Molecular Dynamics Study of Surfactant-Like Peptide Based Nanostructures

Abstract

Surfactant-like peptide (SLP) based nanostructures are investigated using all-atomistic molecular dynamics (MD) simulations. We report structure properties of nanostructures belonging to the A(N)K peptide group. in particular, the mathematical models for the two A(3)K membranes, A(6)K nanotube, and A(9)K nanorod were developed. Our MD simulation results are consistent with the experimental data, indicating that A(3)K membranes are stable in two different configurations: (1) SLPs are tilted relative to the normal membrane plane; (2) SLPs are interdigitated. the former configuration is energetically more stable. the cylindrical nanostructures feature a certain order of the A6K peptides. in turn, the A9K nanorod does not exhibit any long-range ordering. Both nanotube and nanorod structure contain large amounts of water inside. Consequently, these nanostructures behave similar to hydrogels. This property may be important in the context of biotechnology. Binding energy analysis-in terms of Coulomb and van der Waals contributions-unveils an increase as the peptide size increases. the electrostatic interaction constitutes 70-75% of the noncovalent attraction energy between SLPs. the nanotubular structures are notably stable, confirming that A(6)K peptides preferentially form nanotubes and A(9)K peptides preferentially form nanorods.