Abstract
Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.
Highlights
Biological machines are ubiquitous in the cell and typically contain many molecules that include protein, RNA, and other cofactors
The landscape is characterized by energetic barriers that are associated with a hierarchy of length scales (Fig. 1) [6,7], where the effective diffusion is dictated by the magnitude of the short length-scale roughness
We have used an explicit-solvent simulation (2.1 million atoms, 1.3 microseconds) to measure the diffusion along multiple structural coordinates that have been implicated in tRNA translocation in the ribosome
Summary
Biological machines are ubiquitous in the cell and typically contain many molecules that include protein, RNA, and other cofactors. To bridge discrete and continuous descriptions for a molecular machine, such as the ribosome, it is necessary to quantify the diffusive properties of functionally-relevant collective rearrangements. The observed, or effective, diffusion of each component of a biomolecular complex is determined by the intrinsic diffusion of that component (free in solution) as well as the short-scale energetic roughness that is introduced by molecular interfaces [1,2,3,4,5]. The landscape is characterized by energetic barriers that are associated with a hierarchy of length scales (Fig. 1) [6,7], where the effective diffusion is dictated by the magnitude of the short length-scale roughness. By measuring the effective diffusion, one may determine the relationship between the long length-scale freeenergy barriers and the kinetics associated with interconversion between well-defined states
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