Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?
Fig 3
Residue-specific Aβ10-40 secondary structure in different force fields.
Distributions of secondary structure in Aβ10-40 peptide with respect to sequence positions i for five force fields: (a) helix propensities 〈H(i)〉; (b) turn propensities 〈T(i)〉; (c) random coil propensities 〈RC(i)〉; (d) β propensities 〈S(i)〉. For clarity, sampling errors represented by vertical bars are shown for the C36 simulations only. Sequence regions are identified by the color scheme used in Fig 1a. C22* force field displays a significant helix structure in S3 and S4 regions, and the OPLS-AA system has a propensity for β-structure in S2 and S4.