Laminar peptide structure: energetic and structural evaluation using molecular dynamics

Abstract

In this work, we performed classical molecular dynamics simulations to evaluate laminar structures formed by peptides with the (RF)5 primary sequence. The alternating arginine (R) and phenylalanine (F) amino acids provide to the (RF)5 peptide a facially amphipathic sheets characteristic. Experimental studies report that the (RF)5 macromolecules can self-assembly into membrane-like or fiber-like nanostructures, however, our theoretical results indicate that the structures present more similarity with a laminar form. Our results demonstrate the existence of a dense mesh of hydrogen bonds that allows the separation of the hydrophilic and hydrophobic parts of the nanostructures in solution. Our theoretical results indicate properties that are perfectly compatible with experimental data. As an application, we noticed a dense charge distribution on the hydrophilic surfaces that allows efficient capture of ions in solutions.