Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes

Abstract

A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

“…A recent work has analyzed all possible RNA : protein π interactions involving base or sugar moieties of rNs and amino acids using a dataset similar to our dataset [40] . However, the total number of π interactions (1532 (897 π‐π and 635 sugar‐π)) is far less than the hydrogen‐bonding interaction identified in our study (Table 3).…”

“…However, the total number of π interactions (1532 (897 π‐π and 635 sugar‐π)) is far less than the hydrogen‐bonding interaction identified in our study (Table 3). [40] More specifically, in contrast to 11–20 hydrogen bonds that commonly occur in a PDB file, only 1–3 π interactions mostly occur in crystal structures [40] . This highlights the greater abundance of rN:amino acid hydrogen bonding compared to π interactions at the RNA : protein interface, and thereby points towards their hitherto unknown or less‐appreciated functional roles in biochemistry.…”

“…Perhaps the most important factors among these are the relatively small and variable number of high‐resolution X‐ray crystal structures searched, and the differences in hydrogen bonding search criteria followed (Table S1). However, the deposition of new structures in PDB in the past decade has nearly quadrupled the total of RNA : protein X‐ray structures, and therefore, more fairly represented all RNA types [40] . Despite the fact that the enhanced structural diversity in the now‐available larger dataset can help better understand RNA : protein interactions, analysis of the frequency, composition and structure has, however, most recently been carried out only on RNA : protein π‐π interactions [40] .…”

“…However, the deposition of new structures in PDB in the past decade has nearly quadrupled the total of RNA : protein X‐ray structures, and therefore, more fairly represented all RNA types [40] . Despite the fact that the enhanced structural diversity in the now‐available larger dataset can help better understand RNA : protein interactions, analysis of the frequency, composition and structure has, however, most recently been carried out only on RNA : protein π‐π interactions [40] . In contrast, despite their greater strength, specificity and thereby functional importance, the most‐recent analysis of hydrogen bonding in RNA : protein complexes was carried out more than five years ago, [17] and involved a dataset that included only half of the crystal structures searched for RNA : protein π‐π interactions [40] .…”

“…For this, within the “Advanced Search” option available on the PDB website (https://www.rcsb.org/), the “Experimental Method” was chosen to be equal to X‐ray diffraction and the “Data Collection Resolution” filter was applied by fixing the resolution to be better than 2.5 Å. This resolution cut‐off was chosen in alignment with the most‐recent analysis of RNA : protein crystal structures [40] . The structures were then filtered using the “Release Date” criterion, which was set to ≤ 23 rd March 2021.…”