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Article

The Dynamics of Subunit Rotation in a Eukaryotic Ribosome

1
Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
2
Department of Biological Sciences, The RNA Institute, University at Albany, 1400 Washington Ave, Albany, NY 12222, USA
3
Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
4
Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Shin-ichi Tate
Received: 19 April 2021 / Revised: 16 May 2021 / Accepted: 18 May 2021 / Published: 24 May 2021
Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ∼1 MDa) undergoes spontaneous and reversible rotation events (∼8). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines. View Full-Text
Keywords: molecular dynamics simulation; energy landscape; entropy molecular dynamics simulation; energy landscape; entropy
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MDPI and ACS Style

Freitas, F.C.; Fuchs, G.; de Oliveira, R.J.; Whitford, P.C. The Dynamics of Subunit Rotation in a Eukaryotic Ribosome. Biophysica 2021, 1, 204-221. https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1020016

AMA Style

Freitas FC, Fuchs G, de Oliveira RJ, Whitford PC. The Dynamics of Subunit Rotation in a Eukaryotic Ribosome. Biophysica. 2021; 1(2):204-221. https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1020016

Chicago/Turabian Style

Freitas, Frederico C., Gabriele Fuchs, Ronaldo J. de Oliveira, and Paul C. Whitford 2021. "The Dynamics of Subunit Rotation in a Eukaryotic Ribosome" Biophysica 1, no. 2: 204-221. https://0-doi-org.brum.beds.ac.uk/10.3390/biophysica1020016

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