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8QU2

NF-YB/C Heterodimer in Complex with a 16-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker

Summary for 8QU2
Entry DOI10.2210/pdb8qu2/pdb
Related8QU3
DescriptorNuclear transcription factor Y subunit alpha, Nuclear transcription factor Y subunit beta, Nuclear transcription factor Y subunit gamma, ... (7 entities in total)
Functional Keywordspeptidometic inhibitor, transcription
Biological sourceHomo sapiens (human)
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Total number of polymer chains3
Total formula weight24534.60
Authors
Durukan, C.,Arbore, F.,Klintrot, C.I.R.,Grossmann, T.N.,Hennig, S. (deposition date: 2023-10-13, release date: 2024-03-20, Last modification date: 2024-11-13)
Primary citationDurukan, C.,Arbore, F.,Klintrot, R.,Bigiotti, C.,Ilie, I.M.,Vreede, J.,Grossmann, T.N.,Hennig, S.
Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y.
Chembiochem, 25:e202400020-e202400020, 2024
Cited by
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.
PubMed: 38470946
DOI: 10.1002/cbic.202400020
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.45 Å)
Structure validation

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