Molecular Dynamics Simulation for the β-Sheet Aggregation of Peptides

The aggregations and thermodynamics stability of a nine peptide forming amyloidal fibril were studied using molecular dynamics simulation methods under acidic and alkaline condition, respectively. The results show that the peptide can form parallel beta-sheet under alkaline condition, whereas forms anti-parallel beta-sheet under acidic condition, and thermodynamics stability of the anti-parallel beta-sheet is more stable than that of parallel beta-sheet. The above observations are consistent with the experimental results. In addition, in the two beta-sheet forms, the peptide chain both extends along direction of the corresponding sheet and forms left-helix, but the angle between adjacent peptide chains are different: the angel in parallel beta-sheet form is less than that in anti-parallel beta-sheet form. Therefore, it is concluded that parallel beta-sheet is form easily aggregation, comparing with the anti-parallel beta-sheet. The conclusion can explain why the diameter of amyloidal fibril under alkaline condition is larger than that under acidic condition in experiment.