DNA nano-mechanics: how proteins deform the double helix
arXiv:0809.3938 · doi:10.1063/1.3082157
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.
accepted for publication in JCP; some minor changes in response to review 18 pages, 5 figure + supplement: 4 pages, 3 figures
References in corpus (2)
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