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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD

Eider Nuñez1,2, Prithwidip Saha1, Markel G Ibarluzea3,4

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|December 11, 2025
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Summary
This summary is machine-generated.

Trigger Factor (TF) is a bacterial chaperone that helps proteins fold during translation. This study visualizes TF

Keywords:
atomic force microscopy imagingmolecular dynamics simulationsprotein foldingribosometrigger factor (chaperone)

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Trigger Factor (TF) is a crucial ATP-independent molecular chaperone in bacteria.
  • TF assists nascent polypeptide chains emerging from the ribosome during protein synthesis.
  • Real-time dynamics of TF during active translation under physiological conditions are not well understood.

Purpose of the Study:

  • To visualize the real-time dynamics of TF on *Escherichia coli* ribosomes during active translation.
  • To investigate the conformational changes and binding interactions of TF in a near-physiological context.
  • To elucidate the role of TF in cotranslational folding.

Main Methods:

  • High-speed atomic force microscopy (HS-AFM) for real-time imaging of TF on intact ribosomes.
  • All-atom molecular dynamics (MD) simulations to complement experimental observations.
  • Visualization of TF interactions with ribosomal proteins uL23 and bL17.

Main Results:

  • TF exhibits dynamic transitions between compact and extended conformations.
  • TF forms stable and transient contacts with specific ribosomal proteins (uL23 and bL17).
  • Multivalent interactions were observed, with TFs engaging distinct sites on the ribosome-nascent chain complex.

Conclusions:

  • This study provides unprecedented insights into the real-time dynamics of ribosome-associated chaperones.
  • The findings reveal TF's conformational flexibility and multivalent binding capabilities.
  • The integrative approach establishes a platform for studying cotranslational folding dynamics.