Noncovalent Interactions in Specific Recognition Motifs of Protein–DNA Complexes

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• 作者：Olga A. Stasyuk ; David Jakubec ; Jiří VondrášekPavel Hobza
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2017
• 出版时间：February 14, 2017
• 年：2017
• 卷：13
• 期：2
• 页码：877-885
• 全文大小：409K
• ISSN：1549-9626

文摘

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.