Switching from the unfolded to the folded state of the helix-loop-helix domain of the Id proteins based on the O-acyl isopeptide method.

The inhibitors of DNA binding and cell differentiation Id1-4 are helix-loop-helix (HLH) proteins that negatively regulate DNA transcription by forming inactive dimers with ubiquitous and tissue-specific bHLH proteins, including E47 and MyoD, respectively. Their highly conserved HLH domains are essential for heterodimerization, but can also self-associate to highly stable, alpha-helix-rich structures at low micromolar peptide concentrations. Here, we show that the introduction of an O-acyl isodipeptide unit involving the putative N-cap serine residue of the C-terminal helix completely abrogates the propensity of the Id HLH analogue for any secondary and tertiary structure, resulting in a random coil, as shown by CD measurements in nonbuffered aqueous solutions. However, the HLH fold reappears as soon as an O-->N intramolecular acyl migration, which occurs spontaneously under physiological conditions, restores the native N-cap serine residue. These results show that changes addressing the N-terminus of the C-terminal helix can dramatically influence the HLH structure, and suggest that local interactions at the junction between the loop and the C-terminal helix might be crucial during the HLH folding process. Furthermore, the present study contributes to the evaluation of the O-acyl isodipeptide unit as a powerful tool to introduce a conformational switch into peptides. Copyright (c) 2008 European Peptide Society and John Wiley & Sons, Ltd.