Knot-controlled ejection of a polymer from a virus capsid

TL;DR

This study uses numerical simulations to show that knots in polymers significantly slow their ejection from virus-like capsids, with knot complexity and type being key factors influencing the process.

Contribution

It reveals that the knot acts as a ratchet controlling ejection rate, emphasizing the role of knot complexity over polymer flexibility in viral DNA ejection.

Findings

More complex knots slow ejection more

Knot type, not flexibility, governs ejection rate for large knots

Knot acts as a ratchet controlling polymer ejection

Abstract

We present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, virus-like capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the capsid and then acts as a ratchet. Polymers with more complex knots eject more slowly and, for large knots, the knot type, and not the flexibility of the polymer, determines the rate of ejection. We discuss the relation of our results to the ejection of DNA from viral capsids and conjecture that this process has the biological advantage of unknotting the DNA before it enters a cell.