The ribosome is an important subject for investigation because it performs a universal and key biochemical process for which the molecular details are not known. Our understanding of the catalytic capabilities of RNA and our general knowledge of RNA and ribonucleoprotein structure will be greatly increased by an elucidation of the rRNA machinery. An important aspect of the proposed studies is that many antibiotics exert their activities on the ribosome. It is necessary to understand the nature of these interactions and their effects on the ribosome if there is to be rational design of synthetic antibiotics. We have developed strategies to determine the locations and frequencies of intramolecular photo- and photochemical crosslinks in the 16S rRNA which reflect its conformation status. We know that the 16SrRNA is subject to specific and discrete conformation changes that depend on its interactions and environment.
The specific aims are designed to obtain more information about the details of the rRNA structure, to determine the role of the rRNA conformation in controlling tRNA binding and translocation, and to determine how antibiotics interfere with protein synthesis. The techniques needed for these experiments are available and the specific aims will proceed independent of one another.
The specific aims of the work are: (1) Complete crosslinking experiments to refine a model for the rRNA handling region of the 16S rRNA in the 30S subunit and 70S ribosome; (2) Determine the details of the structural changes that occur during tetracycline and spectinomycin binding and determine how these changes interfere with tRNA binding and the translocation process; (3) Determine how the 16S rRNA conformation determines tRNA binding and tRNA translocation; and (4) Determine the global structural consequences of the 16S rRNA secondary structure change in the interval 885-914 that occurs in the 16S rRNA, determine how association of aminoacyl-tRNA.EFTu.GTP ternary complex affects 16S rRNA structure, and them determine how the different conformations affects aminoacyl-tRNA-binding.
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