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arXiv · 0809.3938

DNA nano-mechanics: how proteins deform the double helix

Nils B. Becker·Ralf Everaers
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Abstract

It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with proteins. We extract the local mean forces and torques acting on each base-pair of bound DNA from high-resolution complex structures. Our method relies on known elastic potentials and a careful choice of coordinates of the well-established rigid base-pair model of DNA. The results are robust with respect to parameter and conformation uncertainty. They reveal the complex nano-mechanical patterns of interaction between proteins and DNA. Being non-trivially and non-locally related to observed DNA conformations, base-pair forces and torques provide a new view on DNA-protein binding that complements structural analysis.

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Nils B. Becker, Ralf Everaers. 2008-12-17. DNA nano-mechanics: how proteins deform the double helix. https://doi.org/10.1063/1.3082157

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