Is the Conformational Ensemble of Alzheimer's Aß10-40 Peptide Force Field Dependent?

ABSTRACT

By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aß10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aß10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aß10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aß1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aß adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aß10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate ß-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aß collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aß10-40 and experimental Aß1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aß1-40 or Aß1-42. This observation suggests that the differences in the conformational ensembles of Aß10-40 and Aß1-40 are small and the former can be used as proxy of the full-length peptide. Based on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most accurate representation of Aß10-40 conformational ensemble.