Knotted protein

Although number of computational methods have been developed to detect protein knots, there are still no completely automatic methods to detect protein knots without necessary manual intervention due to the missing residues or chain breaks in the X-ray structures or the nonstandard PDB formats.

Mathematically, a knot is defined as a subset of three-dimensional space that is homeomorphic to a circle.

For more complex knots, it is theoretically possible to have the loop to twist multiple times around itself, meaning that one end of the chain gets wrapped around at least once, and then threading to occur.

[7] The folding of knotted proteins may be explained by interaction of the nascent chain with the ribosome.

[9] In another experimental study, a 91-residue-long protein was attached to the termini of YibK and YbeA.

[12] Another topologically complex structure is the link formed by covalent loops, closed by disulfide bridges.

[15] Yet another complex structures arising as a result of the existence of disulfide bridges are the cystine knots, for which two disulfide bridges form a closed, covalent loop, which is threaded by third chain.

[16] One can also consider loops in proteins formed by pieces of the main chain and the disulfide bridges and interaction via ions.

Such loops can also be knotted of form links even within structures with unknotted main chain.

Human carbonic anhydrase was identified to have a low unknot score (22).

If there is no knot, the algorithm eventually produces a straight line that joins both termini.

Some proposals about the function of knots have been that it might increase thermal and kinetic stability.

It was also shown that the knot in proteins creates the places on the verge of hydrophobic and hydrophilic parts of the chain, characteristic for active sites.

The rotating view of a smoothed chain of a knotted protein (PDB ID: 1xd3)
Four knot types identified in proteins: the 3 1 knot (upper left), the 4 1 knot (upper right), the 5 2 knots (lower left) and the 6 1 knot (lower right). These images were produced by KnotPlot. [ 5 ] Note that the 3 1 knot has in fact two distinct forms: left-handed and right-handed. What is shown here is a right-handed 3 1 knot.
(A) A protein is an open chain. (B) To create a closed loop, we pick a point at an infinite distance, and connect it to the N and C termini, thus the whole topological structure becomes a closed loop.
A possible slipknot in a protein. If the terminus is cut from the red line (1), a trefoil knot is created (2).