DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA neucleobases or deoxyribose sugar

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dc.contributor.authorWilson, Katie A.
dc.contributor.authorKellie, Jennifer L.
dc.contributor.authorWetmore, Stacey D.
dc.date.accessioned2016-08-16T21:21:00Z
dc.date.available2016-08-16T21:21:00Z
dc.date.issued2014
dc.descriptionSherpa Romeo green journal, open accessen_US
dc.description.abstractFour 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.en_US
dc.description.peer-reviewYesen_US
dc.identifier.citationWilson, 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/gku269en_US
dc.identifier.urihttps://hdl.handle.net/10133/4584
dc.language.isoen_CAen_US
dc.publisherOxford University Pressen_US
dc.publisher.departmentDepartment of Chemistry and Biochemistryen_US
dc.publisher.facultyArts and Scienceen_US
dc.publisher.institutionUniversity of Lethbridgeen_US
dc.subjectDNA-proteinen_US
dc.subjectDNA nucleobasesen_US
dc.subjectAromatic amino acidsen_US
dc.subjectPi-interactionsen_US
dc.subjectDeoxyriboseen_US
dc.titleDNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA neucleobases or deoxyribose sugaren_US
dc.typeArticleen_US
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