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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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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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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
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Structure-Based Energetics of Stop Codon Recognition by Eukaryotic Release Factor.

Amit Kumar1, Debadrita Basu1, Priyadarshi Satpati1

  • 1Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati , Guwahati 781039, Assam, India.

Journal of Chemical Information and Modeling
|August 22, 2017
PubMed
Summary

Eukaryotic release factor 1 (eRF1) uses distinct energetic principles to recognize stop codons during translation termination. This study reveals how eRF1 achieves high specificity through mRNA interactions and desolvation effects.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Eukaryotic release factor 1 (eRF1) mediates translation termination by recognizing mRNA stop codons.
  • Unlike bacteria, eukaryotes use a single eRF1 to decode all three stop codons (UAA, UAG, UGA).
  • eRF1 stabilizes a compact mRNA structure, accommodating four nucleotides, differing from bacterial factors.

Purpose of the Study:

  • To quantitatively investigate the energetic basis of eRF1's stop codon recognition selectivity.
  • To elucidate the molecular mechanisms underlying eRF1's discrimination between cognate and near-cognate codons.

Main Methods:

  • Utilized cryo-electron microscopy (cryo-EM) structures of translation termination complexes.
  • Performed molecular dynamics free energy simulations on cognate and near-cognate eRF1-mRNA complexes.

Main Results:

  • eRF1 exhibits enhanced discriminatory power against sense codons compared to bacterial factors.
  • Specific intra-mRNA interactions within the compact structure contribute to stop codon specificity.
  • Loss of protein-mRNA interactions and desolvation of incorrect codons enhance specificity.

Conclusions:

  • eRF1 employs a unique combination of mRNA structural stabilization and desolvation effects for precise stop codon recognition.
  • These findings provide insights into the molecular energetics governing translation termination fidelity in eukaryotes.