Formation of amphipathic alpha helices under laboratory conditions has been demonstrated for part of the sequence believed to have a role in mediating dimerization and oligomerization of the protein.

[1][2][4] The BK, JC, and SV40 agnoproteins have all been experimentally demonstrated to be phosphorylated in vivo, which appears to improve both protein stability and viral propagation, but no other post-translational modifications have been detected.

[2] Agnoprotein is a regulatory protein required for efficient proliferation of the viruses in which it is present, although many polyomaviruses do not have the gene.

[4] It has also been suggested that agnoprotein functions as a viroporin – that is, a viral protein that alters membrane permeability to facilitate the virus particles' exit from the cell.

[2] A large number of protein-protein interactions have been reported between agnoprotein and other proteins of both viral and host cell origin.

[2] Host cell proteins reported as binding partners for at least one virus species' agnoprotein include p53, Ku70, PP2A, YB-1, FEZ1, HP1α, α-SNAP, PCNA, and AP-3.

[3] The distribution of agnoprotein among polyomaviruses has prompted speculation that there is little evolutionary selection pressure in favor of its presence.