Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations

FIGURE 1. (A) Molecular model of a tail-truncated myosin V. (B,C) Molecular models of the complexes of an actin filament with myosin V in (B) the down-up state and (C) down-down state. Two heavy chains of myosin V are shown in blue and red. Twelve light chains of myosin V in compact or extended conformations are colored in green. The actin filament is indicated in yellow. All structures were drawn using PyMOL version 1.8.4.0 (http://www.pymol.org/).

FIGURE 2. Flexible fitting simulation of the actin-myosin complex in the down-up state. (A) The corrected experimental AFM image used as a reference in the simulation; scale bar, 10 nm; color bar in nm. (B) Time series of the cosine similarity for ten independent simulation runs are shown in brown. The trajectory involving the largest value is colored in red. (C) The pseudo-AFM image with the highest cosine similarity created using afmize (Niina et al., 2020a; Niina et al., 2020b); scale bar, 10 nm; color bar in nm. (D) The structure model of actin-myosin complex with the highest cosine similarity on top of the reference AFM image; scale bar, 10 nm.

FIGURE 3. Flexible fitting simulation of the actin-myosin complex in the down-down state. (A) The corrected experimental AFM image used as a reference in the simulation; scale bar, 10 nm; color bar in nm (same as Figure 2A). (B) Time series of the cosine similarity for ten independent simulation runs are shown in brown. The trajectory involving the largest value is colored in red. (C) The pseudo-AFM image with the highest cosine similarity created using afmize (Niina et al., 2020a; Niina et al., 2020b); scale bar, 10 nm; color bar in nm. (D) Structure model of the actin-myosin complex with the highest cosine similarity on top of the reference AFM image; scale bar, 10 nm.

FIGURE 4. (A,B) Probability density distributions of the cosine similarity of pseudo-AFM images using (A) the region of 40 × 30 pixels used for the flexible fitting and (B) the region of 25 × 12 pixels corresponding to the myosin neck. The distributions of the down-up state and the down-down state are shown in red and blue, respectively. (C) The region of AFM image corresponding to the myosin neck is shown in color. Scale bar, 10 nm.