IPM Calendar  School/Center

Weekly Seminar
Mechanisms of the Self-assembly of EAK16 Peptides and Formation of Nanostructures in the Presence and Absence of a Hydrophobic Surface
Dr. Soheila Emamyari

Date : Wednesday , January 4, 2023
           14:00 - 15:00    

In this work, self-assembly of EAK16 ionic complementary peptides under different pH conditions in the presence and absence of a hydrophobic surface has been studied. In the first part, some self-assembly experiments with EAK16-II and EAK16-IV peptides have been performed. In addition to the experiments, the self-assembly behavior of EAK16 peptides has been studied by using molecular dynamics (MD) simulation in two sections. In the first section, all-atom MD simulations have been used to study the single chain equilibrium conformation and the dimerization of the three types of ionic EAK16 peptide under three pH conditions. Formation of different assemblies of these peptides that has been observed in experiments, has been described by analyzing the peptides behavior in the single- and double-chain levels. In the second section, the pH dependent self-assembly behavior of the three types of EAK16 peptide in the presence of a hydrophobic surface has been studied by using coarse-grained MD simulations. The results show that EAK16-I and EAK16-II peptides assemble into ribbon-like structures, regardless of the value of pH. EAK16-IV peptides however, assemble into ribbon-like structures at pH<4.3 and pH>10.53, and form disc-shaped assemblies on the hydrophobic surface under neutral pH conditions.