Rational design of TNFα binding proteins based on the de novo designed protein DS119 |
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| Authors: | Xiaoling Zhang Qi Shen Bo Tang Huanhuan Liang Luhua Lai |
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| Institution: | 1. Center for Quantitative Biology, Peking University, Beijing, China;2. National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China;3. BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China;4. Peking‐Tsinghua Center for Life Sciences, Peking University, Beijing, China |
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| Abstract: | 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. De 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. |
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| Keywords: | protein design protein‐protein interaction TNF inhibitor de novo |
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