Mass spectrometry-complemented molecular modeling predicts the interaction interface for a camelid single-domain antibody targeting the Plasmodium falciparum circumsporozoite protein’s C-terminal domain
Kwabena F.M. Opuni, Manuela Ruß, Rob Geens, Line De Vocht, Pieter Van Wielendaele, Christophe Debuy, Yann G.-J. Sterckx, Michael O. Glocker
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引用次数: 0
Abstract
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. 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. 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 complex dissociation constant is 5 × 10 M. Combining AlphaFold2 modeling with mass spectrometry/limited proteolysis generated a trustworthy model for the sdAbCSP1 – PfCSP-Cext complex interaction interface.
期刊介绍:
Computational and Structural Biotechnology Journal (CSBJ) is an online gold open access journal publishing research articles and reviews after full peer review. All articles are published, without barriers to access, immediately upon acceptance. The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together through the application of computational methods. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. Specific areas of interest include, but are not limited to:
Structure and function of proteins, nucleic acids and other macromolecules
Structure and function of multi-component complexes
Protein folding, processing and degradation
Enzymology
Computational and structural studies of plant systems
Microbial Informatics
Genomics
Proteomics
Metabolomics
Algorithms and Hypothesis in Bioinformatics
Mathematical and Theoretical Biology
Computational Chemistry and Drug Discovery
Microscopy and Molecular Imaging
Nanotechnology
Systems and Synthetic Biology