Capturing knots in (bio)polymers

Dr. Peter Virnau, Institut of Physics, Johannes Gutenberg-University of Mainz, Germany.


In this talk, I will give an overview on the appearance of knots in polymers, DNA and proteins. To begin with, I will present the statistics of knots with numerical simulations of a model polyethylene, spanning high temperature (coil) and low temperature (globule) phases and investigate the location and the distribution of knot sizes in random walks. Although globular homopolymers display an abundance of knots, only about one in a thousand protein structures are knotted. Can this absence of entanglement be explained in terms of statistical mechanics or is there an evolutionary bias? Do knots in proteins serve a purpose and how do they actually fold? To elaborate on this, I will present an overview of knotted proteins from the current version of the Protein Data Bank. I will also discuss some particularly intriguing examples of this set and explain how knots probably appeared in the cause of evolution.