Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes
Result description
In-view of the importance of protein-DNA interactions in biological processes, we extracted from the Protein Data Bank several one-to-one complexes of amino acids with nucleotides that matched certain geometric and energetic specificity criteria and investigated them using quantum chemistry methods. The CCSD(T)/CBS interaction energies were used as a benchmark to compare the performance of the MP2.5, MP2-F12, DFT-D3, and PM6-D3H4 methods. All methods yielded good agreement with the reference values, with declining accuracy from MP2.5 to PM6-D3H4. Regardless of the site of interaction, the minima found after full optimization in implicit solvent with high dielectric constant were close to the structures experimentally detected in protein-DNA complexes. According to DFT-SAPT analysis, the nature of noncovalent interactions strongly depends on the type of amino acid. The negatively charged sugar-phosphate backbone of DNA heavily influences the strength of interactions and must be included in the computational model, especially in the case of interactions with charged amino acids.
Keywords
density functional theoryside chain interactionsinteraction energies
The result's identifiers
Result code in IS VaVaI
Alternative codes found
RIV/00216208:11310/17:10368324 RIV/61989592:15310/17:73584596
Result on the web
DOI - Digital Object Identifier
Alternative languages
Result language
angličtina
Original language name
Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes
Original language description
In-view of the importance of protein-DNA interactions in biological processes, we extracted from the Protein Data Bank several one-to-one complexes of amino acids with nucleotides that matched certain geometric and energetic specificity criteria and investigated them using quantum chemistry methods. The CCSD(T)/CBS interaction energies were used as a benchmark to compare the performance of the MP2.5, MP2-F12, DFT-D3, and PM6-D3H4 methods. All methods yielded good agreement with the reference values, with declining accuracy from MP2.5 to PM6-D3H4. Regardless of the site of interaction, the minima found after full optimization in implicit solvent with high dielectric constant were close to the structures experimentally detected in protein-DNA complexes. According to DFT-SAPT analysis, the nature of noncovalent interactions strongly depends on the type of amino acid. The negatively charged sugar-phosphate backbone of DNA heavily influences the strength of interactions and must be included in the computational model, especially in the case of interactions with charged amino acids.
Czech name
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Czech description
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Classification
Type
Jimp - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2017
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
13
Issue of the periodical within the volume
2
Country of publishing house
US - UNITED STATES
Number of pages
9
Pages from-to
877-885
UT code for WoS article
000394924000044
EID of the result in the Scopus database
2-s2.0-85012880758
Result type
Jimp - Article in a specialist periodical, which is included in the Web of Science database
OECD FORD
Physical chemistry
Year of implementation
2017