Challenges in describing ribosome dynamics

Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments

Computational coarse-grained models play a fundamental role as a research tool in protein folding, and they are important in bridging theory and experiments. Folding mechanisms are generally discussed using the energy landscape framework, which is well mapped within a class of simplified structure-based models. In this chapter, simplified computer models are discussed with special focus on structure-based ones.

Diffusion of tRNA inside the ribosome is position-dependent

In recent years, there has been a growing interest to quantify the energy landscape that governs ribosome dynamics. However, in order to quantitatively integrate theoretical predictions and experimental measurements, it is essential that one has a detailed understanding of the associated diffusive properties. Here, all-atom explicit-solvent simulations (50 μs of aggregate sampling) predict that the diffusion coefficient of a tRNA molecule will depend on its position within the ribosome. Specifically, during aa-tRNA accommodation (i.e., the process by which tRNA enters the ribosome), the apparent diffusion coefficient decreases by approximately an order of magnitude. By comparing these to values obtained with an energetically "smooth" model, we show that the observed nonuniform behavior likely arises from electrostatic and solvation interactions between the tRNA and ribosome. These calculations also reveal the hierarchical character of ribosomal energetics, where steric interactions induce a large-scale free-energy barrier, and short-scale roughness determines the rate of diffusive movement across the landscape.

Ensemble and single-molecule FRET studies of protein synthesis

Protein synthesis is a complex, multi-step process that involves large conformational changes of the ribosome and protein factors of translation. Over the last decade, Förster resonance energy transfer (FRET) has become instrumental for studying structural rearrangements of the translational apparatus. Here, we discuss the design of ensemble and single-molecule (sm) FRET assays of translation. We describe a number of experimental strategies that can be used to introduce fluorophores into the ribosome, tRNA, mRNA and protein factors of translation. Alternative approaches to tethering of translation components to the microscope slide in smFRET experiments are also reviewed. Finally, we discuss possible challenges in the interpretation of FRET data and ways to address these challenges.