within this 20 amino acid peptide. A model of the peptide was developed based on hydropathicity and structure prediction calculations and these indicated that the repeated structure is dominated by a hydrophilic domain of seven amino acids, extending into two flanking beta turns. NMR analysis of the 20 amino acid peptide was undertaken to probe the secondary structure. Epitope mapping experiments involving solid phase synthesis of overlapping heptapeptides in the repeat unit identified the minimum structures for antibody binding as Arg-Pro-Ala-Pro and Arg-Pro-Ala for the C595 and NCRC-11 antibodies, respectively. These determinants were found within the predicted hydrophilic turn region domain of the peptide. The epitopes for six other PEM-reactive monoclonal antibodies were also determined to reside within the predicted hydrophilic turn domain. This evidence is in accord with the disposition of this region of the PEM peptide core being at the exterior of the glycoprotein where it would be accessible to antibody recognition and binding events.

Recent advances in solid-phase peptide synthesis and preparation of antibodies to synthetic peptides

Peptides prepared by the solid-phase peptide synthesis (SPPS) approach are used increasingly in biological research, for instance to elicit anti-peptide antibodies that will recognize the intact, cognate protein. Recent advances in SPPS are reviewed, including the use of new coupling reagents, new methods for evaluating peptide purity and new techniques of automated and multiple peptide synthesis. Methods for enhancing peptide immunogenicity are discussed such as the use of adjuvants and liposomes, and of synthetic branched polypeptides as carriers.

The antibody response to the HIV-1 specific "out" (vpu) protein: identification of an immunodominant epitope and correlation of antibody detectability to clinical stages

Overlapping decapeptides based on the sequences of two human immunodeficiency virus type 1 (HIV-1) strains (HXB2 and ELI) were used to identify an immunodominant epitope of the nonstructural protein "out" (vpu) of the human immunodeficiency virus type 1. Of 29 HIV-1 antibody-positive sera, 6 reacted with decapeptides corresponding to the C-terminal amino acid sequence VEMGVEMGHHAPWDVDDL of the "out" (vpu) protein. This oligopeptide was synthesized by the solid phase method and used to develop an enzyme-linked immunosorbent assay (ELISA) for screening of 243 HIV-1-seropositive and 75 HIV-1-seronegative sera. It was found that 26% of the HIV-1 antibody-positive sera were reactive in the "out" (vpu) peptide ELISA, whereas none of the HIV-1-negative sera reacted with the oligopeptide. Correlation of reactivity of sera with the Walter Reed (WR) staging classification demonstrated that individuals classified WR 1 (36%) and WR 2 (42%) were more often reactive than patients classified WR 3-6 (11%).

Deduced amino acid sequences of class 1 protein (PorA) from three strains of Neisseria meningitidis. Synthetic peptides define the epitopes responsible for serosubtype specificity

The previously determined nucleotide sequence of the porA gene, encoding the class 1 outer membrane protein of meningococcal strain MC50, has been used to clone and sequence the porA gene from two further strains with differing serosubtype specificities. Comparison of the predicted amino acid sequences of the three class 1 proteins revealed considerable structural homology with major variation confined to two discrete regions (VR1 and VR2). The high degree of structural homology between the sequences gave predicted secondary structures that were almost identical, with the variable domains located in hydrophilic regions that are likely to be surface located and hence accessible to antibody binding. The predicted amino acid sequences have been used to define the epitopes recognized by mAbs with serosubtype specificity. A series of overlapping decapeptides spanning each of the class 1 protein sequences have been synthesized on solid-phase supports and probed with mAbs. Antibodies with P1.16 and P1.15 subtype specificity reacted with sequences in the VR2 domain, while antibodies with P1.7 subtype specificity reacted with sequences in the VR1 domain. Further peptides have been constructed to define the minimum epitopes recognized by each antibody. Thus we have been able to define linear peptides on each class 1 protein molecule that are responsible for subtype specificity and that represent targets for a protective immune response.

Vaccination against gonorrhoea: the potential protective effect of immunization with a synthetic peptide containing a conserved epitope of gonococcal outer membrane protein IB

Monoclonal antibody SM24 recognizes a protective, highly conserved but non-immunogenic epitope on outer membrane protein PIB of Neisseria gonorrhoeae. A series of overlapping synthetic peptides, spanning the deduced amino acid sequence of PIB from strain R10, have been synthesized on solid phase supports. Monoclonal antibody SM24 reacted with two adjacent decapeptides corresponding to residues 191-200 and 196-205, containing the common sequence TYSIP. Following localization of the epitope recognized, a peptide was synthesized corresponding to residues 193-204. The peptide was coupled to a carrier protein (KLH) and both the free peptide and peptide-KLH conjugate were used for immunization of rabbits. The resulting antisera reacted with the immunizing peptide, with denatured PIB on Western blots and, in addition, with native PIB in outer membranes of both the homologous and a heterologous strain. In the presence of human complement the sera were bactericidal for both the homologous and the heterologous strain. Thus synthetic peptides may be used to induce a protective polyclonal immune response against epitopes on gonococcal PI which are normally only weakly or non-immunogenic.

Antigenic epitopes of NEF proteins from different HIV-1 strains as recognized by sera from patients with manifest and latent HIV infection

Human immunodeficiency virus (HIV) infection that generally causes a strong antibody response toward HIV may sometimes occur in a latent form, characterized by seronegativity in assays based on structural HIV proteins. Latently infected individuals, however, often have an antibody response against the nonstructural regulatory HIV-1 protein NEF, a factor implicated in down-regulation of viral expression. In order to define the specificity of NEF antibodies, we looked for antibody response against more than 600 overlapping nonapeptides representing the total NEF sequence of three different HIV-1 isolates BRU, SF2, and MAL. Nine distinct homologous antigenic epitopes were recognized by sera from seropositive HIV-1-infected individuals by the peptide ELISA. We further demonstrated that sera from "at risk" individuals, with no antibodies to HIV structural proteins but reacting with the recombinant NEF protein in Western blot, recognize the same epitopes. Immunological assays based on the defined NEF epitopes can therefore be used to diagnose early or latent HIV Infection.

Antibody-directed drug discovery

By harnessing the remarkable power of the immune system to access the three-dimensional chemical information sequestered in target sites for drug ligands, antibody-directed drug discovery speeds the design of new therapeutic entities.

Mapping antigenic sites on the major outer membrane protein of Chlamydia trachomatis with synthetic peptides

The antigenicity of the major outer membrane protein (MOMP) of Chlamydia trachomatis was comprehensively evaluated by using overlapping hexapeptide homologs of serovar B MOMP and polyclonal rabbit antisera in a peptide enzyme-linked immunosorbent assay. Of 367 hexapeptides, 152 showed reactivities with at least one antiserum. Seven hexapeptides located within variable domain (VD) IV (residues 288 to 316) were found to be most reactive in terms of their binding titer and frequency, suggesting that VD IV is the immunodominant region within the MOMP as detected by this assay. Peptide-reactive antibodies could also recognize corresponding epitopes on either viable or acetone-permeabilized organisms. The antigenic specificity and immunoaccessibility of epitopes located in VD IV were resolved by absorbing antisera with chlamydial elementary bodies. Six antigenic sites were found in this region and included a B-type-specific site (S1), four subserogroup-specific sites (S2 and S4 to 6), and one species-specific site (S3), each displaying varying degrees of surface exposures on elementary bodies from different C. trachomatis serovars.

Antibody activity in ankylosing spondylitis sera to two sites on HLA B27.1 at the MHC groove region (within sequence 65-85), and to a Klebsiella pneumoniae nitrogenase reductase peptide (within sequence 181-199)

74 overlapping peptides of varying lengths from Klebsiella pneumoniae nitrogenase reductase (residues 181-199) and from the HLA B27.1 molecule (residues 65-85) were synthesized and tested by ELISA against sera from HLA B27+ ankylosing spondylitis (AS) patients, and sera from HLA B27+ and HLA B27- healthy first-degree relatives. Antibody activity in AS sera to Klebsiella peptides of four to eight amino acids was maximal with the peptide NSRQTDR. Activity to HLA B27 peptides was maximal with the peptide KAKAQTDR (named epitope I). These peptides overlap with, but are proximal to the NH2 terminus from QTDRED, which is homologous in HLA B27.1 and K. pneumoniae nitrogenase reductase. A second weaker reactive site was noted in the HLA B27.1 peptides, proximal to the COOH terminus from the homologous sequence, namely peptide REDLRTLL (named epitope II). Little activity was seen against peptides that included the entire homologous sequence. Sera from 50 AS patients showed higher total Ig activity against peptides KAKAQTDR (p less than 0.001) and NSRQTDR (p less than 0.02) than did sera from 22 B27+ and 22 B27- healthy controls. These data indicate that AS patient sera contain antibodies that bind to K. pneumoniae nitrogenase peptides and HLA B27.1 peptides, and that there are at least two epitopes on HLA B27.1 in the alpha 1 domain, at the MHC groove region, that are autoantigenic in AS patients. Epitope I may be a site for crossreactivity between HLA B27 and Klebsiella.

Epitope mapping of the HIV-1 gag region with monoclonal antibodies

A new type of immunochemical mapping of the human immunodeficiency virus type 1 (HIV-1) gag region was performed. By use of native HIV-1 viral lysates or the gag recombinant p24-15 antigen, a new set of monoclonal antibodies (Mabs) to the gag region proteins was generated. Synthetic HIV-1 peptides covering the entire gag region were used to specifically localize the continuous epitopes by direct binding to the Mabs and by blocking the Mab immunoreactivity. The identified immunogenic epitopes were localized between the gag amino acids (aa) 108-127, 203-217, 208-222, 248-282, 273-302, 288-307, 308-322, 331-354 and 408-422. These continuous epitopes formed seven immunogenic regions. One strongly p17-reactive Mab appeared to react with a discontinuous epitope, the components of which were 110 aa distant in the linear sequence: aa 23-27 and 128-132. The synthetic peptides appeared to be more congruent with the Mab-reactive sites in solution than when coated to a solid phase.

Immunogenic domains of hepatitis delta virus antigen: peptide mapping of epitopes recognized by human and woodchuck antibodies

Hepatitis delta virus (HDV) is a defective RNA virus which is dependent on hepatitis B virus for essential helper functions. Only a single highly basic phosphoprotein, HDV antigen (HDAg), is expressed by the HDV genome during infection in humans. Antibody directed to HDAg is important in the diagnosis of HDV infection, and it is likely but not yet proven that the immune response to HDAg provides significant protection against subsequent exposures to HDV. In an effort to map the antigenic domains of HDAg, 209 overlapping hexapeptides, spanning the entire 214 amino acid residues of the protein, were synthesized on polyethylene pins and probed by enzyme-linked immunosorbent assay with sera containing high titers of anti-HD antibodies. Domains recognized by antibodies present in serum from human chronic carriers of this virus included residues 2 to 7, 63 to 74, 86 to 91, 94 to 100, 159 to 172, 174 to 195, and 197 to 207. Antibody from an acutely superinfected woodchuck recognized similar epitopes, as well as a domain spanning residues 121 to 128. Together, residues in these antigenic domains constitute 41% of the HDAg molecule. Oligopeptides 15 to 29 residues in length and representing epitopes of HDAg found to be dominant in humans (residues 2 to 17, 156 to 184, and 197 to 211) were synthesized in bulk and found to possess significant antigenic activity by microdilution enzyme-linked immunosorbent assay. The reactivity of peptide 197-211 with human sera confirms that the entire 214 amino acids of HDAg are expressed during infection in vivo. In addition, these results suggest that synthetic peptides may be useful reagents for development of new and improved diagnostic tests for HDV infection.

Chemical characterization of the parasitophorous vacuole membrane antigen QF 116 from Plasmodium falciparum

On the basis of amino acid sequencing and immunological cross-reactivity, the Plasmodium falciparum parasitophorous vacuole antigens QF116 and exp-1/CRA are apparently identical. The epitope recognized by an inhibitory monoclonal antibody directed against QF116 is located proximal to the C-terminus of the protein. The QF116 protein is processed during maturation by the cleavage of a 22-amino-acid signal peptide and acylated as measured by labeling with myristic acid.

Mapping of viral epitopes with prokaryotic expression products

Several systems are available for the expression of foreign gene sequences in Escherichia coli. We describe the use of prokaryotic expression products of viral gene fragments in order to identify the regions that specify the binding sites of antibodies. This approach is particularly successful if the antigenicity does not depend on the native protein, but only on the amino acid sequence, i.e., if the epitope is sequential. Combining prokaryotic expression with the use of synthetic peptides often permits a fast and accurate mapping of an epitope. The occurrence of immunodominant sequential epitopes on the surfaces of viruses seems to be a widespread phenomenon.

Detection of P-glycoprotein isoforms by gene-specific monoclonal antibodies

P-glycoprotein is a highly conserved membrane protein shown to be overexpressed in many multidrug-resistant tumor cell lines. P-glycoprotein is encoded by a small gene family in mammalian cells. Class I and II isoforms cause multidrug resistance, whereas class III does not. In this report, we have characterized three P-glycoprotein-specific monoclonal antibodies (mAbs) by high-resolution epitope mapping with a series of hexapeptides. mAb C494 is gene specific, binding to a sequence present only in the class I isoform of hamster and human. The mAb C32 recognizes a sequence conserved in hamster class I and II isoforms but not in class III isoforms. In contrast, the mAb C219 recognizes a highly conserved amino acid sequence found in all P-glycoprotein isoforms characterized to date. These mAbs were used to reveal differential expression and specific localization of the three P-glycoprotein isoforms in hamster tissues by immunohistochemical staining and competition with epitope-specific peptides. Colonic epithelial cells expressed predominantly the class I isoform in a polarized manner, adrenal cortical cells expressed predominantly the class II isoform, whereas a small percentage of skeletal muscle fibers expressed the class III isoform of P-glycoprotein. These findings suggest that the P-glycoprotein isoforms have distinct physiological roles associated with specialized cell functions.

The main immunogenic region of the nicotinic acetylcholine receptor: interaction of monoclonal antibodies with synthetic peptides

Monoclonal antibodies to the main immunogenic region of the nicotinic acetylcholine receptor have been studied with regard to their binding to synthetic peptides. It was found that monoclonal antibody 210 to the main immunogenic region binds to the synthetic fragment spanning residues 66 to 76 of the alpha subunits of the acetylcholine receptor from human muscle, but not to the homologous sequence from Xenopus. This parallels the reactivities of antibodies to the main immunogenic region with intact receptors from two species, and confirms the biological significance of the weak interactions observed between antibodies to this region and synthetic peptides. It also suggests that N alpha 68 and D alpha 71 are critical contact residues.

Influence of the peptide insolubilization method on detection of anti-peptide antibodies in ELISA. Evaluation of nonspecific interactions

Different methods of peptide insolubilization in solid phase were compared in ELISA, to verify the influence of the peptide antigen presentation in the interaction with related antibodies. Our studies were performed using as model the peptide fragment 163-171 of human Interleukin 1 beta, and polyclonal or monoclonal anti-peptide antibodies. It was found that the peptide, N-terminally linked to a protein carrier before the adsorption on microtiter wells, interacted with specific polyclonal and monoclonal antibodies with high sensitivity and specificity. In contrast the recognition of similar random conjugates, prepared using a bivalent cross-linking reagent or the peptide covalently linked to poly-L-Lysine-pretreated wells, was hampered generally by very high levels of nonspecific binding. On the other hand, the free peptide adsorbed directly to the solid phase interacted with antibodies with very low sensitivity and specificity. Nonspecific interactions were found in particular between peptides and hyperimmune sera or nonrelated monoclonal antibodies. On the contrary pre-immune sera and normal mouse immunoglobulins never showed significant interactions with any of peptides. This nonspecificity was also overcome when N-terminally linked peptide-protein conjugates were used for the assay.

Multiple peptide synthesis (Pepscan method) for the systematic analysis of B- and T-cell epitopes: Application to parasite proteins

In 1984 Mario Geysen and his colleagues described a technique for the simultaneous synthesis of hundreds of peptides on polyethylene rods. The peptides, still on the rods, could be used directly in enzyme-linked immunosorbent assays (ELISAs) and in this way linear parts of B-cell epitopes could be mapped. For the analysis of T-cell epitopes, peptides can be cleaved from the rods and incorporated into proliferation assays. This method, called the 'Pepscan' procedure, has been used for the detailed characterization of epitopes of viruses, Chlamydia and Mycobacteria: it is a powerful new approach to the epitope mapping of parasite proteins.

Bands, interbands and puffs in native Drosophila polytene chromosomes are recognized by a monoclonal antibody to an epitope in the carboxy-terminal tail of histone H1

A monoclonal antibody was raised against Drosophila melanogaster histone H1. Immunoscreening of proteolytic cleavage fragments of H1 and of a set of all possible overlapping synthetic octapeptides corresponding to the amino acid sequence of H1, revealed that the antibody recognizes an epitope within the sequence 207VTAAKPKA214 near the centre of the carboxy-terminal tail. This antibody gives positive immunofluorescence over the entire length of native D. melanogaster polytene chromosomes isolated from salivary glands by microdissection at physiological pH and ionic strength. Bands, interbands and puffs are all seen to contain H1. The immunofluorescence over puffs, albeit lower than that over bands and interbands, indicates that chromatin decondensation can occur without complete loss of H1 in these structures. The reaction of the antibody with bands suggests that the segment of the C-terminal tail containing the epitope may be exposed in the condensed 30 nm chromatin filament.

The NK model of rugged fitness landscapes and its application to maturation of the immune response

Adaptive evolution is, to a large extent, a complex combinatorial optimization process. Such processes can be characterized as "uphill walks on rugged fitness landscapes". Concrete examples of fitness landscapes include the distribution of any specific functional property such as the capacity to catalyze a specific reaction, or bind a specific ligand, in "protein space". In particular, the property might be the affinity of all possible antibody molecules for a specific antigenic determinant. That affinity landscape presumably plays a critical role in maturation of the immune response. In this process, hypermutation and clonal selection act to select antibody V region mutant variants with successively higher affinity for the immunizing antigen. The actual statistical structure of affinity landscapes, although knowable, is currently unknown. Here, we analyze a class of mathematical models we call NK models. We show that these models capture significant features of the maturation of the immune response, which is currently thought to share features with general protein evolution. The NK models have the important property that, as the parameter K increases, the "ruggedness" of the NK landscape varies from a single peaked "Fujiyama" landscape to a multi-peaked "badlands" landscape. Walks to local optima on such landscapes become shorter as K increases. This fact allows us to choose a value of K that corresponds to the experimentally observed number of mutational "steps", 6-8, taken as an antibody sequence matures. If the mature antibody is taken to correspond to a local optimum in the model, tuning the model requires that K be about 40, implying that the functional contribution of each amino acid in the V region is affected by about 40 others. Given this value of K, the model then predicts several features of "antibody space" that are in qualitative agreement with experiment: (1) The fraction of fitter variants of an initial "roughed in" germ line antibody amplified by clonal selection is about 1-2%. (2) Mutations at some sites of the mature antibody hardly affect antibody function at all, but mutations at other sites dramatically decrease function. (3) The same "roughed in" antibody sequence can "walk" to many mature antibody sequences. (4) Many adaptive walks can end on the same local optimum. (5) Comparison of different mature sequences derived from the same initial V region shows evolutionary hot spots and parallel mutations. All these predictions are open to detailed testing by obtaining monoclonal antibodies early in the immune response and carrying out in vitro mutagenesis and adaptive hill climbing with respect to affinity for the immunizing antigen.

Localization of virus-specific and group-specific epitopes of plant potyviruses by systematic immunochemical analysis of overlapping peptide fragments

Virus-specific or group-specific antibody probes to potyviruses can be produced by targeting the immune response to the virus-specific, N-terminal region of the capsid protein (29-95 amino acids depending on the virus) or to the conserved core region (216 amino acids) of the capsid protein, respectively. Immunochemical analysis of overlapping, synthetic octapeptides covering the capsid protein of the Johnsongrass strain of Johnsongrass mosaic virus (JGMV-JG) has delineated the peptide sequences recognized by five polyclonal rabbit antisera and two mouse monoclonal antibodies (mAbs). The antibodies characterized were (i) three virus-specific rabbit polyclonal antisera and one virus-specific mouse mAb (1/25) raised against native virus particles, (ii) one polyclonal antiserum raised against trypsin-derived core particles of JGMV-JG, (iii) one group-specific polyclonal antiserum raised against the denatured, truncated coat protein from trypsin-derived core particles of JGMV-JG, and (iv) one group-specific mouse mAb (1/16) raised against native virus particles. The two epitopes seen by mAb 1/25 occurred at residues 18-27 and 43-52 and overlapped with the two major epitopes seen by the virus-specific polyclonal antiserum. The group-specific epitope seen in JGMV-JG by mAb 1/16 was also recognized strongly in potato virus Y, the type member of the potyvirus group. The multiple epitopes seen by the cross-reactive polyclonal antisera were distributed across the entire core region of the coat protein and their relative antibody binding responses varied between JGMV-JG, potato virus Y, and six other distinct potyviruses.

Cross-reactivity of antibody against an epitope of the Plasmodium falciparum second merozoite surface antigen

Monoclonal antibodies directed against the 51 kD merozoite surface antigen of Plasmodium falciparum also bind to other antigens within the infected cell. The sizes of these cross-reacting antigens have been characterized. Immunofluorescence due to the reaction of one of the monoclonal antibodies with these cross-reacting antigens was localized in the intra-erythrocytic parasite and in granules in the infected red cell cytoplasm. This immunofluorescence could be distinguished from the merozoite surface antigen in parasite lines with a variant serotype of the merozoite surface antigen which fails to react with the monoclonal antibodies. It was found that the in-vitro growth inhibition caused by the presence of one of the monoclonal antibodies, 8G10/48, was dependent on the expression of the corresponding serotype of merozoite surface antigen, a finding consistent with the inhibitory effect of this antibody being primarily directed against the merozoite surface antigen and not the cross-reacting antigens. Analysis of the frequency at which epitopes occur suggests that such cross-reacting proteins will be commonly seen in malaria, without the need to postulate a selective advantage for such cross-reacting specificities.

The chemistry of site-directed serology for HIV infections

The advent of site-directed serology has provided a specific and simplified means of distinguishing antibody responses to the two types of human immunodeficiency virus (HIV) in an outbred population. Remarkably, human sera containing HIV antibodies and simian sera containing simian immunodeficiency virus (SIV) antibodies had a very narrow amino acid dependence in the 23 residue long peptide, 582Ala-604Cys, used as antigen. A single dominating antigenic site was demonstrated in the C-terminal part of the peptide--596Trp-602Gln for HIV-2 and SIV antibodies and 597Gly-602Leu for HIV-1. A minor fraction of HIV-1 antibodies also reacted with a second site, 588Lys and 589Asp. These data define the precise amino acid dependence of a uniquely immunogenic site in the folded transmembrane protein of HIV and facilitate the optimizing of peptide antigens for site-directed serology.

Serologically defined linear epitopes in the envelope protein of dengue 2 (Jamaica strain 1409)

Antisera from dengue patients and dengue virus infected rabbits recognized octapeptides corresponding to linear amino acid sequences in the envelope protein of dengue 2 (Jamaica 1409). Although no peptide was recognized by sera from all dengue infected hosts, two peptides (216LPLPWLPG223 and 448FSGVSWTM455) were recognized by sera from all dengue 2 infected rabbits. One of these 448FSGVSWTM455 was also recognized by sera from both the dengue 2 patients tested. No peptides were identified which reacted exclusively with all dengue 2 infected animals. Use of a mouse monoclonal antibody (1B7) enabled identification of two regions (50AKQPATLR57 and 127GKVVLPEN134) and possibly a third (349GRLITVNP356) in the envelope protein of dengue 2 likely to be involved in haemagglutination inhibition and virus neutralization in vitro.

Identification and classification of potyviruses on the basis of coat protein sequence data and serology. Brief review

The identification and classification of potyviruses has been in a very unsatisfactory state due to the large size of the group, the apparent vast variation among the members and the lack satisfactory taxonomic parameters that will distinguish distinct viruses from strains. In the past, use of classical methods, such as host range and symptomatology, cross-protection, morphology of cytoplasmic inclusions and conventional serology, revealed a "continuum" implying that the "species" and "strain" concepts cannot be applied to potyviruses. In contrast nucleic acid and amino acid sequence data of coat proteins has clearly demonstrated that potyviruses can be divided into distinct members and strains. This sequence data in combination with information of the structure of the potyvirus particle has been used to develop simple techniques such as HPLC peptide profiling, serology (using polyclonal antibody probes obtained by cross-adsorption with core protein from trypsin treated particles) and cDNA hybridization. These findings, along with immunochemical analyses of overlapping synthetic peptides have established the molecular basis for potyvirus serology; explained many of the problems associated with the application of conventional serology; and provided a sound basis for the identification and classification of potyviruses. As a result, the virus/strain status of some potyviruses has been redefined, requiring a change in the potyvirus nomenclature. These new developments necessitate a re-evaluation of the earlier literature on symptomatology, cross-protection, cytoplasmic inclusion body morphology and serology.

Similar binding properties of peptide ligands for a human immunoglobulin and its light chain dimer

The urinary light chain dimer and serum monoclonal IgG1 protein from a patient (Mcg) with multiple myeloma and amyloidosis were systematically tested for their binding activities to peptides presented on solid supports. The system was validated using a series of enkephalins, beta-casomorphins and DNP-lysine derivatives which were known to complex with the dimer. Sets of peptide ligands binding to the proteins were constructed by incremental additions of amino acid residues to minimal binding units [Geysen et al., J. Immun. Meth. 102, 259-274 (1987)]. Both the amino acid sequences and the combinations of optical isomers were optimized at each stage of the syntheses. Binding could be demonstrated for ligands ranging in size from a tethered single amino acid to pentapeptides. At the dipeptide levels, the dimer and the IgG1 protein showed different preferences (Hp versus qf, where lower case letters designate D-amino acid residues). However, in a tetrapeptide ligand (qfHp) for the dimer, both of these initial preferences had converged. With few exceptions, the IgG1 molecule showed binding activity for the ligands developed for the dimer. Two sets of selected peptides, one based on Hp and the other on mW, were synthesized for diffusion into crystals of the dimer. X-ray analyses showed that these peptides bound exclusively in the main binding cavity between the "variable" domains of the dimer. As predicted from the ELISA results with tethered ligands, the relative occupancies in the crystals followed the order of tetrapeptide greater than tripeptide much greater than dipeptide. The crystallographic studies confirmed that peptides with very different sequences can bind in the same cavity.

A protective monoclonal antibody recognizes a linear epitope in the precursor to the major merozoite antigens of Plasmodium chabaudi adami

The monoclonal antibody 5C10/66 was shown to afford strong protection in mice against fulminating Plasmodium chabaudi adami infection. This was remarkable, as immunity to this organism is regarded to be mainly T-cell mediated. This antibody identified a 250-kDa molecule in schizonts and an 83-kDa fragment in merozoites. A cDNA clone selected by 5C10/66 was the homologue of the Plasmodium falciparum precursor to the major merozoite surface antigen (PMMSA). Comparison with the P. falciparum sequence showed that the P. chabaudi adami clone encoded the middle portion of the gene and that it can also be divided into variable and conserved blocks. Screening of a set of all possible octamer peptides predicted by the cDNA clone revealed that the core epitope of 5C10/66 was Glu-Thr-Thr-Glu-Thr. This region resides in a variable block of PMMSA.

The major outer membrane protein of Chlamydia trachomatis: critical binding site and conformation determine the specificity of antibody binding to viable chlamydiae

The major outer membrane protein (MOMP) is the prime candidate for the development of a chlamydial vaccine. Antibodies to the subspecies-specific epitope neutralize chlamydial infection. Monoclonal antibodies (MAbs) to this epitope were prepared either by immunization with whole chlamydiae or with a 16 amino acid synthetic peptide. The critical binding site on the subspecies epitope for these MAbs was determined to single amino acid resolution using several hundred solid-phase peptides. A frame shift of just one amino acid in critical binding site completely prevented antibody binding to viable chlamydiae. A single MAb to whole organisms was capable of spanning both the surface-exposed, conformation-dependent, subspecies epitope and a buried, conformation-independent species epitope some 10 A distant. Immunization with peptide generated an MAb with reduced binding constraints which permitted the antibody to bind with broadened species-specificity at the subspecies binding site. The results show for the first time the importance of both critical binding site and conformation at the subspecies epitope. We suggest that the conformational flexibility of short, epitopic peptide vaccines may in some cases be advantageous, giving rise to extended specificity not attained with the natural protein.

The structural basis of allergenicity: recombinant DNA-based strategies for the study of allergens

The use of recombinant DNA techniques for the study of allergenicity of proteins is a viable, and in many ways a preferred, alternative to the traditional procedures of protein purification, digestion and analysis of peptides for both allergenicity and amino acid sequence. The process of protein purification can be difficult and in many instances workers are forced to use only partially pure fractions that make the identification of the allergenic proteins uncertain. Furthermore, the purification and sequencing of peptides and their testing for retention of allergenic properties, represents a substantial and time-consuming work load. The synthesis of families of synthetic peptides to characterize the amino acids important for allergenic properties is also expensive and time-consuming. On the other hand, the preparation of a cDNA library from an allergen source is today a relatively easy and inexpensive task. The isolation and purification of cDNA clones is comparatively trivial compared to protein purification. Using the techniques described in this text, it can be seen that the molecular biological approach, although in some respects similar in principle to those of the protein chemist to study allergens, provides the capability to study several clones at the same time, and to compare clones for the presence of conserved regions corresponding to allergenic determinants. In addition, the techniques for generating mutant sequences provides perhaps the most powerful and simple set of procedures available for defining the amino acid structures essential for proteins or peptides to behave as allergens.

Hepatic and biliary autoantigens

Chronic active hepatitis (CAH) and primary biliary cirrhosis (PBC) are two enigmatic liver diseases in which autoimmunity is implicated. Provisional criteria to separate the autoimmune type of CAH (A-CAH) from others are specified. Western immunoblotting using disease sera and antibody screening of a rat liver gene expression library were used to identify hepatic and biliary autoantigens relevant to the pathogenesis of A-CAH or PBC. With all reported putative liver-specific autoantigen preparations, serum reactivity in A-CAH and CAH due to infection with hepatitis B virus tends to be similar. In A-CAH, immunoblotting showed multiple reactivities with all liver preparations used, including hepatocyte membrane. In PBC, immunoblotting showed two disease-specific polypeptide antigens of MW 70 and 45 kD. A cDNA clone derived from a rat liver gene expression library was shown to encode the antigenic site of the 70 kD polypeptide. Recently published work in two other laboratories has established that the 70 kD autoantigen is the E2 component of the pyruvate dehydrogenase enzyme (PDH), and a proposed antibody-binding site (autoepitope) is a conserved decapeptide, corresponding to residues 83-92 of the deduced amino acid sequence of M2, which is the binding site of lipoic acid to the E2 component of PDH.

Epitope mapping with solid-phase peptides: identification of type-, subspecies-, species- and genus-reactive antibody binding domains on the major outer membrane protein of Chlamydia trachomatis

The major outer membrane protein (MOMP) of Chlamydia trachomatis carries serovar-, subspecies-, species- and genus immunodomains, antibodies to which may be protective. We have compared the inferred amino acid sequences for MOMP from different serovars of C. trachomatis and from Chlamydia psittaci to identify the likely locations of these sero-taxonomic epitopes. Overlapping peptides corresponding to each of these regions were synthesized on a solid phase and probed with monoclonal antibodies (MAbs) of appropriate specificities. We describe the primary structures of the binding sites of MAb to each of these four epitopes on C. trachomatis serovar L1 MOMP.

Epitope-mapping on the Epstein-Barr virus major capsid protein using systematic synthesis of overlapping oligopeptides

Systematic solid-phase synthesis of all possible overlapping nonapeptides of the 1381 amino acid sequence of the Epstein-Barr virus major capsid protein (EBV-MCP) was used to identify the position of linear antigen epitopes on this protein as recognised by human polyclonal antisera. Antisera were selected for reactivity with EBV-MCP on immunoblots. The results show that antibodies from different individual donors may recognise EBV-MCP through binding to a variety of different epitopes. These epitopes are localized at random over the protein backbone though some non-binding areas are also present. In addition, ten 'hot-spots' were identified containing closely-spaced reactive peptides (epitope-clusters) recognised by most (greater than or equal to 70%) individuals. No significant correlation was found between the actual location of these epitope-clusters and computer predictions using either hydrophilicity plots, secondary structure plots or a combination of (additional) parameters. Epitope-clusters generally were located in regions of indifferent or hydrophilic nature and mostly contained predicted beta-turn configurations. Only one epitope-cluster was located within a region of sequence homology with the MCPs of herpes simplex virus type 1 and varicella-zoster virus. The present study demonstrates the potential of using systematic peptide synthesis to define serologically relevant linear epitopes on large and relatively unexplored viral polypeptides.

Size-exclusion HPLC analysis of epitopes

A size-exclusion chromatography method based on competition between intact antibodies and antigen-binding fragments (Fabs) is used to evaluate relative spatial location of epitopes recognized by monoclonal antibodies. If epitopes are spatially distinct, the presence of a potentially competitive Fab results in formation of complexes of higher molecular weight than those formed by antigen and intact IgG. Complexes of lower molecular weight are formed if the epitopes overlap, are identical, or if, upon formation of the antigen-antibody complex, conformational change occurs that results in loss of epitope. Size-exclusion chromatography of the relevant mixtures reveals these shifts in molecular weight distribution and, therefore, provides an unambiguous determination of spatially independent epitopes. In addition, chromatographic analysis of competition between IgG and its enzymatically prepared Fab is used to evaluate the dissociation rate constant of the antigen-antibody reaction in re-equilibrating mixtures.