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

Saghiri, Afsane; Bozorgmehr, Mohammad Reza; Morsali, Ali

doi:10.22036/pcr.2022.327519.2024

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

Document Type : Regular Article

Authors

Afsane Saghiri

Mohammad Reza Bozorgmehr

Ali Morsali

Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran

https://doi.org/10.22036/pcr.2022.327519.2024

Abstract

Sodium dodecyl sulfate (SDS) solution is considered as a cell membrane mimicking solution. Here, the effect of beta amyloid peptide on the structure and diffusion coefficient of SDS by molecular dynamics simulation is investigated. 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 results and the results of other simulations. The results obtained here are in good agreement with the experimental results and the results of other simulations. The simulations in presence of beta amyloid were performed at two concentrations of SDS, below the critical micelle concentration and the higher than the critical micelle concentration. The results show as the concentration of SDS increased, the diffusion coefficient of peptide and sodium ion increased, while the diffusion coefficient of water and SDS decreased. Calculation of the moment of inertia ratios in different directions shows that at sub-critical micelle concentration of SDS the micelles deviate from the ellipsoidal shape.

Graphical Abstract