Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session II

53 – POS Board 25 Thermal Properties of Polymer Knots in the Presence of Short-range Interactions Yani Zhao . Institute of Physics, University of Szczecin, Szczecin, Poland. Polymer rings forming complex topological configurations are studied in connection with several applications ranging from biochemistry to mechanical engineering. A brief account on the latest experimental results in the subject will be reviewed. The most difficult problem in dealing with the statistical mechanics of polymer knots is to distinguish their topological configurations. In this talk the results of extensive simulations of single polymer knots on a simple cubic lattice and with lengths up to thousand segments will be presented. To equilibrate the knots and for the Monte Carlo sampling, which is based on the Wang-Landau algorithm, a set of pivot moves is used. To preserve the topology of the knots after each move, two recently developed techniques have been employed. One is the so-called PAEA method. It is able to detect the changes of topology exactly and is very fast. The other method uses the Vassiliev knot invariant of degree 2 represented in the form of contour integrals. This invariant has the great advantage of allowing large pivot moves, which are able to accelerate the Monte Carlo sampling procedure. As an application of these methods, the calculation of the specific energy, the radius of gyration and the heat capacity of several types of polymer knots in a solution with poor or good solvents will be presented. Some consequences on the thermodynamics of polymer knots will be drawn. The problem of sampling certain rare knot conformations and of detecting pseudo phase transitions associated with these conformations will be discussed. A comparison with the previously known result will be made. Board 26 Unknotting the Gordian Knot: Single Molecule Force Spectroscopy on UCH-L1 Fabian Ziegler 1 , Nicole Lim 2 , Benjamin Pelz 1 , Mathias Arens 1 , Soumit Mandal 1 , Wei-Ping Ng 2 , Sophie E. Jackson 2 .Matthias Rief 1 . 1 Technische Universität München, Garching, Germany, 2 University of Cambridge, Cambridge, United Kingdom. We perform Single Molecule Force Spectroscopy with Optical Tweezers to single molecules of the knotted protein UCH-L1, a protein knot with a 5 2 (so called "Gordian") topology. Force offers ideal possibilities to control the conformation of the knotted chain. Here we apply force in the range of several piconewton to single molecules of UCH-L1. With mutations of single amino acids in the sequence of UCH-L1 we can pull with different geometries. Pulling at the n- and c-terminus of the sequence leads to unfolding and tightening the knot, while other pulling positions can reduce the knot from a 5 2 to a 3 1 structure or even completely unknot the polypeptide chain. With these mutants, we study the folding kinetics in dependence of the knot formation of UCH-L1. 54 – POS

- 98 -