DNA nanomechanics: How proteins deform the double helix

摘要

It is a standard exercise in mechanical engineering to infer the external forces and torques on a bodyfrom a given static shape and known elastic properties. Here we apply this kind of analysis todistorted double-helical DNA in complexes with proteins: We extract the local mean forces andtorques acting on each base pair of bound DNA from high-resolution complex structures. Ouranalysis relies on known elastic potentials and a careful choice of coordinates for thewell-established rigid base-pair model of DNA. The results are robust with respect to parameter andconformation uncertainty. They reveal the complex nanomechanical patterns of interaction betweenproteins and DNA. Being nontrivially and nonlocally related to observed DNA conformations,base-pair forces and torques provide a new view on DNA-protein binding that complementsstructural analysis.