The ultimate goal of this project is to understand the molecular mechanisms of protein synthesis. The wealth of structural information obtained from cryoEM reconstructions and x-ray crystallography in recent years has provided a strong basis for studying the molecular basis of ribosome function and has led to proposal of numerous mechanistic models. However, it is essential to subject such structure-based models to experimental test. Moreover, the realization that ribosomes are highly dynamic structures, whose functional capabilities are based on both large- and small-scale molecular movements, requires experimental approaches that will be able to correlate specific dynamic events with function. This project will investigate the mechanisms of crucial steps in translation, in particulr, steps where ribosome structural dynamics play an important role and including experiments specifically designed to critically test mechanisms based on structural observations. The experimental approaches are based on biochemical and biophysical solution methods, including in vitro testing of specific functions in mutationally altered ribosomes, bulk and single-molecule FRET approaches and the use of optical tweezers. The principle aims are to investigate (i) the molecular basis of ribosomal translocation;(ii) the mechanism of translation termination;and (iii the ribosomal mRNA helicase and measurement of ribosomal forces using optical tweezers. The proposed research is of strong clinical relevance because bacterial ribosomes are a major target for numerous antibiotics. Elucidation of the structures of functional complexes of bacterial ribosomes will provide a rigorous basis for development of novel antibiotics to address the crisis of emerging drug-resistant strains of bacterial pathogens. Studying the mechanism of action of the ribosomal helicase will help to understand how retroviruses, including HIV, use pseudoknots to create programmed frame-shifting during their infectious cycle, providing clues to the design of anti-retroviral therapeutics.
This research is of strong clinical relevance because bacterial ribosomes are a major target for numerous antibiotics. Elucidation of the mechanisms of action of bacterial ribosomes, together with knowledge of their high-resolution structures, will therefore provide a rigorous basis for development of novel antibiotics to address the crisis of emerging drug-resistant strains of bacterial pathogens. Studies on the mechanism of action of the ribosomal helicase will help to understand how retroviruses, including HIV, use pseudoknots to create programmed frame-shifting during their infectious cycle, providing clues to the design of anti-retroviral therapeutics.
|Colussi, Timothy M; Costantino, David A; Zhu, Jianyu et al. (2015) Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature 519:110-3|
|Mohan, Srividya; Donohue, John Paul; Noller, Harry F (2014) Molecular mechanics of 30S subunit head rotation. Proc Natl Acad Sci U S A 111:13325-30|
|Zhou, Jie; Lancaster, Laura; Donohue, John Paul et al. (2014) How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Science 345:1188-91|
|Liu, Tingting; Kaplan, Ariel; Alexander, Lisa et al. (2014) Direct measurement of the mechanical work during translocation by the ribosome. Elife 3:e03406|
|Ramrath, David J F; Lancaster, Laura; Sprink, Thiemo et al. (2013) Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Proc Natl Acad Sci U S A 110:20964-9|
|Ermolenko, Dmitri N; Cornish, Peter V; Ha, Taekjip et al. (2013) Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. RNA 19:158-66|
|Noller, Harry F (2013) How does the ribosome sense a cognate tRNA? J Mol Biol 425:3776-7|
|Zhou, Jie; Lancaster, Laura; Donohue, John Paul et al. (2013) Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science 340:1236086|
|Santos, Natalia; Zhu, Jianyu; Donohue, John Paul et al. (2013) Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2. Structure 21:1258-63|
|Qu, Xiaohui; Lancaster, Laura; Noller, Harry F et al. (2012) Ribosomal protein S1 unwinds double-stranded RNA in multiple steps. Proc Natl Acad Sci U S A 109:14458-63|
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