Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?
Fig 4
Aβ backbone fluctuations in different force fields.
Root-mean-square fluctuations (RMSF), δϕ(i) (black bars) and δψ(i) (red bars), in the backbone dihedral angles ϕ and ψ for Aβ10-40 amino acids i computed in five force fields: (a) C36, (b) C36s, (c) C22*, (d) C22cmap, and (e) OPLS-AA. Sampling errors are shown by vertical bars. Sequence regions are identified by the color scheme used in Fig 1a. The plots show that out of all force fields C22* predicts the most rigid backbone, especially in S2 and S4 regions.