# Pearl-Necklace-Like Local Ordering Drives Polypeptide Collapse

## TL;DR

This paper investigates the nonequilibrium collapse pathways of polypeptides, revealing a pearl-necklace-like intermediate structure driven by local ordering and hydrogen bonding, which accelerates protein folding.

## Contribution

It introduces the concept of pearl-necklace-like local ordering as a key intermediate in polypeptide collapse, highlighting the role of local interactions in fast protein folding.

## Key findings

- Collapse involves pearl-necklace-like local clusters
- Collapse dynamics follow a linear growth of a length scale
- Dynamical critical exponent z=0.5 indicates rapid folding

## Abstract

Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between hydration effects and intra-peptide interactions. Once intra-peptide van der Waal interactions dominate, the chain collapses along a nonequilibrium pathway characterized by formation of pearl-necklace-like local clusters as intermediates that eventually coagulate into a single globule. By describing this coarsening through the contact probability as a function of distance along the chain, we extract a time-dependent length scale that grows in linear fashion. The collapse dynamics is characterized by a dynamical critical exponent $z=0.5$ that is much smaller than the values of $z=1-2$ reported for non-biological polymers. This difference in the exponents is explained by the instantaneous formation of intra-chain hydrogen bonds and local ordering that may be correlated with the observed fast folding times in proteins.