A novel target recognition revealed by calmodulin in complex with the basic helix–loop–helix transcription factor SEF2‐1/E2‐2

Calmodulin is the predominant intracellular receptor for Ca2+ signals, mediating the regulation of numerous cellular processes. It can inhibit the DNA binding of basic helix–loop–helix transcription factors by a direct interaction of a novel type. To structurally characterize this novel calmodulin‐target interaction, we decided to study the complex of calmodulin with a dimeric peptide corresponding to the DNA‐binding domains of the dimeric basic helix–loop–helix transcription factor SEF2‐1 (SEF2‐1mp) using NMR. Here, we report that the stoichiometry of the calmodulin:SEF2‐1mp complex is one dimeric peptide binding two calmodulin molecules. We also report the 1H, 13C, and 15N resonance assignments and the secondary structure of calmodulin in this for NMR large (∼38 kD) complex, as well as the 1H assignments and secondary structure of SEF2‐1mp. In addition, we determined the amide proton exchange rates of calmodulin and measured intermolecular calmodulin:SEF2‐1mp and calmodulin:calmodulin NOE contacts. The isotope‐filtered experiments show a large number of SEF2‐1mp to calmodulin NOE contacts indicating that a tight complex is formed, which is confirmed by an intermolecular calmodulin:calmodulin NOE contact. The secondary structure and amide proton exchange data show that the binding does not occur via the classical wraparound binding mode. Instead, the data indicate that calmodulin interacts with SEF2‐1mp in a more open conformation, although the hydrophobic surfaces of the N‐ and C‐terminal domains still form the main interaction sites. Interactions involving charged residues are also identified in agreement with the known relatively high sensitivity of the binding to ionic strength. Finally, the peptide does not form an α‐helix as in the classical wraparound binding mode.