Figure 4. The proposed mechanism of kinetic annealing of the EOT ensemble.
(A) Representative configurations visited by EmrE, T28R, and nR111 mutants within 1 s of simulation time following the end of ribosomal translation; this set of configurations for each mutant is called the EOT ensemble. The most-charged loop is indicated in red to highlight its position relative to the membrane. (B) The average loop positions from the EOT ensemble of each mutant is presented in terms of the fraction of configurations for which each loop occupies the cytoplasm. Adding charge to a loop biases towards a cytoplasmic position. (C) Post-translational annealing of representative EOT configurations for each mutant. Horizontal arrows indicate possible transitions as loops stochastically flip across the membrane to correct misintegrated TMDs. In each case, the position of the slowest-flipping loop (loop in red) determines the fully integrated topology by retaining its initial EOT position.