Dresden 2009 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Poster I

BP 7.57: Poster

Monday, March 23, 2009, 17:45–20:00, P3

Stretching of a DNA/HU-protein complexes in SMD simulations — •Carsten Olbrich and Ulrich Kleinekathöfer — Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany

The protein HU is a member of a family of prokaryotic proteins that interacts with the DNA in a non-specific way [1]. Its major function is the binding, compaction and stabilization of DNA. Steered molecular dynamic (SMD) simulations are applied to DNA which is either bound to the HU protein of the bacteria Anabaena (AHU) or of the Thermotoga maritima (TmHU). Using these all-atom simulations including explicit water and about 80,000 atoms in total, we are able to gain insight into the discrete disruptions events which occur when the DNA releases from the protein body. These disruptions were first observed in experiments performed with optical tweezers [2]. By comparing the unbinding pathways of the complexes, different binding strengths of AHU and TmHU to DNA can be found.
[1] R. Dame and N. Goosen, FEBS Lett. 529, 151 (2006).
[2] M. Salomo, F. Kremer et al., J. Mol. Biol. 359, 769 (2006).