DNA nanomechanics: how proteins deform the double helix.
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from a given 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 analysis relies on known elastic potentials and a careful choice of coordinates for the well-established rigid base-pair model of DNA. The results are robust with respect to parameter and conformation uncertainty. They reveal the complex nanomechanical patterns of interaction between proteins 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 complements structural analysis.
Laboratoire de Physique de l'Ecole Normale Supérieure, Université de Lyon, 69007 France. nils.becker@ens-lyon.fr
Nils B
NB
Becker
Ralf
R
Everaers
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D049329:Nanostructures; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D035181:TATA-Box Binding Protein / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
D035181:TATA-Box Binding Protein; D004247:DNA; D004706:Endodeoxyribonucleases; C064579:I-Ppo endonuclease