Dissecting protein–RNA recognition sites

Abstract

We analyze the protein–RNA interfaces in 81 transient binary complexes taken from the Protein Data Bank. Those with tRNA or duplex RNA are larger than with single-stranded RNA, and comparable in size to protein–DNA interfaces. The protein side bears a strong positive electrostatic potential and resembles protein–DNA interfaces in its amino acid composition. On the RNA side, the phosphate contributes less, and the sugar much more, to the interaction than in protein–DNA complexes. On average, protein–RNA interfaces contain 20 hydrogen bonds, 7 that involve the phosphates, 5 the sugar 2′OH, and 6 the bases, and 32 water molecules. The average H-bond density per unit buried surface area is less with tRNA or single-stranded RNA than with duplex RNA. The atomic packing is also less compact in interfaces with tRNA. On the protein side, the main chain NH and Arg/Lys side chains account for nearly half of all H-bonds to RNA; the main chain CO and side chain acceptor groups, for a quarter. The 2′OH is a major player in protein–RNA recognition, and shape complementarity an important determinant, whereas electrostatics and direct base–protein interactions play a lesser part than in protein–DNA recognition.