Single Molecule Force Spectroscopy to Compare Natural versus Artificial Antibody-Antigen Interaction

Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization

Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions.

Molecular Recognition of Proteins through Quantitative Force Maps at Single Molecule Level

Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific tip-sample forces. Remarkably, adhesion images give only specific rupture events, becoming qualitative and quantitative molecular recognition maps obtained at reasonably fast rates, which is a great advantage compared to the force–volume modes. This procedure has been used to go further in discriminating between two similar protein molecules, avidin and streptavidin, in hybrid samples. The adhesion maps generated scanning with biotinylated probes showed features identified as avidin molecules, in the range of 40–80 pN; meanwhile, streptavidin molecules rendered 120–170 pN at the selected working conditions. The gathered results evidence that repulsive jumping force mode applying very small forces allows the identification of biomolecules through the specific rupture forces of the complexes and could serve to identify receptors on membranes or samples or be applied to design ultrasensitive detection technologies.

Evaluating effect of metallic ions on aggregation behavior of β-amyloid peptides by atomic force microscope and surface-enhanced Raman Scattering

Background

Excessive aggregation of β-amyloid peptides (Aβ) is regarded as the hallmark of Alzheimer’s disease. Exploring the underlying mechanism regulating Aβ aggregation remains challenging and investigating aggregation events of Aβ in the presence and absence of metallic ions at molecular level would be meaningful in elucidating the role of metal cations on interactions between Aβ molecules. In this study, chemical self-assembled monolayer (SAM) method was employed to fabricate monolayer of β-amyloid peptides Aβ42 on gold substrate with a bolaamphiphile named 16-Mercaptohexadecanoic acid (MHA). Firstly, the samples of gold substrate (blank control), the MHA-modified substrate, and the Aβ42-modified substrate were detected by X-ray photoelectron spectroscopy (XPS) to track the self-assembly process. Aggregation behaviors of Aβ42 before and after metallic ions (Zn²⁺, Ca²⁺, Al³⁺) treatment were monitored by atomic force microscopy (AFM) and the interaction between Aβ42 and metallic ions (Zn²⁺, Ca²⁺, Al³⁺) was investigated by surface-enhanced Raman Scattering (SERS).

Results

The XPS spectra of binding energy of gold substrate (blank control), the MHA-modified substrate, and the Aβ42-modified substrate are well fitted with the corresponding monolayer’s composition, which indicates that Aβ42 monolayer is well formed. The recorded surface morphology of different experimental groups obtained by AFM showed markedly different nanostructures, indicating occurrence of aggregation events between Aβ42 molecules after adding metal ions to the solution. Compared to the control group, the presence of metallic ions resulted in the increased size of surface structures on the observed 3D topography. Besides, the intermolecular rupture force of Aβ42 increased with the addition of metallic ions. Further study by SERS showed that the Raman strength of Aβ42 changes significantly after the metal cation treatment. A considerable part of the amide bonds interacts with metal cations, leading to a structural change, which is characterized by the weakened β-fold Raman peak.

Conclusion

The AFM imaging results suggest that aggregation events occurred between Aβ42 molecules with the addition of metal cations. In addition, the results of force tests indicate that the presence of metallic ions could promote adhesion between Aβ42 molecules, which is likely to be the trigger for aggregation behavior of Aβ42. Furthermore, the effect of metallic cations on the conformational change of Aβ42 studied by SERS supported the results obtained by AFM. Taken together, the results showed that the presence of substoichiometric metal cations promotes aggregation behavior between Aβ42 molecules on the substrate at pH 7.4.

Stabilization of surface-bound antibodies for ELISA based on a reversable zeolitic imidazolate framework-8 coating

Immunoassays typically must be stored under refrigerated conditions because antibodies, after being immobilized to solid surfaces, tend to lose their recognition capabilities to target antigens under non-refrigerated conditions. This requirement hinders application of immunoassays in resource-limited settings including rural clinics in tropical regions, disaster struck areas, and low-income countries, where refrigeration may not be feasible. In this work, a facile approach based on a reversable zeolitic imidazolate framework-8 (ZIF-8) coating is introduced to stabilize surface-bound antibodies on enzyme-linked immunosorbent assay (ELISA) plates under non-refrigerated conditions. Using a sandwich ELISA for the detection of neutrophil gelatinase-associated lipocalin (NGAL), a urine biomarker for acute kidney injury, as a model system, ZIF-8 is demonstrated to be able to uniformly coat the surface-bound anti-NGAL IgG, and stabilize the dynamic range and detection sensitivity of the assay after storage at an elevated temperature (50 °C) for at least 4 weeks. The stabilization efficacy of the ZIF-8 coating is comparable to the current "gold standard" refrigeration approach, and superior to the commonly used sucrose coating method. This approach will greatly improve the shelf-life and stability of antibody-coated ELISAs and other types of assays which utilize surface-bound antibodies, thus extending biomedical research and medical diagnostics to resource-limited settings.

Scanning Probe Microscopies: Imaging and Biomechanics in Reproductive Medicine Research

Basic and translational research in reproductive medicine can provide new insights with the application of scanning probe microscopies, such as atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM). These microscopies, which provide images with spatial resolution well beyond the optical resolution limit, enable users to achieve detailed descriptions of cell topography, inner cellular structure organization, and arrangements of single or cluster membrane proteins. A peculiar characteristic of AFM operating in force spectroscopy mode is its inherent ability to measure the interaction forces between single proteins or cells, and to quantify the mechanical properties (i.e., elasticity, viscoelasticity, and viscosity) of cells and tissues. The knowledge of the cell ultrastructure, the macromolecule organization, the protein dynamics, the investigation of biological interaction forces, and the quantification of biomechanical features can be essential clues for identifying the molecular mechanisms that govern responses in living cells. This review highlights the main findings achieved by the use of AFM and SNOM in assisted reproductive research, such as the description of gamete morphology; the quantification of mechanical properties of gametes; the role of forces in embryo development; the significance of investigating single-molecule interaction forces; the characterization of disorders of the reproductive system; and the visualization of molecular organization. New perspectives of analysis opened up by applying these techniques and the translational impacts on reproductive medicine are discussed.

Imprinted Polymer Beads Loaded with Silver Nanoparticles for Antibacterial Applications

After the emergence of multidrug-resistant strains, antibiotic resistance in bacteria has become an important problem. Thus, materials for combating multidrug-resistant bacteria are of vital importance. In this work, we developed an antibacterial material that can selectively capture and destruct bacteria on the basis of their physical characteristics. To achieve bacterial capture and deactivation with a single material, we used bacterial cells as templates to synthesize surface-imprinted polymer beads in bacteria-stabilized Pickering emulsions. Acrylate-functionalized polyethylenimine was used to coat the bacterial surface so that the coated bacteria can act as a particle stabilizer to establish an oil-in-water Pickering emulsion. Hydrophobic Ag nanoparticles were introduced into the oil phase composed of cross-linking monomers. Bacteria-imprinted beads (BIB) were obtained after the oil phase was polymerized. Bacterial binding experiments confirmed the importance of the imprinted sites for specific recognition with the target bacteria. The Ag nanoparticles embedded inside the polymer beads enhanced bacterial inactivation and reduced the leakage of heavy metal in aquatic environment. The combination of bacteria-imprinting with delivery of general-purpose antibacterial reagents offers a useful approach toward selective capture and destruction of bacteria.

Development of a universal method for the measurement of binding affinities of antibody drugs towards a living cell based on AFM force spectroscopy

A universal method to measure the binding affinities of antibody drugs towards their targets on the surface of living cells was developed based on atomic force microscopy (AFM) analysis. Nivolumab, an antibody drug targeting programmed cell death 1 (PD-1), was mainly used as a model for this evaluation. The surface of a tip-less AFM cantilever was coated with nano-capsules, on which immunoglobulin G-binding ZZ domains of protein A were exposed, and nivolumab molecules were immobilized on the cantilever through binding between the antibody Fc domains and the ZZ domains, which controlled the molecular orientation of the antibodies. Model human T lymphocytes (Jurkat), on which PD-1 molecules were highly expressed, were immobilized on a glass substrate via a lipid bilayer-anchoring reagent. The nivolumab-coated AFM cantilever was moved to approach the T cells, and the rupture forces between nivolumab molecules on the AFM cantilever and PD-1 molecules on the cell surface were measured. The average values of the rupture forces were 0.18 ± 0.10, 0.21 ± 0.18, 0.12 ± 0.07, 0.11 ± 0.06, and 0.12 ± 0.06 nN μm-2 at loading forces of 10, 20, 30, 40, and 50 nN, respectively. Application of significantly higher loading forces decreased the S/N ratio, as confirmed by comparison with control T cells with low PD-1 expression, which suggested that a low loading force of less than 20 nN was sufficient for these measurements. A correlation between the expression levels of PD-1 and the rupture force values was confirmed using immunofluorescence. A similar assay was performed by using an antibody drug targeting epidermal growth factor receptor (EGFR) and a model cancer cell expressing EGFR molecules (A431) to evaluate the universal application of the developed method for various antibody drugs, and the same conclusions as that in nivolumab's case were obtained. This method can be applied to living cells without any chemical treatment, which allows the present method to compare the affinities of various antibody drugs towards the same single cell. These results indicated that the present method is useful for selecting the most effective candidates from various antibody drugs from the point of view of binding forces between antibodies and living cells.

Metal-Organic Framework Preserves the Biorecognition of Antibodies on Nanoscale Surfaces Validated by Single-Molecule Force Spectroscopy

Antibody biorecognition forms the basis for numerous biomedical applications such as diagnostic assays, targeted drug delivery, and targeted cancer imaging. However, antibodies, especially after being conjugated to surfaces or nanostructures, suffer from stability issues when stored under nonrefrigeration conditions. Therefore, enhancing the stability of antibodies on surfaces and nanostructures under ambient and elevated temperatures is of paramount importance for many nanobiotechnology applications. In this study, we introduce a simple and facile approach based on a metal-organic framework (MOF) coating to preserve the biorecognition capability of antibodies immobilized on nanoscale surfaces after exposure to elevated temperatures for a prolonged period. By using atomic force microscopy (AFM)-based force spectroscopy, we demonstrate that the MOF coating is able to preserve the binding force and binding frequency of the anti-CD-146 antibody attached to an AFM tip to CD-146 antigen on the surface of melanoma cells at the single-molecule level. We also demonstrate that the MOF coating outperforms another commonly used sucrose coatings in terms of maintaining the binding force and binding frequency of the antibody to antigen. Herein, the AFM tip functionalized with antibodies provides a nanoscale testbed (analogous to an antibody-conjugated nanostructure) to assess antibody biorecognition at the single-molecule level and preservation efficacy under antibody denaturing conditions. This MOF coating approach should be applicable to the preservation of a variety of antibody-conjugated nanostructures aiming for targeted drug delivery, targeted cancer imaging, and nanobiosensors. The improved stability and elimination of refrigeration requirements will facilitate wide applications of antibody-enabled nanobiotechnology in resource-limited environments and populations.

Label-Free Detection of Transferrin Receptor by a Designed Ligand-Protein Sensor

Advanced detection of biomarkers in biofluids plays an important role in disease diagnosis and prognosis. Current techniques with pre-labelling suffer from high cost and complicated operation, etc. Herein, we designed a label-free electrochemical biosensor for rapid detection of transferrin receptor with desirable linear range, sensitivity, specificity, reproducibility, and stability for practical applications.

Miniaturized magnetic bead-actuators for force-clamp spectroscopy-based single-molecule measurements

Force-clamp spectroscopy can mimic the physiological conditions for the proteins under investigation. In addition, it is a direct way of observing the relationship between bond lifetime and molecular forces. However, traditional force-clamp methods rely on active feedback controllers that can introduce artefacts. In this work, we introduce a new method to enable force-clamp spectroscopy without a need for an active feedback. The method is based on miniaturized magnetic beads offering improved stability. As a case study, we performed force-clamp experiments using biotin-streptavidin molecule pairs with and without active feedback. Our results demonstrate the feasibility of force-clamp experiments without feedback and illustrate the advantages of our method.

Environmental Stability of Plasmonic Biosensors Based on Natural versus Artificial Antibody

Plasmonic biosensors based on the refractive index sensitivity of localized surface plasmon resonance (LSPR) are considered to be highly promising for on-chip and point-of-care biodiagnostics. However, most of the current plasmonic biosensors employ natural antibodies as biorecognition elements, which can easily lose their biorecognition ability upon exposure to environmental stressors (e.g., temperature and humidity). Plasmonic biosensors relying on molecular imprints as recognition elements (artificial antibodies) are hypothesized to be an attractive alternative for applications in resource-limited settings due to their excellent thermal, chemical, and environmental stability. In this work, we provide a comprehensive comparison of the stability of plasmonic biosensors based on natural and artificial antibodies. Although the natural antibody-based plasmonic biosensors exhibit superior sensitivity, their stability (temporal, thermal, and chemical) was found to be vastly inferior to those based on artificial antibodies. Our results convincingly demonstrate that these novel classes of artificial antibody-based plasmonic biosensors are highly attractive for point-of-care and resource-limited conditions where tight control over transport, storage, and handling conditions is not possible.

Single-Molecule Force Spectroscopy Reveals Self-Assembly Enhanced Surface Binding of Hydrophobins

Hydrophobins have raised lots of interest as powerful surface adhesives. However, it remains largely unexplored how their strong and versatile surface adhesion is linked to their unique amphiphilic structural features. Here, we develop an AFM-based single-molecule force spectroscopy assay to quantitatively measure the binding strength of hydrophobin to various types of surfaces both in isolation and in preformed protein films. We find that individual class II hydrophobins (HFBI) bind strongly to hydrophobic surfaces but weakly to hydrophilic ones. After self-assembly into protein films, they show much stronger binding strength to both surfaces due to the cooperativity of different interactions at nanoscale. Such self-assembly enhanced surface binding may serve as a general design principle for synthetic bioactive adhesives.

Ultrarobust Biochips with Metal-Organic Framework Coating for Point-of-Care Diagnosis

Most biosensors relying on antibodies as recognition elements fail in harsh environment conditions such as elevated temperatures, organic solvents, or proteases because of antibody denaturation, and require strict storage conditions with defined shelf life, thus limiting their applications in point-of-care and resource-limited settings. Here, a metal-organic framework (MOF) encapsulation is utilized to preserve the biofunctionality of antibodies conjugated to nanotransducers. This study investigates several parameters of MOF coating (including growth time, surface morphology, thickness, and precursor concentrations) that determine the preservation efficacy against different protein denaturing conditions in both dry and wet environments. A plasmonic biosensor based on gold nanorods as the nanotransducers is employed as a model biodiagnostic platform. The preservation efficacy attained through MOF encapsulation is compared to two other commonly employed materials (sucrose and silk fibroin). The results show that MOF coating outperforms sucrose and silk fibroin coatings under several harsh conditions including high temperature (80 °C), dimethylformamide, and protease solution, owing to complete encapsulation, stability in wet environment and ease of removal at point-of-use by the MOF. We believe this study will broaden the applicability of this universal approach for preserving different types of on-chip biodiagnostic reagents and biosensors/bioassays, thus extending the benefits of advanced diagnostic technologies in resource-limited settings.

Universal Mussel-Inspired Ultrastable Surface-Anchoring Strategy via Adaptive Synergy of Catechol and Cations

An outstanding anchoring ligand with robust anchoring ability and universal applicability is highly desirable in materials science and surface engineering. This work reports a novel and universal mussel-inspired anchoring strategy based on a cationic amine-modified catechol ligand coupled with the 2-methacryloyloxyethyl phosphorylcholine moiety. The ligand shows substrate-independent anchoring capability, and the deposited film possesses excellent antifouling properties and superior ultrasonic stability as compared to the conventional catechol ligand. Single-molecule force spectroscopy based on atomic force microscopy reveals that the enhanced ultrastable anchoring is attributed to the synergistic binding effect of cationic amine and catechol. Our results provide new nanomechanical insights into the development of novel coating strategies underwater based on amine-incorporated catechol derivatives for a wide range of materials engineering, bioengineering, and environmental applications.