Folding and dimerization of the ionic peptide EAK16-IV

Folding and dimerization of an ionic polyalanine-based peptide chain (EAK16-IV) are simulated with nonspecific interactions. It is found that there is a competition between two kinds of structural motifs under different strengths of electrostatic interactions. The dominance of hairpin-like structures would be realized with a strong electrostatic interaction both thermodynamically and kinetically, showing the importance of the electrostatic interaction on the formation of hairpin-like structures. Simulations on the dimerization with strong electrostatic interaction are also carried out It is found that the concentration contributes essentially to the shape of the dimers. These studies demonstrate that the strong interactions and kinetic factors might be important for the ordered amyloid aggregates.