Quantifying the transition state ensembles of biomolecular function

Abstract

Quantifying the molecular mechanism that governs biomolecular function poses significant challenges, as it often involves large-scale collective motions with coupled degrees of freedom. To properly characterize the energetics and kinetics of biomolecules, we employ statistical-mechanical principles such as the energy land- scape theory and transition state analysis. In this formulation, biological dynamics can be described in terms of diffusion on a free-energy surface, where the process may be described by a few relevant variables. In this body of work, the focus is on the 70S bacterial ribosome, a biomolecular machine that undergoes multiple conformational rearrangements during protein elongation. In particular, we are interested in the relationship between tRNA movement and ribosome rotation during hybrid state formation. To approach this, we developed molecular models of the ribosome and tRNA molecules and simulated the system under various conditions. Through the structure-based energetic description we were able to elucidate the interplay be- tween structure and molecular flexibility and demonstrate how it affects functional dynamics. Additionally, with the use of optimized measures that accurately captured barrier-crossing events, we were able to identify interactions that have a significant effect on the free-energy landscape. This framework provides a baseline where global properties of a molecular machine are largely dependent on structural features.