ArticleProtein engineering, design & selection : PEDS2019
Conformational selection of allergen-antibody complexes-surface plasticity of paratopes and epitopes.
Article in Protein engineering, design & selection : PEDS, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 22 citations in OpenAlex.
- Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations.Protein science : a publication of the Protein Society · 2025Article
- AllergyPred: a web server for allergen prediction.Nucleic acids research · 2025Article
- Conformational Flexibility of a Lipocalin Allergen (Mus m 1): Implications for Molecular Allergy Diagnostics.Current issues in molecular biology · 2025Article
- CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis.Journal of chemical information and modeling · 2024Article
- In-silico analysis of potent Mosquirix vaccine adjuvant leads.Journal, genetic engineering & biotechnology · 2023Article
- Recent Progress in Antibody Epitope Prediction.Antibodies (Basel, Switzerland) · 2023Review
- Functional antibody characterization via direct structural analysis and information-driven protein-protein docking.Proteins · 2022Article
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats.Frontiers in molecular biosciences · 2022Article
- The influence of antibody humanization on shark variable domain (VNAR) binding site ensembles.Frontiers in immunology · 2022Article
- Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens.Scientific reports · 2021Article
- Germline-Dependent Antibody Paratope States and Pairing Specific VFrontiers in immunology · 2021Article
- Shark Antibody Variable Domains Rigidify Upon Affinity Maturation-Understanding the Potential of Shark Immunoglobulins as Therapeutics.Frontiers in molecular biosciences · 2021Article
- Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning.Frontiers in chemistry · 2021Article
- Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments.Frontiers in molecular biosciences · 2020Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.