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Rational design of TNFα binding proteins based on the de novo designed protein DS119
Author(s) -
Zhu Cheng,
Zhang Changsheng,
Zhang Tao,
Zhang Xiaoling,
Shen Qi,
Tang Bo,
Liang Huanhuan,
Lai Luhua
Publication year - 2016
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3029
Subject(s) - protein design , rational design , protein engineering , computational biology , synthetic biology , scaffold protein , biology , protein structure , protein–protein interaction , biochemistry , microbiology and biotechnology , enzyme , genetics , signal transduction
De novo protein design offers templates for engineering tailor‐made protein functions and orthogonal protein interaction networks for synthetic biology research. Various computational methods have been developed to introduce functional sites in known protein structures. D e novo designed protein scaffolds provide further opportunities for functional protein design. Here we demonstrate the rational design of novel tumor necrosis factor alpha (TNFα) binding proteins using a home‐made grafting program AutoMatch. We grafted three key residues from a virus 2L protein to a de novo designed small protein, DS119, with consideration of backbone flexibility. The designed proteins bind to TNFα with micromolar affinities. We further optimized the interface residues with RosettaDesign and significantly improved the binding capacity of one protein Tbab1‐4. These designed proteins inhibit the activity of TNFα in cellular luciferase assays. Our work illustrates the potential application of the de novo designed protein DS119 in protein engineering, biomedical research, and protein sequence‐structure‐function studies.