Fig 2. Typical biasing forces used in LRPF simulations.

(a-b) Typical biasing forces, ${\mathbf{F}}_{matrix}^{bias}$ (a) and ${\mathbf{F}}_{cytoplasm}^{bias}$ (b), applied to C_α-atoms in LRPF2 and LRPF2+ simulations, respectively, are represented by black cones. Protein backbone is drawn in ribbon representation. C_α-atoms to which the perturbative forces, ${\mathbf{F}}_{matrix}^{perturb}$ and ${\mathbf{F}}_{cytoplasm}^{perturb}$, are applied are indicated by spheres. The biasing forces were frequently updated during the LRPF simulations.