Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40).

ABSTRACT: Using a predictive coarse-grained protein force field, we compute and compare the free energy landscapes and relative stabilities of amyloid-? protein (1-42) and amyloid-? protein (1-40) in their monomeric and oligomeric forms up to the octamer. At the same concentration, the aggregation free energy profile of A?42 is more downhill, with a computed solubility that is about 10 times smaller than that of A?40. At a concentration of 40 ?M, the clear free energy barrier between the pre-fibrillar tetramer form and the fibrillar pentamer in the A?40 aggregation landscape disappears for A?42, suggesting that the A?42 tetramer has a more diverse structural range. To further compare the landscapes, we develop a cluster analysis based on the structural similarity between configurations and use it to construct an oligomerization map that captures the paths of easy interconversion between different but structurally similar states of oligomers for both species. A taxonomy of the oligomer species based on ?-sheet stacking topologies is proposed. The comparison of the two oligomerization maps highlights several key differences in the landscapes that can be attributed to the two additional C-terminal residues that A?40 lacks. In general, the two terminal residues strongly stabilize the oligomeric structures for A?42 relative to A?40, and greatly facilitate the conversion from pre-fibrillar trimers to fibrillar tetramers.

SUBMITTER: Zheng W 

PROVIDER: S-EPMC5805378 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature