Abstract
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.
Highlights
The topology of a folded polymer chain is one of its key, yet less understood properties
The physics of protein folding has been dominated by several theoretical frameworks including the nucleation–propagation mechanism and the diffusion–collision model, and none address the topological properties of a chain during a folding process.[1,2,3,4,5]
Of monomers spaced at the equilibrium bond length while the initial configuration of the latter is sampled from the thermalized conformations of the chain in a good solvent
Summary
The topology of a folded polymer chain is one of its key, yet less understood properties.
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