Can solvents tie knots? Helical folds of biopolymers in liquid environments

Abstract

Helices are the quintessential geometric motif of the microscale, from alpha-helices in proteins to double helices in DNA. Assembly of the helical geometry of biopolymers is a foundational step in a hierarchy of structure that eventually leads to biological activity. By simulating folding in a simplified setting we probe the role of the solvent in the collaborative processes governing biomaterials. Using a simulation technique based on the morphometric approach to solvation, we performed computer experiments in which a short, flexible tube-modelling a biopolymer in an aqueous environment-folds solely based on the interaction of the tube with the solvent. Our findings reveal a variety of helical structures that assemble depending on solvent conditions, including overhand knots and symmetric double helices. By differentiating the role of solvation, our work illuminates the environment of all soluble biomolecules, demonstrating that the solvent can drive fundamental rearrangements, even up to tying a simple overhand knot.