Figure 2

Scheme of the mathematical model encoding the dynamics of SpoIIIE/DNA interaction. (A,B) In the model SpoIIIE can interact with non-specific DNA (DNA _NS , A) and SRS containing DNA (DNA _SRS , B). The dynamics of non-active SpoIIIE (i) were modelled as a Markov process controlled by the SpoIIIE binding/unbinding probabilities (p _on /p _off ) to/from non-specific or SRS regions of DNA (orange and green solid lines respectively). Once bound to DNA, SpoIIIE can undergo 1D diffusion defined by the sliding length sld. In the presence of ATP (ii), SpoIIIE can become active with a probability p _ATP and translocate at constant velocity (v _trans ). Probabilities of binding, unbinding, sliding lengths and activation by ATP could be set to distinct values depending on the DNA substrate. When the triplex was present (iii), translocating SpoIIIE can displace the triplex when reaching the corresponding DNA end with probability p _triplex . See Material and Methods and Supplementary Information for additional details.