Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model.

[Display omitted] • An implicit solvent/implicit surface model parameterization for gold surface. • Adsorption free energy calculation for amino acids using molecular dynamics (MD). • In silico evaluation of free energy of adsorption for the set of peptides and gold. • Comparison and discussion of results obtained with experimental data. The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides. [ABSTRACT FROM AUTHOR]