Figure 2.

Equilibrium helix-coil transitions in capped αI and αII peptides (with primary sequences of NYDKFMEKM and NIVKRKLAA, respectively). (A and B) RMSD_dihed of isolated αI (A) and αII (B) with respect to the initial conformations in 10 μs MD trajectories is shown. The first and last residues of the peptides were excluded for the calculation. (C) The helix state population of each residue in αI (αII), with simulation data as solid circles (triangles) and predictions from the L-R model as solid (dashed) lines. Minor deviations partly arise from the simple form of the L-R model that assumes a common set of parameters for all amino acids. A more complex L-R model with amino-acid-specific treatment, however, was found to overfit the simulation data.