Figure 1.

Schematic representation of the physical parameters used in the L1 and L2 models (color online). (a) Basic modes of motion related to longitudinal interactions: interdimer stretching, intra- and interdimer bending, and interdimer torsional motion. (b) Basic modes of motions related to lateral interactions: stretching, translational shift, and torsion. (c) Conversion between two types of lateral bonds that result from the combinations of lateral modes. (d) Four coordinates (L, θ, ϕ, ψ) describe the relative position and orientation between two neighboring monomers. Monomers, each treated as a rigid body, are connected head to tail along the longitudinal direction (protofilament). All energy terms are expressed as functions of these four coordinates. (e) The relative coordinates (d, θ_s, ϕ_r), describing the relative position and orientation between two lateral neighboring monomers, represent the distance and the translational angle between the centers of mass of two monomers, and the reorientation of the monomer internal coordinate system, respectively. These values are derived from the four coordinates in (d). (f) Schematic illustration of the truncated harmonic potential form used, where x_e stands for the equilibrium value in the corresponding dimension, and x_c is the critical value where the interaction becomes zero. (g–h) Schematic comparison between the L2 and L1 models. The former generalizes the latter by adding one more type of lateral interaction (sheet bond in red) in addition to besides the traditional tube bond (in blue). (i) Schematic illustration of the composite double-well (for the L2 model) and single well (for the L1 model) potentials along the lateral bond conversion coordinate. The blue and green curves for the L1 model correspond to stiff and soft tube bonds, respectively. The lateral transition coordinate is defined as an effective coordinate that combines the effects of stretching, shifting and rotating movements.