In silico investigation on the inhibition of Aβ42 aggregation by Aβ40 peptide by potential of mean force study

Abstract

Recent experimental data revealed that small, soluble Amyloid beta (Aβ42) oligomers, especially dimers impair synaptic plasticity and memory leading to Alzheimer’s disease. Here, we have studied dimerization of Aβ42/Aβ42 homo-dimer and Aβ40/Aβ42 hetero-dimer in terms of free energy profile by all-atom simulations using the ff99SB force field. We have found that in the presence of Aβ40 peptide, there exists a strong tendency to form a hetero-dimer with Aβ42 peptide, suggesting that a possible co-oligomerization. Furthermore, we have investigated the effects of Aβ40 on the Aβ42 peptide. Our study also shows that in presence of Aβ40, the beta-content of Aβ42 monomer is reduced. Additionally, certain residues important for bending in Aβ42 peptide attained an increased flexibility in the presence of Aβ40. The salt-bridge destabilization also manifested the impact of Aβ40 on Aβ42 peptide as a whole. Based on this, one may expect that Aβ40 inhibits the aggregation propensity of Aβ42. Moreover, the binding free energy obtained by the molecular mechanics–Poisson–Boltzmann surface area method also revealed a strong affinity between the two isoforms thereby suggests that Aβ40 binding induces conformational change in Aβ42. Our results suggest that co-oligomerization of Aβ isoforms may play a substantial role in Alzheimer’s disease.