Force history dependence of receptor-ligand dissociation

Catch Bonds in Immunology

Catch bonds are molecular bonds that last longer under force than slip bonds, which become shorter-lived under force. Although catch bonds were initially discovered in studies of leukocyte and bacterial adhesions two decades ago, they have since been found in many other contexts, including platelet binding to blood vessel walls during clotting, structural support within the cell and between cells, force transmission in the cell's machineries for motility and mechanotransduction, viral infection of host cells, and immunoreceptor mechanosensing. Catch bonds are strengthened by increasing force, which induces structural changes in one or both interacting molecules either locally or allosterically to enable additional contacts at their binding interface, thus lengthening bond lifetimes. They can be modeled by the kinetics of a system escaping from the energy well(s) of the bound state(s) over the energy barrier(s) to the free state by traversing along the dissociation path(s) across a hilly energy landscape modulated by force. Catch bond studies are important for understanding the mechanics of biological systems and developing treatment strategies for infectious diseases, immune disorders, cancer, and other ailments.

Receptor-Ligand Binding: Effect of Mechanical Factors

Gaining insight into the in situ receptor-ligand binding is pivotal for revealing the molecular mechanisms underlying the physiological and pathological processes and will contribute to drug discovery and biomedical application. An important issue involved is how the receptor-ligand binding responds to mechanical stimuli. This review aims to provide an overview of the current understanding of the effect of several representative mechanical factors, such as tension, shear stress, stretch, compression, and substrate stiffness on receptor-ligand binding, wherein the biomedical implications are focused. In addition, we highlight the importance of synergistic development of experimental and computational methods for fully understanding the in situ receptor-ligand binding, and further studies should focus on the coupling effects of these mechanical factors.

Quantifying Shear-induced Margination and Adhesion of Platelets in Microvascular Blood Flow

Platelet margination and adhesion are two critical and closely related steps in thrombus formation. Using dissipative particle dynamics (DPD) method that seamlessly models blood cells, blood plasma, and vessel walls with functionalized surfaces, we quantify the shear-induced margination and adhesion of platelets in microvascular blood flow. The results show that the occurrence of shear-induced RBC-platelet collisions has a remarkable influence on the degree of platelet margination. We characterize the lateral motion of individual platelets by a mean square displacement analysis of platelet trajectories, and find that the wall-induced lift force and the shear-induced displacement in wall-bounded flow cause the variation in near-wall platelet distribution. We then investigate the platelet adhesive dynamics under different flow conditions, by conducting DPD simulations of blood flow in a microtube with fibrinogen-coated wall surfaces. We find that the platelet adhesion is enhanced with the increase of fibrinogen concentration level but decreased with the increase of shear rate. These results are consistent with available experimental results. In addition, we demonstrate that the adherent platelets have a negative impact on the margination dynamics of the circulating platelets, which is mainly due to the climbing effect induced by the adherent ones. Taken together, these findings provide useful insights into the platelet margination and adhesion dynamics, which may facilitate the understanding of the predominant processes governing the initial stage of thrombus formation.

Immune-mediated alopecias and their mechanobiological aspects

Alopecia is a non-specific term for hair loss clinically diagnosed by the hair loss pattern and histological analysis of patient scalp biopsies. The immune-mediated alopecia subtypes, including alopecia areata, lichen planopilaris, frontal fibrosing alopecia, and central centrifugal cicatricial alopecia, are common, significant forms of alopecia subtypes. For example, alopecia areata is the most common autoimmune disease with a lifetime incidence of approximately 2% of the world's population. In this perspective, we discuss major results from studies of immune-mediated alopecia subtypes. These studies suggest the key event in disease onset as the collapse in immune privilege, which alters the hair follicle microenvironment, e.g., upregulation of major histocompatibility complex molecules and increase of cytokine production, and results in immune cell infiltration, inflammatory responses, and damage of hair follicles. We note that previous studies have established that the hair follicle has a complex mechanical microenvironment, which may regulate the function of not only tissue cells but also immune cell infiltrates. This suggests a potential for mechanobiology to contribute to alopecia research by adding new methods, new approaches, and new ways of thinking, which is missing in the existing literature. To fill this a gap in the alopecia research space, we develop a mechanobiological hypothesis that alterations in the hair follicle microenvironment, specifically in the mechanically responsive tissues and cells, partially due to loss of immune privilege, may be contributors to disease pathology. We further focus our discussion on the potential for applying mechanoimmunology to the study of T cell infiltrates in the hair follicle, as they are considered primary contributors to alopecia pathology. To establish the connection between the mechanoimmunological hypothesis and immune-mediated alopecia subtypes, we discuss what is known about the role of T cells in immune-mediated alopecia subtypes, using the most extensively studied AA as our model.

Flow driven vesicle unbinding under mechanosensitive adhesion

Ligand receptor based adhesion is the primary mode of interaction of cellular blood constituents with the endothelium. These adhered entities also experience shear flow imposed by the blood which may lead to their detachment due to the viscous lift forces. Here, we have studied the role of the ligand-receptor bond kinetics in the detachment of an adhered vesicle (a simplified cell model) under shear flow. Using boundary integral formulation we performed numerical simulation of a two dimensional vesicle under shear flow for different values of applied shear rates and time scale of bond kinetics. We observe that the vesicle demonstrates three steady state configurations - adhered, pinned and detached for fast enough ligand-receptor kinetics (akin to Lennard-Jones adhesion). However, for slow bond kinetics the pinned state is not observed. We present scaling laws for the critical shear rates corresponding to the transitions among these three states. These results can help with identifying the processes of cell adhesion/detachment in the blood stream, prevalent features during the immune response and cancer metastasis.

Mechanotransduction as a major driver of cell behaviour: mechanisms, and relevance to cell organization and future research

How do cells process environmental cues to make decisions? This simple question is still generating much experimental and theoretical work, at the border of physics, chemistry and biology, with strong implications in medicine. The purpose of mechanobiology is to understand how biochemical and physical cues are turned into signals through mechanotransduction. Here, we review recent evidence showing that (i) mechanotransduction plays a major role in triggering signalling cascades following cell-neighbourhood interaction; (ii) the cell capacity to continually generate forces, and biomolecule properties to undergo conformational changes in response to piconewton forces, provide a molecular basis for understanding mechanotransduction; and (iii) mechanotransduction shapes the guidance cues retrieved by living cells and the information flow they generate. This includes the temporal and spatial properties of intracellular signalling cascades. In conclusion, it is suggested that the described concepts may provide guidelines to define experimentally accessible parameters to describe cell structure and dynamics, as a prerequisite to take advantage of recent progress in high-throughput data gathering, computer simulation and artificial intelligence, in order to build a workable, hopefully predictive, account of cell signalling networks.

Numerical study on the adhesion of a circulating tumor cell in a curved microvessel

The adhesion of a circulating tumor cell (CTC) in a three-dimensional curved microvessel was numerically investigated. Simulations were first performed to characterize the differences in the dynamics and adhesion of a CTC in the straight and curved vessels. After that, a parametric study was performed to investigate the effects of the applied driven force density f (or the flow Reynolds number Re) and the CTC membrane bending modulus K_b on the CTC adhesion. Our simulation results show that the CTC prefers to adhere to the curved vessel as more bonds are formed around the transition region of the curved part due to the increased cell-wall contact by the centrifugal force. The parametric study also indicates that when the flow driven force f (or Re) increases or when the CTC becomes softer (K_b decreases), the bond formation probability increases and the bonds will be formed at more sites of a curved vessel. The increased f (or Re) brings a larger centrifugal force, while the decreased K_b generates more contact areas at the cell-wall interface, both of which are beneficial to the bond formation. In the curved vessel, it is found that the site where bonds are formed the most (hotspot) varies with the applied f and the K_b. For our vessel geometry, when f is small, the hotspot tends to be within the first bend of the vessel, while as f increases or K_b decreases, the hotspot may shift to the second bend of the vessel.

Analysing the Initial Bacterial Adhesion to Evaluate the Performance of Antifouling Surfaces

The aim of this work was to study the initial events of Escherichia coli adhesion to polydimethylsiloxane, which is critical for the development of antifouling surfaces. A parallel plate flow cell was used to perform the initial adhesion experiments under controlled hydrodynamic conditions (shear rates ranging between 8 and 100/s), mimicking biomedical scenarios. Initial adhesion studies capture more accurately the cell-surface interactions as in later stages, incoming cells may interact with the surface but also with already adhered cells. Adhesion rates were calculated and results shown that after some time (between 5 and 9 min), these rates decreased (by 55% on average), from the initial values for all tested conditions. The common explanation for this decrease is the occurrence of hydrodynamic blocking, where the area behind each adhered cell is screened from incoming cells. This was investigated using a pair correlation map from which two-dimensional histograms showing the density probability function were constructed. The results highlighted a lower density probability (below 4.0 × 10⁻⁴) of the presence of cells around a given cell under different shear rates irrespectively of the radial direction. A shadowing area behind the already adhered cells was not observed, indicating that hydrodynamic blocking was not occurring and therefore it could not be the cause for the decreases in cell adhesion rates. Afterward, cell transport rates from the bulk solution to the surface were estimated using the Smoluchowski-Levich approximation and values in the range of 80–170 cells/cm².s were obtained. The drag forces that adhered cells have to withstand were also estimated and values in the range of 3–50 × 10⁻¹⁴ N were determined. Although mass transport increases with the flow rate, drag forces also increase and the relative importance of these factors may change in different conditions. This work demonstrates that adjustment of operational parameters in initial adhesion experiments may be required to avoid hydrodynamic blocking, in order to obtain reliable data about cell-surface interactions that can be used in the development of more efficient antifouling surfaces.

Single-molecule investigations of T-cell activation

T-cell activation is the central event governing its development, differentiation, and effector functions. T-cell activation is initiated by the direct physical interaction of the T cell antigen receptor (TCR) with cognate peptide presented by the major histocompatibility complex (pMHC) molecule expressed on the antigen presenting cell (APC) surface. Since the identification of TCR as the only receptor for antigen on T cells three decades ago, studies have elucidated the major molecular players and signaling events responding to TCR stimulation. However, the question of how the physical event of pMHC binding is converted across the membrane into chemical events to initiate signal transduction remains elusive. Here we review recent investigations of T-cell activation using single-molecule force and fluorescence techniques that shed new light on this key question.

Dynamic bonds and their roles in mechanosensing

Mechanical forces are ubiquitous in a cell's internal structure and external environment. Mechanosensing is the process that the cell employs to sense its mechanical environment. In receptor-mediated mechanosensing, cell surface receptors interact with immobilized ligands to provide a specific way to receive extracellular force signals to targeted force-transmitting, force-transducing and force-supporting structures inside the cell. Conversely, forces generated endogenously by the cell can be transmitted via cytoplasmic protein-protein interactions and regulate cell surface receptor activities in an 'inside-out' manner. Dynamic force spectroscopy analyzes these interactions on and inside cells to reveal various dynamic bonds. What is more, by integrating analysis of molecular interactions with that of cell signaling events involved in force-sensing and force-responding processes, one can investigate how dynamic bonds regulate the reception, transmission and transduction of mechanical signals.

Mechanical properties of P-selectin PSGL-1 bonds

The accurate determination of the mechanical properties of P-selectin and PSGL-1 is crucial for design and optimization of applications utilizing such bonds, e.g. biosensors and targeted drug delivery systems, as adhesion and mechanical interactions play a critical role in several key functions of biological cells. In current work, the spring constant and rupture force of a single P-selectin PSGL-1 ligand receptor bond and the Young's modulus of a layer made of these ligand receptors are reported. The work-of-adhesion of the P-selectin PSGL-1 interface is also characterized. In the reported experiments, PSGL-1 coated particles are deposited on a P-selectin coated substrate and their transient nanometer scale out-of-plane displacements are acquired employing a laser Doppler vibrometer as they are excited by an ultrasonic field. From the spectral response of a single particle, the resonance frequencies of its vibrational motion are identified, and with help of a particle adhesion model, the average rupture force and stiffness of a single P-selectin PSGL-1 ligand receptor are determined as F^rupt = 171 ± 56 pN and k^b = 0.56 ± 0.04 mN/m, respectively. Furthermore, the Young's modulus and work-of-adhesion of a layer of P-selectin PSGL-1 ligand receptors are extracted as E = 28.74 ± 3.96 MPa and W^A = 70.0 ± 8.0 mJ/m², respectively. Unlike Atomic Force Microscopy (AFM) and other probe-based techniques, the reported approach eliminates the need for direct contact with the sample, which could compromise the accuracy of the results by imposing unspecified additional contact interactions. Further, the current technique can be employed for measurements under various fluid flow conditions.

History, rare, and multiple events of mechanical unfolding of repeat proteins

Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

Lipid rafts enhance the binding constant of membrane-anchored receptors and ligands

Gaining insights into the binding of membrane-anchored receptors and ligands that mediate cell adhesion and signal transduction is of great significance for understanding numerous physiological processes driven by intercellular communication. Lipid rafts, microdomains in cell membranes enriched in cholesterol and saturated lipids such as sphingomyelin, are believed to serve as the essential platforms to recruit protein molecules for biological functions. An important question remains how the lipid rafts affect the binding constant of membrane-anchored receptors and ligands. We have investigated the adhesion of multicomponent membranes by using Monte Carlo simulations of a mesoscopic model with biologically relevant parameters. We find that the preferential partitioning of membrane-anchored receptor and ligand proteins in the lipid rafts significantly increases the binding constant of those proteins, in cooperation with the shape fluctuations of the membranes caused by thermal excitations. The binding constant can even be greater than that of the same receptors and ligands anchored to two apposing supported, planar membranes without shape fluctuations. The membrane shape fluctuations facilitate the binding of the anchored receptors and ligands, in contrast to the case of homogeneous membranes. Our results suggest that cells might regulate the binding of membrane-anchored receptor and ligand proteins by modulating the properties of lipid rafts such as area fraction, size and the affinity of rafts to the proteins.

Control of interface interactions between natural rubber and solid surfaces through charge effects: an AFM study in force spectroscopic mode

Adhesion of nanoparticles (natural rubber) is monitored by slight changes in the surface charge state of the contacting solid surfaces.

A model for cyclic mechanical reinforcement

Mechanical force regulates a broad range of molecular interactions in biology. Three types of counterintuitive mechanical regulation of receptor–ligand dissociation have been described. Catch bonds are strengthened by constant forces, as opposed to slip bonds that are weakened by constant forces. The phenomenon that bonds become stronger with prior application of cyclic forces is termed cyclic mechanical reinforcement (CMR). Slip and catch bonds have respectively been explained by two-state models. However, they assume fast equilibration between internal states and hence are inadequate for CMR. Here we propose a three-state model for CMR where both loading and unloading regulate the transition of bonds among the short-lived, intermediate, and long-lived state. Cyclic forces favor bonds in the long-lived state, hence greatly prolonging their lifetimes. The three-state model explains the force history effect and agrees with the experimental CMR effect of integrin α₅β₁–fibronectin interaction. This model helps decipher the distinctive ways by which molecular bonds are mechanically strengthened: catch bonds by constant forces and CMR by cyclic forces. The different types of mechanical regulation may enable the cell to fine tune its mechanotransduction via membrane receptors.

BROWNIAN DYNAMICS SIMULATION OF CATCH TO SLIP TRANSITION OVER A MODEL ENERGY LANDSCAPE

We perform Brownian dynamics simulation (BDS) of catch to slip transition over a model energy landscape. Through our BDS we demonstrate that for forces below the critical force the bond rupture occurs mostly through the catch pathway while for forces above the critical force the bond rupture occurs mostly through the slip pathway. We also demonstrate that the shoulder in the bond rupture force distribution switches to peak as the loading rate increases progressively and the bond lifetime is maximized at the model dependent critical force. The force dependent bond lifetime obtained via transforming the bond rupture force distribution at a given loading rate is in excellent agreement with that obtained from our BDS at constant forces. An alternative to the current mechanism of catch to slip transition is presented and validated through BDS.

Early T cell activation: integrating biochemical, structural, and biophysical cues

T cells carry out the formidable task of identifying small numbers of foreign antigenic peptides rapidly and specifically against a very noisy environmental background of endogenous self-peptides. Early steps in T cell activation have thus fascinated biologists and are among the best-studied models of cell stimulation. This remarkable process, critical in adaptive immune responses, approaches and even seems to exceed the limitations set by the physical laws ruling molecular behavior. Despite the enormous amount of information concerning the nature of molecules involved in the T cell antigen receptor (TCR) signal transduction network, and the description of the nanoscale organization and real-time analysis of T cell responses, the general principles of information gathering and processing remain incompletely understood. Here we review currently accepted key data on TCR function, discuss the limitations of current research strategies, and suggest a novel model of TCR triggering and a few promising ways of going further into the integration of available data.

Stiff substrates enhance monocytic cell capture through E-selectin but not P-selectin

The stiffening of blood vessel walls is associated with inflammatory diseases, including atherosclerosis, diabetes, and obesity. These diseases are driven by the excessive recruitment of inflammatory leukocytes out of the bloodstream and into tissues, but whether vascular stiffening plays a direct role in this process is not clear. In this study, we investigated the possibility that leukocyte capture from blood flow is enhanced on stiffer substrates. We modeled blood flow in vitro by perfusing monocytic cells over hydrogels that matched the stiffness of healthy and diseased arteries. The hydrogels were coated with either E-selectin or P-selectin, which are the endothelial adhesion proteins known to mediate immune cell capture from flow. Interestingly, we discovered that cell attachment to P-selectin coated gels was not dependent on substrate stiffness, while attachment through E-selectin was enhanced on stiffer gels. Specifically we found that on E-selectin coated gels, cells attached in greater numbers, remained attached for longer time periods, and rolled more slowly on stiff gels than soft gels. These results suggest that vascular stiffening could promote leukocyte adhesion to vessel walls where E-selectin is expressed, but may have less of an effect when P-selectin is also present.

Fluorescence Biomembrane Force Probe: Concurrent Quantitation of Receptor-ligand Kinetics and Binding-induced Intracellular Signaling on a Single Cell

Membrane receptor-ligand interactions mediate many cellular functions. Binding kinetics and downstream signaling triggered by these molecular interactions are likely affected by the mechanical environment in which binding and signaling take place. A recent study demonstrated that mechanical force can regulate antigen recognition by and triggering of the T-cell receptor (TCR). This was made possible by a new technology we developed and termed fluorescence biomembrane force probe (fBFP), which combines single-molecule force spectroscopy with fluorescence microscopy. Using an ultra-soft human red blood cell as the sensitive force sensor, a high-speed camera and real-time imaging tracking techniques, the fBFP is of ~1 pN (10(-12) N), ~3 nm and ~0.5 msec in force, spatial and temporal resolution. With the fBFP, one can precisely measure single receptor-ligand binding kinetics under force regulation and simultaneously image binding-triggered intracellular calcium signaling on a single live cell. This new technology can be used to study other membrane receptor-ligand interaction and signaling in other cells under mechanical regulation.

Effects of cellular viscoelasticity in lifetime extraction of single receptor-ligand bonds

Single-molecule force spectroscopy is widely used to determine kinetic parameters of dissociation by analyzing bond rupture data obtained via applying mechanical force to cells, capsules, and beads that are attached to an intermolecular bond. The bond rupture data are obtained in experiments either at a constant force or at a constant loading rate. We explore the effect of cellular viscoelasticity in constant-force experiments. Specifically, we perform Monte Carlo simulations of bond rupture at a given constant force to obtain the bond lifetime as a function of force in the absence and in the presence of bond force modulation due to cellular viscoelasticity, to explore its effect on the bond lifetime.

Molecular force spectroscopy on cells

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Contribution of the CR domain to P-selectin lectin domain allostery by regulating the orientation of the EGF domain

The allostery of P-selectin has been studied extensively with a focus on the Lec and EGF domains, whereas the contribution of the CR domain remains unclear. Here, molecular dynamics simulations (MDS) combined with homology modeling were preformed to investigate the impact of the CR domain on P-selectin allostery. The results indicated that the CR domain plays a role in the allosteric dynamics of P-selectin in two ways. First, the CR1 domain tends to stabilize the low affinity of P-selectin during the equilibration processes with the transition inhibition from the S1 to S1’ state by restraining the extension of the bent EGF orientation, or with the relaxation acceleration of the S2 state by promoting the bending of the extended EGF orientation. Second, the existence of CR domain increases intramolecular extension prior to complex separation, increasing the time available for the allosteric shift during forced dissociation with a prolonged bond duration. These findings further our understanding of the structure-function relationship of P-selectin with the enriched micro-structural bases of the CR domain.

Probing time-dependent mechanical behaviors of catch bonds based on two-state models

With lifetime counter-intuitively being prolonged under forces, catch bonds can play critical roles in various sub-cellular processes. By adopting different “catching” strategies within the framework of two-state models, we construct two types of catch bonds that have a similar force-lifetime profile upon a constant force-clamp load. However, when a single catch bond of either type is subjected to varied forces, we find that they can behave very differently in both force history dependence and bond strength. We further find that a cluster of catch bonds of either type generally becomes unstable when subjected to a periodically oscillating force, which is consistent with experimental results. These results provide important insights into versatile time-dependent mechanical behaviors of catch bonds. We suggest that it is necessary to further differentiate those bonds that are all phenomenologically referred to as “Catch bonds”.

Cell adhesion. The minimal cadherin-catenin complex binds to actin filaments under force

Linkage between the adherens junction (AJ) and the actin cytoskeleton is required for tissue development and homeostasis. In vivo findings indicated that the AJ proteins E-cadherin, β-catenin, and the filamentous (F)-actin binding protein αE-catenin form a minimal cadherin-catenin complex that binds directly to F-actin. Biochemical studies challenged this model because the purified cadherin-catenin complex does not bind F-actin in solution. Here, we reconciled this difference. Using an optical trap-based assay, we showed that the minimal cadherin-catenin complex formed stable bonds with an actin filament under force. Bond dissociation kinetics can be explained by a catch-bond model in which force shifts the bond from a weakly to a strongly bound state. These results may explain how the cadherin-catenin complex transduces mechanical forces at cell-cell junctions.

Stochastic simulation of single-molecule pulling experiments

Single-molecule pulling experiments are widely used for studying the structure, dynamics, and function of single biological molecules via applying mechanical forces on them in a controlled way. Pulling at a constant speed or at a constant force builds up a mechanical force on a molecule or molecular complex leading to a molecular transition such as the dissociation of a molecular complex, unfolding of a protein, or unwrapping of a higher-order structure. We perform Brownian dynamics and Monte Carlo simulations of single-molecule pulling experiments. Through our simulations we demonstrate that the molecular transition rate based on the Kramers theory in the high-barrier limit becomes unsuitable as the applied force approaches the critical force at which the barrier disappears. We also demonstrate that use of molecular transition rate based on mean first passage time (MFPT) approach would be more relevant in describing molecular transition especially as the applied force approaches the critical force.

Antigen-antibody biorecognition events as discriminated by noise analysis of force spectroscopy curves

Atomic force spectroscopy is able to extract kinetic and thermodynamic parameters of biomolecular complexes provided that the registered unbinding force curves could be reliably attributed to the rupture of the specific complex interactions. To this aim, a commonly used strategy is based on the analysis of the stretching features of polymeric linkers which are suitably introduced in the biomolecule-substrate immobilization procedure. Alternatively, we present a method to select force curves corresponding to specific biorecognition events, which relies on a careful analysis of the force fluctuations of the biomolecule-functionalized cantilever tip during its approach to the partner molecules immobilized on a substrate. In the low frequency region, a characteristic 1/f (α) noise with α equal to one (flickering noise) is found to replace white noise in the cantilever fluctuation power spectrum when, and only when, a specific biorecognition process between the partners occurs. The method, which has been validated on a well-characterized antigen-antibody complex, represents a fast, yet reliable alternative to the use of linkers which may involve additional surface chemistry and reproducibility concerns.

P-fimbriae in the presence of anti-PapA antibodies: new insight of antibodies action against pathogens

Uropathogenic strains of Escherichia coli establish urinary tract infections by attaching to host epithelial cells using adhesive organelles called fimbriae. Fimbriae are helix-like structures with a remarkable adaptability, offering safeguarding for bacteria exposed to changing fluid forces in the urinary tract. We challenged this property of P-fimbriae by cross-linking their subunits with shaft-specific antibodies and measuring the corresponding force response at a single organelle level. Our data show compromised extension and rewinding of P-fimbriae in the presence of antibodies and reduced fimbrial elasticity, which are important properties of fimbriae contributing to the ability of bacteria to cause urinary tract infections. The reduced elasticity found by cross-linking fimbrial subunits could thus be another assignment for antibodies; in addition to marking bacteria as foreign, antibodies physically compromise fimbrial function. We suggest that our assay and results will be a starting point for further investigations aimed at inhibiting sustained bacterial adhesion by antibodies.

Rupture of multiple catch-slip bonds: Two-state two-pathway catch-slip bonds

We performed Monte Carlo simulation of the detachment of a polymorphonuclear (PMN) leukocyte immersed in a Newtonian fluid and adhered to a substrate by multiple catch-slip bonds. We found that at certain loading rates the interplay of multiple catch-slip bonds leads to a bimodal distribution of the bond rupture force. We also found that the low force peak in these bond rupture force distributions switches to a high force peak with a gradual increase in the loading rate. These trends in the bond rupture force distributions are characteristics of two-state systems. Consequently, though individual catch-slip bonds follow one-state two-pathway energy landscape, their interplay mimics a two-state two-pathway energy landscape.

Mechanochemitry: a molecular biomechanics view of mechanosensing

Molecular biomechanics includes two themes: the study of mechanical aspects of biomolecules and the study of molecular biology of the cell using mechanical tools. The two themes are interconnected for obvious reasons. The present review focuses on one of the interconnected areas-the mechanical regulation of molecular interaction and conformational change. Recent conceptual developments are summarized, including catch bonds, regulation of molecular interaction by the history of force application, and cyclic mechanical reinforcement. These studies elucidate the mechanochemistry of some of the candidate mechanosensing molecules, thereby providing a natural connection to mechanobiology.

Biophysical description of multiple events contributing blood leukocyte arrest on endothelium

Blood leukocytes have a remarkable capacity to bind to and stop on specific blood vessel areas. Many studies have disclosed a key role of integrin structural changes following the interaction of rolling leukocytes with surface-bound chemoattractants. However, the functional significance of structural data and mechanisms of cell arrest are incompletely understood. Recent experiments revealed the unexpected complexity of several key steps of cell-surface interaction: (i) ligand-receptor binding requires a minimum amount of time to proceed and this is influenced by forces. (ii) Also, molecular interactions at interfaces are not fully accounted for by the interaction properties of soluble molecules. (iii) Cell arrest depends on nanoscale topography and mechanical properties of the cell membrane, and these properties are highly dynamic. Here, we summarize these results and we discuss their relevance to recent functional studies of integrin-receptor association in cells from a patient with type III leukocyte adhesion deficiency. It is concluded that an accurate understanding of all physical events listed in this review is needed to unravel the precise role of the multiple molecules and biochemical pathway involved in arrest triggering.

Effect of viscoelasticity on the analysis of single-molecule force spectroscopy on live cells

Single-molecule force spectroscopy is used to probe the kinetics of receptor-ligand bonds by applying mechanical forces to an intermediate media on which the molecules reside. When this intermediate media is a live cell, the viscoelastic properties can affect the calculation of rate constants. We theoretically investigate the effect of media viscoelasticity on the common assumption that the bond force is equal to the instantaneous applied force. Dynamic force spectroscopy is simulated between two cells of varying micromechanical properties adhered by a single bond with a constant kinetic off-rate. We show that cell and microvilli deformation, and hydrodynamic drag contribute to bond forces that can be 28-90% lower than the applied force for loading rates of 10(3)-10(7) pN/s, resulting in longer bond lifetimes. These longer bond lifetimes are not caused by changes in bond kinetics; rather, they are due to the mechanical response of the intermediate media on which the bonds reside. Under the assumption that the instantaneous bond force is equal to the applied force--thereby ignoring viscoelasticity--leads to 14-39% error in the determination of off-rates. We present an approach that incorporates viscoelastic properties in calculating the instantaneous bond force and kinetic dissociation parameter of the intermolecular bond.

Quantitative modeling assesses the contribution of bond strengthening, rebinding and force sharing to the avidity of biomolecule interactions

Cell adhesion is mediated by numerous membrane receptors. It is desirable to derive the outcome of a cell-surface encounter from the molecular properties of interacting receptors and ligands. However, conventional parameters such as affinity or kinetic constants are often insufficient to account for receptor efficiency. Avidity is a qualitative concept frequently used to describe biomolecule interactions: this includes incompletely defined properties such as the capacity to form multivalent attachments. The aim of this study is to produce a working description of monovalent attachments formed by a model system, then to measure and interpret the behavior of divalent attachments under force. We investigated attachments between antibody-coated microspheres and surfaces coated with sparse monomeric or dimeric ligands. When bonds were subjected to a pulling force, they exhibited both a force-dependent dissociation consistent with Bell’s empirical formula and a force- and time-dependent strengthening well described by a single parameter. Divalent attachments were stronger and less dependent on forces than monovalent ones. The proportion of divalent attachments resisting a force of 30 piconewtons for at least 5 s was 3.7 fold higher than that of monovalent attachments. Quantitative modeling showed that this required rebinding, i.e. additional bond formation between surfaces linked by divalent receptors forming only one bond. Further, experimental data were compatible with but did not require stress sharing between bonds within divalent attachments. Thus many ligand-receptor interactions do not behave as single-step reactions in the millisecond to second timescale. Rather, they exhibit progressive stabilization. This explains the high efficiency of multimerized or clustered receptors even when bonds are only subjected to moderate forces. Our approach provides a quantitative way of relating binding avidity to measurable parameters including bond maturation, rebinding and force sharing, provided these parameters have been determined. Also, this provides a quantitative description of the phenomenon of bond strengthening.

Rupture of multiple receptor-ligand bonds: bimodal distribution of bond rupture force

Monte Carlo simulation of the rupture of multiple receptor-ligand bonds between two PMN cells suspended in a Newtonian fluid is performed. In the presence of a hydrodynamic drag force acting on two PMN cells the interplay of multiple receptor-ligand bonds between these cells leads to a bimodal distribution of the bond rupture force at certain loading rates. Specifically, it is found that the interplay of multiple bonds between two PMN cells in the presence of hydrodynamic drag force acting on these cells modifies the bond energy landscape in such a way as to lead to a bimodal distribution of the bond rupture force where a low force peak switches to a high force peak as the loading rate is increased progressively, characteristics of two-state systems.

Kinetics and mechanics of two-dimensional interactions between T cell receptors and different activating ligands

Adaptive immune responses are driven by interactions between T cell antigen receptors (TCRs) and complexes of peptide antigens (p) bound to Major Histocompatibility Complex proteins (MHC) on the surface of antigen-presenting cells. Many experiments support the hypothesis that T cell response is quantitatively and qualitatively dependent on the so-called strength of TCR/pMHC association. Most available data are correlations between binding parameters measured in solution (three-dimensional) and pMHC activation potency, suggesting that full lymphocyte activation required a minimal lifetime for TCR/pMHC interaction. However, recent reports suggest important discrepancies between the binding properties of ligand-receptor couples measured in solution (three-dimensional) and those measured using surface-bound molecules (two-dimensional). Other reports suggest that bond mechanical strength may be important in addition to kinetic parameters. Here, we used a laminar flow chamber to monitor at the single molecule level the two-dimensional interaction between a recombinant human TCR and eight pMHCs with variable potency. We found that 1), two-dimensional dissociation rates were comparable to three-dimensional parameters previously obtained with the same molecules; 2), no significant correlation was found between association rates and activating potency of pMHCs; 3), bond mechanical strength was partly independent of bond lifetime; and 4), a suitable combination of bond lifetime and bond strength displayed optimal correlation with activation efficiency. These results suggest possible refinements of contemporary models of signal generation by T cell receptors. In conclusion, we reported, for the first time to our knowledge, the two-dimensional binding properties of eight TCR/pMHC couples in a cell-free system with single bond resolution.

The two-pathway model of the biological catch-bond as a limit of the allosteric model

Catch-binding is a counterintuitive phenomenon in which the lifetime of a receptor/ligand bond increases when a force is applied to break the bond. Several mechanisms have been proposed to rationalize catch-binding. In the two-pathway model, the force drives the system away from its native dissociation pathway into an alternative pathway involving a higher energy barrier. Here, we analyze an allosteric model suggesting that a force applied to the complex alters the distribution of receptor conformations, and as a result, induces changes in the ligand-binding site. The model assumes explicitly that the allosteric transitions govern the properties of the ligand site. We demonstrate that the dynamics of the ligand is described by two relaxation times, one of which arises from the allosteric site. Therefore, we argue that one can characterize the allosteric transitions by studying the receptor/ligand binding. We show that the allosteric description reduces to the two-pathway model in the limit when the allosteric transitions are faster than the bond dissociation. The formal results are illustrated with two systems, P-selectin/PSGL-1 and FimH/mannose, subjected to both constant and time-dependent forces. The report advances our understanding of catch-binding by combining alternative physical models into a unified description and makes the problem more tractable for the bond mechanics community.

Mechanobiology of platelets: techniques to study the role of fluid flow and platelet retraction forces at the micro- and nano-scale

Coagulation involves a complex set of events that are important in maintaining hemostasis. Biochemical interactions are classically known to regulate the hemostatic process, but recent evidence has revealed that mechanical interactions between platelets and their surroundings can also play a substantial role. Investigations into platelet mechanobiology have been challenging however, due to the small dimensions of platelets and their glycoprotein receptors. Platelet researchers have recently turned to microfabricated devices to control these physical, nanometer-scale interactions with a higher degree of precision. These approaches have enabled exciting, new insights into the molecular and biomechanical factors that affect platelets in clot formation. In this review, we highlight the new tools used to understand platelet mechanobiology and the roles of adhesion, shear flow, and retraction forces in clot formation.

DISSECTING INDIVIDUAL LIGAND–RECEPTOR BONDS WITH A LAMINAR FLOW CHAMBER

The most important function of proteins may well be to bind to other biomolecules. It has long been felt that kinetic rates of bond formation and dissociation between soluble receptors and ligands might account for most features of the binding process. Only theoretical considerations allowed to predict the behaviour of surface-attached receptors from the properties of soluble forms. During the last decade, experimental progress essentially based on flow chambers, atomic force microscopes or biomembrane force probes allowed direct analysis of biomolecule interaction at the single bond level and gave new insight into previously ignored features such as bond mechanical properties or energy landscapes. The aim of this review is (i) to describe the main advances brought by laminar flow chambers, including information on bond response to forces, multiplicity of binding states, kinetics of bond formation between attached structures, effect of molecular environment on receptor efficiency and behaviour of multivalent attachment, (ii) to compare results obtain by this and other techniques on a few well defined molecular systems, and (iii) to discuss the limitations of the flow chamber method. It is concluded that a new framework may be needed to account for the effective behaviour of biomolecule association.

Minimal encounter time and separation determine ligand-receptor binding in cell adhesion

The binding properties of biomolecules play a crucial role in many biological phenomena, especially cell adhesion. Whereas the attachment kinetics of soluble proteins is considered well known, complex behavior arises when protein molecules are bound to the cell membrane. We probe the hidden kinetics of ligand-receptor bond formation using single-molecule flow chamber assays and Brownian dynamics simulations. We show that, consistent with our recently proposed hypothesis, association requires a minimum duration of contact between the reactive species. In our experiments, ICAM-1 anchored on a flat substrate binds to anti-ICAM-1 coated onto flowing microbeads. The interaction potential between bead and substrate is measured by microinterferometry and is used as an ingredient to simulate bead movement. Our simulation calculates the duration of ligand-receptor contacts imposed by the bead movement. We quantitatively predict the reduction of adhesion probability measured for shorter tether length of the ligand or if a repulsive hyaluronan layer is added onto the surface. To account for our results, we propose that bond formation may occur in our system by crossing of a diffusive plateau in the energy landscape, on the timescale of 5 ms and an energy barrier of 5 k(B)T, before reaching the first detectable bound state. Our results show how to relate cell-scale behavior to the combined information of molecular reactivity and biomolecule submicron-scale environment.

Force measurements of TCR/pMHC recognition at T cell surface

The rupture forces and adhesion frequencies of single recognition complexes between an affinity selected peptide/MHC complex and a TCR at a murine hybridoma surface were measured using Atomic Force Microscopy. When the CD8 coreceptor is absent, the adhesion frequency depends on the nature of the peptide but the rupture force does not. When CD8 is present, no effect of the nature of the peptide is observed. CD8 is proposed to act as a time and distance lock, enabling the shorter TCR molecule to bridge the pMHC and have time to finely read the peptide. Ultimately, such experiments could help the dissection of the sequential steps by which the TCR reads the peptide/MHC complex in order to control T cell activation.

Regulation of catch bonds by rate of force application

The current paradigm for receptor-ligand dissociation kinetics assumes off-rates as functions of instantaneous force without impact from its prior history. This a priori assumption is the foundation for predicting dissociation from a given initial state using kinetic equations. Here we have invalidated this assumption by demonstrating the impact of force history with single-bond kinetic experiments involving selectins and their ligands that mediate leukocyte tethering and rolling on vascular surfaces during inflammation. Dissociation of bonds between L-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) loaded at a constant ramp rate to a constant hold force behaved as catch-slip bonds at low ramp rates that transformed to slip-only bonds at high ramp rates. Strikingly, bonds between L-selectin and 6-sulfo-sialyl Lewis X were impervious to ramp rate changes. This ligand-specific force history effect resembled the effect of a point mutation at the L-selectin surface (L-selectinA108H) predicted to contact the former but not the latter ligand, suggesting that the high ramp rate induced similar structural changes as the mutation. Although the A108H substitution in L-selectin eliminated the ramp rate responsiveness of its dissociation from PSGL-1, the inverse mutation H108A in P-selectin acquired the ramp rate responsiveness. Our data are well explained by the sliding-rebinding model for catch-slip bonds extended to incorporate the additional force history dependence, with Ala-108 playing a pivotal role in this structural mechanism. These results call for a paradigm shift in modeling the mechanical regulation of receptor-ligand bond dissociation, which includes conformational coupling between binding pocket and remote regions of the interacting molecules.

Effect of cell and microvillus mechanics on the transmission of applied loads to single bonds in dynamic force spectroscopy

Receptor-ligand interactions that mediate cellular adhesion are often subjected to forces that regulate their detachment via modulating off-rates. Although the dynamics of detachment is primarily controlled by the physical chemistry of adhesion molecules, cellular features such as cell deformability and microvillus viscoelasticity have been shown to affect the rolling velocity of leukocytes in vitro through experiments and simulation. In this work, we demonstrate via various micromechanical models of two cells adhered by a single (intramolecular) bond that cell deformability and microvillus viscoelasticity modulate transmission of an applied external load to an intramolecular bond, and thus the dynamics of detachment. Specifically, it is demonstrated that the intermolecular bond force is not equivalent to the instantaneous applied force and that the instantaneous bond force decreases with cellular and microvillus compliance. As cellular compliance increases, not only does the time lag between the applied load and the bond force increase, an initial response time is observed during which cell deformation is observed without transfer of force to the bond. It is further demonstrated that following tether formation the instantaneous intramoleular bond force increases linearly at a rate dependent on microvillus viscosity. Monte Carlo simulations with fixed kinetic parameters predict that both cell and microvillus compliance increase the average rupture time, although the average rupture force based on bond length remains nearly unchanged.

Force-clamp measurements of receptor-ligand interactions

Protein-protein interactions are the basis of both biochemical and biophysical signaling of living cells. In many cases, the receptor is present on the cell surface while the ligand is in solution or linked to another support (extracellular matrix or another cell). In the case of cellular adhesion, forces are continuously applied to receptor-ligand complexes and, as a consequence, the dissociation kinetics of the bonds may change. It is, thus, relevant to study the kinetics of protein-protein interactions in response to applied forces, as this is the most physiologically relevant situation. The atomic force microscope (AFM) was one of the first nanotools to be applied to this end. However, new approaches need to be developed to better understand the complex energy landscape of molecular interactions under applied stress. In this chapter, we described the use of the AFM to carry out force-clamp measurements on receptor-ligand bonds. Force-clamp measurements on bonds consist of applying a constant and controlled force to a receptor-ligand bond and measure the resulting dissociation lifetime. The described methods include the required materials, functionalization of tips and substrates, force-clamping measurements, and processing and interpretation of the results. An illustrative example is given with the well-studied streptavidin-biotin complex.

Interaction of p53 with Mdm2 and azurin as studied by atomic force spectroscopy

Azurin, a bacterial protein, can be internalized in cancer cells and induce apoptosis. Such anticancer effect is coupled to the formation of a complex with the tumour-suppressor p53. The mechanism by which azurin stabilizes p53 and the binding sites of their complex are still under investigation. It is also known that the predominant mechanism for p53 down-regulation implies its association to Mdm2, the main ubiquitin ligase affecting its stability. However, the p53/Mdm2 interaction, occurring at the level of both their N-terminal domains, has been characterized so far by experiments involving only partial domains of these proteins. The relevance of the p53/Mdm2 complex as a possible target of the anticancer therapies requires a deeper study of this complex as made up of the two entire proteins. Moreover, the apparent antagonist action of azurin against Mdm2, with respect of p53 regulation, might suggest the possibility that azurin binds p53 at the same site of Mdm2, preventing in such a way p53 and Mdm2 from association and thus p53 from degradation. By following the interaction of the two entire proteins by atomic force spectroscopy, we have assessed the formation of a specific complex between p53 and Mdm2. We found for it a binding strength and a dissociation rate constant typical of dynamical protein-protein interactions and we observed that azurin, even if capable to bind p53, does not compete with Mdm2 for the same binding site on p53. The formation of the p53/Mdm2/azurin ternary complex might suggest an alternative anti-cancer mechanism adopted by azurin.

Effects of tip-induced material reorganization in dynamic force spectroscopy

Dynamic force spectroscopy (DFS) has become a well-established method for characterizing bond strength, yet may also be useful for examining more complex phenomena such as dynamic processes or multiple reaction pathways. Here, we analyze the case where contact between an atomic force microscopy (AFM) tip and the sample induces sample reorganization during testing. Surface contact often causes molecular rearrangement in soft materials, which could also result in an altered reaction energy landscape. We model this situation by allowing the energy barrier position and magnitude to be time-dependent functions with a characteristic time scale τ . We find dynamic energy barriers result in two linear regimes with a dramatic transition near t=τ in the DFS analysis. The sharp transition region is a hallmark of a moving energy barrier and indicates the time scale of reorganization. These results illustrate that DFS may be useful to monitor dynamic transitions and also highlight the importance of extending the loading rate range used in DFS studies.

Long-lived, high-strength states of ICAM-1 bonds to beta2 integrin, I: lifetimes of bonds to recombinant alphaLbeta2 under force

Using single-molecule force spectroscopy to probe ICAM-1 interactions with recombinant alphaLbeta2 immobilized on microspheres and beta2 integrin on neutrophils, we quantified an impressive hierarchy of long-lived, high-strength states of the integrin bond, which start from basal levels with integrin activation in solutions of divalent cations and shift dramatically upward to hyperactivated states with cell signaling in leukocytes. Taking advantage of very rare events, we used repeated measurements of bond lifetimes under steady ramps of force to achieve a direct assay for the off-rates of ICAM-1 from beta2 integrin in each experiment. Of fundamental importance, the assay for off-rates does not depend on how the force is applied over time, and remains valid when the rates of dissociation change with different levels of force. In this first article, we present results from tests of a monovalent ICAM-1 probe against immobilized alphaLbeta2 in environments of divalent cations (Ca2+, Mg2+, and Mn2+) and demonstrate in detail the method for assay of off-rates. When extrapolated to zero force, the force-free values for the off-rates are found to be consistent with published solution-based assays of soluble ICAM-1 dissociation from immobilized LFA-1, i.e., approximately 10(-2)/s in Mg2+ or Mn2+ and approximately 1/s in Ca2+. At the same time, as expected for adhesive function, we find that the beta2 integrin bonds activated in Mn2+ or Mg2+ possess significant and persistent mechanical strength (e.g., >20 pN for >1 s) even when subjected to slow force ramps (<10 pN/s). As discussed in our companion article, using the same assay, we find that although the rates of dissociation for diICAM-1fc bonds to LFA-1 on neutrophils in Mn2+ are similar to those for mICAM-1 bonds to recombinant alphaLbeta2 on microspheres, they appear to represent a dimeric attachment to a pair of tightly clustered integrin heterodimers. The mechanical strengths and lifetimes of the dimeric interactions increase dramatically when the neutrophils are stimulated by the chemokine IL-8 or are bound with an allosterically activating (anti-CD18) monoclonal antibody, demonstrating the major impact of cell signaling on LFA-1.

The viscoelastic properties of microvilli are dependent upon the cell-surface molecule

We studied at nanometer resolution the viscoelastic properties of microvilli and tethers pulled from myelogenous cells via P-selectin glycoprotein ligand 1 (PSGL-1) and found that in contrast to pure membrane tethers, the viscoelastic properties of microvillus deformations are dependent upon the cell-surface molecule through which load is applied. A laser trap and polymer bead coated with anti-PSGL-1 (KPL-1) were used to apply step loads to microvilli. The lengthening of the microvillus in response to the induced step loads was fitted with a viscoelastic model. The quasi-steady state force on the microvillus at any given length was approximately fourfold lower in cells treated with cytochalasin D or when pulled with concanavalin A-coated rather than KPL-1-coated beads. These data suggest that associations between PSGL-1 and the underlying actin cytoskeleton significantly affect the early stages of leukocyte deformation under flow.