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 in

SUBMITTER: Bahadur RP 

PROVIDER: S-EPMC2377425 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature