The inhibitory effects of vinylphosphonate-linked thymidine dimers on the unidirectional translocation of PcrA helicase along DNA: a molecular modelling study

The PcrA DNA helicases are important bacterial enzymes and quintessential examples of molecular motors. Through conformational changes caused by ATP hydrolysis, they move along the template double helix, breaking the hydrogen bonds holding the two strands together, and separating the template chains so that the genetic information can be accessed. The flexibility of the DNA backbone is essential for the unidirectional translocation of PcrA. A modified DNA substrate with reduced backbone rotational flexibility (via an incorporated vinylphosphonate linkage) has previously been designed and tested as a helicase substrate. The results show that a single modification on the backbone is sufficient to inhibit the activity of PcrA. In this paper a range of molecular simulation methods have been applied to examine the structural origins of this inhibitory effect, as it tests our theories of the mechanism of action of this motor. We observe that the chemical modification has different effects on the energetics of DNA translocation through the protein as it reaches different sub-sites.