Modeling interactions between peptides and metal ions

The role of cofactors, like transition metal ions, in folding, misfolding and aggregating proteins and peptides within cells and tissues is now well recognized [1]. Due to the low degree of structure in protein regions involved in such important interactions, experimental methods need complementary information provided by models, these latter ranging from coarse-grained electrostatics to accurate quantum-mechanical descriptions of forces, passing through empirical force-fields used in atomistic simulations. In this contribution, the role of different types of modeling techniques and of high-performance computing infrastructures will be described, with particular emphasis on the contributions provided to the understanding of the interactions between Zn/Cu and peptides involved in neurodegenerative disorders like Creutzfeldt-Jacob (prion protein) [2,3] and Alzheimer's diseases (amyloid-beta peptides) [4,5,6].