Optimizing Protein-Polymer Interactions in a Poly(ethylene glycol) Coarse-Grained Model.

Increasing demand for hybrid materials that merge the synthetic and biological areas in drug industries requires in-depth knowledge of the individual components and their contributions to these complexes. Coarse-grained (CG) models developed for proteins and polymers exist, yet there is a lack of understanding of the cross interactions when these two groups of materials integrate to build a complex. In this work, we characterized the nonbonded interactions between poly(ethylene glycol) (PEG) and amino acids in a Martini CG model utilizing state-of-the-art quantum mechanics calculations of interaction energies. The parameter set proposed, was validated by assessing the polymer density in the vicinity of individual amino acids obtained from available all-atomistic molecular dynamic simulations of plasma proteins. Our results revealed the necessity of protein-polymer interaction parameterization at the CG level to avoid overestimation of polymer association when employing other PEG models within the Martini framework.