Extended Data Fig. 6: Structural stability of the β-propeller of TcB during molecular dynamics simulations.

Principal component analysis of the trajectories started from the closed (a–c) or open (d–f) states of the TcB–TcC complex. The plots show the root mean square fluctuation associated with the first (a, d), second (d, e) and third (c, f) principal components. The percentages in the legends indicate the fractional contribution that each component makes to the total variance. The structures show the range of conformations observed along their corresponding component. The colour scale in the structures represents the position along each principal component going between the extremes, from red to green to blue. For guidance, the blades of the β-propeller are labelled in structures and plots, with blades 3 and 4 highlighted in blue. g, h, Graphical representation of the hybrid potentials used for the dual conformation structure-based SMOG force field. A Gaussian potential (g) can be used to create a contact term that includes exactly two minima (states a and b) with equal well depth, corresponding to the observed distance in two independent structures. In addition, by using a Gaussian potential the excluded volume of the contact can be independently controlled. A representation of the hybrid dihedral angle potential used in this study is shown in h. Starting from the dihedral functions for states a and b, the functions are combined as described in Methods. The regions between the averages (av1 and av2) and the closest extrema are connected using a polynomial function, to guarantee continuity and differentiability.