Figure 8. Simulated dynamics of Swi4,... | Rockefeller University Press

Figure 8.

$Simulated dynamics of Swi4, Mbp1, and Swi6 are multimodal.(A) Example trajectories of individual Swi4 (left, green), Mbp1 (middle, red), and Swi6 (right, blue) dimers from the simulations in 3D, showing for each dimer particle alternations between anomalous sub-diffusive motion confined within cluster and fast, freely diffusive motion between clusters. Black circles represent DNA G1/S promoter target sites. Black arrows indicate positions of multiple binding/unbinding events within given promoter clusters. (B) Example of MSD versus time lag curves corresponding to individual Swi4 (left), Mbp1 (middle), and Swi6 (right) dimer trajectories (color curves) of one small cell simulation. The thick black curves represent the MSD averaged over all the trajectories for each protein. Computation of MSD curves were restricted to the steady-state section of each trajectory, corresponding to simulated times beyond 0.6 s from the onset of the simulation. (C) Histograms of single-trajectory diffusion coefficients extracted from the slope of linear fits of the first four points of individual MSD curves from B. Data were gathered from five to seven independent simulations. Red arrows indicate the approximate positions of main peaks underlying the distribution. We note that simulations predicted a significant fraction of quasi-immobile molecules with an effective diffusion coefficient lower than 0.001. We did not observe this fraction in experiments, possibly due to instrument jitter, which sets a lower bound to the slowness of quantifiable motions.$

Simulated dynamics of Swi4, Mbp1, and Swi6 are multimodal. (A) Example trajectories of individual Swi4 (left, green), Mbp1 (middle, red), and Swi6 (right, blue) dimers from the simulations in 3D, showing for each dimer particle alternations between anomalous sub-diffusive motion confined within cluster and fast, freely diffusive motion between clusters. Black circles represent DNA G1/S promoter target sites. Black arrows indicate positions of multiple binding/unbinding events within given promoter clusters. (B) Example of MSD versus time lag curves corresponding to individual Swi4 (left), Mbp1 (middle), and Swi6 (right) dimer trajectories (color curves) of one small cell simulation. The thick black curves represent the MSD averaged over all the trajectories for each protein. Computation of MSD curves were restricted to the steady-state section of each trajectory, corresponding to simulated times beyond 0.6 s from the onset of the simulation. (C) Histograms of single-trajectory diffusion coefficients extracted from the slope of linear fits of the first four points of individual MSD curves from B. Data were gathered from five to seven independent simulations. Red arrows indicate the approximate positions of main peaks underlying the distribution. We note that simulations predicted a significant fraction of quasi-immobile molecules with an effective diffusion coefficient lower than 0.001. We did not observe this fraction in experiments, possibly due to instrument jitter, which sets a lower bound to the slowness of quantifiable motions.