SIB Group paves a new way to analyse protein knots

Some proteins form a specific knot when they fold into their native structures. The function of knots in proteins and the mechanism of their formation are still poorly understood. In order to study protein knots, it is necessary to identify knotted proteins and also pinpoint the location of knotted regions.

Until now, to find out whether a given protein is knotted or not it was necessary to close its polypeptide chain, as mathematically the concept of knotting was only defined for closed curves in space.
Although the closure was only performed in silico, at the level of protein coordinates, the process of closure by itself can produce knots when the closing segment passes through the complex windings of a protein chain. Therefore, researchers studying protein knots had to accept that their detection method had intrinsic problems.

In 2012, Russian mathematician Vladimir Turaev introduced a new concept of knotoids that allowed him to characterize entanglements of curves in space without their closure.

A SIB group composed of a mathematician, physicists and a biologist worked out a new method that allows to characterize the entanglement of protein chains using the concept of knotoids. This method will allow other groups to characterize knots in studied proteins without any need of closure. This new study entitled “Studies of global and local entanglements of individual protein chains using the concept of knotoids” by D. Gkountaroulis, J. Dorier, F. Benedetti and A. Stasiak will be published in Scientific Reports on 24 July 2017.

www.nature.com/articles/s41598-017-06649-3

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