Epitopes prediction for microcystin-LR by molecular docking

Microcystin-LR (MC-LR) is one of the most worldwide harmful cyanobacterial toxins. A lots of antibodies against MC-LR have been generated and characterized. However, the knowledge about the epitopes of MC-LR was still limited. The objective of this study was to analyze the epitopes of MC-LR and demo...

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Autores principales:	Yuan Liu, Shu Liu, Chongxin Xu, Manman Lin, Yihang Li, Cheng Shen, Ying Liang, Xing Sun, Donglan Wang, Peng Lü, Xianjin Liu
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Microcystin-LR Single chain variable fragment Epitope Molecular docking Environmental pollution TD172-193.5 Environmental sciences GE1-350
Acceso en línea:	https://doaj.org/article/b608929e96f642e2964d0d597da327ca
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id	oai:doaj.org-article:b608929e96f642e2964d0d597da327ca
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spelling	oai:doaj.org-article:b608929e96f642e2964d0d597da327ca2021-11-06T04:17:44ZEpitopes prediction for microcystin-LR by molecular docking0147-651310.1016/j.ecoenv.2021.112925https://doaj.org/article/b608929e96f642e2964d0d597da327ca2021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S014765132101037Xhttps://doaj.org/toc/0147-6513Microcystin-LR (MC-LR) is one of the most worldwide harmful cyanobacterial toxins. A lots of antibodies against MC-LR have been generated and characterized. However, the knowledge about the epitopes of MC-LR was still limited. The objective of this study was to analyze the epitopes of MC-LR and demonstrate the binding mode of MC-LR with its antibody. The variable genes of a mouse hybridoma cell line (Mab5H1–3B3) raised against MC-LR have been cloned and assembled in a single chain variable fragment (scFv), and then soluble expressed in E.coli BL21. Based on the scFv, the IC50 and IC10 for MC-LR were determined to be 7.45 nM and 0.30 nM by competitive ELISA. And the scFv also showed 115% and 112% cross-reactivities to MC-RR and MC-YR, and 59% to MC-LA. By molecular docking, the binding mode between MC-LR and its scFv was demonstrated. A hydrogen bond interaction was observed between the carbonyl group of Adda5 residue of MC-LR and its scFv, and the guanidyl group of Arg4 residue and phenyl group of Adda5 residue of MC-LR were also involved in the interaction. These predicted epitopes were supported by antibody cross-reactivity data. By comparing the antibody informatics of MC-LR scFv with its predicted paratopes, VH-CDR1 was crucial for MC-LR binding, and its specificity could be tuned by engineering in Vκ-CDR1 and Vκ-CDR3. These information would be useful for the hapten design for microcystins or improving the properties of MC-LR scFv in vitro.Yuan LiuShu LiuChongxin XuManman LinYihang LiCheng ShenYing LiangXing SunDonglan WangPeng LüXianjin LiuElsevierarticleMicrocystin-LRSingle chain variable fragmentEpitopeMolecular dockingEnvironmental pollutionTD172-193.5Environmental sciencesGE1-350ENEcotoxicology and Environmental Safety, Vol 227, Iss , Pp 112925- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microcystin-LR Single chain variable fragment Epitope Molecular docking Environmental pollution TD172-193.5 Environmental sciences GE1-350
spellingShingle	Microcystin-LR Single chain variable fragment Epitope Molecular docking Environmental pollution TD172-193.5 Environmental sciences GE1-350 Yuan Liu Shu Liu Chongxin Xu Manman Lin Yihang Li Cheng Shen Ying Liang Xing Sun Donglan Wang Peng Lü Xianjin Liu Epitopes prediction for microcystin-LR by molecular docking
description	Microcystin-LR (MC-LR) is one of the most worldwide harmful cyanobacterial toxins. A lots of antibodies against MC-LR have been generated and characterized. However, the knowledge about the epitopes of MC-LR was still limited. The objective of this study was to analyze the epitopes of MC-LR and demonstrate the binding mode of MC-LR with its antibody. The variable genes of a mouse hybridoma cell line (Mab5H1–3B3) raised against MC-LR have been cloned and assembled in a single chain variable fragment (scFv), and then soluble expressed in E.coli BL21. Based on the scFv, the IC50 and IC10 for MC-LR were determined to be 7.45 nM and 0.30 nM by competitive ELISA. And the scFv also showed 115% and 112% cross-reactivities to MC-RR and MC-YR, and 59% to MC-LA. By molecular docking, the binding mode between MC-LR and its scFv was demonstrated. A hydrogen bond interaction was observed between the carbonyl group of Adda5 residue of MC-LR and its scFv, and the guanidyl group of Arg4 residue and phenyl group of Adda5 residue of MC-LR were also involved in the interaction. These predicted epitopes were supported by antibody cross-reactivity data. By comparing the antibody informatics of MC-LR scFv with its predicted paratopes, VH-CDR1 was crucial for MC-LR binding, and its specificity could be tuned by engineering in Vκ-CDR1 and Vκ-CDR3. These information would be useful for the hapten design for microcystins or improving the properties of MC-LR scFv in vitro.
format	article
author	Yuan Liu Shu Liu Chongxin Xu Manman Lin Yihang Li Cheng Shen Ying Liang Xing Sun Donglan Wang Peng Lü Xianjin Liu
author_facet	Yuan Liu Shu Liu Chongxin Xu Manman Lin Yihang Li Cheng Shen Ying Liang Xing Sun Donglan Wang Peng Lü Xianjin Liu
author_sort	Yuan Liu
title	Epitopes prediction for microcystin-LR by molecular docking
title_short	Epitopes prediction for microcystin-LR by molecular docking
title_full	Epitopes prediction for microcystin-LR by molecular docking
title_fullStr	Epitopes prediction for microcystin-LR by molecular docking
title_full_unstemmed	Epitopes prediction for microcystin-LR by molecular docking
title_sort	epitopes prediction for microcystin-lr by molecular docking
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/b608929e96f642e2964d0d597da327ca
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Epitopes prediction for microcystin-LR by molecular docking

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