The effect of sodium dodecyl sulfate concentration on the aggregation behavior of Aβ (1–42) peptide: Molecular dynamics simulation approach

Abstract

Beta-amyloid (1–42) is the most effective peptide in the formation of inter-synaptic aggregate structures. These complex structures lead to disruption of the neural network and the development of Alzheimer's disease. Here, the effect of sodium dodecyl sulfate concentration on Aβ (1–42) structure has been investigated by molecular dynamics simulation. The calculations were performed at concentrations lower than and above than the critical micelle concentration. Two single and six peptide systems were used for each concentration. Calculations were also repeated in the absence of sodium dodecyl sulfate. The secondary structure of Aβ (1–42) was calculated in the designed systems. The results showed that the dominant secondary structure in monomeric systems is the helix. Also, the calculation of the Aβ (1–42) secondary structure shows that the behavior of the peptides is heterogeneous in the hexamer systems. The length of the Lys28-Ala42 salt bridge was calculated in different systems as criterion of peptide toxicity. The results showed that the length of the salt bridge is increased at both SDS concentrations. The radial distribution function was used to investigate the interaction of the peptide with SDS. The result revealed that the distribution of SDS molecules around the amyloid-β peptide residues is great in the presence of low SDS concentration. Also, the interaction intensity between the peptide and SDS at low SDS concentrations is higher than that at high SDS concentration.