PDB 2ZPX deposited: 2008-07-29 modified: 2009-08-18
Title TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity; R1antTNF-T8
Authors Abe, Y., Kamada, H., Mukai, Y., Nakagawa, S., Nakamura, T., Nomura, T., Ohta, T., Shibata, H., Taniai, M., Tsunoda, S., Tsutsumi, Y., Yamagata, Y., Yoshioka, Y.
Structure factors resolution 2.83 rfactor 0.268 rfree 0.309
DPI 1.38 theoretical min: 0.59

Tumour necrosis factor (TNF) is an important cytokine that induces an inflammatory response predominantly through the TNF receptor-1 (TNFR1). A crucial strategy for the treatment of many autoimmune diseases, therefore, is to block the binding of TNF to TNFR1. We previously identified a TNFR1-selective antagonistic mutant TNF (R1antTNF) from a phage library containing six randomized amino acid residues at the receptor-binding site (amino acids 84-89). Two R1antTNFs, R1antTNF-T2 (A84S, V85T, S86T, Y87H, Q88N and T89Q) and R1antTNF-T8 (A84T, V85P, S86A, Y87I, Q88N and T89R), were successfully isolated from this library. Here, we analysed R1antTNF-T8 using surface plasmon resonance spectroscopy and X-ray crystallography to determine the mechanism underlying the antagonistic activity of R1antTNF. The kinetic association/dissociation parameters of R1antTNF-T8 were higher than those of wild-type TNF, indicating more rapid bond dissociation. X-ray crystallographic analysis suggested that the binding mode of the T89R mutation changed from a hydrophobic to an electrostatic interaction, which may be responsible for the antagonistic behaviour of R1antTNF. Knowledge of these structure-function relationships will facilitate the design of novel TNF inhibitors based on the cytokine structure.

J.Biochem. 2009 Aug; 146(2):167-172 doi:10.1093/jb/mvp065

Cross References
Database source Identifier Description
PubMed 19386778
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
2ZPX/1 2ZPX 1 trimer 0 3 0 2976