Unfolding of globular polymers by external force

Mapping a single-molecule folding process onto a topological space

Physics of protein folding has been dominated by conceptual frameworks including the nucleation-propagation mechanism and the diffusion-collision model, and none address the topological properties of a chain during a folding process. Single-molecule interrogation of folded biomolecules has enabled real-time monitoring of folding processes at an unprecedented resolution. Despite these advances, the topology landscape has not been fully mapped for any chain. Using a novel circuit topology approach, we map the topology landscape of a model polymeric chain. Inspired by single-molecule mechanical interrogation studies, we restrained the ends of a chain and followed fold nucleation dynamics. We find that, before the nucleation, transient local entropic loops dominate. Although the nucleation length of globules is dependent on the cohesive interaction, the ultimate topological states of the collapsed polymer are largely independent of the interaction but depend on the speed of the folding process. After the nucleation, transient topological rearrangements are observed that converge to a steady-state, where the fold grows in a self-similar manner.

Unfolding of polymers tethered to viscoelastic substrates

The problem of globular polymer unfolding under applied force is a widely-studied fundamental topic in biological and chemical physics, with important applications in cell biology. Much of the existing theoretical and experimental literature focuses on the case where force is applied while fixing the opposite end of the polymer chain in space. However, in a realistic biological microenvironment, forces will be applied against viscoelastic references, and the deformation of the folded polymer chain will be combined with the deformation of viscoelastic substrate. In this paper, we consider several simple viscoelastic models for the substrate, and show that its relaxation properties determine the unfolding kinetics. In particular, for low pulling forces, substrates with longer relaxation times cause lower unfolding rates for the pulled polymer chain, whereas for high forces, those substrates with longer relaxation times instead produce higher unfolding rates.

Globule-stretch transition of a self-attracting chain in the repulsive active particle bath

Folding and unfolding of a chain structure are often manipulated in experiments by tuning the pH, temperature, single-molecule forces or shear fields. Here, we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting chain in a suspension of self-propelling particles (SPPs). As the propelling force increases, the globule-stretch (G-S) transition of the chain occurs due to the enhanced disturbance from the SPPs. Two distinct mechanisms of the transition in the limits of low and high rotational diffusion rates of SPPs have been observed: shear-induced stretching at a low rate and collision-induced melting at a high rate. The G-S and S-G (stretch-globule) curves form a hysteresis loop at the low rate, while they merge at the high rate. Besides, we find that two competing effects result in a non-monotonic dependence of the G-S transition on SPP density at the low rate. Our results suggest an alternative approach to manipulating the folding and unfolding of (bio)polymers by utilizing active agents.