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Article
Open AccessMitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk
The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated ...
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Article
The energetics of subunit rotation in the ribosome
Protein synthesis in the cell is controlled by an elaborate sequence of conformational rearrangements in the ribosome. The composition of a ribosome varies by species, though they typically contain ...
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Article
Open AccessA steric gate controls P/E hybrid-state formation of tRNA on the ribosome
The ribosome is a biomolecular machine that undergoes multiple large-scale structural rearrangements during protein elongation. Here, we focus on a conformational rearrangement during translocation, known as P...
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Protocol
Using SMOG 2 to Simulate Complex Biomolecular Assemblies
Over the last 20 years, the application of structure-based (Gō-like) models has ranged from protein folding with coarse-grained models to all-atom representations of large-scale molecular assemblies. While the...
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Article
Open AccessHow EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome
It has long been recognized that the thermodynamics of mRNA–tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize t...
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Article
Open AccessSteric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocation
Translocation of mRNA and tRNA through the ribosome is associated with large-scale rearrangements of the head domain in the 30S ribosomal subunit. To elucidate the relationship between 30S head dynamics and mR...
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Chapter
Molecular Dynamics Simulations of the Ribosome
Structural biology techniques such as crystallography and cryo-EM produce high resolution snap shots of the ribosome at various stages of protein synthesis. Single molecule studies yield time-resolved measurem...
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Article
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites
During translation, transfer RNAs enter the ribosome and then move sequentially through three sites, known as A, P and E, as they transfer their attached amino acids onto the growing peptide chain. How the rib...
