Structural properties of amyloid [beta](1-40) dimer explored by replica exchange molecular dynamics simulations

Replica exchange molecular dynamics simulations (300 ns) were used to study the dimerization of amyloid [beta](1-40) (A[beta](1-40)) polypeptide. Configurational entropy calculations revealed that at physiological temperature (310 K, 37°C) dynamic dimers are formed by randomly docked monomers. Free energy of binding of the two chains to each other was -93.56±6.341 kJ mol-1. Prevalence of random coil conformations was found for both chains with the exceptions of increased [beta]-sheet content from residues 16-21 and 29-32 of chain A and residues 15-21 and 30-33 of chain B with [beta]-turn/[beta]-bend conformations in both chains from residues 1-16, 21-29 of chain A, 1-16, and 21-29 of chain B. There is a mixed [beta]-turn/[beta]-sheet region from residues 33-38 of both chains. Analysis of intra- and interchain residue distances shows that, although the individual chains are highly flexible, the dimer system stays in a loosely packed antiparallel [beta]-sheet configuration with contacts between residues 17-21 of chain A with residues 17-21 and 31-36 of chain B as well as residues 31-36 of chain A with residues 17-21 and 31-36 of chain B. Based on dihedral principal component analysis, the antiparallel [beta]-sheet-loop-[beta]-sheet conformational motif is favored for many low energy sampled conformations. Our results show that A[beta](1-40) can form dynamic dimers in aqueous solution that have significant conformational flexibility and are stabilized by collapse of the central and C-terminal hydrophobic cores with the expected [beta]-sheet-loop-[beta]-sheet conformational motif. Proteins 2017; 85:1024-1045. © 2017 Wiley Periodicals, Inc.