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

• DOI: 10.1021/acs.jpcb.6b04476
• Publication Date: 2016-08-01T18:34:10Z
• Authors: Kien Nguyen; Paul C. Whitford
• Keywords: Energy landscape; Transition state

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