Figure 1.

Definitions of the variables of the UNRES model. The virtual-bond angle θ_i is determined by the three C^α carbons at sites i, i + 1, i + 2 and is defined as the angle between the ${\mathrm{C}}_i^{\alpha }\cdots {\mathrm{C}}_{i+1}^{\alpha }$ virtual-bond vector and the ${\mathrm{C}}_{i+1}^{\alpha }\cdots {\mathrm{C}}_{i+2}^{\alpha }$ virtual-bond vector [Eq. 11]. It should be noted that, for consistency with the notation of Sec. 2B, the angles θ used in this work are complements of the original angles θ, i.e., π − θ (see, e.g. Ref. 39). The C^α carbon atoms are represented by small open circles. The virtual-bond-dihedral angle γ_i it the angle between the two planes, determined by the C^α at sites (i, i + 1, i + 2) and (i + 1, i + 2, i + 3) [Eqs. 12, 13]. In addition, the UNRES energy function [Eqs. 32, 33, 34, 35] involves the following structure, shown in the Figure: The interaction sites are peptide-bond centers (p), and side-chain ellipsoids of different sizes (SC) attached to the corresponding α-carbons with different virtual-bond lengths b_SC. The UNRES energy is also a function of the coordinates of the SC and p sites which are functions of (θ, γ, α, β) and also contains terms that depend explicitly on these angles.