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In another study, knotting fingerprint analyses of transmembrane transporting channels from five different families of proteins showed that the slipknotted topology is conserved.

Alternatively, DCL-based approaches utilise the fact that a number of building blocks can come together to form chains of different lengths which can then fold to a thermodynamically stable state. Whereas, in some cases, the molecules are rigid in the presence of the templating metal ion, they can clearly undergo conformational change and their flexibility can alter when the metal ion is removed.

In contrast to small monomeric proteins with simple folds, it is clear that proteins with topologically knotted or slipknotted structures have much more complex energy landscapes with many intermediate states and parallel pathways. The fusion proteins created in this study represent some of the most deeply knotted proteins known, the C-terminal fusions requiring some or more residues to pass through a loop to form the knotted native state.

Numerous simulation studies have shown that a slipknot may be an important intermediate configuration in the folding of knotted proteins [,] and thus, understanding the mechanisms involved in their formation could offer insights into how deeply knotted proteins fold.

In all of these cases, the link or knot is created by a covalent bond or oligomeric structure. Much research effort has been undertaken to address the question of whether a knot can provide additional thermodynamic, kinetic or mechanical stability to a protein structure.

Further studies by the same group demonstrated that a more topologically complex protein knot, the 5 2 knot, clearly enhanced the protein’s kinetic stability in comparison to that of a protein containing a 3 1 knot [ ].

Furthermore, it was shown that specific native contacts within the trefoil-knotted core are crucial in maintaining the knot in the denatured state, and that threading occurs in the late stages of folding [ ]. For each fold, the PDB code for the structure of the protein or a typical protein in the family is given. The procedure is repeated many times and a spectrum of knots is obtained, in which the knot type that is dominant is labelled as the knot type of the chain. In each case, an x-ray crystal structure left and a schematic representation of the link right are shown.


The results were consistent with the protein knotting and folding from an initially unknotted nascent chain, thus demonstrating that a process associated with the knotting step is rate limiting. Importantly, this translational mechanism is known to be essential for the replication and proliferation of all retroviruses. This review highlights some of the molecular knotted structures discovered in biology and chemistry.

This is due to the increased compactness of the molecule as the ACN increases. The mechanism of action of this family of enzymes is known, and involves cutting of the DNA chain, movement of one part of the chain relative to another, and the ligation of the two ends of the cut chain to form a closed system.

They speculate on why naturally occurring RNAs do not contain knots and suggest a number of possible causes: It is interesting to note that topoisomerases, known to work on DNA, can also catalyse knotting and unknotting events in synthetic forms of RNA, even though there is no known biological activity associated with this.

Knots were generated using KnotPlot http: More complex knots have also been identified in proteins that catalyse various enzymatic reactions.

Molecular knots in biology and chemistry

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It is worth noting that this behavior of slipknotted structures is different to that observed for uniformly elastic polymers [ ].

Sequences and structures of RNA pseudoknots. These include structures that contain a trefoil 3 1figure-of-eight 4 1Gordian 5 2 and stevedore 6 1 knot with three, four, five and six projected crossings of the polypeptide backbone, respectively figure 9.


A tetrahedral copper I ion acts as a template to coordinate a single polypyridyl ligand and form the crossing points, while another copper I ion binds to the functional end groups of the ligand, threads the loop through its coordination geometry and subsequently catalyses the covalent bond formation to create the trefoil knot motif figure 14 c.

These computational studies revealed non-trivial behaviour in which the extremes i. Lopez and co-workers demonstrated that Topo IV in bacteria can not only form knots in DNA during replication but it is also responsible in unknotting them later on so that DNA can get correctly segregated to every daughter cell [ 44 ].

Recently, the same group extended these studies and used the same model to investigate in further detail the effect of knots, knot depth and motif on folding properties of 3 1 -knotted proteins [ ]. Most recently, Soler and co-workers extended their studies to investigate the folding mechanism of the more complex 5 2 -knot [ ].

Molecular knots in biology and chemistry – IOPscience

As yet, it remains to be seen what factors actually determine viral genome organisation in terms of its knot types and distribution. It has been speculated that a knotted topology could play a key role in increasing catalytic activity or ligand binding affinity potentially by decreasing dynamics or enhancing stability thermodynamic, kinetic and mechanical of a protein. In addition, it is only recently that chemists have been able to synthesise knotted molecular species and they are only just beginning to study the properties of these types of structures.

In brief, the DCL 15088 allows the molecules themselves to discover different conformations in solution until those, which are thermodynamically the most stable, persist in the mixture once equilibrium is reached. Interested readers are directed towards the following references for a more detailed discussion of all of these topics [ 101114636869 ].