Knotted protein

Knotted proteins are proteins whose backbones entangle themselves in a knot. One can imagine pulling a protein chain from both termini, as though pulling a string from both ends. When a knotted protein is “pulled” from both termini, it does not get disentangled. Knotted proteins are very rare, making up only about one percent of the proteins in the Protein Data Bank, and their folding mechanisms and function are not well understood. Although there are experimental and theoretical studies that hint to some answers, systematic answers to these questions have not yet been found.

Although number of computational methods have been developed to detect protein knots, there are still no completely automatic methods to detect protein knots without necessary manual intervention due to the missing residues or chain breaks in the X-ray structures or the nonstandard PDB formats.

Most of the knots discovered in proteins are deep trefoil (3₁) knots. Figure eight knots (4₁), three-twist knots (5₂), Stevedore knots (6₁) and Septoil knot (7₁) have also been discovered. Recently, use of machine learning techniques for predicting protein structure, resulted in highly accurate prediction of 6₃ knot. Furthermore, using same techniques, composite knots (namely 3₁#3₁) were found and crystallised.