Fig. 3: Anle138b binds dynamically inside the α-synuclein protofilament.

a Starting structures for MD simulations for the four principal poses of anle138b: Pyrazole nitrogen atoms of anle138b (indicated by blue arrows) are oriented either to residues ₆₇GGAV₇₀ (inward-facing, yellow) or to residues ₈₀KTVEGAGSI₈₈ (outward-facing, green) inside the cavity (cyan) of α-synuclein protofilament L2. The bromophenyl moiety can point up or down the protofilament (small panels). A color code denotes the individual simulation sets for each binding pose in all following panels (inward-facing—yellow, outward-facing—green). b, c Orientation (left) and distributions of minimal distances (right) between nitrogen atoms of anle138b and C_γ1 of I88 (light-blue), and C_α of G67, G68, G84, G86 (magenta) as described in a. Dashed lines indicate the initial positions of anle138b at the start of the simulation. d Snapshots and e, i trajectories (representative trajectories as bold lines; others as thin lines for clarity) illustrate discrete translational motion along the protofilament axis and alignment of anle138b with individual β-strand layers. Relative free-energy binding profiles G(x) as a function of anle138b insertion depth x for combined simulation sets of f inward-facing and j outward-facing pose. Data are presented as mean values ± SEM (depicted by shading). g, k Isosurfaces of corresponding anle138b occupancy. h, l Cumulative histogram of dwell times calculated from anle138b displacements inside the tubular cavity for h inward-facing (n = 24) and l outward-facing (n = 218) pose. Data are presented as mean values ± SEM (indicated by error bars). Water and lipid molecules omitted for clarity in all renderings.