KnotProt: a database of proteins with knots and slipknots

Abstract

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.

Characterization of the Folding of a 5 2 -Knotted Protein Using Engineered Single-Tryptophan Variants

“…The knot is relatively shallow compared with some other deeply knotted protein structures, since only five to six residues need to pass through a loop to make the knot (43). Within the 5 2 knot, there is a 3 1 knot that resides between residues 6 and 163 (43). Although we cannot state categorically whether the intermediate states observed are knotted or not, it is possible to use the structural information we obtained to speculate about the knotted state of the intermediates.…”

“…The knot is relatively shallow compared with some other deeply knotted protein structures, since only five to six residues need to pass through a loop to make the knot (43). Within the 5 2 knot, there is a 3 1 knot that resides between residues 6 and 163 (43).…”

Knots in knots: A study of classical knot diagrams

“…Subsequent to these discussions, Rawdon, Stasiak and I studied the presence of subknots, using the spatial closure method discussed earlier, in ideal and random knots [4], the knotting fingerprint, in a generalization of the earlier protein structural analysis [2,6] in which we used another version of a knotting fingerprint. Here, each cell in the circular fingerprint expresses the strength of the knotting of …”

Structural entanglements in protein complexes

“…Chronologically, the first entry on the list of such proteins appears to be carbonic anhydrase B 4,5 and the current status of the list can be obtained, for instance, at the KnotProt database 6 . The protein backbones do not form closed loops, however, and the presence of a knot cannot be assessed in absolute terms as it depends on the method used to connect the termini beyond the backbone in order to generate a closed line.…”