Abstract
The elongation cycle of the ribosome requires rapid and regulated dynamics of numerous large-scale conformational rearrangements. While these are high-dimensional processes, single-molecule experiments typically measure a small number of interatomic distances. Thus, an outstanding challenge is to identify the most kinetically-relevant degrees of freedom. Our strategy for addressing this gap is to use simplified theoretical models and molecular dynamics simulations to simulate many (100-1000) spontaneous large-scale (∼30-50 Å) conformational transitions for each step (accommodation, A/P and P/E formation, translocation, subunit rotation). These vast data sets then allow us to identify suitable experimental strategies for precisely probing the free-energy landscape and rate-limiting barriers in the ribosome. In addition to having utility in experimental studies, these simulations are also revealing the pronounced influence of molecular sterics and flexibility on the kinetics of elongation.
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