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

The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technolog-ical 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 model-ing. 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 demon-strate the parametrization of the model and compare the results with all-atom simulations and experi-mental results for specific peptides. (c) 2021 Published by Elsevier Inc.

Automated summary

This study presents a computational protocol, the effective implicit surface model (EISM), for evaluating the binding affinity trends of peptides on parameterized surfaces, specifically focusing on the widely studied gold surface. By utilizing an amino-acid and surface specific implicit solvent model, researchers can explore peptide conformational degrees of freedom rapidly, while also demonstrating model parametrization and comparison with experimental results.