How a Paraflagellum Rod Works
As the PFR and the axoneme are very tightly connected, both structures have to move together. It can be argued that the PFR contributes to regulate the flagellar movements. This could be done by providing a more rigid structure that can vary its stiffness in time, that is, modifying flagellum beating pattern.

We need only one protein to build a device for information transfer and control, that is, a protein with two conformational, alternate states such as intermediate filament proteins, which can form lattice-like structures. The propagation of conformational changes along these proteins can be used to transport or transduce sensory information. Each protein can be considered as a dipole in one of the two possible states. We can imagine that the conformational change is transmitted by one dipole to the neighbor proteins as a wave. Therefore, a current flow through these lattice-like structures could be generated by the mobile electrons of the proteins that interact with their immediate neighbors via dipole–dipole forces.

The α-helical coiled-coils structural motif in the rod filament is well suited for electron propagation. A current might be propagated distally via PFR₁ and PFR₂ protein–protein charge transfers in the lattice-like rod filaments. The current flows through these lattice-like structures and the sole constraint is that each lattice site should possess a dipole moment proportional to the magnitude of the mobile charge unit and the distance over which it hops, that is, about 1 or 2 nm. This wave produces a contraction in the PFR and a varying internal resistance that modulates the flagellar beats. The contraction occurs by displacement of the goblet appendages of the PFR along the axonemal microtubules, which reduces the distance between the coiled filaments hence generating longitudinal waves of contraction along the paraxial rod. The stiffening should swing the flagellum sideways, damping out some undulatory waves of the axoneme.