A Systematic Test of Receptor Binding Kinetics for Ligands in Tumor Necrosis Factor Superfamily by Computational Simulations

International Journal of Molecular Sciences
Zhaoqian Su, Yinghao Wu

Abstract

Ligands in the tumor necrosis factor (TNF) superfamily are one major class of cytokines that bind to their corresponding receptors in the tumor necrosis factor receptor (TNFR) superfamily and initiate multiple intracellular signaling pathways during inflammation, tissue homeostasis, and cell differentiation. Mutations in the genes that encode TNF ligands or TNFR receptors result in a large variety of diseases. The development of therapeutic treatment for these diseases can be greatly benefitted from the knowledge on binding properties of these ligand-receptor interactions. In order to complement the limitations in the current experimental methods that measure the binding constants of TNF/TNFR interactions, we developed a new simulation strategy to computationally estimate the association and dissociation between a ligand and its receptor. We systematically tested this strategy to a comprehensive dataset that contained structures of diverse complexes between TNF ligands and their corresponding receptors in the TNFR superfamily. We demonstrated that the binding stabilities inferred from our simulation results were compatible with existing experimental data. We further compared the binding kinetics of different TNF/TNFR systems, a...Continue Reading

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Citations

Sep 15, 2020·Journal of Biomolecular Structure & Dynamics·Fortunatus C Ezebuo, Ikemefuna C Uzochukwu
Apr 20, 2021·Computational and Structural Biotechnology Journal·Zhaoqian SuYinghao Wu

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Methods Mentioned

BETA
enzyme-linked immunosorbent assay

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