Role of repulsive forces on self-assembly behavior of amyloid β -peptide (1-40): Molecular dynamics simulation approach

A-amyloid self-assembly is related to the changing the structure of the -amyloid from the helix to the sheet. This structural change is one of the main reasons for developing Alzheimer’s disease. Usually, the addition of non-polar solvents to water is used to study the role of hydrophobic forces in the self-assembly behavior. However, adding non-polar solvents also causes unwanted structural changes. Here, by changing the Lennard-Jones potential repulsion expression, structural changes in Amyloid -peptide (1-40) (A40) have been studied using molecular dynamics simulation. For this purpose, in the Lennard-Jones potential and , 9, 10, 11, 12 were placed in attractive and repulsion terms, respectively. Then this change in the potential was applied to the GROMOS96 and OPLS-AA/L force fields. Molecular dynamics simulations of A40 were performed based on these 10 potentials. The results show that the change in the Lennard-Jones repulsion term in both of the applied force fields does not have a regular impact on the structure and dynamics of the A40. For example, with the change of to 11 in the GROMOS96 force field, the diffusion coefficient of A40 decreases, while with the change of to 10, the diffusion coefficient increases in this force field. The change zones in the secondary and tertiary structures are also different. However, the results indicate that the OPLS AA/L force field is more sensitive to the change in the Lennard-Jones potential repulsion term.

Self-assembly;Alzheimer’s disease;Force field;Hydrophobic forces