RNA recognition by the human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface

James K. Kranz, Kathleen B. Hall

Research output: Contribution to journalArticlepeer-review

59 Scopus citations

Abstract

One of the most common structural motifs in RNA-binding proteins is the RNA-binding domain (RBD). These domains share a common α/β sandwich tertiary fold, and highly conserved, though they bind diverse RNA targets with a wide range of binding affinities. The N-terminal RNA-binding domain (RBD1) of the human U1A protein binds specifically to stem/loop II of the U1 snRNA with sub-nanomolar affinity. Solvent-exposed aromatic residues on the β-sheet surface are highly conserved among RBD domains; in RBD1, these are Tyr13 and Phe56, with a unique Gln at position 54. Effects of substitutions at these positions were examined using energetic pairwise coupling to describe the communication between these residues in both the free and RNA-bound states of the protein. 15N NMR experiments were used to determine effects of the β-sheet substitutions on the structural and dynamic properties of this domain. The combination of thermodynamic pairwise coupling and 15N-backbone dynamics provides direct evidence for local cooperative interactions among Y13, Q54, and F56, and a non-conserved loop that directly affect RNA-binding. The results describe how conserved and non-conserved regions of an RBD can communicate with each other to mediate recognition of the RNA.

Original languageEnglish
Pages (from-to)215-231
Number of pages17
JournalJournal of Molecular Biology
Volume285
Issue number1
DOIs
StatePublished - Jan 8 1999

Keywords

  • Human U1A RBD(1)
  • N NMR spectroscopy
  • Pairwise coupling, free energy
  • Protein backbone dynamics
  • RNA:protein recognition

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