Topological aspects in biological macromolecules

10/10/2007, 14:15, Room D6-135

Peter Virnau, Institut für Physik, Johannes Gutenberg-Universität

In the first part of the talk I will present preliminary work on the protein-DNA recognition problem. The challenge can be formulated as follows: Given the structure of a protein-DNA binding complex, predict sites in the genome which the protein recognizes, i.e., to which it binds with significant affinity, or vice versa optimize a given transcription factor such that related genes can be regulated. In particular, I will focus on testing the predictive quality of atomistic force-fields in conjunction with molecular mechnics calculations.

Although globular homopolymers display an abundance of knots, only about one in a thousand proteins contains a knot in its backbone. In the second part of my talk I will focus on these peculiar structures and 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 as well as evolutionary and functional implications.