Protein synthesis is a fundamental process in all living organisms. Ribosomes are the ribonucleoprotein complexes responsible for protein synthesis. Recent atomic resolution structures of the large and small ribosomal subunits provide a unique opportunity to understand the mechanism by which ribosomes perform the complex task of protein synthesis. One of the important steps in the elongation cycle of protein synthesis is the iterative movement of the tRNA-mRNA complex, a process called translocation. In Escherichia coli, elongation factor G (EF-G) catalyzes translocation. The mechanism of EF-G-dependent translocation is poorly understood. The long-term goal of my laboratory is to elucidate the molecular basis of translocation. Several lines of studies indicate that the ribosomal RNAs (rRNAs) may play a functional role during translocation. We recently developed a novel modification-interference approach that will permit us to examine the role of 16S rRNA in translocation. The method uses a highly efficient site-specific cross-link between P site bound tRNA and 16S rRNA to select ribosomes that are active in translocation. We will use a combinatorial approach for identifying bases, non-bridging phosphate oxygens, and ribose 2'-hydroxyl groups within 16S rRNA that are critical for translocation. This study will provide information about the dynamics of ribosome structure that cannot be easily acquired by X-ray crystallography. Ribosomes are the target for inactivation by several classes of antibiotics. Antibiotics such as eiythromycin, spectionmycin, viomycin, thiostrepton, and the aminoglycosides specifically inhibit translocation. Some of these antibiotics prevent the 16S rRNA from undergoing structural changes that are critical for translocation. Antibiotic-resistant strains of bacteria are on the rise, causing a crisis in the management and treatment of these infections throughout the world. Understanding the mechanism of translocation will provide insights for developing more effective antibiotics that target the ribosome of these drug-resistant strains of bacteria.
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