Are there knots in proteins?

Conservation of complex knotting and slipknotting patterns in proteins

“…Of course, the characterization of the knotting within the protein structures makes sense only if one considers fixed configurations, in this case proteins in their native folded structures. Then they may be treated as frozen and thus unable to undergo any deformation.Several papers have described various interesting closure procedures to capture the knot type of the native structure of a protein or a subchain of a closed chain (1,3,(29)(30)(31)(32)(33). In general, the strategy is to ensure that the closure procedure does not affect the inherent entanglement in the analyzed protein chain or subchain.…”

“…However, the shortening method applied to the same starting configuration can result in different knot types depending on the order of the shortening moves (30). Because the order of the shortening moves is not determined by the actual configuration but depends on arbitrarily chosen parameters, this method also is confronted with the problem that the linear chains do not totally determine the knot type of the frozen chain.Limitations in these single closure methods stimulated interest in probabilistic methods of defining the most likely knot type of linear chains with a given geometry (1,3,30). One relatively simple, unbiased method consists of placing the analyzed linear chain near the center of a large sphere and closing it by adding to each end one long segment connecting it with the same, randomly chosen point on the enclosing sphere.…”

“…protein knots | knot theory | topology T here are increasing numbers of known proteins that form linear open knots in their native folded structure (1,2). In general, knots in proteins are orders of magnitude less frequent than would be expected for random polymers with similar length, compactness, and flexibility (3).…”

“…Therefore, it is believed that knotted protein structures were, in part, eliminated during evolution because proteins that fold slowly and/or nonreproducibly should be evolutionarily disadvantageous for the hosting organisms. Nevertheless, there are several families of proteins that reproducibly form simple knots, complex knots, and slipknots (1,2). In these proteins, the disadvantage of less efficient folding may be balanced by a functional advantage connected with the presence of these knots.…”

“…To shed light on the function and formation of protein knots, we performed a thorough characterization of knotting within protein structures deposited in the Protein Data Bank (PDB) (28) by creating a precise mapping of the position and size of the knotted and slipknotted domains and knot tails (1,2). We identified the types of knots that are formed by the backbone of the entire polypeptide chain and also by all continuous backbone portions of a given protein (1,2).…”