Cation-Pi Interactions at Non-Redundant Protein-RNA Interfaces
Cation-pi interactions have proved to be important in proteins and protein-ligand complexes. Here cation-pi interactions are analyzed for 282 non-redundant protein-RNA interfaces. The statistical results show that this kind of interaction exists in 65% of the interfaces. The four RNA bases are ranked as Gua > Ade > Ura > Cyt according to their propensity to participate in cation-pi interactions. The corresponding ranking for the involved amino acid residues is: Arg > Lys > Asn > Gln. The same trends are obtained based on empirical energy calculation. The Arg-Gua pairs have the highest stability and are also most frequently observed. The number of cation-pi pairs involving unpaired bases is 2.5-fold greater than those involving paired bases. Hence, cation-pi interactions show sequence and structural specificities. For the bicyclic bases, Gua and Ade, their 5-atom rings participate in cation-pi interactions a little more than 6-atom rings, with the percentages of 54 and 46% respectively, which is due to the higher cation-pi participation proportion (63%) of 5-atom rings in the paired bases. These results give a general view of cation-pi interactions at protein-RNA interfaces and are helpful in understanding the specific recognition between protein and RNA.