### abstract ###
Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date.
We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the role of the enzyme in protein degradation.
While knots are usually preserved among homologues, we also identify an exception in a transcarbamylase.
This allows us to exemplify the function of knots in proteins and to suggest how they may have been created.
### introduction ###
Although knots are abundant and complex in globular homopolymers CITATION CITATION, they are rare and simple in proteins CITATION CITATION.
Sixteen methyltransferases in bacteria and viruses can be combined into the / knot superfamily CITATION, and several isozymes of carbonic anhydrase are known to be knotted.
Apart from these two folds, only a few insular knots have been reported CITATION, CITATION, CITATION, CITATION, some of which were derived from incomplete structures CITATION, CITATION.
For the most part, knotted proteins contain simple trefoil knots that can be represented by three essential crossings in a projection onto a plane.
Only three proteins were identified with four projected crossings .
In this report we provide the first comprehensive review of knots in proteins, which considers all entries in the Protein Data Bank CITATION, and not just a subset.
This allows us to examine knots in homologous proteins.
Our analysis reveals several new knots, all in enzymes.
In particular, we discovered the most complicated knot found to date in human ubiquitin hydrolase, and suggest that its entangled topology protects it against being pulled into the proteasome.
We also noticed that knots are usually preserved among structural homologues.
Sequence similarity appears to be a strong indicator for the preservation of topology, although differences between knotted and unknotted structures are sometimes subtle.
Interestingly, we have also identified a novel knot in a transcarbamylase that is not present in homologues of known structure.
We show that the presence of this knot alters the functionality of the protein, and suggest how the knot may have been created in the first place.
Mathematically, knots are rigorously defined in closed loops CITATION.
Fortunately, both the N- and C-termini of open proteins are typically accessible from the surface and can be connected unambiguously: we reduce the protein to its C - backbone, and draw two lines outward starting at the termini in the direction of the connection line between the center of mass of the backbone and the respective ends CITATION.
The lines are joined by a big loop, and the structure is topologically classified by the determination of its Alexander polynomial CITATION, CITATION.
Applying this method to the Protein Data Bank in the version of January 3, 2006, we found 273 knotted structures in the 32,853 entries that contain proteins.
Knots formed by disulfide CITATION, CITATION or hydrogen bonds CITATION were not included in the study.
