Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F16%3A00463502" target="_blank" >RIV/61388963:_____/16:00463502 - isvavai.cz</a>
Alternative codes found
RIV/00216208:11310/16:10332095
Result on the web
<a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158704" target="_blank" >http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158704</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1371/journal.pone.0158704" target="_blank" >10.1371/journal.pone.0158704</a>

Result language
angličtina
Original language name
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis
Original language description
Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue-amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein-DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
<a href="/en/project/LH11020" target="_blank" >LH11020: Systematic mapping of the conformational space of short peptides through molecular dynamics simulation - a way to understanding of protein structure formation.</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2016
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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