Molecular dynamics simulation of the synthesis of protein-like copolymers via conformation-dependent design

We propose a computer model to describe the synthesis of protein-like copolymers in a polar solvent via irreversible polymerization of hydrophobic and hydrophilic monomers with simultaneous globule formation. In the model, growing chain macroradical, polymerizing monomers, and the preferential absorption of hydrophobic monomers in the core of the globule are taken into account explicitly. The effect of monomer concentrations and reaction rate on the conformational properties and primary copolymer sequences is investigated. We find that, under certain conditions, the resulting copolymers can form protein-like globules with hydrophobic core wrapped in a hydrophilic envelope. Also, a gradient structure of primary sequences of the copolymers is revealed. Such sequences are formed due to both a change in the chain conformation and a continuous redistribution of comonomers between the globule and the solution in the course of the polymerization.