An increasing number of peptides with specific binding affinity to various protein and even non-protein targets are being discovered from phage display libraries. The power of this method lies in its ability to efficiently and rapidly identify ligands with a desired target property from a large population of phage clones displaying diverse surface peptides. However, the search for the needle in the haystack does not always end successfully. False positive results may appear. Thus instead of specific binders phage with no actual affinity toward the target are recovered due to their propagation advantages or binding to other components of the screening system, such as the solid phase, capturing reagents, contaminants in the target sample or blocking agents, rather than the target. Biopanning experiments on different targets performed in our laboratory revealed some previously identified and many new target-unrelated peptide sequences, which have already been frequently described and published, but not yet recognized as target-unrelated. Distinguishing true binders from false positives is an important step toward phage display selections of greater integrity. This article thoroughly reviews and discusses already identified and new target-unrelated peptides and suggests strategies to avoid their isolation.
Despite available treatment, there is still significant morbidity and mortality present among patients with the autoimmune thrombophilic condition termed 'antiphospholipid syndrome' (Espinosa, G. and Cervera, R. 2009. Morbidity and mortality in the antiphospholipid syndrome. Curr. Opin. Pulm. Med. 15:413.). High-avidity (HAv) anti-β(2)-glycoprotein I (anti-β(2)GPI) antibodies, shown to correlate with thrombotic events in patients, could represent the much needed improved prognostic marker. By studying their effect on crystalline annexin A5 shield on phospholipid surfaces (one of proposed pathogenic mechanisms), with the use of atomic force microscopy, the pathogenic potential of HAv anti-β(2)GPI antibodies was confirmed. Furthermore, by using surface plasmon resonance and enzyme-linked immunosorbent assays, unique binding characteristics of HAv antibodies in comparison with low avidity antibodies were established. HAv anti-β(2)GPI were confirmed to (i) recognize β(2)-glycoprotein I in a solution, (ii) interact predominantly monovalently (much lower dependency on the antigen density) and (iii) form more stable complexes with the antigen. Since enzyme-linked immunosorbent assays currently used in routine diagnostics detect anti-β(2)GPI antibodies of unknown avidity, our observations are potentially useful for the development of improved diagnostic tests capable of detecting clinically relevant antibodies.
Studies concerning interactions between anti-β2-glycoprotein I antibodies (anti-β2GPI) and β2-glycoprotein I (β2GPI) suggest relevance of charge interactions and hydrogen bonds. However, paratope of diagnostically and clinically relevant anti-β2GPI and epitope characteristics of β2GPI, still remain unclear. The aim of our study was to determine paratope characteristics of various anti-β2GPI antibodies and epitope characteristics of β2GPI using phage display. Monoclonal IgG anti-β2GPI, purified polyclonal high avidity and low avidity IgG anti-β2GPI derived from plasma of APS patients were used to screen phage display libraries. The affinity and competition ability of selected clones were evaluated. Various heptapeptides presenting putative paratopes of anti-β2GPI and specific heptapeptides presenting putative epitopes of β2GPI were determined. Epitope presenting peptides bind to the respective anti-β2GPI and consequently interrupt antibody-antigen interaction. The amino acid composition of selected peptides confirmed the importance of hydrogen bonds and charge interactions in the binding of anti-β2GPI to the antigen. Epitopes recognized by high avidity anti-β2GPI predominately contain hydrogen bond forming side chains, while in low avidity anti-β2GPI epitope the charged side chains prevail. The alignment of selected sequences to three-dimensional antigen structure revealed that polyclonal high avidity anti-β2GPI recognize native epitopes that are accessible regardless of β2GPI's conformation whereas the epitope recognized by low avidity anti-β2GPI is cryptic and cannot be accessed when β2GPI takes the closed plasma conformation.
Isolation buffer characteristics and storage conditions could partially transform natural antibodies. 50 IgG factions were isolated from seven healthy donors' sera using various protein G columns and buffers. PAGE revealed no major antibody cleavages; purity of IgGs eluted at pH 2.4-3.5 was close to homogeneity, independent of buffer composition. Although eluting at pH 2.4 resulted in 3.5- or 17-fold higher antibody yield compared to pH 3.0 or 3.5, respectively, it distorted the antibody molecule. IgGs eluted at pH 2.4 acquired reactivity against diagnostically important autoantigens, confirmed by standardized ELISAs. Preserved antibodies' natural activity is important in further experiments with oxidatively-induced autoantibodies.
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