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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Ribosomes01:27

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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Ribosomal RNA Synthesis

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
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Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis
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Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.

G I Makarov1, T M Makarova, N V Sumbatyan

  • 1Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia. bogdanov@belozersky.msu.ru.

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Molecular dynamics simulations reveal ribosome conformational changes during protein synthesis. All-atom modeling details tRNA translocation, nascent peptide behavior, and drug interactions within the ribosome.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biochemistry

Background:

  • The ribosome is a complex molecular machine responsible for protein synthesis.
  • Conformational changes are integral to ribosomal function.
  • Traditional structural and biochemical methods leave some questions about ribosome dynamics unanswered.

Purpose of the Study:

  • To review the utility of all-atom molecular dynamics (MD) simulations in studying ribosome dynamics.
  • To highlight how MD simulations complement experimental techniques like X-ray crystallography and cryo-EM.
  • To demonstrate the application of MD in understanding specific ribosomal processes.

Main Methods:

  • All-atom molecular dynamics simulations of the ribosome.
  • Integration of simulation data with experimental structural and biochemical data.

Main Results:

  • MD simulations provide atomic-level insights into tRNA translocation.
  • All-atom modeling elucidates the behavior of nascent peptides within the ribosomal tunnel.
  • Simulations reveal the interactions of antibiotics and small molecules with the ribosome.
  • MD helps in understanding the mechanism of allosteric signal transmission in the ribosome.

Conclusions:

  • All-atom molecular dynamics is a powerful tool for investigating ribosome function at an atomic level.
  • MD simulations offer unique perspectives on dynamic processes that are difficult to capture with static structural methods.
  • This approach is crucial for understanding drug mechanisms and developing new therapeutics targeting the ribosome.