Figure 3

Model predicted dynamics and distributions of SpoIIIE in DNA _SRS in the absence of ATP. (A) Representative trajectories of SpoIIIE interacting with DNA _SRS in the absence of ATP. Each panel represents a DNA molecule where the sliding properties of SpoIIIE when interacting with SRS and non-specific DNA were varied with parameter values shown on the right of each panel. The rest of the parameters were set to the optimal values depicted in Table 1. Horizontal and vertical axis represent time evolution in Monte Carlo steps (MCS) and DNA coordinate (in base pairs, bp), respectively. SpoIIIE binding events are shown by solid blue hexagons and trajectories are shown in orange and green when interacting with non-specific DNA and SRS, respectively. Scheme on the right depicts non-specific DNA regions (solid black line) and SRS sites (semi-transparent green triangles). (B,C) The model-predicted relative frequency of SpoIIIE at SRS sequences in the absence of ATP was evaluated as function of the SpoIIIE/SRS association and dissociation probabilities (p _on ^SRS and p _off ^SRS for panels B and C, respectively) one order of magnitude above and below the values reproducing AFM distributions while the rest of the parameter values were set to the values described in Table 1. Simulations were performed in the absence of 1D diffusion (grey triangles), including homogeneous (orange circles) and anomalous (green squares) sliding between non-specific DNA and SRS with values depicted in the inset of the figure. Solid lines connecting dots are only a guide to the eye. Blue dotted line and grey shaded area indicate the mean experimental relative frequency of SpoIIIE binding at SRS and standard deviation respectively as obtained from Fig. 1C. Dotted black vertical line indicates the association and dissociation probability values defined from experimental data (see Methods and Supplementary Information). Upper scheme represents SpoIIIE bound to SRS.