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Human DND1-RRM2 forms a non-canonical domain swapped dimer.

Pooja Kumari1, Neel Sarovar Bhavesh1

  • 1Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.

Protein Science : a Publication of the Protein Society
|April 16, 2021
PubMed
Summary
This summary is machine-generated.

The human DND1-RRM2 domain forms a unique 3D domain-swapped dimer, revealing a non-canonical RNA recognition motif (RRM) fold. This structural insight explains the molecular basis of domain-swapped dimerization in RRM domains.

Keywords:
DND1NMR spectroscopyRNA binding proteinRNA recognition motifcrystal structuredomain swapped dimerization

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Area of Science:

  • Structural Biology
  • Molecular Biology
  • Biochemistry

Background:

  • RNA recognition motifs (RRMs) are abundant RNA-binding domains crucial for eukaryotic cellular regulation.
  • While canonical RRM structures are known, variations in their topology exist.
  • The DND1 protein's RRM2 domain is implicated in cellular processes, but its structural characteristics are not fully understood.

Purpose of the Study:

  • To determine the crystal structure of the human DND1-RRM2 domain.
  • To elucidate the structural basis for any observed non-canonical fold.
  • To investigate the molecular mechanisms underlying domain-swapped dimerization in RRMs.

Main Methods:

  • X-ray crystallography to determine the 2.3 Å resolution structure of human DND1-RRM2.
  • Nuclear Magnetic Resonance (NMR) spectroscopy to explore protein dynamics at the residue level.
  • Molecular Dynamics (MD) simulations to complement experimental dynamics data.

Main Results:

  • The human DND1-RRM2 domain adopts a non-canonical RRM fold.
  • A stable 3D domain-swapped dimer is formed through interactions between β1 and β4 strands across protomers.
  • NMR and MD simulations identified key residues and dynamics responsible for the stable domain-swapped dimer formation.

Conclusions:

  • The study reveals a novel, non-canonical RRM fold in human DND1-RRM2, characterized by 3D domain-swapped dimerization.
  • The findings provide a detailed molecular understanding of the determinants and mechanisms driving this unique dimerization.
  • This work expands the known structural diversity of RRM domains and their regulatory potential.