ArticleBiophysical journal2005
Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 26 citations in OpenAlex.
- Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding.Nucleic acids research · 2020Article
- How methyl-sugar interactions determine DNA structure and flexibility.Nucleic acids research · 2019Article
- DNA conformational transitions inferred from re-evaluation of m|FActa crystallographica. Section D, Structural biology · 2017Article
- Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions.PloS one · 2010Article
- DNA structures from phosphate chemical shifts.Nucleic acids research · 2010Article
- Evolutionary and biophysical relationships among the papillomavirus E2 proteins.Frontiers in bioscience (Landmark edition) · 2009Review
- Insights on protein-DNA recognition by coarse grain modelling.Journal of computational chemistry · 2008Article
- MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.Biophysical journal · 2008Article
- Switching control of expression of ptsG from the Mlc regulon to the NagC regulon.Journal of bacteriology · 2008Article
- Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites.Nucleic acids research · 2008Article
- Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides.Nucleic acids research · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations of a total duration of 30 ns in explicit solvent were carried out on the BPV-1-E2 protein complexed to a high-affinity DNA target containing the two hydrogen-bonded ACCG.CGGT half-sites separated by the noncontacted ACGT sequence. The analysis of the trajectories focuses on the DNA structure and on the dynamics. The data are compared to those issued from recent simulations made on three free targets that recognize E2 with different affinities. E2 does not drastically perturb the mechanic properties of the free DNA: the structural relationships between the BI/BII backbone substates and some helical parameters are preserved in the complex despite a severe slowing down of the phosphate group motions. The structures of both free and bound half-sites are very close to each other although the conformational space explored by these regions is narrowed when they are contacted by the protein. The enhanced plasticity found in the best free target spacers, mainly manifested through the backbone motions, allows a clear overlap between several free and bound global DNA features such as the base displacement. Furthermore, this flexibility is preserved in the complex. Our results support the hypothesis that E2 takes advantage of free predistorted structures that may minimize the DNA deformation cost. In addition, we observe that E2 is far from totally stiffening the DNA, suggesting that the entropic penalty inherent in the complex formation could be limited.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.