Extended Data Fig. 9: The structured domains of TPC provide the force for membrane deformation.
a) Side and top view images of representative timepoints from the MD simulation of a membrane without TPC. The 0 µs time point represents the starting point and the membrane is roughly 60 nm x 60 nm in size. At 5 µs, the membrane has essentially the same size. The height of the simulation box remains constant throughout the simulation, indicating that no membrane deformations occur. Different colors indicate different simulation repeats. b) Side and top view images of representative timepoints from the MD simulation of a membrane with a single TPC. The 0 µs time point represents the starting point and the membrane is roughly 40 nm x 40 nm in size. At 5 µs, the membrane has essentially the same size. The height of the simulation box remains constant throughout the simulation, indicating that no membrane deformations occur. Different colors indicate different simulation repeats. c) Visualization of the deformation of the simulation box over the time of the simulation for 3x TPC (Fig. 5g) extended up to 5 µs. The increased height of the simulation box (4 out of 5 simulation repeats) indicates membrane deformations. Different colors indicate different simulation repeats. This panel represents an extension of the simulation shown in Fig. 5g. d) Side and top view images of representative timepoints from the MD simulation of a membrane with a single AP-2. The 0 µs time point represents the starting point and the membrane is roughly 40 nm x 40 nm in size. At 5 µs, the membrane has essentially the same size. The height of the simulation box remains constant throughout the simulation, indicating that no membrane deformations occur. Different colors indicate different simulation repeats. e) Side and top view images of representative timepoints from the MD simulation of a membrane with 3x AP-2. The 0 µs time point represents the starting point and the membrane is roughly 60 nm x 60 nm in size. At 4.7 µs, the membrane is deformed. The increased height of the simulation box (3 out of 5 simulation repeats) indicates membrane deformations. Different colors indicate different simulation repeats. This panel represents an extension of the simulation shown in Fig. 5g. f) Side and top view images of representative timepoints from the MD simulation of a membrane with a single AP180 ANTH domain. The 0 µs time point represents the starting point and the membrane is roughly 40 nm x 40 nm in size. At 5 µs, the membrane has essentially the same size. The height of the simulation box remains constant throughout the simulation, indicating that no membrane deformations occur. Different colors indicate different simulation repeats. g) Side and top view images of representative timepoints from the MD simulation of a membrane with 3x AP180 ANTH domain. The 0 µs time point represents the starting point and the membrane is roughly 60 nm x 60 nm in size. At 5 µs, the membrane has essentially the same size. The height of the simulation box remains constant throughout the simulation, indicating that no membrane deformations occur. Different colors indicate different simulation repeats. This panel represents an extension of the simulation shown in Fig. 5g. h) Visualization of the membrane deformations along the Z axis (brown line and area) over the time alongside with the positions of the center of mass of the three TPLATE complexes (red, blue and green lines). Four MD simulation repeats that were not included in Fig. 5f are shown here. The time indications represent computational time of CG-MD simulations, which cannot be easily compared to the actual endocytic life times observed in microscopy experiments.
