At one time, molecular biologists swore blind that proteins would never become knotted, at least not in the natural course of things.

But in recent years, they’ve been forced to eat their words as  one protein after another has been shown to have a knotted structure.

The question is why; what purpose do knots serve in protein structures?

We know how they form: in exactly the same way that string becomes knotted in your pocket, by the random motion of the protein.

But it turns out that knots do not occur as frequently as you’d expect if proteins became knotted at random. In fact most proteins never become knotted. It “has remained largely unclear why nature steers some proteins to form a complicated knotted structure, while most are discouraged,” say Thomas Bornschlögl from the Technische Universität München in Germany and colleagues.

One possibility is that knots make proteins more mechanically stable. To test this idea, Bornschlögl and pals set out to measure how much force is needed to untangle a knotted protein called apo phytochrome using an atomic force microscope as a pair of tweezers.

It turns out that it unfolds with only 47 picoNewtons of force, making it less stable than many proteins that aren’t knotted. Nature can’t have chosen that structure for its superstability then, reason Bornschlögland and co.

Instead they think that the knot prevents the protein domains from slipping relative to each other when the structure absorbs light energy. The knot helps turn this energy into free vibrations which dissipate as heat.

That’s an interesting idea but by no means a slam dunk. So we’re back to square one: why are some proteins knotted and what advantage does this confer on them?

Ref: arxiv.org/abs/0809.1067: Tightening the knot in phytochrome by single molecule atomic force microscopy

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