Figure 1

Analysis of TM6 irregularities computed from MD simulations of polyalanine peptides containing the CAAP, SAAP, TAAP motifs in the gauche-, gauche + and trans conformers. Difference between average Φ (A) and Ψ (B) dihedral angles, unit bend (C) and unit twist (D) profiles. CtAAP and Cg+AAP are the unique peptide conformations that present very similar helical geometrical parameters to AAAP. Sg+AAP peptide present certain distortion relative to AAAP peptide and Cg-AAP, Sg-AAP, StAAP, Tg+AAP, Tg-AAP, TtAAP present the most distorted helical geometrical parameters relative to AAAP peptide. Bend and twist angles assigned at position i corresponds to the value computed for (i-3, i) and (i, i + 3) and for (i-3, i), respectively.