9r17

De novo designed homodimeric NTF2-like protein with a hydrophobic pocket

spinqualitylabelsall models 9r17, resolution 1.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9r17 is a 1 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.5Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed NTF2-like proteins are compact alpha + beta fold domains with cone-shaped architectures and internal pockets, making them attractive scaffolds for the de novo design of small-molecule binders and enzymes. However, creating ligand-binding pockets often compromises folding stability, posing a key challenge in de novo protein design. Here, we introduce strategies to stabilize NTF2-like domains while preserving pocket geometry and accessibility. By expanding the hydrophobic core through computationally designed alpha-helical subdomains or homodimer interfaces buttressing the beta-sheet's convex face, we enhance structural stability without blocking pocket access on the concave face. Biochemical, biophysical, and crystallographic analyses confirm that the designed buttressing elements maintain the intended fold and support diverse, well-formed hydrophobic ligand-binding pockets with increased preorganization. Our results demonstrate that structural stabilization and pocket optimization need not be mutually exclusive, providing a generalizable approach to create robust ligand-binding proteins. This framework addresses a major bottleneck in protein design and should fuel the development of NTF2-based scaffolds for applications in small-molecule biosensing and enzyme catalysis. Buttressing ligand-binding pockets in de novo designed NTF2-like domains.,Nadal M, Albi-Puig J, Castellvi A, Garcia-Franco PM, Vega S, Velazquez-Campoy A, Marcos E Protein Sci. 2025 Nov;34(11):e70323. doi: 10.1002/pro.70323. PMID:41074781 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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