DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA neucleobases or deoxyribose sugar
Date
2014
Authors
Wilson, Katie A.
Kellie, Jennifer L.
Wetmore, Stacey D.
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Abstract
Four hundred twenty-eight high-resolution DNA–
protein complexes were chosen for a bioinformatics
study. Although 164 crystal structures (38% of those
searched) contained no interactions, 574 discrete pi-
contacts between the aromatic amino acids and the
DNA nucleobases or deoxyribose were identified using
strict criteria, including visual inspection. The
abundance and structure of the interactions were determined
by unequivocally classifying the contacts
as either pi–pi stacking, Pi–pi T-shaped or sugar–
pi contacts. Three hundred forty-four nucleobase–
amino acid pi–pi contacts (60% of all interactions
identified) were identified in 175 of the crystal structures
searched. Unprecedented in the literature, 230
DNA–protein sugar–pi contacts (40% of all interactions
identified) were identified in 137 crystal structures,
which involve C–H···pi and/or lone–pair···pi interactions,
contain any amino acid and can be classified
according to sugar atoms involved. Both pi–pi
and sugar–pi interactions display a range of relative
monomer orientations and therefore interaction energies
(up to –50 (–70) kJ mol−1 for neutral (charged)
interactions as determined using quantum chemical
calculations). In general, DNA–protein pi-interactions
are more prevalent than perhaps currently accepted
and the role of such interactions in many biological
processes may yet to be uncovered.
Description
Sherpa Romeo green journal, open access
Keywords
DNA-protein , DNA nucleobases , Aromatic amino acids , Pi-interactions , Deoxyribose
Citation
Wilson, K. A., Kellie, J. L., & Wetmore, S. D. (2014). DNA-protein, pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Research, 43(10), 672-6741. doi:10.1093/nar/gku269