Determining the specificity of monoclonal antibody HPT-101 to tau-peptides with optical tweezers

Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers

The Sec61 translocon allows the translocation of secretory preproteins from the cytosol to the endoplasmic reticulum lumen during polypeptide biosynthesis. These proteins possess an N-terminal signal peptide (SP) which docks at the translocon. SP mutations can abolish translocation and cause diseases, suggesting an essential role for this SP/Sec61 interaction. However, a detailed biophysical characterization of this binding is still missing. Here, optical tweezers force spectroscopy was used to characterize the kinetic parameters of the dissociation process between Sec61 and the SP of prepro-alpha-factor. The unbinding parameters including off-rate constant and distance to the transition state were obtained by fitting rupture force data to Dudko-Hummer-Szabo models. Interestingly, the translocation inhibitor mycolactone increases the off-rate and accelerates the SP/Sec61 dissociation, while also weakening the interaction. Whereas the translocation deficient mutant containing a single point mutation in the SP abolished the specificity of the SP/Sec61 binding, resulting in an unstable interaction. In conclusion, we characterize quantitatively the dissociation process between the signal peptide and the translocon, and how the unbinding parameters are modified by a translocation inhibitor.

Determination of protein-protein interactions at the single-molecule level using optical tweezers

Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (k_off, k_on), affinity values (K_D), energy to the transition state ΔG^≠, distance to the transition state Δx^≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.

Model systems for optical trapping: the physical basis and biological applications

The micromechanical methods, among which optical trapping and atomic force microscopy have a special place, are widespread currently in biology to study molecular interactions between different biological objects. Optical trapping is reported to be quite applicable to study the mechanical properties of surface structures onto bacterial (pili and flagella) and eukaryotic (filopodia) cells. The review briefly summarizes the physical basis of optical trapping, as well as the principles of calculating the van der Waals, electrostatic, and donor-acceptor forces when two microparticles or a microparticle and a flat surface are used. Three main types of model systems (abiotic, biotic, and mixed) used in trapping experiments are described, and the peculiarities of manipulation with living (bacteria, fungal spores, etc.) and non-spherical objects (e.g., rod-shaped bacteria) are summarized.

Application of Force to a Syndecan-4 Containing Complex With Thy-1-αVβ3 Integrin Accelerates Neurite Retraction

Inflammation contributes to the genesis and progression of chronic diseases, such as cancer and neurodegeneration. Upregulation of integrins in astrocytes during inflammation induces neurite retraction by binding to the neuronal protein Thy-1, also known as CD90. Additionally, Thy-1 alters astrocyte contractility and movement by binding to the mechano-sensors α_Vβ₃ integrin and Syndecan-4. However, the contribution of Syndecan-4 to neurite shortening following Thy-1-α_Vβ₃ integrin interaction remains unknown. To further characterize the contribution of Syndecan-4 in Thy-1-dependent neurite outgrowth inhibition and neurite retraction, cell-based assays under pro-inflammatory conditions were performed. In addition, using Optical Tweezers, we studied single-molecule binding properties between these proteins, and their mechanical responses. Syndecan-4 increased the lifetime of Thy-1-α_Vβ₃ integrin binding by interacting directly with Thy-1 and forming a ternary complex (Thy-1-α_Vβ₃ integrin + Syndecan-4). Under in vitro-generated pro-inflammatory conditions, Syndecan-4 accelerated the effect of integrin-engaged Thy-1 by forming this ternary complex, leading to faster neurite retraction and the inhibition of neurite outgrowth. Thus, Syndecan-4 controls neurite cytoskeleton contractility by modulating α_Vβ₃ integrin mechano-receptor function. These results suggest that mechano-transduction, cell-matrix and cell-cell interactions are likely critical events in inflammation-related disease development.

A QCM-based rupture event scanning technique as a simple and reliable approach to study the kinetics of DNA duplex dissociation

Rupture Event Scanning (REVS) is applied for the first time within an approach based on dynamic force spectroscopy. Using model DNA duplexes containing 20 pairs of oligonucleotides including those containing single mismatches, we demonstrated the possibility of reliable determination of the kinetic parameters of dissociation of biomolecular complexes: barrier positions, the rate constants of dissociation, and the lifetime of complexes. Within this approach, mechanical dissociation of DNA duplexes occurs according to a mechanism similar to unzipping. It is shown that this process takes place by overcoming a single energy barrier. In the case where a mismatch is located at the farthest duplex end from the QCM surface, a substantial decrease in the position of the barrier between the bound and unbound states is observed. We suppose that this is due to the formation of an initiation complex containing 3-4 pairs of bases, and this is sufficient for starting duplex unzipping.

On the interpretation of kinetics and thermodynamics probed by single-molecule experiments

Single-molecule pulling experiments are widely used to extract both thermodynamic and kinetic data on ligand-receptor pairs, typically by fitting different models to the probability distribution of rupture forces of the corresponding bond. Here, a theoretical model is presented that shows how a measurement of the number of binding and unbinding events as a function of the observation time can also give access to both the binding (kon) and the unbinding (koff) rates of bonds, which combined provide a well-defined bond free-energy ΔGbond. The connection between ΔGbond and the ligand-receptor binding constant measured by typical binding essays is critically discussed. The role played by the molecular construct used to tether ligands and receptors to a surface is considered, highlighting the various approximations necessary to derive general expressions that connect its structure to its contribution, termed ΔGcnf, to the bond free-energy. In this way, the validity and the assumptions underpinning widely employed formulas and experimental protocols used to extract binding constants from single-molecule experiments are assessed. Finally, the role of ΔGcnf in processes mediated by ligand-receptor binding is briefly considered, and an experiment to unambiguously measure this quantity proposed.

Force interactions between Yersiniae lipopolysaccharides and monoclonal antibodies: An optical tweezers study

This article reports the force spectroscopy investigation of interactions between lipopolysaccharides (LPSs) of two species from Yersinia genus and complementary (or heterologous) monoclonal antibodies (mAbs). We have obtained the experimental data by optical trapping on the "sensitized polystyrene microsphere - sensitized glass substrate" model system at its approach - retraction in vertical plane. We detected non-specific interactions in low-amplitude areas on histograms mainly due to physicochemical properties of abiotic surface and specific interactions in complementary pairs "antigen - antibodies" in high-amplitude areas (100-120 pN) on histograms. The developed measurement procedure can be used for detection of rupture forces in other molecular pairs.

Single-molecule measurements of the effect of force on Thy-1/αvβ3-integrin interaction using nonpurified proteins

Single-molecule measurements combined with a novel mathematical strategy were applied to accurately characterize how bimolecular interactions respond to mechanical force, especially when protein purification is not possible. Specifically, we studied the effect of force on Thy-1/αvβ3 integrin interaction, a mediator of neuron-astrocyte communication.

Thy-1 and αvβ3 integrin mediate bidirectional cell-to-cell communication between neurons and astrocytes. Thy-1/αvβ3 interactions stimulate astrocyte migration and the retraction of neuronal prolongations, both processes in which internal forces are generated affecting the bimolecular interactions that maintain cell–cell adhesion. Nonetheless, how the Thy-1/αvβ3 interactions respond to mechanical cues is an unresolved issue. In this study, optical tweezers were used as a single-molecule force transducer, and the Dudko-Hummer-Szabo model was applied to calculate the kinetic parameters of Thy-1/αvβ3 dissociation. A novel experimental strategy was implemented to analyze the interaction of Thy-1-Fc with nonpurified αvβ3-Fc integrin, whereby nonspecific rupture events were corrected by using a new mathematical approach. This methodology permitted accurately estimating specific rupture forces for Thy-1-Fc/αvβ3-Fc dissociation and calculating the kinetic and transition state parameters. Force exponentially accelerated Thy-1/αvβ3 dissociation, indicating slip bond behavior. Importantly, nonspecific interactions were detected even for purified proteins, highlighting the importance of correcting for such interactions. In conclusion, we describe a new strategy to characterize the response of bimolecular interactions to forces even in the presence of nonspecific binding events. By defining how force regulates Thy-1/αvβ3 integrin binding, we provide an initial step towards understanding how the neuron–astrocyte pair senses and responds to mechanical cues.

Epitope mapping of monoclonal antibody HPT-101: a study combining dynamic force spectroscopy, ELISA and molecular dynamics simulations

By combining enzyme-linked immunosorbent assay (ELISA) and optical tweezers-assisted dynamic force spectroscopy (DFS), we identify for the first time the binding epitope of the phosphorylation-specific monoclonal antibody (mAb) HPT-101 to the Alzheimer's disease relevant peptide tau[pThr231/pSer235] on the level of single amino acids. In particular, seven tau isoforms are synthesized by replacing binding relevant amino acids by a neutral alanine (alanine scanning). From the binding between mAb HPT-101 and the alanine-scan derivatives, we extract specific binding parameters such as bond lifetime τ0, binding length x(ts), free energy of activation ΔG (DFS) and affinity constant K(a) (ELISA, DFS). Based on these quantities, we propose criteria to identify essential, secondary and non-essential amino acids, being representative of the antibody binding epitope. The obtained results are found to be in full accord for both experimental techniques. In order to elucidate the microscopic origin of the change in binding parameters, we perform molecular dynamics (MD) simulations of the free epitope in solution for both its parent and modified form. By taking the end-to-end distance d(E-E) and the distance between the α-carbons d(C-C) of the phosphorylated residues as gauging parameters, we measure how the structure of the epitope depends on the type of substitution. In particular, whereas d(C-C) is sometimes conserved between the parent and modified form, d(E-E) strongly changes depending on the type of substitution, correlating well with the experimental data. These results are highly significant, offering a detailed microscopic picture of molecular recognition.