Figure 2.

Structure (A) and orientation (B) of PGLa in the S-state. (A) The CHARMM simulation (red) reveals a full α-helix, whereas PGLa partially unfolds in the OPLS simulation (black), with loss of helicity prominent at G7 and G11. (B) The orientation is described by two angles: the tilt angle (τ) is the angle between the membrane normal and the helix long axis, which is defined to point from the N- to the C-terminus. The azimuthal rotation angle (ρ) is defined as a right-handed rotation around the helix long axis, with 0° defined to place the vector from the helix axis to the C_α atom of K12 parallel to the membrane plane. Both angles show similar behavior in the CHARMM and helically restrained (R) OPLS simulations. The rotation angle slowly fluctuates over a wide range at 35°C (orange vector, blue curves), resulting in large uncertainties in ρ. Convergence can be accelerated by use of high temperature (120°C) using a helically restrained peptide (R), which yields rapid convergence of τ and ρ without noticeably changing the averages obtained at 35°C.