MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.

ABSTRACT: The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA

SUBMITTER: Falconi M 

PROVIDER: S-EPMC2479573 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature