Quantifying the energy landscape of the ribosome

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The energy landscape perspective provides both a conceptual and computational framework for describing the functional dynamics of biomolecules. With continued advances in structural biology and high-performance computing, the field is positioned to extend this approach to large biomolecular machines. One of the most central machines in living cells is the ribosome, a highly complex assembly that is responsible for the production of proteins. During the translocation step of protein synthesis, tRNA molecules transit through the ribosomal binding sites, which is associated with large-scale conformational rearrangements of the ribosome. Here, we use molecular simulations to elucidate the physical relationship between ribosome dynamics and tRNA movement. Specifically, this dissertation aims to reveal how biomolecular sterics and flexibility can contribute to the free-energy barriers associated with function. In Chapter 2, we present the first spontaneous and complete simulations of mRNA-tRNA movement through the ribosome, at atomic resolution. These calculations suggest that specific steric interactions between tRNA and the 30S subunit give rise to an intermediate that involves a novel tilting motion of the ribosome. Next, to provide precise characterization of the barriers (i.e. kinetics), Chapter 3 discusses an analysis for identifying reaction coordinates that most closely follow the lowest free-energy pathway. For this study, we performed long simulations of tRNA movement during A/P hybrid-state formation and projected the dynamics along interatomic distances. Our analysis shows that the distance employed in previous single-molecule experiments underestimates the free-energy barrier, while alternative coordinates are accurate. Finally, in Chapter 4, we provide a theoretical comparison of A/P hybrid-state formation for different tRNA species. These simulations demonstrate how differences in tRNA size and shape can lead to species-dependent free energies, and thus kinetics. With this foundation, we further show that specific motions of the ribosomal A-site finger are highly predictive of tRNA transition events. Taken together, the findings from this dissertation open up new strategies for experimental techniques that aim at modulating ribosome function.