Download MendeleyBinding dynamics of a stapled peptide targeting the transcription factor NF-Y.
Durukan, C., Arbore, F., Klintrot, R., Bigiotti, C., Ilie, I.M., Vreede, J., Grossmann, T.N., Hennig, S.(2024) Chembiochem : e202400020-e202400020
- PubMed: 38470946
- DOI: https://doi.org/10.1002/cbic.202400020
- Primary Citation of Related Structures:
8QU2, 8QU3, 8QU4 - PubMed Abstract:
Transcription factors (TFs) play a central role in gene regulation, and their malfunction can result in a plethora of severe diseases. TFs are therefore interesting therapeutic targets, but their involvement in protein-protein interaction networks and the frequent lack of well-defined binding pockets render them challenging targets for classical small molecules. As an alternative, peptide-based scaffolds have proven useful, in particular with an α-helical active conformation. Peptide-based strategies often require extensive structural optimization efforts, which could benefit from a more detailed understanding of the dynamics in inhibitor/protein interactions. In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.
Organizational Affiliation:
VU Amsterdam Faculty of Sciences, Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS.
