Absence of knots in known RNA structures

Abstract

The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed.RNA structure | RNA knots | physical knots | PDB-wide topological profiling T he notion that biomolecules should be minimally entangled to fold efficiently and reproducibly and sustain functionally oriented structural arrangements seems so intuitive that viable biological molecules have long been thought to be practically free of physical knots (1, 2).Indeed, it was only relatively recently that the occurrence of deeply knotted proteins was shown (3). Several other instances of knotted and slipknotted proteins have been discovered more recently (4), and it is now established that a sizeable fraction of the protein chains deposited in the Protein Data Bank (PDB) (5) host physical knots (1, 6). The latter range in complexity from the simplest trefoil knot to the six-crossing Stevedore's knot (7). The functional implications of these knots are still unclear. Nevertheless, several hypotheses have been formulated to rationalize the functional advantage that arguably leads specific knotted proteins to evolve from unknotted ones (6, 8). For instance, knots have been argued to enhance the mechanical stability of active sites and prevent proteolytic degradation (8, 9).Although empirical evidence shows de facto that knotted proteins do exist, it also confirms the expectations that physical knots can significantly hinder and slow down the spontaneous folding process (10). This occurs because the various folding steps need to be well-coordinated to ensure the formation of the correct knot type in the correct protein location (11-13). This limited kinetic accessibility is likely responsible for the much lower incidence of knots in proteins compared with generic equilibrated polymers (14), where entanglement inevitably arises with increasing chain length and compactness (15-18).Physical knots have also been shown t...

Multiple folding pathways of proteins with shallow knots and co-translational folding

“…On the other hand, there are very few knotted RNA molecules -in a recent assessment [3] only three cases have been identified, but the corresponding structures are resolved poorly. Occurrence of knotted proteins is in between -several hundreds of knot-containing structure files and a dozen of truly independent structures [4,5,6,7] in the Protein Data Bank (PDB).…”

Molekulare Knoten

“…[146] Es mag überraschen, dass natürlich verknotete RNA bisher noch nicht entdeckt wurde,die Gründe fürihr Fehlen sind unklar. [147] In bahnbrechenden Arbeiten von Seemans Gruppe wurden auch künstliche DNA-Knoten vorgestellt. [148] [149][150][151] Das erste Protein, in dem ein verknotetes Rückgrat identifiziert wurde,w ar eine a-Carboanhydrase.…”

A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds

“…A survey showed that knotted RNA molecules are rare among currently known RNA structures [18]: Only 3 knotted RNA chains, with 3, 4 and 16 crossings, respectively, are found among 2,863 RNA structures contained in the PDB. However, conventional knot polynomials only consider phosphodiester bonds in an RNA molecule, and completely ignores the topological effects of hydrogen bonds in stem regions, the basis of the formation of RNA secondary structures.…”