The Molecular Dynamics study of atomic structure behavior of LL-37 peptide as the antimicrobial agent, derived from the human cathelicidin, inside a nano domain filled by the aqueous environment

Abstract

The LL-37 peptide is an antimicrobial agent derived from human cathelicidin. In addition to their antimicrobial properties, these peptides can activate the immune system through various mechanisms and contribute to autoimmune diseases. In the current study, we describe the atomic behavior of this protein in an aqueous environment inside of metallic nanochannel (Fe nanochannel). For this purpose, Molecular Dynamics (MD) approach was implemented in equilibrium conditions. A Large Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used in this computational study. Computationally, the various atoms interaction described by Universal Force Field (UFF), TIP4P, and Embedded Atom Model (EAM). Furthermore, physical factors like potential energy, temperature, Radial Distribution Function (RDF), density/velocity/temperature profiles, and protein volume were calculated for atomic behavior description of the LL-37 protein-water system. MD outputs indicated the atomic stability of protein structure in an aqueous environment inside metallic nanochannels. Numerically, the LL-37 protein volume changes from 3906.81 Å3 to 3900.11 Å3 value after t = 10 ns. Also, the maximum density and velocity/temperature profiles reach 0.0225 atoms/Å3 and 0.0124 Å/fs/435.22 K (respectively), values detected in the initial/final and middle bins MD box.