Protein and Mg²⁺-induced conformational changes in the S15 binding site of 16 S ribosomal RNA

The Bacillus stearothermophilus ribosomal protein S15 binds to the central domain of the 16 S rRNA inducing a conformational change in a threeway helical junction. To understand the nature of this conformational change, extended-helical junctions were prepared to examine the effects of S15 or Mg²⁺ binding on the relative helical orientation using native gel electrophoretic mobility and transient electric birefringence. The free junction is planar with ~120°interhelical angles, whereas S15 and Mg²⁺ yield a junction conformation that remains planar in which two helices, 21 and 22, become colinear and the third, helix 20, forms a 60°angle with respect to helix 22. This conformational change is thought to be important for directing the assembly of the central domain of the 30 S ribosomal subunit.