A topological refactoring design strategy yields highly stable granulopoietic proteins

• Published in: Nature communications Vol. 13; no. 1; p. 2948
• Main Authors: Skokowa, Julia, Hernandez Alvarez, Birte, Coles, Murray, Ritter, Malte, Nasri, Masoud, Haaf, Jérémy, Aghaallaei, Narges, Xu, Yun, Mir, Perihan, Krahl, Ann-Christin, Rogers, Katherine W., Maksymenko, Kateryna, Bajoghli, Baubak, Welte, Karl, Lupas, Andrei N., Müller, Patrick, ElGamacy, Mohammad
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/6; 631/114/469; 631/250/2520; 631/61/51/2314; 64/116; 64/60; 82/103; 82/16; 82/80; 82/83; Atomic structure; Cell differentiation; Colony-stimulating factor; Cytokines; Design; Granulocyte colony-stimulating factor; Granulocyte Colony-Stimulating Factor - genetics; Hematopoiesis; Hematopoietic Stem Cells; Humanities and Social Sciences; Humans; In vivo methods and tests; Leukocytes (granulocytic); Leukocytes (neutrophilic); multidisciplinary; Neutropenia; Neutrophils; Protein folding; Protein structure; Proteins; Science; Science (multidisciplinary); Stem cells; Topology
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-30157-2

Protein therapeutics frequently face major challenges, including complicated production, instability, poor solubility, and aggregation. De novo protein design can readily address these challenges. Here, we demonstrate the utility of a topological refactoring strategy to design novel granulopoietic proteins starting from the granulocyte-colony stimulating factor (G-CSF) structure. We change a protein fold by rearranging the sequence and optimising it towards the new fold. Testing four designs, we obtain two that possess nanomolar activity, the most active of which is highly thermostable and protease-resistant, and matches its designed structure to atomic accuracy. While the designs possess starkly different sequence and structure from the native G-CSF, they show specific activity in differentiating primary human haematopoietic stem cells into mature neutrophils. The designs also show significant and specific activity in vivo. Our topological refactoring approach is largely independent of sequence or structural context, and is therefore applicable to a wide range of protein targets. Skokowa et al. reconstruct the fold of a granulopoietic cytokine, resulting in de novo, hyperstable, highly active proteins with therapeutic potential for treating several neutropenia disorders.