Modeling, energetic and structural analysis of peptide membranes formed by arginine and phenylalanine (R2F4R2) using fully atomistic molecular dynamics

Abstract

The use of computational resources for modeling organic nanostructures from peptides has an incredible potential to elucidate fundamental characteristics that guide molecular interactions and that collaborate with the understanding of the self-assembly process of these materials. In this work we describe a structural and energetic study of a membrane formed by the sequence R2F4R2 using molecular dynamics. Our simulations were carried out exploring three forms of juxtaposition between the peptides that shape the organic nanostructure. They also show that the three forms of organization are viable during the self-assembly process leading to similar structures. Our results reinforce the importance of hydrogen bonds and the correct characterization of the hydrophobic and hydrophilic structure of the peptide in the nanomembrane idealization process (especially bola-amphiphile peptides). Our results obtained by molecular dynamics indicate that the thickness of the peptide sheets observed experimentally may be related to the superposition of monolayer membranes with thicknesses close to 2.3 nm, characterizing multilaminar membranes with thicknesses close to 4 nm in full agreement with experimental data.