Studies of global and local entanglements of individual protein chains using the concept of knotoids

Abstract

Abstract We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open curves in 3D space, in contrast to knot diagrams which represent projections of closed curves in 3D space. The intrinsic difference with classical knot theory is that the generalization provided by knotoids admits non-trivial topological entanglement of the open curves provided that their geometry is frozen as it is the case for crystallized proteins. Consequently, our approach doesn’t require the closure of chains into loops which implies that the geometry of analysed chains does not need to be changed by closure in order to characterize their topology. Our study revealed that the knotoid approach detects protein regions that were classified earlier as knotted and also new, topologically interesting regions that we classify as pre-knotted.