Journal of Physical Chemistry B, Vol.123, No.31, 6750-6756, 2019
Tetrameric A beta 40 and A beta 42 beta-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution
Alzheimer's disease (AD) is characterized by the accumulation of extracellular A beta 42 and A beta 40 oligomers and plaques. In a recent computational study, we found that the presence of the residues 141 and A42 increases significantly the propensity of A beta to form a tetrameric beta-barrel structure in a bilayer mimicking a neuronal membrane. In this work, we have determined the propensity of the two A beta proteins to form tetrameric beta-barrel structures in aqueous solution using four atomistic protein fields, that is, Amber99SB-ILDN/TIP3P, OPLS/TIP3P, CHARMM36m/TIP3P-modified, and Amber99SB/DISP. Extensive replica exchange molecular dynamics simulations make it clear that a beta-barrel, made of two distinct beta-hairpin motifs and an asymmetric arrangement of eight antiparallel beta-strands with an inner pore diameter of 0.7 nm, exists transiently for A beta 42 peptide, but this is less the case for A beta 40 peptide, due to the change of the CHC-CHC and the Cter-Cter interfaces. This study has several implications in AD.