Flux-based model for midnucleoid positioning.

(A) In our mathematical model, ATP-bound PomZ dimers can attach to the nucleoid (1) and then diffuse along it (2). The elasticity of the chromosome and the PomZ dimers is effectively included by modelling the PomZ dimers as springs. A nucleoid-bound PomZ dimer has a free binding site available to bind to the PomXY cluster (3). When also bound to the PomXY cluster, a PomZ dimer can diffuse both on the cluster and on the nucleoid (4). The interaction of PomZ with the PomXY cluster (and DNA) leads to a stimulation of the ATPase activity of PomZ, which in turn causes a conformational change in the ATP-bound PomZ dimer and the release of two ADP-bound monomers into the cytosol (5). ADP-bound PomZ monomers must exchange ADP for ATP and form dimers before they can bind to the nucleoid again (these processes are not explicitly included in the model). Hence, there is a delay between release of the inactive, ADP-bound form and reconstitution of the active, ATP-bound form (6). (B) Details of the PomZ interactions with the PomXY cluster. Not only PomZ dimers with a nucleoid binding site below the PomXY cluster, but also PomZ dimers outside of the cluster region can attach to the cluster, in a stretched configuration. The edges of the PomXY cluster are reflecting boundary conditions for the movement of PomZ’s cluster binding site (indicated by the crossed arrow).