Design and analysis of polypeptide nanofiber using full atomistic Molecular Dynamic

Abstract In this work, surfactant-like peptides (SLP) pre-organized forming nanofibers are investigated by using all-atomistic Molecular Dynamics (MD) simulations. The nanofibers were investigated using two different ensembles: isobaric-isothermal and isovolumetric-isothermal. The nanofibers present a neutral hydrophobic tail made up of 12 amino-acids residues, three glycines (GLY), three alanines (ALA), three valines (VAL) and three isoleucines (ILE), and a charged hydrophilic head composed of three amino-acids residues, three lysines (LYS). The amino acids were linked in two different primary sequences, NH2-G3A3V3I3K3-COOH and NH2-K3I3V3A3G3-COOH, with differences on the torsion angles, in the positional disorder of the side-chain group and at the termination (N or C). We have analyzed the hydrogen bonds, Coulombic and vdW interactions to allow a better understanding of interactions influence between the peptide and the solvent medium (PEP-SOL), as well as the role of each group of amino acid residues (PEP-PEP) in the nanofiber's stability. The influence of the termination (N or C) on the fiber interactions was also observed. Our results indicate that G3A3V3I3K3 nanofiber, with the C-terminal attached to the charged lysine, presents more interactions with water and fewer interactions between its residues than the K3I3V3A3G3 nanofiber, indicating that this nanofiber would be more hydrophilic and its residues less hidden in the inner core.