Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?
Fig 5
Aβ10-40 tertiary interactions in different force fields.
Intrapeptide contact maps, 〈C(i, j)〉, present the probabilities of forming contacts between residues i and j in Aβ10-40 peptide for five force fields: (a) C36, (b) C36s, (c) C22*, (d) C22cmap [44], and (e) OPLS-AA. The bars on the right-side color code 〈C(i, j)〉 values. Sequence regions are identified by the color scheme used in Fig 1a. C36, C36s, and C22cmap contact maps reveal lack of stable long-range interactions, whereas C22* displays few exceptionally strong long- and short-range contacts. OPLS-AA contact map is characterized by extensive but flickering tertiary interactions.