T‐Helper‐Cell Determinants in Protein Antigens are Preferentially Located in Cysteine‐Rich Antigen Segments Resistant to Proteolytic Cleavage by Cathepsin B, L, and D

Abstract

We report on a computer algorithm capable of predicting the location of T-helper-cell epitopes in protein antigen (Ag) by analysing the Ag amino acid sequence. The algorithm was constructed with the aim of identifying segments in Ag which are resistant to proteolytic degradation by the enzymes cathepsin B, L, and D. These are prominent enzymes in the endocytic pathway through which soluble protein Ag enter APC, and resistant segments in Ag may, therefore, be expected to contain more T-cell determinants than susceptible segments. From information available in the literature on the substrate specificity of the three enzymes, it is clear that a cysteine is not accepted in any of the S2, S1, S1', and S2' subsites of cathepsin B and L, and not in the S1 and S1' subsites of cathepsin D. Moreover, we have noticed that cysteine-containing T-cell determinants in a number of protein Ag are particularly rich in the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine. By searching protein Ag for clusters of amino acids containing cysteine and two of the other amino acids we were able to predict 17 out of 23 empirically known T-cell determinants in the Ag with a relatively low number of false (positive) predictions. Furthermore, we present a new principle for searching Ag for potential amphipatic alpha-helical protein segments. Such segments accord well with empirically known T-cell determinants and our algorithm produces a lower number of false positive predictions than the principle based on discrete Fourier transformations previously described.

Novel sequences and epitopes of diagnostic value derived from the Anisakis simplex Ani s 7 major allergen*

“…In our opinion, there are several factors that may contribute to the increased antigenicity/allergenicity of Ani s 7, namely: (i) the way in which the allergen is released (direct ‘inoculation’ into disrupted host tissues); (ii) the repeating amino acid composition of the motifs and (iii) its high cysteine content, which may render the allergen resistant to proteolytic degradation by certain prominent enzymes (i.e. cathepsins) in the endocytic pathway of antigen‐presenting cells, thus favouring recognition by specific T cells (25). Furthermore, the existence of another Anisakis antigen with several homologous repeats of the rAni s 7 sequence (as indicated above) probably constitutes a second source of antigenic stimulus for induction of anti‐Ani s 7 IgE antibodies.…”

Presentation of the Goodpasture Autoantigen to CD4 T Cells Is Influenced More by Processing Constraints Than by HLA Class II Peptide Binding Preferences

“…All except one of the peptides contain one or more cysteine residues likely to be involved in disulfide bonds (based on the reported structure of the highly homologous ␣1(IV) chain, see Ref. 30), and many known T cell epitopes derive from regions of proteins involved in disulfide bonds, possibly because the presence of the disulfide linkage affords some protection from proteolytic attack (31). The preparation of ␣3(IV)NC1 used in this study was reduced during purification but had ample opportunity to oxidize prior to and during pulsing of the APC.…”

Hypothesis for the Control of Clotting Factor VIII Inhibitory Antibodies by Decreasing Potency of Helper T‐Cell‐Recognized Epitopes in Factor VIII

“…32]. This strip is hypothesized to regulate scavenging of the sequence presented to T cells [33][34][35] by promoting adsorption to the wall of an endosomal vesicle as a helix (Fig, 3), Such adsorbed. amphipathic helices may be relatively resistant to further proteolysis.…”