Berlin 2008 – scientific programme

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BP: Fachverband Biologische Physik

BP 26: Posters II

BP 26.6: Poster

Thursday, February 28, 2008, 17:00–19:30, Poster A

Stretching of a DNA/HU-protein complex 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 interact with the DNA in a non-specific way [1]. Its major function is the binding, compaction and stabilization of DNA. We applied steered molecular dynamic (SMD) simulations to DNA which is bound to a HU protein. 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].
[1] R. Dame and N. Goosen, FEBS Lett. 529, 151 (2006).
[2] M. Salomo, F. Kremer et al., J. Mol. Biol. 359, 769 (2006).