Open AccessDesign of novel granulopoietic proteins by topological rescaffolding
Author(s) -
Birte Hernandez Alvarez,
Julia Skokowa,
Murray Coles,
Perihan Mir,
Masoud Nasri,
Kateryna Maksymenko,
Laura Weidmann,
Katherine W. Rogers,
Karl Welte,
Andrei N. Lupas,
Patrick Müller,
Mohammad ElGamacy
Publication year - 2020
Publication title -
plos biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 4.127
H-Index - 271
eISSN - 1545-7885
pISSN - 1544-9173
DOI - 10.1371/journal.pbio.3000919
Subject(s) - biology , computational biology , microbiology and biotechnology , haematopoiesis , protein design , protein engineering , set (abstract data type) , protein stability , in vitro , stem cell , topology (electrical circuits) , computer science , protein structure , genetics , biochemistry , enzyme , engineering , programming language , electrical engineering
Computational protein design is rapidly becoming more powerful, and improving the accuracy of computational methods would greatly streamline protein engineering by eliminating the need for empirical optimization in the laboratory. In this work, we set out to design novel granulopoietic agents using a rescaffolding strategy with the goal of achieving simpler and more stable proteins. All of the 4 experimentally tested designs were folded, monomeric, and stable, while the 2 determined structures agreed with the design models within less than 2.5 Å. Despite the lack of significant topological or sequence similarity to their natural granulopoietic counterpart, 2 designs bound to the granulocyte colony-stimulating factor (G-CSF) receptor and exhibited potent, but delayed, in vitro proliferative activity in a G-CSF-dependent cell line. Interestingly, the designs also induced proliferation and differentiation of primary human hematopoietic stem cells into mature granulocytes, highlighting the utility of our approach to develop highly active therapeutic leads purely based on computational design.