Figure 2.

Helicity changes upon protonation in ScaDMT. (A) Time average of helicity of each residue as observed in simulations of ScaDMT in various protonation states, quantified using STRIDE²⁴. The indicated transmembrane regions were taken from the PDBTM database⁶². Regions with most differences in helicity are shown, which are TMH 6 (top) and TMH 8 (bottom). (B) Helicity changes in each MD trajectory were also quantitated by calculating the time average of the sum of dihedral angles ψ _i + ϕ _i+1 along the protein chain. For an ideal α-helix, this value is ≈−105°. Large values around 200° correspond to local peptide bond flips.