The influence of polar and non-polar interactions on the self-assembly of peptide nanomembranes and their applications: an atomistic study using classical molecular dynamics

Abstract

In this work, structural and energetic properties of five peptide membranes are investigated via fully atomistic molecular dynamics simulations. The membranes are made up of peptides with the Ac-I3XGK (X = glutamine (Q), serine (S), asparagine (N), glycine (G) or leucine (L)) amino acid primary sequence. That is, peptides with a charged polar head, composed of one lysine residue, and a neutral tail (I3XG). This work seeks to understand how the insertion of polar amino acids (Q, S, or N) in the peptide neutral tail, at the X position, changes the energetic and structural properties of the peptide membranes, contrasting with membranes composed of just non-polar amino acids (G or L) at this position. We report the results of hydrogen bonds, Coulombic, and van der Waals interactions between the membranes' peptide residues, as well as between each peptide residue and water. It was seen that the I3QGK, I3SGK, and I3NGK membranes perform more hydrogen bonds between their residues than the I3GGK and I3LGK ones. Besides, an important observation is that the polar amino acids would allow the appearance of hydrogen bonds between the peptide β-sheet side chains (forming polar zipper) instead of just between the peptide main chains. This work elucidate importance results that can help in the interpretation of experimental investigations, and the construction of structures in a bottom-up process by given a detailed understanding of the polar zippers formation, which can allow the emergence of flat and wide structures.