8IRW

Structure of nanobody Nb9 against parathion

Summary for 8IRW

• Entry DOI: 10.2210/pdb8irw/pdb
• Descriptor: nanobody Nb9 against parathion (2 entities in total)
• Functional Keywords: nanobody, parathion, immune system
• Biological source: Camelus bactrianus
• Total number of polymer chains: 2
• Total formula weight: 36761.04

Authors

Wang, H.,Li, J.D.,Shen, X.,Xu, Z.L.,Sun, Y.M. (deposition date: 2023-03-19, release date: 2024-03-20, Last modification date: 2025-04-02)

Primary citation

Li, J.D.,Shen, X.,Xu, Z.L.,Liang, Y.F.,Shen, Y.D.,Yang, J.Y.,Wang, H.
Molecular Evolution of Antiparathion Nanobody with Enhanced Sensitivity and Specificity Based on Structural Analysis.
J.Agric.Food Chem., 71:14758-14768, 2023

PubMed Abstract: Nanobody (Nb) has gained significant attention in immunoassays owing to its numerous advantages, particularly its ease of molecular evolution. However, the limited understanding of how high sensitivity and specificity attained for antihapten Nbs hamper the development of high-performance Nbs. Herein, the antiparathion Nb (Nb9) we prepared previously was chosen as the model, and an approach based on X-ray crystallography, molecular docking, and rational site-directed saturation mutation for constructing a rapid and effective platform for nanobody evolution was described. Based on the structural analysis, two mutants, namely Nb-D5 (IC = 2.4 ± 0.2 ng/mL) and Nb-D12 (IC = 2.7 ± 0.1 ng/mL), were selected out from a six-sites directed saturation mutation library, 3.5-fold and 3.1-fold sensitivity enhancement over Nb9 to parathion, respectively. Besides, Nb-D12 exhibited improved sensitivity for quinalphos, triazophos, and coumaphos (5.4-35.4 ng/mL), indicating its broader detection potential. Overall, our study advances an effective strategy for the future rational evolution of Nbs with desirable performance.

PubMed: 37768036
DOI: 10.1021/acs.jafc.3c05176

Experimental method

X-RAY DIFFRACTION (1.55 Å)