DOI: 10.1101/514448Jan 8, 2019Paper

Dissecting the energetics of subunit rotation in the ribosome

BioRxiv : the Preprint Server for Biology
Mariana Levi, Paul Charles Whitford

Abstract

The accurate expression of proteins requires the ribosome to efficiently undergo elaborate conformational rearrangements. The most dramatic of these motions is subunit rotation, which is necessary for tRNA molecules to transition between ribosomal binding sites. While rigid-body descriptions provide a qualitative picture of the process, obtaining quantitative mechanistic insights requires one to account for the relationship between molecular flexibility and collective dynamics. Using simulated rotation events, we assess the quality of experimentally-accessible measures for describing the collective displacement of the ~4000-residue small subunit. For this, we ask whether each coordinate is able to identify the underlying free-energy barrier and transition state ensemble (TSE). We find that intuitive structurally-motivated coordinates (e.g. rotation angle, inter-protein distances) can distinguish between the endpoints, though they are poor indicators of barrier-crossing events, and they underestimate the free-energy barrier. In contrast, coordinates based on inter-subunit bridges can identify the TSE. We additionally verify that the committor probability for the putative TSE configurations is 0.5, a hallmark feature of any trans...Continue Reading

Related Concepts

Gene Rearrangement
Ribosomes
Transfer RNA
Site
Description
Simulation
Landscapes
Protein Expression
Ribosome Binding
Orientation (spatial)

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