ArticleComputational and structural biotechnology journal2024
Mass spectrometry-complemented molecular modeling predicts the interaction interface for a camelid single-domain antibody targeting the
Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Conserved Motifs in the Ligand-Binding Domain of TetR Family Regulators: Identification and Analysis.Computational and structural biotechnology journal · 2026Article
- Evidence for a model of conformational change by theInfection and immunity · 2025Article
- Mass Spectrometric ITEM-FOUR Analysis Reveals Coding Single-Nucleotide Polymorphisms in Human Cardiac Troponin T That Evade Detection by Sandwich ELISAs Which Use Monoclonal Antibodies M7 and M11.7 from the Elecsys Troponin TInternational journal of molecular sciences · 2025Article
- AlphaFold in protein structure and function prediction.Computational and structural biotechnology journal · 2025Article
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8 authors.
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Abstract
Background: Bioanalytical methods that enable rapid and high-detail characterization of binding specificities and strengths of protein complexes with low sample consumption are highly desired. The interaction between a camelid single domain antibody (sdAbCSP1) and its target antigen (PfCSP-Cext) was selected as a model system to provide proof-of-principle for the here described methodology. Research design and methods: The structure of the sdAbCSP1 - PfCSP-Cext complex was modeled using AlphaFold2. The recombinantly expressed proteins, sdAbCSP1, PfCSP-Cext, and the sdAbCSP1 - PfCSP-Cext complex, were subjected to limited proteolysis and mass spectrometric peptide analysis. ITEM MS (Intact Transition Epitope Mapping Mass Spectrometry) and ITC (Isothermal Titration Calorimetry) were applied to determine stoichiometry and binding strength. Results: The paratope of sdAbCSP1 mainly consists of its CDR3 (aa100-118). PfCSP-Cext's epitope is assembled from its α-helix (aa40-52) and opposing loop (aa83-90). PfCSP-Cext's GluC cleavage sites E46 and E58 were shielded by complex formation, confirming the predicted epitope. Likewise, sdAbCSP1's tryptic cleavage sites R105 and R108 were shielded by complex formation, confirming the predicted paratope. ITEM MS determined the 1:1 stoichiometry and the high complex binding strength, exemplified by the gas phase dissociation reaction enthalpy of 50.2 kJ/mol. The Conclusions: Combining AlphaFold2 modeling with mass spectrometry/limited proteolysis generated a trustworthy model for the sdAbCSP1 - PfCSP-Cext complex interaction interface.
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