Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin

The core ribosomal protein S8 binds to the central domain of 16S rRNA indep endently of other ribosomal proteins and is required for assembling the 30S subunit. It has been shown with E. colt ribosomes that a short rRNA fragme nt restricted by nucleotides 588-602 and 636-651 is sufficient for strong a nd specific protein S8 binding. In this work, we studied the complexes form ed by ribosomal protein S8 from Thermus thermophilus and Methanococcus jann aschii with short rRNA fragments isolated from the same organisms. The diss ociation constants of the complexes of protein S8 with rRNA fragments were determined. Based on the results of binding experiments, rRNA fragments of different length were designed and synthesized in preparative amounts in vi tro using T7 RNA-polymerase. Stable S8-RNA complexes were crystallized.. Cr ystals were obtained both for homologous bacterial and archaeal complexes a nd for, hybrid complexes of archaeal protein with bacterial rRNA. Crystals of the complex of protein S8 from M. jannaschii with the 37-nucleotide rRNA fragment from the same organism suitable for X-ray analysis were obtained.