6QMP image
Deposition Date 2019-02-08
Release Date 2019-10-02
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6QMP
Keywords:
Title:
NF-YB/C Heterodimer in Complex with NF-YA Peptide
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Nuclear transcription factor Y subunit alpha
Gene (Uniprot):NFYA
Chain IDs:A
Chain Length:31
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Nuclear transcription factor Y subunit beta
Gene (Uniprot):NFYB
Chain IDs:B
Chain Length:95
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Nuclear transcription factor Y subunit gamma
Gene (Uniprot):NFYC
Chain IDs:C
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly.
Angew.Chem.Int.Ed.Engl. 58 17351 17358 (2019)
PMID: 31539186 DOI: 10.1002/anie.201907901

Abstact

Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors. We developed a peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility. In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability. Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target DNA.

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