DNA nano-mechanics: how proteins deform the double helix

TL;DR

This paper introduces a method to analyze the nano-mechanical forces and torques exerted on DNA by proteins using high-resolution structures, revealing complex interaction patterns that enhance understanding of DNA-protein binding.

Contribution

It applies mechanical analysis to DNA-protein complexes, providing a novel way to infer forces and torques from static structures, complementing traditional structural approaches.

Findings

Revealed complex force and torque patterns in DNA-protein interactions

Demonstrated robustness of the method against parameter uncertainties

Provided new insights into DNA-protein binding mechanics

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.