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Mapping Protein-Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome-Nascent Globin Complex.

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This study reveals how apomyoglobin (apoMb) interacts with the ribosome during cotranslational folding. Nascent chains interact with ribosomal proteins (r-proteins) and RNA, particularly L23, on the ribosome

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Ribosome-bound nascent chain (RNC) interactions with ribosomal components are crucial for cotranslational protein folding.
  • Previous studies on RNC-ribosome contacts primarily used C-terminal stalling sequences, leaving a gap in understanding interactions without these motifs.
  • Information regarding interactions between nascent chains and ribosomal proteins (r-proteins) on the ribosome's outer surface is scarce.

Purpose of the Study:

  • To investigate the structural features of ribosome-bound apomyoglobin (apoMb) and its interactions with the ribosome.
  • To explore nascent chain-ribosome contacts within the ribosomal exit tunnel and on its outer surface, especially in the absence of strong stalling sequences.
  • To elucidate the role of specific ribosomal components, including r-proteins and rRNA, in nascent chain folding and interaction.

Main Methods:

  • Chemical cross-linking to identify proximal residues between the nascent chain and ribosome.
  • Single-particle cryo-electron microscopy (cryo-EM) for high-resolution structural determination.
  • Fluorescence anisotropy decays to assess the dynamics of the nascent chain and its interactions.

Main Results:

  • Within the ribosomal exit tunnel core, apoMb interactions resemble previously reported findings.
  • As the RNC enters the tunnel vestibule, it exhibits increased dynamics and interacts with ribosomal RNA (rRNA) and the L23 r-protein.
  • On the ribosome's outer surface, RNCs primarily interact with a conserved nonpolar patch on the L23 r-protein.
  • The N-terminal region of apoMb is dynamic and compact, lacking direct contact with the ribosome.
  • Apomyoglobin interacts with the ribosome via its C-terminal region during translocation.

Conclusions:

  • Apomyoglobin's cotranslational folding involves dynamic interactions with the ribosome, particularly with rRNA and the L23 r-protein in the tunnel vestibule and on the outer surface.
  • The C-terminal region of the nascent chain mediates ribosome interaction, while the N-terminal region remains dynamic and compact.
  • These findings provide new insights into the mechanisms of cotranslational protein folding and the role of specific ribosomal components in guiding this process.