A Stevedore's Protein Knot

Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered α-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.Author Summary: Knots are ubiquitous in many aspects of our life, but remain elusive in proteins. The multitude of protein structures archived in the Protein Data Bank can be grouped into several hundred patterns, but only a handful are folded into knots. Combing through the recently added structures we found several novel knotted proteins. A microbial enzyme that catalyzes the breakdown of pollutants is the most complex protein knot encountered so far (similar to a knot used by stevedores for lifting cargo). The smallest knotted protein on the other hand consists of only 92 amino acids. The existence of these complex motifs demonstrates that the ability of self assembly goes far beyond normal expectations. Aided by computer simulations we present evidence which suggests that the Stevedore protein knot, despite its topological complexity, may actually form in a single flipping movement.