All-atom molecular dynamics of the cyanopodophage A4 portal-tail complex reveals dynamic asymmetry in tail fiber chains

Abstract Cyanophages are key regulators of cyanobacterial populations in aquatic ecosystems, yet little is known about the conformational dynamics of their infection machinery. We performed a 250 ns all-atom molecular dynamics simulation of the cyanopodophage A4 portal-tail complex (PDB: 9K09), a 48-chain assembly of approximately 4 million atoms in explicit solvent. The simulation revealed two distinct groups: a rigid scaffold formed by the portal, adaptor, and nozzle, and significantly more flexible tail fibers. Within each tail fiber, the most mobile regions are in the C-terminal cell wall binding domain (CBD), which recognizes the Anabaena lipopolysaccharide receptor, while the disordered central stem is stabilized by inter-chain contacts. The three tail fiber chains in each trimer are sequence-identical, but their dynamics differ by position: the chain whose CBD points toward the capsid is more mobile than the other two. These results provide the first dynamic characterization of cyanopodophage A4.