Abstract

A model for the cytoplasmic domain of the M2 proton channel of influenza A virus was formulated based primarily on the cytoplasmic domain of the Vpu protein of HIV-1 using sequence similarity and structure prediction techniques. The model consists of a pair of antiparallel helices followed by a strand parallel to the first helix. Structural analogies with other proteins contribute support for features of the model and suggest ways in which the M2 cytoplasmic domain can interact with other viral and cellular factors.

Keywords: Influenza a virus, m2 protein, hiv-1 vpu protein, cytoplasmic domain structure, sequence analysis, fold recognition