Structures and Thermodynamics of Alzheimer's Amyloid-β Aβ(16-35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

Many proteins display a strand-loop-strand motif in their amyloid fibrillar states. For instance, the amyloid beta-protein, A beta 1-40, associated with Alzheimer's disease, displays a loop at positions 22-28 in its amyloid fibril state. It has been suggested that this loop could appear early in the aggregation process, but quantitative information regarding its presence in small oligomers remains scant. Because residues 1-15 are disordered in A beta 1-42 fibrils and A beta 10-35 forms fibrils in vitro, we select the peptide A beta 16-35, centered on residues 22-28 and determine the structures and thermodynamics of the monomer and dimer using coarse-grained implicit solvent replica exchange molecular dynamics simulations. Our simulations totalling 5 mu s for the monomer and 12 mu s for the dimer show no sign of strong secondary structure signals in both instances and the significant impact of dimerization on the global structure of A beta 16-35. They reveal however that the loop 22-28 acts as a quasi-independent unit in both species. The loop structure ensemble we report in A beta 16-35 monomer and dimer has high similarity to the loop formed by the A beta 21-30 peptide in solution and, to a lesser extent, to the loop found in A beta 1-40 fibrils. We discuss the implications of our findings on the assembly of full-length A beta.