Hemagglutinin (HA) is a glycoprotein found on the surface of the influenza virus, acting as a molecular spike that protrudes from the viral envelope. Its name derives from its ability to cause red blood cells to clump together, a process known as hemagglutination. HA mediates the virus’s successful entry into a host cell by performing both the initial attachment to the cell surface and the subsequent fusion of the viral and cellular membranes.
Molecular Architecture of Hemagglutinin
Hemagglutinin is a large, rod-shaped homotrimer, composed of three identical protein units. Each unit is initially synthesized as a single polypeptide chain, HA0, before being processed into its mature, active form. The mature protein is structurally divided into two distinct, covalently linked subunits: HA1 and HA2. The structure resembles a lollipop, with a membrane-distal globular head sitting atop a fibrous stalk region. The HA1 subunit primarily forms the globular head, positioned furthest from the viral surface, and is responsible for binding to the host cell. The HA2 subunit, along with a small portion of HA1, forms the stalk that anchors the structure to the viral membrane.
For the protein to become competent for membrane fusion, the precursor HA0 must undergo proteolytic cleavage by host cellular proteases. This cleavage separates the HA0 chain into the HA1 and HA2 subunits, which remain connected by a disulfide bond. This process is a prerequisite for infectivity because it exposes the hydrophobic N-terminus of the HA2 subunit, known as the fusion peptide, tucking it into a stabilized internal position.
Receptor Recognition and Viral Attachment
The first step in the influenza infection process is attachment, mediated by the globular head (HA1) of the hemagglutinin trimer. Located at the tip of the globular domain is a shallow pocket that serves as the receptor-binding site. This site specifically recognizes and binds to sialic acid molecules, which are carbohydrates found on the surface of host cells. The chemical linkage of the sialic acid to the underlying sugar chain determines which species a particular influenza virus can infect.
Human-adapted influenza viruses preferentially bind to sialic acids linked by an alpha-2,6 configuration, abundant in the human upper respiratory tract. In contrast, avian influenza viruses are specialized to bind to sialic acids with an alpha-2,3 linkage, common in the avian gut and lower human respiratory tract. A change in just a few amino acids within the HA1 globular head can alter the binding preference, allowing a virus to jump the species barrier. Successful binding locks the virus onto the host cell.
The pH-Triggered Membrane Fusion Mechanism
Following attachment, the host cell internalizes the viral particle through receptor-mediated endocytosis, enclosing it within an endosome. As the endosome travels deeper inside the cell, its internal environment acidifies, with the pH dropping toward 5.0 to 5.5. This drop in acidity triggers the hemagglutinin protein. The low pH causes an irreversible conformational change in the HA trimer. This rearrangement exposes the previously buried hydrophobic fusion peptide, located at the N-terminus of the HA2 subunit.
The fusion peptide inserts itself into the membrane of the endosome, anchoring the viral protein. As the protein continues refolding, the stalk domain elongates and folds back upon itself, forming a stable, rod-like coiled-coil structure. This action pulls the viral membrane and the endosomal membrane closer together. The force generated by this structural collapse ultimately forces the two lipid bilayers to merge, creating a pore that allows the viral genetic material to escape the endosome and enter the host cell cytoplasm.
Hemagglutinin as a Target for Vaccines and Antivirals
Hemagglutinin is the main antigen included in seasonal influenza vaccines. Antibodies generated by the vaccine or a prior infection bind to the globular head of HA, physically blocking the receptor-binding site and preventing viral attachment. The virus constantly evolves to evade this immune response through two main mechanisms.
Antigenic Drift
Antigenic drift involves the accumulation of minor point mutations primarily in the HA1 globular head, leading to subtle changes in the binding site and its surrounding regions. These alterations allow the virus to escape recognition by existing antibodies, necessitating the frequent update of the seasonal vaccine composition.
Antigenic Shift
Antigenic shift occurs when a human-infecting virus acquires an entirely novel HA gene segment from an animal influenza strain through genetic reassortment.
The stalk region (HA2) is conserved across different influenza strains because its structure is required for the fusion mechanism and cannot easily be mutated. This conserved nature makes the stalk an attractive target for developing “universal” influenza vaccines intended to provide broad, long-lasting protection against all subtypes. While neuraminidase inhibitors are the most common influenza antivirals, some drug development efforts focus on small molecules that interfere directly with HA’s function, either by blocking attachment or by preventing the low pH-induced conformational change required for membrane fusion.