We have developed a means of using atomic force microscopy (AFM) to repeatedly localize a small area of interest (4 x 4 microm(2)) within a 0.5-cm(2) area on a heterogeneous sample, to obtain and localize high-resolution images and force measurements on nonideal samples (i.e., samples that better reflect actual biological systems, not prepared on atomically flat surfaces). We demonstrate the repeated localization and measurement of unbinding forces associated with antibody--antigen (ab--ag) interactions, by applying AFM in air and in liquid to visualize and measure polyclonal ab--ag interactions, using chicken collagen as a model system. We demonstrate that molecular interactions, in the form of ab--ag complexes, can be visualized by AFM when secondary antibodies are conjugated to 20-nm colloidal gold particles. We then compare those results with established immunological techniques, to demonstrate broader application of AFM technology to other systems. Data from AFM studies are compared with results obtained using immunological methods traditionally employed to investigate ab--ag interactions, including enzyme-linked immunosorbent assay, immunoblotting, and in situ immunofluorescence. Finally, using functionalized AFM tips with a flexible tether [poly(ethylene glycol) 800] to which a derivatized antibody was attached, we analyzed force curve data to measure the unbinding force of collagen antibody from its antigen, obtaining a value of approximately 90 +/- 40 pN with a MatLab code written to automate the analyses of force curves obtained in force--volume mode. The methodology we developed for embedded collagen sections can be readily applied to the investigation of other receptor--ligand interactions.
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http://dx.doi.org/10.1021/la036376i | DOI Listing |
ACS Nano
January 2025
Institute of Biomedical Engineering, University of Toronto, Toronto M5S 2E3, Canada.
Immune complexes (ICs), formed via antibody (Ab)-antigen (Ag) binding, trigger diverse immune responses, which are critical for natural immunity and have uses for vaccines and immunotherapies. While IC-elicited immune responses depend on its structure, existing methods for IC synthesis produce heterogeneous assemblies, which limits control over their cellular interactions and pharmacokinetics. In this study, we demonstrate the use of DNA origami to create synthetic ICs with defined shape, size, and solubility by displaying Ags in prescribed spatial patterns.
View Article and Find Full Text PDFJ Chem Phys
February 2024
Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India.
The intriguing network of antibody-antigen (Ab-Ag) interactions is highly governed by environmental perturbations and the nature of biomolecular interaction. Protein-protein interactions (PPIs) have potential applications in developing protein-adsorption-based sensors and nano-scale materials. Therefore, characterizing PPIs in the presence of a nanomaterial at the molecular level becomes imperative.
View Article and Find Full Text PDFJ Immunol
November 2023
Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
Being able to accurately predict the three-dimensional structure of an Ab can facilitate Ab characterization and epitope prediction, with important diagnostic and clinical implications. In this study, we evaluated the ability of AlphaFold to predict the structures of 222 recently published, high-resolution Fab H and L chain structures of Abs from different species directed against different Ags. We show that although the overall Ab prediction quality is in line with the results of CASP14, regions such as the complementarity-determining regions (CDRs) of the H chain, which are prone to higher variation, are predicted less accurately.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
August 2023
Area of Immunology, Faculty of Biology, and Centro de Investigaciones Biomédicas (Biomedical Research Center), Universidade de Vigo, Vigo 36310, Spain.
Since the pioneering works of Berg and Purcell, discriminating between diffusion followed by binding has played a central role in understanding cell signaling. B cell receptors (BCR) and antibodies (Ab) challenge that simplified view as binding to the antigen follows after a chain of diffusion and rotations, including whole molecule rotation and independent tilts and twists of their Fab arms due to their Y-shaped structure and flexibility. In this paper, we combine analytical calculations with Brownian simulations to derive the first-passage times due to these three rotations positioning the Fab paratopes at a proper distance and orientation required for antigen binding.
View Article and Find Full Text PDFChembiochem
May 2023
Department of Chemistry and Technology of Drugs, Department of Excellence 2018-2022, Sapienza-University of Rome, P.le Aldo, Moro 5, 00185, Rome, Italy.
One of the main problems in developing immunosensors featuring carbon nanotubes (CNTs) is immobilizing antibodies (Abs) onto the CNT surface to afford selective binding to target antigens (Ags). In this work, we developed a practical supramolecular Ab conjugation strategy based on resorc[4]arene modifiers. To improve the Ab orientation on the CNTs surface and optimizing the Ab/Ag interaction, we exploited the host-guest approach by synthesizing two newly resorc[4]arene linkers R1 and R2 via well-established procedures.
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