Role of dimerization in KH/RNA complexes: the example of Nova KH3

Biochemistry. 2002 Apr 2;41(13):4193-201. doi: 10.1021/bi011994o.

Abstract

The K homology module, one of the most common RNA-binding motifs, is present in multiple copies in both prokaryotic and eukaryotic regulatory proteins. Increasing evidence suggests that self-aggregation of KH modules has a functional role. We have used a combination of techniques to characterize the behavior in solution of the third KH domain of Nova-1, a paradigmatic KH protein. The possibility of working on the isolated module allowed us to observe specifically the homodimerization and RNA-binding properties of KH domains. We provide conclusive evidence that self-association of Nova-1 KH3 occurs in solution even in the absence of RNA. Homodimerization involves a specific protein/protein interface. We also studied the dynamical behavior of Nova-1 KH3 in isolation and in complex with RNA. These data provide a model for the mechanism of KH/RNA recognition and suggest functional implications of dimerization in KH complexes. We discuss our findings in the context of the whole KH family and suggest a generalized mode of interaction.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Antigens, Neoplasm*
  • Base Sequence
  • Dimerization
  • Kinetics
  • Magnetic Resonance Spectroscopy
  • Models, Genetic
  • Models, Molecular
  • Molecular Sequence Data
  • Nerve Tissue Proteins*
  • Neuro-Oncological Ventral Antigen
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA / chemistry
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry*
  • Ribonucleoproteins / chemistry
  • Sequence Homology, Amino Acid
  • Ultracentrifugation

Substances

  • Antigens, Neoplasm
  • Nerve Tissue Proteins
  • Neuro-Oncological Ventral Antigen
  • RNA-Binding Proteins
  • Ribonucleoproteins
  • RNA