Extended Data Fig. 5: MD simulation of Sam50 and Tom40 in the SAM^Tom40-early intermediate.

a, Time-course changes of secondary structure for the N-terminal region of Tom40 in the Sam^Tom40-early intermediate were calculated using DSSP⁶³. One of the five trajectories is shown as an example. The leftmost part shows the secondary structure of the mature Tom40 (PDB ID: 6JNF). The red and blue colors indicate the residue in α-helix and β-sheet, respectively. The results showed that the residues around the β1-segment of Tom40 are stable as α-helix for a long period of time during the simulation. The tendency was similar for the other four trajectories. b, Using the trajectories after 100 ns, the root-mean-square fluctuation (RMSF) and the fractions of secondary structure were calculated for each trajectory. The RMSF of each residue of Tom40 (upper left) and Sam50 (upper right) of the trajectory corresponding to (a) was plotted. The fractions of secondary structure calculated by DSSP for the same trajectory of Tom40 (lower left) and Sam50 (lower right) were also plotted. The lower part of each panel indicates the secondary structure of mature Tom40 (PDB ID: 6JNF) and the secondary structure of the initial structure of Sam50. The red and blue colors indicate the residue in α-helix and β-sheet, respectively. c, Snapshots of the structures of the Sam50^Tom40-early intermediate at 0 ns, 300 ns (as an example of one state), and 800 ns (as an example of the other state) for one of the trajectories. During the MD simulation, the initially separated Tom40 β5-7 segments develop to form a β-sheet. d, Comparison of the cryo-EM density maps and the model, for β1 and its flanking regions, derived by MD-assisted fitting. e, Stereo view of the cryo-EM density maps for β1 and the surrounding part of the hybrid barrel of Tom40 and Sam50.