A New Model for the Transmembrane Heterocomplex of Hemagglutinin HA and Ionic Channel M2 Proteins in Influenza A Virus

The lipid envelope of the influenza A virus contains two major types of protein spikes formed by the transmembrane hemagglutinin trimers (HA, MW 80 kDa) and neuraminidase tetramers (NA, MW 55 kDa), in quantities of 500 and 120, respectively. The third transmembrane protein, M2 (MW 14 kDa), forms tetramers of ion channels in quantities of about 10-20 per virion. Modeling of the molecular structure using the AlphaFold software tool showed a novel model for a heterocomplex of HA0-M2 proteins, in which the M2 tetramer located inside the HA0 trimer like a "matryoshka doll." Similar models of the HA0-M2 heterocomplex were obtained for the A/Aichi/2/68 (H3N2) and A/WSN/33 (H1N1) viruses. The resulting HA0-M2 heterocomplex possessed a high structural complementarity of the macromolecular interfaces (ipTM = 0.65), had no structural clashes of atoms in the molecular interfaces (clash score = 0.0), and exhibited stable and reliable intermolecular topology with a high ranking score of 0.79. The constructed model allows to explain the phenomenon of blocking the function of M2 ion channels by the rigid conformation of the uncleaved HA0 protein and, in contrast, the activation of M2 channels after (i) specific point proteolysis of HA0 into HA1 (55 kDa) and HA2 (25 kDa) subunits and (ii) exposure to acidic pH of 4.0-5.5, leading to the disclosure of the 3D structure of the HA1/2 molecule and the opening of the M2 channel.