Binding of human ribosomal protein S16 with 18S rRNA fragment 1203-1236/1521-1698

Human ribosomal protein S16 is homologous to prokaryotic S9, which contacts the 16S rRNA region formed by helices H29, H30, H38-H41, and H43 by X-ray data. A study was made of the interaction of recombinant human S16 with an RNA transcript corresponding to human 18S rRNA region 1203-1236/1521-1698 (helices H28-30 and H41-43), homologous to the 16S rRNA region harboring part of the S9-binding site. S16 specifically bound to the transcript with an apparent dissociation constant of (1.3 +/- 0.1) . 10(-8) M at 20 degrees C. Enzymatic and chemical footprinting was used to identify the nucleotides whose accessibility for RNases and modifying chemical agents changes upon S16 binding. In the presence of S16, a substantially higher accessibility was observed for C1544 (internal loop of hairpin H41), C1618-U1622, C1629-A1634 (hairpin H42), C1521-C1523, U1530, C1532 (helix H30), C1645, C1646, and G1648 (base of hairpin H43) and an appreciably lower accessibility was observed for C1670-A1675 (hairpin H43). Many of the 16S rRNA nucleotides corresponding to the above 18S rRNA nucleotides tightly contact S9 residues in the bacterial 30S ribosomal subunit.