Geometry/topology Seminar

A topological selection of knot folding pathways from native states

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Speaker(s): Agnese Barbensi (University of Oxford, Mathematical Institute)
A small percentage of catalogued proteins is known to form open ended knots. Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of their projections using topological objects called knotoids. We define a topologically inspired distance between the knotoid distributions of knotted proteins, and we use it to detect and distinguish specific geometrical features for proteins sharing the same dominant topology. Our method allows us to reveal different folding pathways for proteins forming open ended trefoil knots by directly looking at the geometry and topology of their native states. This is joint work with N.Yerolemou, O.Vipond, B.Mahler, P.Dabrowski-Tumanski and D.Goundaroulis.

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