Quantitative Study of Bio-Nano Interface

Abstract

The free energy of adsorption of proteins onto nanoparticles offers an insight into the biological activity of these particles in the body, but calculating these energies is challenging at the atomistic resolution. In addition, the structural information of the proteins may not be readily available. This work demonstrates how information about the adsorption affinity of proteins onto nanoparticles can be obtained from the first principles with minimum experimental input. We use a multiscale model of protein–nanoparticle interaction to evaluate adsorption energies for a set of proteins on different types of nanoparticles such as metals, metal oxides, and carbon materials and some of its derivatives of various sizes and zeta potentials. For some proteins, we compare the results for 3D structures derived from experiments to those predicted computationally from amino acid sequences using homology modelling. We also compare the results for 3D structures derived from AlphaFold to those predicted computationally from amino acid sequences using homology modelling. Based on these calculations and 2D and 3D protein descriptors, we develop statistical models for predicting the binding energy of proteins, enabling the rapid characterisation of the affinity of nanoparticles to a wide range of proteins.