B-cell epitope prediction for antipeptide paratopes with the HAPTIC2/HEPTAD user toolkit (HUT)

Abstract

B-cell epitope prediction for antipeptide paratopes is key to developing novel vaccines and immunodiagnostics. This entails estimating free-energy changes for paratope binding to variable-length disordered peptidic sequences as has been previously described for the Heuristic Affinity Prediction Tool for Immune Complexes (HAPTIC), which resolves said binding into processes of epitope compaction, collapse and contact by analogy to protein folding. However, HAPTIC analyzes antigen sequence data without excluding potentially problematic candidate epitopes (e.g., comprising inaccessible and/or conformationally rigid residues) while also neglecting the temperature dependence of polyproline II (PPII) helix propensity (for compaction), occurrence of epitope-backbone hydrogen bonding and impact of disulfide bond formation between epitope cysteine residues. The present work thus provides a more physically realistic revision of HAPTIC (HAPTIC2), the HAPTIC2-like Epitope Prediction Tool for Antigen with Disulfide (HEPTAD) and the HAPTIC2/HEPTAD Input Preprocessor (HIP), forming the HAPTIC2/HEPTAD User Toolkit (HUT). HIP facilitates tagging of residues (e.g., in hydrophobic blobs, ordered regions and glycosylation motifs) for exclusion from downstream analyses by HAPTIC2 and HEPTAD. HAPTIC2 enables temperature-dependent PPII helix propensity calculations while also regarding glycine and proline as polar residues that form hydrogen bonds with paratopes. HEPTAD analyzes antigen sequences that each contain two cysteine residues for which the impact of disulfide pairing is estimated as a correction to the free-energy penalty of compaction. All components of HUT (i.e., HIT, HAPTIC2 and HEPTAD) are freely accessible online (http://badong.freeshell.org/hut.htm).