Regensburg 2013 – scientific programme

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BP: Fachverband Biologische Physik

BP 2: Proteins

BP 2.10: Talk

Monday, March 11, 2013, 12:15–12:30, H44

Zinc Finger Proteins and the 3D Organization of Chromosomes — •Dieter Heermann¹, Christoph Feinauer¹, Sebastian Goldt², Andreas Hofmann¹, Lei Liu¹, and Gabriell Mate¹ — ¹Institut für Theoretische Physik, Universität Heidelberg, Philosophenweg 19, 69120 Heidelberg — ²Fitzwilliam College, Cambridge University, Cambridge, England

Zinc finger domains are one of the most common structural motifs in eukaryotic cells. These DNA-binding proteins contain up to 37 zinc finger domains connected by flexible linker regions. They have shown to be important organizers of the 3D structure of chromosomes and as such are called the master weaver of the genome.

Our results indicate that the binding affinity is increased by the flexible linkers by several orders of magnitude. Moreover, the binding map for proteins with more than one domain exhibits interesting structures which, having been neither observed nor described before can be interpreted to fit very well with existing theories of facilitated target location.

We have developed a methodology to characterize these flexible proteins. Employing the concept of barcodes we propose a measure to compare such flexible proteins in terms of a similarity measure. This measure is validated by a comparison between a geometric similarity measure and the topological similarity measure that takes geometry as well as topology into account.