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The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer.

Jens Danielsson1, Leena Liljedahl, Elsa Bárány-Wallje

  • 1Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.

Biochemistry
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Small ribonucleotide reductase (RNR) regulatory protein Sml1 in yeast is intrinsically disordered. Dimerization of Sml1 enhances its stability and protects functional regions from degradation, a potential general mechanism for disordered proteins.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Sml1 is a regulatory protein controlling ribonucleotide reductase (RNR) activation in Saccharomyces cerevisiae.
  • Intrinsically disordered proteins (IDPs) exhibit high dynamics and lack stable structures, posing challenges for characterization.
  • Previous studies suggested a dimeric structure for Sml1, but its molecular properties required further investigation.

Purpose of the Study:

  • To characterize the molecular properties of Sml1, including its structure, dynamics, and oligomerization state.
  • To investigate the functional implications of Sml1's disordered nature and its dimeric form.
  • To explore the potential role of Sml1's structure in protecting functionally important regions.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy, including studies on 15N-labeled Sml1 and a truncated variant.
  • Translation diffusion NMR measurements to determine dimerization constants.
  • Hydrodynamic radius measurements using NMR diffusion.
  • Spin-labeling studies to probe long-range interactions.
  • Protease degradation assays combined with mass spectrometry.

Main Results:

  • Sml1 was confirmed as an intrinsically disordered protein with transient helical segments and restricted motion.
  • Dimerization of Sml1 was confirmed, with a dissociation constant of 0.1 mM at 4°C.
  • Hydrodynamic radii determined for monomeric (23.4 Å) and dimeric (34.4 Å) Sml1.
  • Long-range interactions suggest N-terminal folding onto the C-terminal domain.
  • Protease degradation revealed preferential degradation of the N-terminal domain, protecting the C-terminal region.
  • Dimer formation offered additional protection against proteolysis without inducing significant structure.

Conclusions:

  • Sml1 exists as a dynamic, intrinsically disordered protein that dimerizes.
  • Dimerization enhances the stability of Sml1 by protecting its functionally important C-terminal region from proteolysis.
  • This protective mechanism mediated by dimerization may be a general feature of other natively disordered proteins.