Dresden 2009 – scientific programme

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BP: Fachverband Biologische Physik

BP 20: DNA, RNA and Chromatin

BP 20.10: Talk

Thursday, March 26, 2009, 16:45–17:00, HÜL 186

Extracting intermolecular forces in protein-DNA complexes from structural data — •Nils Becker and Ralf Everaers — Laboratoire de Physique, École Normale Supérieure, Université de Lyon

It is a standard exercise in mechanical engineering to infer external forces acting on a body, when given its shape and elastic properties. We apply this kind of analysis to distorted double-helical DNA in complexes with proteins, and extract the local mean forces and torques acting on each base-pair of bound DNA from high-resolution complex structures. The analysis relies on known elastic potentials and a careful choice of coordinates for the well-established rigid base-pair model of DNA. The results reveal the complex nano-mechanical patterns of interaction between proteins and DNA. An application of this idea to 146bp and 147bp crystal structures of the nucleosome core particle reveals a characteristic force pattern at the well-known DNA contact sites, and leads to an explanation of twist defect placement in the irregular 146bp structure.