Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue-amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein-DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties.

• MeSH
• adenin chemie   metabolismus   MeSH
• aminokyselinové motivy * MeSH
• aminokyseliny chemie   metabolismus   MeSH
• cytosin chemie   metabolismus   MeSH
• databáze proteinů MeSH
• DNA vazebné proteiny chemie   genetika   metabolismus   MeSH
• DNA chemie   genetika   metabolismus   MeSH
• guanin chemie   metabolismus   MeSH
• konformace nukleové kyseliny MeSH
• krystalografie rentgenová MeSH
• molekulární modely MeSH
• statistika jako téma metody   MeSH
• terciární struktura proteinů MeSH
• termodynamika MeSH
• thymin chemie   metabolismus   MeSH
• vazba proteinů MeSH
• vazebná místa genetika   MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenin MeSH
• aminokyseliny MeSH
• cytosin MeSH
• DNA vazebné proteiny MeSH
• DNA MeSH
• guanin MeSH
• thymin MeSH

In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution.

• MeSH
• konformace nukleové kyseliny MeSH
• kvantová teorie * MeSH
• nukleové kyseliny chemie   MeSH
• RNA chemie   MeSH
• výpočetní biologie * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• nukleové kyseliny MeSH
• RNA MeSH

The pi-pi interactions between benzene and the aromatic nitrogen heterocycles pyridine, pyrimidine, 1,3,5-triazine, 1,2,3-triazine, 1,2,4,5-tetrazine, and 1,2,3,4,5-pentazine are systematically investigated. The T-shaped structures of all complexes studied exhibit a contraction of the C--H bond accompanied by a rather large blue shift (40-52 cm(-1)) of its stretching frequency, and they are almost isoenergetic with the corresponding displaced-parallel structures at reliable levels of theory. With increasing number of nitrogen atoms in the heterocycle, the geometries, frequencies, energies, percentage of s character at C, and the electron density in the C--H sigma antibonding orbital of the complexes all increase or decrease systematically. Decomposition analysis of the total binding energy showed that for all the complexes, the dispersion energy is the dominant attractive contribution, and a rather large attraction originating from electrostatic contribution is compensated by its exchange counterpart.

• MeSH
• benzen chemie   MeSH
• chemické modely * MeSH
• dusík chemie   MeSH
• elektrony MeSH
• heterocyklické sloučeniny chemie   MeSH
• molekulární modely MeSH
• přenos energie MeSH
• stereoizomerie MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• benzen MeSH
• dusík MeSH
• heterocyklické sloučeniny MeSH