Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F17%3A00475097" target="_blank" >RIV/61388963:_____/17:00475097 - isvavai.cz</a>
Alternative codes found
RIV/00216208:11310/17:10368324 RIV/61989592:15310/17:73584596
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.6b00775" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.6b00775</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.6b00775" target="_blank" >10.1021/acs.jctc.6b00775</a>

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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Type
J<sub>imp</sub> - 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

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)

Publication year
2017
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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