Knots in biopolymers

Knotted macromolecular chains are common in living organisms. For example, knots existing in certain enzymes and DNA molecules are crucial to their biological function. Knotted structures have also been synthesized for use as novel building blocks for nanotechnological applications. Because of their small size, DNA and proteins undergo incessant random motion. Consequently, knots tied in those tiny molecular ropes are quite unlike the knots we are accustomed to in our everyday life. For example, rock climbers and sailors who use knots to join ropes (below) are fortunate that they do not have to deal with thermal motion, which can “lubricate” a pair of molecular strands so that they easily come apart when one pulls on them.

Click here to see what happens when two polymer strands joined by a knot are pulled apart (simulation by Serdal Kirmizialtin)

For further details see [Serdal Kirmizialtin and Dmitrii E. Makarov, Simulations of the untying of molecular friction knots between individual polymer strands, J. Chem. Phys. 128 (2008) 094901]  link

Knots in polymer chains are not static. For example, a simple knot tied in a tensioned polymer will move randomly (simulation by Lei Huang)

  • For details see [Lei Huang and Dmitrii E. Makarov, Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains, J. Phys. Chem. A 111(2007)  10338-10344] link

Knots existing in certain protein structures can prevent passage of those proteins through narrow constrictions (such as the proteasome entrance). Here we illustrate this by simulating translocation of knotted and unknotted peptides through a pore (courtesy of Lei Huang).

Translocation of an unknotted protein

Translocation of a knotted protein

  • For details see [Lei Huang and Dmitrii E. Makarov, Translocation of a knotted polypeptide through a pore, J. Chem. Phys. 129 (2008), 121107.] link