scholarly journals Dissecting the Energetics of Subunit Rotation in the Ribosome

2019 ◽  
Vol 123 (13) ◽  
pp. 2812-2823 ◽  
Author(s):  
Mariana Levi ◽  
Paul C. Whitford
Keyword(s):  
Subunit Rotation

scholarly journals The Dynamics of Subunit Rotation in a Eukaryotic Ribosome

Biophysica ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 204-221
Author(s):  
Frederico Campos Freitas ◽  
Gabriele Fuchs ◽  
Ronaldo Junio de Oliveira ◽  
Paul Charles Whitford
Keyword(s):  
Free Energy ◽  
Large Scale ◽  
Small Subunit ◽  
Free Energy Barrier ◽  
Temperature Dependent ◽  
Molecular Flexibility ◽  
Subunit Rotation ◽  
Biological Kinetics ◽  
Rate Limiting ◽  
Reversible Rotation

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.

scholarly journals Large Terminase Conformational Change Induced by Connector Binding in Bacteriophage T7

2013 ◽  
Vol 288 (23) ◽  
pp. 16998-17007 ◽  
Author(s):  
María I. Daudén ◽  
Jaime Martín-Benito ◽  
Juan C. Sánchez-Ferrero ◽  
Mar Pulido-Cid ◽  
José M. Valpuesta ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Bacteriophage T7 ◽  
Crystallographic Structure ◽  
Dna Translocation ◽  
Phage T4 ◽  
Subunit Rotation ◽  
Molecular Bases ◽  
Mechanical Movement ◽  
Large Terminase ◽  
Shed Light

During bacteriophage morphogenesis DNA is translocated into a preformed prohead by the complex formed by the portal protein, or connector, plus the terminase, which are located at an especial prohead vertex. The terminase is a powerful motor that converts ATP hydrolysis into mechanical movement of the DNA. Here, we have determined the structure of the T7 large terminase by electron microscopy. The five terminase subunits assemble in a toroid that encloses a channel wide enough to accommodate dsDNA. The structure of the complete connector-terminase complex is also reported, revealing the coupling between the terminase and the connector forming a continuous channel. The structure of the terminase assembled into the complex showed a different conformation when compared with the isolated terminase pentamer. To understand in molecular terms the terminase morphological change, we generated the terminase atomic model based on the crystallographic structure of its phage T4 counterpart. The docking of the threaded model in both terminase conformations showed that the transition between the two states can be achieved by rigid body subunit rotation in the pentameric assembly. The existence of two terminase conformations and its possible relation to the sequential DNA translocation may shed light into the molecular bases of the packaging mechanism of bacteriophage T7.

scholarly journals Subunit rotation in single FRET-labeled F1-ATPase hold in solution by an anti-Brownian electrokinetic trap

2013 ◽  
Author(s):  
Hendrik Sielaff ◽  
Thomas Heitkamp ◽  
Andrea Zappe ◽  
Nawid Zarrabi ◽  
Michael Börsch
Keyword(s):  
F1 Atpase ◽  
Subunit Rotation

scholarly journals Subunit rotation of ATP synthase embedded in membranes: a or   subunit rotation relative to the c subunit ring

2002 ◽  
Vol 99 (21) ◽  
pp. 13448-13452 ◽  
Author(s):  
K. Nishio ◽  
A. Iwamoto-Kihara ◽  
A. Yamamoto ◽  
Y. Wada ◽  
M. Futai
Keyword(s):  
Atp Synthase ◽  
C Subunit ◽  
Subunit Rotation

scholarly journals Subunit rotation in a single F o F 1 -ATP synthase in a living bacterium monitored by FRET

2011 ◽  
Author(s):  
K. Seyfert ◽  
T. Oosaka ◽  
H. Yaginuma ◽  
S. Ernst ◽  
H. Noji ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Living Bacterium ◽  
Subunit Rotation
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