IEEE.DNA.Deformation.Energy.As.An.Indirect.Recognition.Mechanism.In.Protein-DNA.Interactions.2007.RETAiL.eBook-KLIP
PACKS________: idib-ddnade
RELEASE DATE_: 2019.09.29
YEAR_________: 2007
LANGUAGE_____: English
RELEASE SIZE_: 0 Mb - 01 files
PAGES________: 9
SOURCE_______: <a href="https://dereferer.me/?https://ieeexplore.ieee.org/document/4104465" target="_blank">https://ieeexplore.ieee.org/document/4104465</a>
PROTECTION___: -(removed)
FORMAT_______: .pdf
ISBN CODE____: 1545-5963
GENRE________: Scientific Papers
NOTES________: Enjoy
PLOT_________: Abstract: Proteins that bind to specific
locations in genomic DNA control many basic
cellular functions. Proteins detect their
binding sites using both direct and indirect
recognition mechanisms. Deformation energy,
which models the energy required to bend DNA
from its native shape to its shape when bound
to a protein, has been shown to be an
indirect recognition mechanism for one
particular protein, integration host factor
(IHF). This work extends the analysis of
deformation to two other DNA-binding
proteins, CRP and SRF, and two endonucleases,
I-Crel and I-Ppol. Known binding sites for
all five proteins showed statistically
significant differences in mean deformation
energy as compared to random sequences.
Binding sites for the three DNA-binding
proteins and one of the endonucleases had
mean deformation energies lower than random
sequences. Binding sites for I-Ppol had mean
deformation energy higher than random
sequences. Classifiers that were trained
using the deformation energy at each base
pair step showed good cross-validated
accuracy when classifying unseen sequences as
binders or nonbinders. These results support
DNA deformation energy as an indirect
recognition mechanism across a wider range of
DNA-binding proteins. Deformation energy may
also have a predictive capacity for the
underlying catalytic mechanism of DNA-binding
enzymes
KNOWLEDGE IS POWER
