Elucidating the mechanisms that enable translation in bacterial and eukaryotic ribosomes - Project Summary As the sole producer of proteins in the cell, the ribosome is central to all cellular life. With this critical role, ribosome dysfunction can give rise to a host of human disease, which makes it a target for therapeutics. In addition, since ribosomes are organism-specific, several classes of antibiotics function by halting protein synthesis in bacteria, without interfering with the dynamics of human ribosomes. However, efforts to combat bacterial infections face multiple challenges, including antibiotic resistance and side effects. Accordingly, a thorough understanding of bacterial and eukaryotic ribosome dynamics can be used to design more effective antibiotics, as well as provide insights into the molecular origins of various diseases. In the current project, we will apply state-of-the art molecular simulation methods to study how ribosomes are able to accurately and efficiently produce proteins in the cell (i.e., translation). We will apply multiple types of simulation techniques to obtain atomistic insights into the dynamics of the conformational rearrangements that enable translation. These calculations will elucidate the precise interactions that control ribosome kinetics in bacterial and human ribosomes (cytosolic and mitochondrial). These studies will advance our understanding of ribosome dynamics, which will allow for more effective therapeutic strategies to be developed, in order to combat bacterial infections and disease. We will work towards this objective by pursuing multiple avenues of investigation. In collaboration with experimental groups, we will design and execute simulations that will specifically guide the development of next-generation single-molecule methods. Our models will also be used to understand the precise relationship between small-scale conformational motions (identified by nuclear magnetic resonance experiments) and large- scale/long-time dynamics in the ribosome. We will also use computational strategies to identify candidate small molecules that may serve as novel broad-spectrum antibiotics. Promising antibiotic candidates will then be characterized through biochemical, single-molecule and structural biology (cryoelectron microscopy) analysis, performed in well-established experimental laboratories. Finally, our collaborations with structural biology laboratories will allow us to provide the first insights into the dynamics of newly-identified functional states. In addition to immediate therapeutic applications, this broad range of efforts will help establish a comprehensive understanding of ribosome dynamics that connects experimental observables and theoretical principles, such that guiding principles may be identified.
