Structural delineation of stem-loop RNA binding by human TAF15 protein

Sci Rep. 2015 Nov 27:5:17298. doi: 10.1038/srep17298.

Abstract

Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Gene Expression
  • Humans
  • Hydrogen Bonding
  • Molecular Docking Simulation*
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleotide Motifs
  • Oligoribonucleotides / chemistry*
  • Oligoribonucleotides / metabolism
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA / chemistry*
  • RNA / metabolism
  • RNA Recognition Motif Proteins / chemistry*
  • RNA Recognition Motif Proteins / genetics
  • RNA Recognition Motif Proteins / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Alignment
  • TATA-Binding Protein Associated Factors / chemistry*
  • TATA-Binding Protein Associated Factors / genetics
  • TATA-Binding Protein Associated Factors / metabolism

Substances

  • Oligoribonucleotides
  • RNA Recognition Motif Proteins
  • Recombinant Proteins
  • TAF15 protein, human
  • TATA-Binding Protein Associated Factors
  • RNA