The effect of Carbon nanotube on the most effective peptide in Alzheimer’s disease in the presence of Dimethyl Sulfoxide: In Silico approach

Due to the non-polar nature of carbon nanotubes, their use in aqueous environments is limited. Therefore, auxiliary solvents such as dimethyl sulfoxide are used to study the interactions between the amyloid-β peptide and carbon nanotubes. In this work, the interaction of Aβ (1-42), the most effective peptide in the development of Alzheimer s disease, with the carbon nanotube was performed using molecular dynamics simulation method. The simulations were carried out in the presence of various concentrations of dimethyl sulfoxide. The stability change of the salt bridge Lys28-Ala42, used in experimental studies, was investigated as a measure of aggregation tendency. Therefore, the radial distribution function of water oxygen atoms and the atoms involved in the salt bridge were used. The results show that the peak height of the radial distribution function around the oxygen of the residue Ala42 is greater than that of the Nx atom of the residue Lys28. By determining the side-chain orientation of the aromatic residues Phe4, Tyr10, Phe19, Phe20 with the carbon nanotube, it was found that the residues Phe4 and Tyr10 have a stronger π-π interaction with the carbon nanotube than the residues Phe19 and Phe20. The results in this study are in good agreement with the experimental data and could be helpful to understand the mechanism of amyloid-β aggregation.