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

TitleMD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.
Publication TypeJournal Article
Year of Publication2008
AuthorsFalconi, M, Oteri, F, Eliseo, T, Cicero, DO, Desideri, A
JournalBiophys J
Volume95
Issue3
Pagination1108-17
Date Published2008 Aug
ISSN1542-0086
KeywordsBovine papillomavirus 1, Computer Simulation, DNA, Viral, DNA-Binding Proteins, Models, Chemical, Models, Molecular, Structure-Activity Relationship, Viral Proteins
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 readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.

DOI10.1529/biophysj.108.130849
Alternate JournalBiophys. J.
PubMed ID18487311
PubMed Central IDPMC2479573