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Fc-Binding Cyclopeptide Induces Allostery from Fc to Fab: Revealed Through in Silico Structural Analysis to Anti-Phenobarbital Antibody.

作者信息

Zhou Tao, Zhang Huiling, Yu Xiaoting, Pan Kangliang, Yao Xiaojun, Shen Xing, Lei Hongtao

机构信息

Guangdong Provincial Key Laboratory of Food Quality and Safety and Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China.

College of Mathematics and Informatics & College of Software Engineering, South China Agricultural University, Guangzhou 510642, China.

出版信息

Foods. 2025 Apr 15;14(8):1360. doi: 10.3390/foods14081360.


DOI:10.3390/foods14081360
PMID:40282765
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12027427/
Abstract

Allostery is a fundamental biological phenomenon that occurs when a molecule binds to a protein's allosteric site, triggering conformational changes that regulate the protein's activity. However, allostery in antibodies remains largely unexplored, and only a few reports have focused on allostery from antigen-binding fragments (Fab) to crystallizable fragments (Fc). But this study, using anti-phenobarbital antibodies-which are widely applied for detecting the potential health food adulterant phenobarbital-as a model and employing multiple computational methods, is the first to identify a cyclopeptide (cyclo[Link-M-WFRHY-K]) that induces allostery from Fc to Fab in antibody and elucidates the underlying antibody allostery mechanism. The combination of molecular docking and multiple allosteric site prediction algorithms in these methods identified that the cyclopeptide binds to the interface of heavy chain region-1 (CH) in antibody Fab and heavy chain region-2 (CH) in antibody Fc. Meanwhile, molecular dynamics simulations combined with other analytical methods demonstrated that cyclopeptide induces global conformational shifts in the antibody, which ultimately alter the Fab domain and enhance its antigen-binding activity from Fc to Fab. This result will enable cyclopeptides as a potential Fab-targeted allosteric modulator to provide a new strategy for the regulation of antigen-binding activity and contribute to the construction of novel immunoassays for food safety and other applications using allosteric antibodies as the core technology. Furthermore, graph theory analysis further revealed a common allosteric signaling pathway within the antibody, involving residues Q123, S207, S326, C455, A558, Q778, D838, R975, R1102, P1146, V1200, and K1286, which will be very important for the engineering design of the anti-phenobarbital antibodies and other highly homologous antibodies. Finally, the non-covalent interaction analysis showed that allostery from Fc to Fab primarily involves residue signal transduction driven by hydrogen bonds and hydrophobic interactions.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/c34cbcc74f26/foods-14-01360-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/6b87cc1b516f/foods-14-01360-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/0da450e77fb9/foods-14-01360-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/8ccdaf081a8e/foods-14-01360-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/88017ec65631/foods-14-01360-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/106b8984b851/foods-14-01360-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/6740abb71820/foods-14-01360-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/9eceed457716/foods-14-01360-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/e95f68f1754f/foods-14-01360-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/e3b3272e0b25/foods-14-01360-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/c34cbcc74f26/foods-14-01360-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/6b87cc1b516f/foods-14-01360-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/0da450e77fb9/foods-14-01360-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/8ccdaf081a8e/foods-14-01360-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/88017ec65631/foods-14-01360-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/106b8984b851/foods-14-01360-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/6740abb71820/foods-14-01360-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/9eceed457716/foods-14-01360-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/e95f68f1754f/foods-14-01360-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/e3b3272e0b25/foods-14-01360-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2140/12027427/c34cbcc74f26/foods-14-01360-g010.jpg

相似文献

[1]
Fc-Binding Cyclopeptide Induces Allostery from Fc to Fab: Revealed Through in Silico Structural Analysis to Anti-Phenobarbital Antibody.

Foods. 2025-4-15

[2]
Non-covalent Fc-Fab interactions significantly alter internal dynamics of an IgG1 antibody.

Sci Rep. 2022-6-4

[3]
Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fcγ Receptor Binding.

Structure. 2020-5-5

[4]
Antigen-induced conformational changes in antibodies and their Fab fragments studied by circular polarization of fluorescence.

Proc Natl Acad Sci U S A. 1975-7

[5]
Antigen binding allosterically promotes Fc receptor recognition.

MAbs. 2018-10-5

[6]
Full-length recombinant antibodies from : production, characterization, effector function (Fc) engineering, and clinical evaluation.

MAbs. 2022

[7]
Antibody-receptor interactions mediate antibody-dependent cellular cytotoxicity.

J Biol Chem. 2021-7

[8]
Charge-mediated Fab-Fc interactions in an IgG1 antibody induce reversible self-association, cluster formation, and elevated viscosity.

MAbs. 2016

[9]
IgG1 and IgG4 antibodies sample initial structure dependent local conformational states and exhibit non-identical Fab dynamics.

Sci Rep. 2023-3-23

[10]
IgG cooperativity - Is there allostery? Implications for antibody functions and therapeutic antibody development.

MAbs. 2017-8-16

本文引用的文献

[1]
A non-classical view of antibody properties: Allosteric effect between variable and constant regions.

Biotechnol Adv. 2025

[2]
The shortest path method (SPM) webserver for computational enzyme design.

Protein Eng Des Sel. 2024-1-29

[3]
Identification of histidine kinase inhibitors through screening of natural compounds to combat mastitis caused by Streptococcus agalactiae in dairy cattle.

J Biol Eng. 2023-9-26

[4]
PASSer: fast and accurate prediction of protein allosteric sites.

Nucleic Acids Res. 2023-7-5

[5]
Targeting the PEDV 3CL protease for identification of small molecule inhibitors: an insight from virtual screening, ADMET prediction, molecular dynamics, free energy landscape, and binding energy calculations.

J Biol Eng. 2023-4-18

[6]
Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations.

J Enzyme Inhib Med Chem. 2023-12

[7]
Insights on the interaction of SARS-CoV-2 variant B.1.617.2 with antibody CR3022 and analysis of antibody resistance.

J Genet Eng Biotechnol. 2023-3-20

[8]
Comprehensive screening strategy coupled with structure-guided engineering of l-threonine aldolase from for enhanced catalytic efficiency towards l--4-methylsulfonylphenylserine.

Front Bioeng Biotechnol. 2023-1-30

[9]
Insight into free energy and dynamic cross-correlations of residue for binding affinity of antibody and receptor binding domain SARS-CoV-2.

Heliyon. 2023-1

[10]
Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains.

Int J Mol Sci. 2022-11-23

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