Figure 5.

Two kinds of binding modes are involved in the process of a β2e subunit (1–143) binding to membrane phospholipids, as shown by an ATMD simulation of β2e. (A) Correlation between the reaction coordinate Z and the magnitude of interaction energy E_int based on 5000 conformations of a β2e subunit (1–143) in the time window between 90 ns and 100 ns. The top (right) panel shows the distribution of the value of reaction coordinate Z (the interaction energy). As the time advances, the character of the binding mode changes from type II to type I (see also Fig. S3). In the long time limit, binding through type I becomes dominant, giving rise to strong and stable binding. Two dominant modes of binding are explained. (B–D) Type I, the stretched binding mode. The N-terminal residues M1 and K2 first anchor to the membrane and the other residues are then bound sequentially while maintaining their structure, which stretches progressively. (E–G) Type II, the agglomerate binding mode. The initial residues in the β2e N-terminus region do not bind first to the membrane; instead, other residues away from the N-terminus featuring the agglomerate structure make the initial contact with the membrane. (H) Time evolution of |E_int| from a given typical single trajectory. The middle panel of (H) represents the probability distribution of |E_int| constructed from 100 configurations in a given 10 ns time window corresponding to each of B, C, D, E, F, and G in the left panel of (H). The energetic character of |E_int| for configurations in each of these time windows were then clustered into. The right panel shows both the mean value and the error bar of |E_int| for a given time window of B, C, D, E, F, and G. To see this figure in color, go online.