7AVC

DoBi scaffold based on PIH1D1 N-terminal domain

This is a non-PDB format compatible entry.

Summary for 7AVC

• Entry DOI: 10.2210/pdb7avc/pdb
• Descriptor: PIH1 domain-containing protein 1, SODIUM ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: protein scaffold, cytokine binding, protein binding
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 17124.44

Authors

Kolenko, P.,Pham, N.P.,Pavlicek, J.,Mikulecky, P.,Schneider, B. (deposition date: 2020-11-05, release date: 2021-02-10, Last modification date: 2024-01-31)

Primary citation

Pham, P.N.,Huliciak, M.,Biedermannova, L.,Cerny, J.,Charnavets, T.,Fuertes, G.,Herynek, S.,Kolarova, L.,Kolenko, P.,Pavlicek, J.,Zahradnik, J.,Mikulecky, P.,Schneider, B.
Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution.
Viruses, 13:-, 2021

PubMed Abstract: Engineered small non-antibody protein scaffolds are a promising alternative to antibodies and are especially attractive for use in protein therapeutics and diagnostics. The advantages include smaller size and a more robust, single-domain structural framework with a defined binding surface amenable to mutation. This calls for a more systematic approach in designing new scaffolds suitable for use in one or more methods of directed evolution. We hereby describe a process based on an analysis of protein structures from the Protein Data Bank and their experimental examination. The candidate protein scaffolds were subjected to a thorough screening including computational evaluation of the mutability, and experimental determination of their expression yield in , solubility, and thermostability. In the next step, we examined several variants of the candidate scaffolds including their wild types and alanine mutants. We proved the applicability of this systematic procedure by selecting a monomeric single-domain human protein with a fold different from previously known scaffolds. The newly developed scaffold, called ProBi (Protein Binder), contains two independently mutable surface patches. We demonstrated its functionality by training it as a binder against human interleukin-10, a medically important cytokine. The procedure yielded scaffold-related variants with nanomolar affinity.

PubMed: 33514045
DOI: 10.3390/v13020190

Experimental method

X-RAY DIFFRACTION (1.2 Å)