Dimerization of the Full-Length Alzheimer Amyloid β-Peptide (Aβ42) in Explicit Aqueous Solution: A Molecular Dynamics Study

In this study, the mechanism of dimerization of the full-length Alzheimer amyloid beta (A beta 42) peptide and structural properties of the three most stable dimers have been elucidated through 0.8 mu s classical molecular dynamics (MD) simulations. The A beta 42 dimer has been reported to be the smallest neurotoxic species that adversely affects both memory and synaptic plasticity. On the basis of interactions between the distinct regions of the A beta 42 monomer, 10 different starting configurations were developed from their native folded structures. However, only six of them were found to form dimers and among them the three most stable (X-P, C-C-AP, and N-N-P) were chosen for the detailed analysis. The structural properties of these dimers were compared with the available experimental and theoretical data. The MD simulations show that hydrophobic regions of both monomers play critical roles in the dimerization process. The high content of the alpha-helical structure in all the dimers is in line with its experimentally proposed role in the oligomerization. The formation of a zipper-like structure in X-P is also in accordance with its existence in the aggregates of several short amyloidogenic peptides. The computed values of translational (D-T) and rotational (D-R) diffusion constants of 0.63 x 10(-6) cm(2)/s and 0.035 ns(-1), respectively, for this dimer are supported by the corresponding values of the A beta 42 monomer. These simulations have also elucidated several other key structural properties of these peptides. This information will be very useful to design small molecules for the inhibition and disruption of the critical A beta 42 dimers.