Selection of putative immunogenic peptides by molecular modelling of the urease of Helicobacter pylori.

Computational methods such as molecular modelling are becoming an increasingly useful means of rationalising experimental data and creating a hypothesis that can suggest new experiments. In this report we discuss the application of molecular modelling methods to aid the selection of feasible peptide epitopes of the urease enzyme from Helicobacter pylori, an important vaccine candidate. Surface exposure was chosen as a criterion for the selection of three peptides which each had different levels of accessibility according to the 3D model. Antibodies raised against these peptides were analysed for their immunoreactivity with the holo enzyme. Only one anti-peptide antibody showed good reactivity with the urease. Our findings emphasise that surface exposure of peptide is not the only important criterion for the selection of immunogenic peptides.