Interaction with a Gold Surface Reshapes the Free Energy Landscape of Alanine Dipeptide

The adsorption of the alanine dipeptide onto a gold surface in aqueous conditions was explored by using molecular dynamics simulations. In particular, using Metadynamics, we reconstructed a three-dimensional free energy landscape to investigate the effect of the metal surface on such landscape. The results show that the adsorption process is able to strongly modify the internal free energy surface of the molecule, even changing its qualitative appearance. The new free energy global minimum corresponds to elongated conformations of the biomolecule, arranged in preferred orientations with respect to the surface. Therefore, the surface-induced changes in the relative stability of the local free energy minima and in the free-energy barriers between them show that the entire conformational ensemble and the interconformer dynamics are also affected by the presence of the surface. The alanine dipeptide is the simplest molecule that exhibits the main features shown by larger peptides. Therefore, these findings provide a basis to rationalize, at the atomistic level, the effects of metal surfaces and nanoparticles on the structure and function of peptides and proteins, which is of paramount importance to engineer new systems for applications in bionanotechnology