On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules

TitleOn the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules
Publication TypeJournal Article
Year of Publication1998
AuthorsLuisi, B, Orozco M, Sponer J, Luque FJ, Shakked Z
JournalJournal of Molecular Biology
Pagination1123 - 1136
Date Published1998/06/26/
KeywordsAcid, as, Bonding;, Conformation, Crystallography;, Databases, DNA/chemistry;, Hydrogen, Nitrogen/chemistry;, Nucleic, Topic;
AbstractCrystallographic studies of duplex DNA have indicated that opposing exocyclic amino groups may form close NH⋯:N contacts. To study the nature of such interactions, we have examined the database of small molecule, high-resolution crystal structures for more accurate examples of this type of unconventional interaction. We have found cases where the amino groups in guanine and adenine bases accept hydrogen bonds from conventional donors, such as amino or hydroxyl groups. More frequently, the purine amino group was found to contact closely electropositive C-H groups. Searches of the nucleic acid structural databases also yielded several examples where the purine amino group is contacted by hydrogen bond donors in macromolecules. Ab initio calculations indicate that the hydrogen-amino contact is improved energetically when the amino group moves from the conventional geometry, where all atoms are co-planar with the base, to one in which the hydrogen atoms lie out of the plane and the nitrogen is at the apex of a pyramid, resulting in polarization of the amino group. The combined structural and theoretical data suggest that the amino group is flexible, and can accommodate close contacts, because the resulting polarization permits electropositive atoms to approach the amino group nitrogen more closely than expected for their conventional van der Waals radii. The flexibility of the amino group may permit particular DNA conformations that enforce hydrogen-amino contacts to optimize favorable stacking interactions, and it may play a role in the recognition of nucleosides. We speculate that the amino group can accept hydrogen bonds under special circumstances in macromolecules, and that this ability might play a mechanistic role in catalytic processes such as deamination or amino transfer.