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Kinetic control of nascent protein biogenesis by peptide deformylase

Lena A K Bögeholz1, Evan Mercier1, Wolfgang Wintermeyer1

  • 1Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.

Scientific Reports
|December 28, 2021
PubMed

Insights

Peptide deformylase (PDF) rapidly removes N-terminal formyl groups from bacterial proteins during synthesis. The enzyme

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Bacterial protein synthesis initiates with formylated methionine.
  • N-terminal formyl group removal by peptide deformylase (PDF) is essential for further processing.
  • Deformylation occurs co-translationally as the nascent chain emerges from the ribosome.

Purpose of the Study:

  • To elucidate the kinetic mechanism of PDF-mediated deformylation of ribosome-bound nascent chains.
  • To investigate the binding and dissociation kinetics of PDF on ribosomes.
  • To understand the role of PDF in early nascent chain processing and potential chaperone activity.

Main Methods:

  • Kinetic analysis of peptide deformylase activity.
  • Study of PDF interaction with ribosome-bound nascent chains.
  • Observation of co-translational deformylation under ongoing translation conditions.

Main Results:

  • PDF binds to and dissociates from ribosomes rapidly, enabling efficient substrate scanning.
  • The rate-limiting step in PDF's mechanism is a post-cleavage nascent chain conformational rearrangement.
  • PDF rapidly deformylates accessible nascent chains during ongoing translation.
  • PDF exhibits slow release of deformylated chains, potentially acting as an early chaperone.

Conclusions:

  • PDF's rapid ribosomal interaction facilitates efficient deformylation of bacterial proteins.
  • The enzyme's slow release of products suggests a role in protecting short nascent chains.
  • PDF's dual function in deformylation and early nascent chain protection is highlighted.

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