Statistical analysis of atomic contacts at RNA–protein interfaces

Abstract

Forty-five crystals of complexes between proteins and RNA molecules from the Protein Data Bank have been statistically surveyed for the number of contacts between RNA components (phosphate, ribose and the four bases) and amino acid side chains. Three groups of complexes were defined: the tRNA synthetases; the ribosomal complexes; and a third group containing a variety of complexes. The types of atomic contacts were a priori classified into ionic, neutral H-bond, C-H...O H-bond, or van der Waals interaction. All the contacts were organized into a relational database which allows for statistical analysis. The main conclusions are the following: (i) in all three groups of complexes, the most preferred amino acids (Arg, Asn, Ser, Lys) and the less preferred ones (Ala, Ile, Leu, Val) are the same; Trp and Cys are rarely observed (respectively 15 and 5 amino acids in the ensemble of interfaces); (ii) of the total number of amino acids located at the interfaces 22% are hydrophobic, 40% charged (positive 32%, negative 8%), 30% polar and 8% are Gly; (iii) in ribosomal complexes, phosphate is preferred over ribose, which is preferred over the bases, but there is no significant preference in the other two groups; (iv) there is no significant prevalence of a base type at protein-RNA interfaces, but specifically Arg and Lys display a preference for phosphate over ribose and bases; Pro and Asn prefer bases over ribose and phosphate; Met, Phe and Tyr prefer ribose over phosphate and bases. Further, Ile, Pro, Ser prefer A over the others; Leu prefers C; Asp and Gly prefer G; and Asn prefers U. Considering the contact types, the following conclusions could be drawn: (i) 23% of the contacts are via potential H-bonds (including CH...O H-bonds and ionic interactions), 72% belong to van der Waals interactions and 5% are considered as short contacts; (ii) of all potential H-bonds, 54% are standard, 33% are of the C-H...O type and 13% are ionic; (iii) the Watson-Crick sites of G, O6(G) and principally N2(G) and the hydroxyl group O2' is more often involved in H-bonds than expected; the protein main chain is involved in 32% and the side chains in 68% of the H-bonds; considering the neutral and ionic H-bonds, the following couples are more frequent than expected-base A-Ser, base G-Asp/Glu, base U-Asn. The RNA CH groups interact preferentially with oxygen atoms (62% on the main chain and 19% on the side chains); (iv) the bases are involved in 38% of all H-bonds and more than 26% of the H-bonds have the H donor group on the RNA; (v) the atom O2' is involved in 21% of all H-bonds, a number greater than expected; (vi) amino acids less frequently in direct contact with RNA components interact frequently via their main chain atoms through water molecules with RNA atoms; in contrast, those frequently observed in direct contact, except Ser, use instead their side chain atoms for water bridging interactions.

Synthetic antibodies for specific recognition and crystallization of structured RNA

“…For the Fab2-⌬C209 P4-P6 complex, interactions with nucleobase edges and ribose atoms comprise 40% and 32% of the direct contacts, respectively, which is similar to the analysis by Lejeune et al (40) of 49 RNA-binding proteins (35% and 43%). Main-chain atoms contribute 37% of the interactions on the protein side of the interface, which is similar to the analysis of Treger and Westhof (32%) (38). These comparisons suggest that, at the atomic level, the Fab-RNA interface resembles other protein-RNA binding interfaces.…”

Simple, recurring RNA binding sites for L-arginine

“…As might be expected from this robust and widespread association, arginine side-chain-RNA interactions are also among the most frequent contacts observed within the entire population of structurally characterized RNA-peptide interfaces (Allers and Shamoo 2001;Treger and Westhof 2001;Morozova et al 2006;Ellis et al 2007).…”

A chloroplast‐localized PPR protein required for plastid ribosome accumulation

“…Particularly striking is the abundance of asparagine residues on the`lower' edge; indeed, an asparagine at position 4 forms part of the PPR consensus (Small and Peeters, 2000; see Figure 2b). Interestingly, asparagine is highly represented at the RNA/protein interface in structurally characterized RNA/protein complexes, whereas it is less characteristic of protein±protein interaction surfaces (Treger and Westhof, 2001). Among the remaining amino acids, arginine, serine, and lysine are the most frequently found at RNA/protein interfaces (Treger and Westhof, 2001); these are also highly represented on the putative substrate binding surfaces of PPR2 and CRP1 (Figure 8).…”

“…Interestingly, asparagine is highly represented at the RNA/protein interface in structurally characterized RNA/protein complexes, whereas it is less characteristic of protein±protein interaction surfaces (Treger and Westhof, 2001). Among the remaining amino acids, arginine, serine, and lysine are the most frequently found at RNA/protein interfaces (Treger and Westhof, 2001); these are also highly represented on the putative substrate binding surfaces of PPR2 and CRP1 (Figure 8). An appealing possibility is that the arginines and lysines along the upper edge interact with phosphate moieties in the RNA backbone, presenting the nucleotide bases for hydrogen bonding with the asparagines, serines, and threonines along the lower edge.…”