Figure 2. Topologies determined from simulations (blue) and compared to the experiments of Seppälä et al. (2010) (red), reporting the fraction of fully integrated integral membrane protein (IMP) configurations in the Ncyto/Ccyto topology.
Error bars indicate the standard error measured from independent blocks of simulations or taken from Seppälä et al. (2010). The dominant topology for each mutant is indicated schematically with additional positive charges relative to EmrE (top) or nEmrE (bottom) drawn as red dots.
Figure 2—figure supplement 1. Robustness of the distribution of topologies to the trajectory termination criteria.
The distribution of topologies for the EmrE, K3, nK3, and T28R mutants are computed using alternative trajectory termination criteria and compared to the distribution of topologies using the original protocol (shown in Figure 2). At left, the plot illustrates the effect of extending each original CG trajectory by 50 s. At right, the plot illustrates the effect of terminating trajectories at a distance of 20σ, rather than 4.5σ, from the origin. The dashed line indicates perfect correlation. Additional details on these calculations are included in the Robustness checks for the trajectory termination criteria section of the ‘Materials and methods’.
Figure 2—figure supplement 2. Correlation between the topologies determined from simulations (x-axis) and compared to the experiments of Seppälä et al. (2010) (y-axis), reporting the fraction of fully integrated IMP configurations in the Ncyto/Ccyto topology.
Mutants lying in the shaded quadrants have the same dominant topology in both the experiments and simulations. The experimental and simulation measurements are linearly correlated with a Pearson correlation coefficient of r = 0.92.