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Capturing Transition States for tRNA Hybrid-State Formation in the Ribosome.

In order to quantitatively describe the energetics of biomolecular rearrangements, it is necessary to identify reaction coordinates that accurately capture the relevant transition events. Here, we perform simulations of A-site tRNA movement (∼20 Å) during hybrid-state formation in the ribosome and quantify the ability of interatomic distances to capture the transition state ensemble. Numerous coordinates are found to be accurate indicators of the transition state, allowing tRNA rearrangements to be described as diffusion across a one-dimensional free-energy surface. In addition to providing insights into the physical-chemical relationship between biomolecular structure and dynamics, these results can help enable single-molecule techniques to probe the free-energy landscape of the ribosome.