Production of anti-idiotypic antibodies by immunization with a pair of complementary peptides

Using a combined computational-experimental approach to predict antibody-specific B cell epitopes

Antibody epitope mapping is crucial for understanding B cell-mediated immunity and required for characterizing therapeutic antibodies. In contrast to T cell epitope mapping, no computational tools are in widespread use for prediction of B cell epitopes. Here, we show that, utilizing the sequence of an antibody, it is possible to identify discontinuous epitopes on its cognate antigen. The predictions are based on residue-pairing preferences and other interface characteristics. We combined these antibody-specific predictions with results of cross-blocking experiments that identify groups of antibodies with overlapping epitopes to improve the predictions. We validate the high performance of this approach by mapping the epitopes of a set of antibodies against the previously uncharacterized D8 antigen, using complementary techniques to reduce method-specific biases (X-ray crystallography, peptide ELISA, deuterium exchange, and site-directed mutagenesis). These results suggest that antibody-specific computational predictions and simple cross-blocking experiments allow for accurate prediction of residues in conformational B cell epitopes.

The association between anti-plasminogen antibodies and disease activity in ANCA-associated vasculitis

OBJECTIVE

Previous studies have shown that in patients with ANCA-associated vasculitis (AAV), anti-plasminogen antibodies were associated with reduced renal function and the presence of fibrinoid necrosis and cellular crescents in renal histology. The purpose of the current study was to investigate whether anti-plasminogen antibodies are associated with the systemic disease activity of AAV.

METHODS

One hundred and four Chinese patients with AAV were recruited. Anti-plasminogen antibodies were detected in sequential serum samples at initial onset and remission of the disease. Associations of anti-plasminogen antibodies with clinicopathological parameters were analysed.

RESULTS

The prevalence of anti-plasminogen antibodies was significantly higher in AAV patients than in healthy controls (19/104 vs 0/50, χ(2) = 8.8, P = 0.003). The prevalence of anti-plasminogen antibodies was significantly higher in the active stage of AAV than in remission (19/104 vs 1/48, χ(2) = 7.5, P = 0.013). The level of anti-plasminogen antibodies (expressed as a percentage of the positive controls) correlated with the ESR (r = 0.207, P = 0.042), serum creatinine (r = 0.302, P = 0.002), d-dimer (r = 0.273, P = 0.009) and the percentage of glomeruli with crescents in renal specimens (r = 0.393, P = 0.004). The level of Birmingham vasculitis activity scores and the prevalence of arthralgia and gastrointestinal involvement in patients with anti-plasminogen antibodies were significantly higher than in patients without anti-plasminogen antibodies [22.5 (s.d. 5.63) vs. 19.4 (s.d. 4.66), P = 0.015; 63.2% vs. 25.8%, P = 0.002; 57.9% vs. 21.1%, P = 0.001, respectively].

CONCLUSION

Circulating anti-plasminogen antibodies were associated with systemic disease activity and renal disease activity of AAV.

Peptides complementary to the active loop of porin P2 from Haemophilus influenzae modulate its activity

Haemophilus influenzae type b (Hib) is one of the leading causes of invasive bacterial infection in young children. It is characterized by inflammation that is mainly mediated by cytokines and chemokines. One of the most abundant components of the Hib outer membrane is the P2 porin, which has been shown to induce the release of several inflammatory cytokines. A synthetic peptide corresponding to loop L7 of the porin activates JNK and p38 mitogen-activated protein kinase (MAPK) pathways. We report a novel use of the complementary peptide approach to design a peptide that is able to bind selectively to the protein P2, thereby reducing its activity. This work provides insights into essential molecular details of P2 that may affect the pathogenesis of Hib infections where interruption of the signaling cascade could represent an attractive therapeutic strategy.

Design, synthesis and screening of antisense peptide based combinatorial peptide libraries towards an aromatic region of SARS-CoV

A combination of high-performance affinity chromatography and antisense peptide based combinatorial peptide libraries was used to screen a potential inhibitor for SARS-CoV. An aromatic-amino acid-rich region within the transmembrane domain at the C terminal of spike (S) protein identified as a membrane-active region was chosen as the target sense peptide (SP) and immobilized as affinity ligand. Four antisense peptides were designed based on the degeneracy of genetic codes. One of them was screened as the lead peptide to construct the extended peptide libraries (EPL). The library screening was carried out at pH 5.5 so as to mimic the low-pH milieu required by virus fusion. After five cycles of screening, a dodecapeptide KKKKYRNIRRPG (DP) was identified to possess the highest binding affinity to the immobilized sense peptide. The dissociation constant of the complex between the DP and the SP was 5.64 x 10(-7) M in a physiological condition. The recognition between the DP and recombinant SARS S protein was demonstrated by ELISA assay to be in a saturable way. The competitive inhibition of the sense peptide in the competitive ELISA reveals the affinity binding between the DP and SARS S protein is specific and directed towards the target SP of the S protein. The results indicate this preferred polypeptide can be used as a lead compound of potent inhibitor of SARS-CoV. The mechanism study suggests the specific recognition between the DP and the target peptide was due to sequence-dependent and multi-modal affinity interaction.

Antibodies with dual reactivity to plasminogen and complementary PR3 in PR3-ANCA vasculitis

Patients with inflammatory vascular disease caused by anti-neutrophil cytoplasmic autoantibodies (ANCA) can harbor antibodies not only to the autoantigen proteinase 3 (PR3) but also to complementary PR3 (cPR3(105-201)), a recombinant protein translated from the antisense strand of PR3 cDNA. The purpose of this study was to identify potential endogenous targets of anti-cPR3(105-201) antibodies. Patients' plasmapheresis material was tested for the presence of antigens reactive with affinity-purified rabbit and chicken anti-cPR3(105-201) polyclonal antibodies. Antigen-containing fractions were tested with patients' anti-cPR3(105-201) affinity-purified IgG, and putative protein targets were sequenced by mass spectrometry. Unexpectedly, plasminogen was identified as a target of anti-cPR3(105-201). Reactivity of affinity-purified antibodies from two patients was lost when plasminogen was converted to plasmin, indicating restricted specificity. Antiplasminogen antibodies from five patients bound plasminogen at a surface-exposed loop structure within the protease domain. This loop contains an amino acid motif that is also found in a portion of recombinant cPR3(105-201); site-directed mutagenesis of this sequence decreased antibody reactivity by 30%. Functionally, antiplasminogen antibodies delayed the conversion of plasminogen to plasmin and increased the dissolution time of fibrin clots. Serologically, antiplasminogen antibody levels were higher in PR3-ANCA patients (n = 72) than healthy control subjects (n = 63), myeloperoxidase-ANCA patients (n = 34), and patients with idiopathic thrombosis (n = 57; P = 0.001). Of the patients with PR3-ANCA, nine had documented deep venous thrombosis events, five of whom were positive for antiplasminogen antibodies. In summary, capitalizing on interactions with complementary proteins, specifically complementary PR3, this study identified plasminogen as a previously undescribed autoantigen in PR3-ANCA vasculitis.

The Proteomic Code: a molecular recognition code for proteins

Background

The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code.

Review

The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding.

Methods and conclusions

A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.

New insights that link microbes with the generation of antineutrophil cytoplasmic autoantibodies: the theory of autoantigen complementarity

PURPOSE OF REVIEW

Reviewed are recent discoveries that provide insights into novel mechanisms involved in the aetiology and pathology of anti-neutrophil cytoplasmic autoantibodies (ANCA) disease.

RECENT FINDINGS

Gene expression profiles of circulating leukocytes from anti-neutrophil cytoplasmic autoantibody immunogenesis patients revealed high levels of proteinase 3 (PR3) and myeloperoxidase (MPO) mRNA. Combined with reports of increased expression of these proteins, it appears that increased antigen availability is a pathologic component of anti-neutrophil cytoplasmic autoantibody immunogenesis disease, which might be equally as important as the presence of anti-MPO or anti-PR3 autoantibodies. Genetic predisposition to develop anti-neutrophil cytoplasmic autoantibody immunogenesis disease may include a polymorphism in the promoter region of the PR3 gene. Signalling pathways affected by anti-neutrophil cytoplasmic autoantibody immunogenesis binding to neutrophils involve the p21 pathway. Lastly, a topic discussed at length in this review is the seminal observation that PR3-ANCA patients harbour antibodies reactive with a protein produced from PR3-antisense RNA, whose amino acid sequence has homologies with proteins from many microbes and viruses. Delineated in the Theory of Autoantigen Complementarity, it is proposed that the initiator of an autoimmune response is not the autoantigen, but instead is a protein that is 'antisense' or complementary to the autoantigen (e.g. from bacteria or PR3).

SUMMARY

The progress in research efforts in the past year, including the identification of complementary proteins as a potential cause of anti-neutrophil cytoplasmic autoantibody immunogenesis, should highly impact future approaches therapeutic intervention.

Autoantigen complementarity: a new theory implicating complementary proteins as initiators of autoimmune disease

Autoimmune diseases affect approximately 1 in 21 persons in the United States. Treatment often requires long-term cytotoxic therapy. How and why these deleterious diseases occur is unclear. A serendipitous finding in our laboratory using serum from patients with autoimmune vasculitis led us to develop the theory of autoantigen complementarity, a novel concept that may elucidate the etiological and pathogenetic mechanisms underlying autoimmune disease in general. The theory proposes that the inciting immunogen that elicits a cascade of immunological events is not the self-antigen (the autoantigen) or its mimic but rather a protein that is complementary in surface structure to the autoantigen; that is, a protein homologous or identical to the amino acid sequence of translated antisense RNA from the noncoding strand of the autoantigen gene. The cascade begins when this complementary protein initiates the production of antibodies that in turn elicit an anti-antibody or anti-idiotypic response. These anti-idiotypic antibodies can now react with the autoantigen. Strikingly, homology search of complementary proteins yields microbial and fungal proteins, thus indicating that invading micro-organisms can deliver the inciting immunogen. Curiously, approximately 50% of our patients transcribe the complementary protein's antisense RNA. If it transpires that these aberrant RNAs are translated, the complementary protein would be produced by the individual. Here we review published research investigating complementary proteins, anti-idiotypic immune responses, and antisense transcripts, all of which support complementary proteins as initiators of autoimmune disease. In addition, we provide possible microbial and/or fungal organisms that may incite some of the most studied autoimmune diseases. Lastly, we propose mechanisms by which cell-mediated autoimmunity can be triggered by autoantigen complementarity. Based on our data and the contributions of the researchers described in this review, identification of proteins complementary to autoantigens is likely to be informative in most autoimmune diseases. This vein of study is in the early phases; however, we expect "autoantigen complementarity" is an underlying mechanism in many autoimmune diseases.

Rational design of peptide vaccines for autoimmune disease: harnessing molecular recognition to fix a broken network

Autoreactive T-cells and antibodies are found at low levels in normal individuals and are thought to be kept at bay by regulatory T-cells and a network of idiotypic and anti-idiotype-bearing antigen receptors on lymphocytes as well as idiotypic anti-idiotypic antibodies. Disruption of this network by genetic, environmental and unknown factors is thought to result in autoimmune diseases. An obvious, ideal and specific therapy for such disorders would be to harness this regulatory network to re-establish immunologic homeostasis. In practice, however, this is not an easy task as most autoimmune diseases involve polyclonal responses to self antigen. Thus, we are faced with the conundrum of not knowing which autoreactive idiotype-bearing antibody or antigen receptor(s) to target in order to restore or induce network regulatory function. The thesis of this review is that understanding a fundamental property governing peptide/protein shape can be used in part to circumvent the problems of self reactivity and polyclonality in autoimmune disorders. More specifically, an algorithm has been developed to design peptide vaccines with shapes that are thought to be complementary in contour to self epitopes which seem to be the focus of autoimmunity. In theory, such complementary shapes should be engendered in certain autoreactive antigen receptors--these complementary constructs consequently represent receptor mimetics. By targeting an immune response against such mimetics, one generates a polyclonal anti-idiotype response that matches the complexity of the autoimmune response itself. This article will describe the algorithm for vaccine design, summarize the in vitro and in vivo evidence for its efficacy and discuss possible therapeutic utility in human autoimmune diseases.

The antisense homology box: a new motif within proteins that encodes biologically active peptides

Amphiphilic peptides approximately fifteen amino acids in length and their corresponding antisense peptides exist within protein molecules. These regions (termed antisense homology boxes) are separated by approximately fifty amino acids. Because many sense-antisense peptide pairs have been reported to recognize and bind to each other, antisense homology boxes may be involved in folding, chaperoning and oligomer formation of proteins. The antisense homology box-derived peptide CALSVDRYRAVASW, a fragment of human endothelin A receptor, proved to be a specific inhibitor of endothelin peptide (ET-1) in a smooth muscle relaxation assay. The peptide was able to block endotoxin-induced shock in rats as well. Our finding of endothelin receptor inhibitor among antisense homology box-derived peptides indicates that searching proteins for this new motif may be useful in finding biologically active peptides.

Epitope complementarity and idiotypic interactions: a study of idiotypic-like interactions between anti-cytidine and anti-guanosine A/J mouse monoclonal antibodies--I. Characterization of these interactions

Idiotypic-like interactions between mAbs directed against cytidine (Cyd) or guanosine (Guo) nucleosides were characterized. These mAbs, Cyd-1 (IgG2b, kappa), Guo-1 (IgG1, kappa) and Guo-2 (IgG1, kappa) were derived from splenocytes of A/J mice immunized with Cyd-KLH or Guo-KLH and recognized the nucleoside base moieties involved in hydrogen bonding. The interactions between Guo-1 or Guo-2 and Cyd-1 involved cross-reactive or distinct-but-neighboring paratope-associated idiotopes. These interactions were characterized by KD values of 4.6 x 10(-6) and 1.8 x 10(-6)M, respectively. The three anti-nucleoside mAbs exhibited Ab2 beta properties and manifested epibody (Ab2 epsilon) activity towards ssDNA. We compared these idiotypic-like reactivities with the anti-idiotypic activity of an intentionally induced IgG1, kappa anti-idiotype mAb prepared with splenocytes from A/J mice immunized with Cyd-1. This Ab2 antibody which bound to Cyd-1 with a KD of 1.1 x 10(-9) M, manifested an Ab2 gamma activity, i.e. it recognized a paratope-associated idiotope on Cyd-1 without exhibiting Ab2 beta properties. In addition, the anti-(Cyd-1) completely inhibited (Cyd-1)-(Guo-1) and (Cyd-1)-(Guo-2) interactions.

Complementary peptide to the carboxyl-terminal tetrapeptide of gastrin

Codons of noncoding DNA strands for peptides have been found to code for amino acids with hydropathic properties opposite to those of the native peptides. Synthetic peptides, designated as complementary peptides, with amino acid sequences coded by noncoding DNA strands of several peptide hormones have been shown to bind the native peptides. In some instances, antibodies to these complementary peptides have shown agonist or antagonist properties of the native hormones. In this study a peptide was synthesized based on codons complementary to messenger RNA for the carboxyl-terminal gastrin tetrapeptide. This complementary peptide bound radiolabeled human gastrin (G17). Antibodies to the complementary peptide competitively inhibited the binding of 125I-gastrin by canine fundic mucosal membrane preparations. These antibodies also showed gastrin agonist properties in that they stimulated canine gastric mucosal parietal cell [14C]aminopyrine uptake, used as an index of stimulation of gastric acid secretion. Competitive inhibition of 125I-gastrin binding by membrane receptors for gastrin and stimulation of [14C]-aminopyrine uptake by antibodies to the complementary peptide for the gastrin tetrapeptide are consistent with their recognition, binding, and occupancy of gastrin receptors.

Critical evaluation of a theory of molecular recognition using human insulin-like-growth-factor-I fragment 21-40 and its complementary peptide

Using solid-phase methods we have synthesized human insulin-like-growth-factor-I (IGF-I) fragment 21-40 (IGF-I 21-40) and the peptide derived from the 5'----3' translation of the complementary nucleic acid of this peptide, 'I-FGI 20-40' (the complementary peptide). According to a recently proposed theory of molecular recognition, these two peptides should bind specifically to each other. We have tested this theory by using both solid- and solution-phase direct-binding assays for this complementary-peptide pair. We have also investigated the ability of I-FGI 20-40 to interfere with native IGF-I binding during radioimmunoassay (r.i.a.), radio-receptor (r.r.a.) assay and ligand-blot analysis of IGF-binding proteins. We have obtained no evidence of any interaction between IGF-I 21-40 and I-FGI 20-40 in either solid- or solution-phase assays. In addition, I-FGI 20-40 does not interfere in the assays used to detect IGF-I binding antibodies (r.i.a.), receptors (r.r.a.) or binding proteins (ligand blots). Our data therefore question the universality of this particular theory of molecular recognition.