Hydration properties of the polyalanines by atomistic molecular dynamics

Abstract

Polyalanine chains have been extensively considered in the context of the development of peptides for self-organization of peptide nanostructures. Atomistic molecular dynamics simulations allowed us to analyze the structure and thermodynamics of the hydration of four polyalanines: A3, A6, A9 and A12. These chains have been considered to interact exactly as lipid in a peptide nanostructure, however our results show that such a view is inaccurate since alanine tails must interact strongly with each other, not only because of the hydrophobic interactions of side chains but also because of their hydrophilic groups. Our results show that the hydration free energy of such chains varies linearly with the length of the polyalanine, is strongly negative and is mostly driven by enthalpy. There is an entropic penalty, however, which is not enough to compensate for the enthalpic gain obtained in the hydration process.