A Volumetric Survey of Cavities and Electrostatic Patterns in Protein-RNA Binding Sites

Surveys of cavities and electrostatics in protein structures have yielded significant insights into the role of shape and charge at binding sites on proteins and DNA. Due to the irregularities in the RNA backbone, similar studies have not been performed in RNA, to our knowledge. In particular, non-helical regions of RNA structure lack the frames of reference often used in the analysis of DNA, where the helical secondary structure is more common. To enable an exhaustive analysis of all regions of RNA structure, this paper observes that volumetric methods developed originally for the analysis of protein structures to provide the first survey of binding cavity geometry in every region of RNA structure. Volumetric methods also create an opportunity to examine electrostatic fields in the same binding regions. On a nonredundant representative subset of available protein-RNA structures, this paper reports the relationship between cavities and focused electrostatic fields in RNA structures, as well as their relationship to bound proteins, clarifying our understanding of protein-RNA recognition mechanisms.