Angel E. Garcia, Nikolaos G. Sgourakis, Yilin Yan, Scott McCallum, and Chunyu Wang. Rensselaer Polytechnic Institute, Troy, NY
The role of two peptides, A�40 and A�42 in the early pathogenesis of the Alzheimer's disease (AD) is frequently emphasized in the literature. It is known that A�42 is more prone to aggregation than A�40, even though they only differ in two (I,A) amino acid residues at the C-terminal end. A direct comparison of the ensembles of conformations adopted by the monomers in solution has been limited by the inherent flexibility of the unfolded peptides. We characterize the conformations of A�42 and A�40 in water by using a combination of molecular dynamics (MD) and measured scalar 3J-coupling data. We perform replica exchange MD (REMD) simulations and find that various classical forcefields quantitatively reproduce the NMR data when the sampling is extended to the microseconds time scale. Using the quantitative agreement of the NMR data as a validation of the model, we proceed to compare the conformational ensembles of the A�42 and A�40 peptide monomers. Our analysis confirms the existence of structured regions within the otherwise flexible A� peptides. We find that the C-terminus of A�42 is more structured than that of A�40. The formation of a �-hairpin in the sequence 31IIGLMVGGVVIA involving short strands at residues 31-34 and 38-41 reduces the C-terminal flexibility of the A�42 peptide and may be responsible for the higher propensity of this peptide to form amyloids.
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