Fig. 3: 3D-LAFM steered molecular dynamics flexible fitting (MDFF) of annexin-V.

a 3D-LAFM density force field U_AFM for A5. An i-j plane cross-section of the force field is colored according to the local energy density (red to blue: Low to high energy level), the gradient of which is proportional to the force field (black arrows). Inset: surface representation of the 3D-LAFM density map where the red dashed box indicates the cross-section site. b MDFF trajectory of A5 (Supplementary Movie 3). Cyan: Selected frames displayed in a side view. Gray: 3D-LAFM density map. Selected frames: t = 0 ns (initial PDB structure), t ~ 0.5 ns, t ~ 10 ns and t ~ 20 ns (md cycle 1), t ~ 40 ns (md cycle 2), and t ~ 60 ns (md cycle 3, end of MDFF, Methods). c–e Evaluation of the A5 MDFF trajectory. Time-evolution of internal energy (E) (c), root-mean-squared deviation (rmsd) to the initial structure (d), and normalized correlation between structure and density map (e) during MDFF (Methods). Red dashed lines: ends of each MDFF cycle. f Superimposed structures of initial model (purple, PDB 1AVR, t = 0 ns) and final model (scarlet, t ~ 60 ns). A5-monomer in top view (top) and from a side view (bottom). g Time-evolution of annexin-repeat movements during the MDFF trajectory. Left and middle: Height of repeats I (blue), III (green), and IV (yellow) relative to repeat II (black arrowheads in (f) for annexin-repeat assignment). The repeat height was measured as the center-of-mass of either all repeat atoms (left), characterizing the repeat rigid body, or all atoms in the top 20 Å of the liquid-facing side (middle), characterizing the repeat surfaces. Right: Height differences (Mean ± SD) of repeat III relative to IV (clear) as well as repeat IV relative to I (striped) in the initial structure (PDB 1AVR), near the end of cycle 1 (md1), cycle 2 (md2), cycle 3 (md3), and the 3D-LAFM density map (afm) (Methods). For each measurement, 21 structures, giving n = 63 protomers, were selected from each MD cycle (md1, md2, and md3).