Single domain antibodies as a powerful tool for high quality surface plasmon resonance studies

Surface Plasmon Resonance: A Sensitive Tool to Study Protein-Protein Interactions

Surface plasmon resonance (SPR) is one of the most commonly used techniques to study protein-protein interactions. The main advantage of SPR is the ability of measuring binding affinities and association/dissociation kinetics of complexes in real time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, called the "ligand," on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, called the "analyte," over the surface containing the ligand. The binding is monitored by following changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. During the last 15 years, SPR has been intensively used in the study of bacterial secretion systems due to its ability of detecting highly dynamic complexes, which are difficult to investigate by other techniques. This chapter will guide users in setting up SPR experiments in order to identify protein complexes and to assess their binding affinity and/or kinetics. It will include detailed protocols for (i) immobilization of proteins with the amine coupling capture method, (ii) analyte-binding analysis, (iii) affinity/kinetics measurements, and (iv) data analysis.

Construction of Synthetic VHH Libraries in Ribosome Display Format

Single-domain antibodies, or VHH, represent an attractive molecular basis to design affinity proteins with favorable properties. Beyond high affinity and specificity for their cognate target, they usually show high stability and high production yields in bacteria, yeast, or mammalian cells. In addition to these favorable properties, their ease of engineering makes them useful for many applications. Until the past few years, the generation of VHH involved the immunization of a Camelidae with the target antigen, followed by a phage display selection using phage libraries encoding the VHH repertoire of the animal blood sample. However, this approach is constrained by the accessibility to the animals, and the output relies on the animal's immune system.Recently, synthetic VHH libraries have been designed to avoid the use of animals. Here, we describe the construction of VHH combinatorial libraries and their use for the selection of binders by ribosome display, a fully in vitro selection technique.

Light-guided intrabodies for on-demand in situ target recognition in human cells

Due to their high stability and specificity in living cells, fluorescently labeled nanobodies are perfect probes for visualizing intracellular targets at an endogenous level. However, intrabodies bind unrestrainedly and hence may interfere with the target protein function. Here, we report a strategy to prevent premature binding through the development of photo-conditional intrabodies. Using genetic code expansion, we introduce photocaged amino acids within the nanobody-binding interface, which, after photo-activation, show instantaneous binding of target proteins with high spatiotemporal precision inside living cells. Due to the highly stable binding, light-guided intrabodies offer a versatile platform for downstream imaging and regulation of target proteins.

Direct Immobilization of Engineered Nanobodies on Gold Sensors

Single-domain antibodies, known as nanobodies, have great potential as biorecognition elements for sensors because of their small size, affinity, specificity, and robustness. However, facile and efficient methods of nanobody immobilization are sought that retain their maximum functionality. Herein, we describe the direct immobilization of nanobodies on gold sensors by exploiting a modified cysteine strategically positioned at the C-terminal end of the nanobody. The experimental data based on secondary ion mass spectrometry, circular dichroism, and surface plasmon resonance, taken together with a detailed computational work (molecular dynamics simulations), support the formation of stable and well-oriented nanobody monolayers. Furthermore, the nanobody structure and activity is preserved, wherein the nanobody is immobilized at a high density (approximately 1 nanobody per 13 nm²). The strategy for the spontaneous nanobody self-assembly is simple and effective and possesses exceptional potential to be used in numerous sensing platforms, ranging from clinical diagnosis to environmental monitoring.

Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins

Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.

Label-Free Biosensors for Laboratory-Based Diagnostics of Infections: Current Achievements and New Trends

Infections pose a serious global public health problem and are a major cause of premature mortality worldwide. One of the most challenging objectives faced by modern medicine is timely and accurate laboratory-based diagnostics of infectious diseases. Being a key factor of timely initiation and success of treatment, it may potentially provide reduction in incidence of a disease, as well as prevent outbreak and spread of dangerous epidemics. The traditional methods of laboratory-based diagnostics of infectious diseases are quite time- and labor-consuming, require expensive equipment and qualified personnel, which restricts their use in case of limited resources. Over the past six decades, diagnostic technologies based on lateral flow immunoassay (LFIA) have been and remain true alternatives to modern laboratory analyzers and have been successfully used to quickly detect molecular ligands in biosubstrates to diagnose many infectious diseases and septic conditions. These devices are considered as simplified formats of modern biosensors. Recent advances in the development of label-free biosensor technologies have made them promising diagnostic tools that combine rapid pathogen indication, simplicity, user-friendliness, operational efficiency, accuracy, and cost effectiveness, with a trend towards creation of portable platforms. These qualities exceed the generally accepted standards of microbiological and immunological diagnostics and open up a broad range of applications of these analytical systems in clinical practice immediately at the site of medical care (point-of-care concept, POC). A great variety of modern nanoarchitectonics of biosensors are based on the use of a broad range of analytical and constructive strategies and identification of various regulatory and functional molecular markers associated with infectious bacterial pathogens. Resolution of the existing biosensing issues will provide rapid development of diagnostic biotechnologies.

Development of Whole-Porcine Monoclonal Antibodies with Potent Neutralization Activity against Classical Swine Fever Virus from Single B Cells

Classical swine fever (CSF) is a highly contagious swine disease that causes devastating economic losses. However, there are few efficacious therapeutic antibodies against the CSF virus (CSFV). Accordingly, we isolated two whole-porcine anti-CSFV neutralizing antibodies (NAbs) directly from single B cells sorted using the conserved linear epitope of the CSFV E2 protein and goat anti-pig IgG. These mAbs, termed HK24 and HK44, can bind to the E2 protein by recognizing sites within the conserved linear epitope of E2. In addition, these two mAbs can detect virus infection with high specificity and possess potent neutralizing activity. HK24 and HK44 protect PK-15 cells from CSFV infections in vitro with potent IC₅₀ values of 9.3 and 0.62 μg/mL, respectively. We anticipate that these antibodies can be used as diagnostic and antiviral agents for CSFV and that the method we describe here will accelerate the production of therapeutic antibodies for other viruses.

Selectable high-yield recombinant protein production in human cells using a GFP/YFP nanobody affinity support

Recombinant protein expression systems that produce high yields of pure proteins and multi-protein complexes are essential to meet the needs of biologists, biochemists, and structural biologists using X-ray crystallography and cryo-electron microscopy. An ideal expression system for recombinant human proteins is cultured human cells where the correct translation and chaperone machinery are present. However, compared to bacterial expression systems, human cell cultures present several technical challenges to their use as an expression system. We developed a method that utilizes a YFP fusion-tag to generate recombinant proteins using suspension-cultured HEK293F cells. YFP is a dual-function tag that enables direct visualization and fluorescence-based selection of high expressing clones for and rapid purification using a high-stringency, high-affinity anti-GFP/YFP nanobody support. We demonstrate the utility of this system by expressing two large human proteins, TOP2α (340 KDa dimer) and a TOP2β catalytic core (260 KDa dimer). This robustly and reproducibly yields >10 mg/L liter of cell culture using transient expression or 2.5 mg/L using stable expression.

Improving biosensing activity to carcinoembryonic antigen with orientated single domain antibodies

Carcinoembryonic antigen (CEA), also referred as CEACAM5, is integral to the adhesion process during cancer invasion and metastasis and is one of the most widely used tumor markers for assisting the diagnosis of cancer recurrence and cancer metastasis. Antibodies against CEA molecules have been developed for detection and diagnostic applications following tumor removal. Single domain antibodies (sdAbs) against CEA isolated from dromedary and llama exhibited high specificity in binding to tumor cells. However, because these CEA sdAbs were not designed to be orientated when conjugated to surface sensors, there is potential for significant improvements in their activity and limit of detection. Herein we modified the CEA sdAbs with two different C-terminal fusions designed to aid with orientation by way of the tail’s charge and biotin binding. A fusion which incorporated the C-terminus addition of a positively charged tail (B5-GS3K) improved biosensor sensitivity to CEA while also retaining the sub-nanomolar binding affinity and thermal stability of the unmodified sdAb. Using our fabricated surfaces on bare gold chips and a multiplexed surface plasmon resonance imager (SPRi), we quantified the specific binding activities, defined as the percentage of bound epitopes to the total immobilized, of the sdAb fusions and anti-CEA mAb. Our results demonstrate that monovalent B5-GS3K exhibited significantly improved binding activity, approximately 3-fold higher than bivalent mAb.

Protein-Protein Interactions: Surface Plasmon Resonance

Surface plasmon resonance (SPR) is one of the most commonly used techniques to study protein-protein interactions. The main advantage of SPR is it gives on the ability to measure the binding affinities and association/dissociation kinetics of complexes in real time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, called the ligand, on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, called the analyte, over the surface containing the ligand. The binding is monitored by subsequent changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. During the last 10 years, SPR has been intensively used in the study of secretion systems because of its ability to detect highly dynamic complexes that are difficult to investigate using other techniques. This chapter will guide users in the setup of SPR experiments in order to identify protein complexes and to assess their binding affinity or kinetics. It will include detailed protocols for (i) the immobilization of proteins with the amine coupling capture method, (ii) analyte-binding analysis, (iii) affinity/kinetic measurements, and (iv) data analysis.Secretion systems are multiprotein complexes allowing the transport of a large number of effectors from the inside to the outside of bacterial cells. The assembly of these supramolecular machineries is ensured by the formation of protein complexes with extremely different times of stability, from transitory to stable interactions. To understand the function of these machineries as well as their modes of association, it is important to study their building blocks by identifying the different interacting partners and assessing their relative affinities and association/dissociation kinetics. For that purpose, scientists combine genetic, biochemical, and biophysical tools. During the last decade, the use of surface plasmon resonance (SPR) in the study of secretion systems has increased spectacularly [1-12]. This in vitro approach is the method of choice to study such dynamic systems owing to its ability to detect both weak and strong interactions ranging from the millimolar to the nanomolar range [13, 14]. SPR can be used as a primary tool to screen interacting partners or as a validation tool for interactions previously identified by other methods (e.g., bacterial two-hybrid, co-immunoprecipitation, chemical crosslinking). The determination of the affinity or kinetics of an interaction, as can be done by SPR, is fundamental to understanding the nature of binding at the cellular level.