Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes
Result description
The growing number of high-quality experimental (X-ray, NMR) structures of protein-DNA complexes has sufficient enough information to assess whether universal rules governing the DNA sequence recognition process apply. While previous studies have investigated the relative abundance of various modes of amino acid-base contacts (van der Waals contacts, hydrogen bonds), relatively little is known about the energetics of these noncovalent interactions. In the present study, we have performed the first large-scale quantitative assessment of binding preferences in protein-DNA complexes by calculating the interaction energies in all 80 possible amino acid-DNA base combinations. We found that several mutual amino acid-base orientations featuring bidentate hydrogen bonds capable of unambiguous one-to-one recognition correspond to unique minima in the potential energy space of the amino acid-base pairs. A clustering algorithm revealed that these contacts form a spatially well-defined group offer
Keywords
The result's identifiers
Result code in IS VaVaI
Result on the web
DOI - Digital Object Identifier
Alternative languages
Result language
angličtina
Original language name
Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes
Original language description
The growing number of high-quality experimental (X-ray, NMR) structures of protein-DNA complexes has sufficient enough information to assess whether universal rules governing the DNA sequence recognition process apply. While previous studies have investigated the relative abundance of various modes of amino acid-base contacts (van der Waals contacts, hydrogen bonds), relatively little is known about the energetics of these noncovalent interactions. In the present study, we have performed the first large-scale quantitative assessment of binding preferences in protein-DNA complexes by calculating the interaction energies in all 80 possible amino acid-DNA base combinations. We found that several mutual amino acid-base orientations featuring bidentate hydrogen bonds capable of unambiguous one-to-one recognition correspond to unique minima in the potential energy space of the amino acid-base pairs. A clustering algorithm revealed that these contacts form a spatially well-defined group offer
Czech name
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Czech description
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Classification
Type
Jx - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
—
Result continuities
Project
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Theory and Computation
ISSN
1549-9618
e-ISSN
—
Volume of the periodical
11
Issue of the periodical within the volume
4
Country of publishing house
US - UNITED STATES
Number of pages
10
Pages from-to
1939-1948
UT code for WoS article
000353176500058
EID of the result in the Scopus database
2-s2.0-84927762269
Basic information
Result type
Jx - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP
CF - Physical chemistry and theoretical chemistry
Year of implementation
2015