Trajectories of the Ribosome as a Brownian Nanomachine

作者：Ali Dashti, Peter Schwander, Robert Langlois, Russell Fung, Wen Li, Ahmad Hosseinizadeh, Hstau Y. Liao, Jesper Pallesen, Gyanesh Sharma, Vera A. Stupina, Anne E. Simon, Jonathan D. Dinman, Joachim Frank, A. Ourmazd · 年份：2023 · DOI：10.1201/9781003456100-7 · 被引用次数：3 · 研究领域：RNA and protein synthesis mechanisms、Diffusion and Search Dynamics、Nanopore and Nanochannel Transport Studies

This chapter presents a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. The novel capabilities constitute a powerful platform for quantitative study of the conformational and energy trajectories of nanomachines, including those engaged in a wide range of important biological processes. The energy landscape constructed by the analysis of the ribosome ensemble shows multiple interconnected paths of relatively low energy. More generally, the way to the quantitative study of the structure, kinetics, and operational cycles of nanomachines is now open.