Epitope effect

Screening of 152 0/X7 peptide libraries on cytolysis of target cells by several CTL clones showed clone-specific Recognition Patterns which allow the deduction of synthetic T-cell epitopes effective in the concentrations also typical for naturally occurring epitopes [54,55]. The degree of degeneracy is characteristic for a certain CTL clone and is also represented in the Recognition Pattern of the peptide library. 

Some combinatorial synthetic approaches rely on the synthesis and testing of mixtures to achieve high throughput. Typically, one wants to maximize the diversity of each pool, so the activity of a pool is indicative of the activity of its most potent compound. However, when sensitivity of the test or solubility of the compounds has been a problem, some groups have, instead, pooled similar compounds, amplifying a weak signal by the epitope effect, that is, the cumulative activity of many related compounds. Regardless of whether compounds are pooled, the methods described previously allow one to maximize either the similarity or diversity of the pools. 

Antibody A52 with its epitope at residues 657-672 [129,139,274,275] inhibited the vanadate-induced crystallization of Ca " -ATPase and decreased the stability of preformed Ca " -ATPase crystals [285]. The vanadate-induced crystals arise by the association of the ATPase monomers into dimers (type A interaction), the dimers into dimer chains (type B interaction), and the dimer chains into 2-dimensional arrays (type C interaction). It is suggested that antibody A52 interferes with type B interactions, preventing the formation of dimer chains, without exerting major effect on the concentration of Ca -ATPase dimers in the membrane. The simplest interpretation of the destabilization of Ca -ATPase crystals by mAb A52 is that binding of the antibody to its antigenic site physically blocks the interaction between ATPase molecules [285]. Considering the large bulk of the antibody, such interference is not unexpected, yet only a few of the antibodies that bind to the Ca -ATPase in native sarcoplasmic reticulum interfered with crystallization. 

During the tissue fixation process, proteins are cross-linked, causing some epitopes to become undetectable by the staining protocols.10 HIAR reverses this effect, allowing these epitopes to be stained, and therefore has become increasingly important for many IHC staining protocols.19-22 However, the available automated IHC platforms vary in their ability to perform online HIAR. 

In order to model the effect of formalin fixation and antigen retrieval on antibody immunoreactivity, we used a peptide epitope array (Fig. 16.5). The peptide epitopes are derived from the exact sequences in the native proteins. In this experiment, the initial findings are similar to those shown in Figure 16.1, but they are then extended by allowing for the role of adjacent proteins. 

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