title: Rational design of TNFα binding proteins based on the de novo designed protein DS119.
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.
authors: BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors: Cheng
authors: C
authors: Zhu
authors: BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors: Changsheng
authors: C
authors: Zhang
authors: BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors: Tao
authors: T
authors: Zhang
authors: Center for Quantitative Biology, Peking University, Beijing, 100871, China.
authors: Xiaoling
authors: X
authors: Zhang
authors: Center for Quantitative Biology, Peking University, Beijing, 100871, China.
authors: Qi
authors: Q
authors: Shen
authors: Center for Quantitative Biology, Peking University, Beijing, 100871, China.
authors: Bo
authors: B
authors: Tang
authors: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
authors: Huanhuan
authors: H
authors: Liang
authors: BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.|Center for Quantitative Biology, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.
authors: Luhua
authors: L
authors: Lai
mesh_terms: D006801:Humans; D011212:Poxviridae / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D015202:Protein Engineering; D012984:Software; D014409:Tumor Necrosis Factor-alpha / Q000037:antagonists & inhibitors*; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D014409:Tumor Necrosis Factor-alpha; D014764:Viral Proteins
keywords: TNF; de novo; inhibitor; protein design; protein-protein interaction