This asymmetry has major implications for the mechanism of the enzyme. It means that the nucleotide-binding sites (at the interface between the subunits) are not equivalent, and will be likely to have differing affinities for the NTPs. This was confirmed by soaking the non-hydrolysable ATP analogue AMP-PNP into the crystals. Of the six sites, electron density corresponding to bound nucleotide was only seen in four positions (two sets of two equivalent sites). The differences were due to altered binding affinity, since all six sites were equally accessible. Of the four nucleotide-containing sites, two had strong density, suggesting an NTP-binding site, while the other two had weaker density, consistent with NDP+Pi binding sites. The last two sites showed no evidence of nucleotide binding. The states of the three sites may interconvert from NTP-bound to NDP+Pi binding to empty as nucleotide hydrolysis occurs. This would allow a "ripple" of NTP-hydrolysis to run around the ring as shown below.

This model shows some similarities with the "binding-change" model associated with the F1-subunit of the mitochondrial ATPase. However, in the helicase there are two equivalent diametrically-opposed sites for each state, rather than three different sites related by 120 degrees as in the ATPase. Also, unlike the F1-ATPase, all the polypeptide chains of the helicase are equivalent, so it is plausible that the required asymmetry in the structure may arise in a different manner.