Calculation of Structural Parameters and Diffusion Coefficient of Sodium Dodecyl Sulfate at Concentrations Lower and Higher Than the Critical Micelle Concentration in the Presence of Amyloid-Beta Peptide

Sodium dodecyl sulfate (SDS) solution is considered a cell membrane mimicking solution. In this study, the effect of the amyloid-beta peptide on the structure and diffusion coefficient of SDS was investigated by molecular dynamics simulation. To control the accuracy of the calculations, a micelle containing 60 molecules of SDS was simulated. The radius of gyration and the moment of inertia of the micelle were calculated and compared with the experimental and simulation results. The results obtained were in good agreement with the experimental and simulation results. The simulations in the presence of amyloid-beta were performed at two concentrations of SDS, below and above the critical micelle concentration. The results showed that as the concentration of SDS increased, the diffusion coefficient of peptide and sodium ion increased while the diffusion coefficient of water and SDS decreased. The calculation of the moments of inertia in different directions showed that the micelles deviated from the ellipsoidal shape at sub-critical micelle concentrations of SDS.