title: Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes.
abstract: 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.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.
authors.forename: Olga A
authors.initials: OA
authors.lastname: Stasyuk
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.|Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague , Albertov 6, 128 43 Prague, Czech Republic.
authors.forename: David
authors.initials: D
authors.lastname: Jakubec
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.
authors.forename: Jiří
authors.identifier: http://orcid.org/0000-0002-6066-973X
authors.initials: J
authors.lastname: Vondrášek
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.|Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic.
authors.forename: Pavel
authors.identifier: http://orcid.org/0000-0001-5292-6719
authors.initials: P
authors.lastname: Hobza
mesh_terms: D020816:Amino Acid Motifs; D004247:DNA / Q000378:metabolism*; D030562:Databases, Protein; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D011506:Proteins; D004247:DNA