Protein-Like Dynamics of Polycarbonate Polymers in Water B

The dynamics of amphiphilic peptide-mimicking polycarbonate polymers are investigated, considering variations in polymer length, monomer sequence, and monomer modification. The polymers are simulated in aqueous solution with atomistic molecular dynamics simulations and an empirical force field. Various structural polymer properties, interaction strengths, and solvation free energies are derived. It is found that water is a less favorable solvent for these polymers than for peptides. Moreover, polymers readily adopt irreversibly a compact state that consists of a variety of distinct compact conformations that are adopted through frequent transitions. Furthermore, the polymers exhibit a strong propensity to form large aggregates. The driving forces for these processes appear to be a hydrophobic effect and more favorable polymer–solvent interactions of aggregates that overcome the otherwise strong mutual repulsion between the positively charged polymers. Replacing hydrophobic residues with polar side chains destabilizes the compact conformations of the polymers. Our results also indicate that the monomer sequence has little effect on the overall solvation properties of the polymer molecule. However, the sequence influences flexibility and compactness of the monomer in solution. Overall, the results of this work confirm the protein-like characteristics of these polymers and elucidate the role of single residues in influencing the structure and aggregation in aqueous solution.