Allosteric role of the large-scale domain opening in biological catch-binding

PDZ Domains from the Junctional Proteins Afadin and ZO-1 Act as Mechanosensors

Intercellular adhesion complexes must withstand mechanical forces to maintain tissue cohesion while also retaining the capacity for dynamic remodeling during tissue morphogenesis and repair. Many cell-cell adhesion complexes contain at least one PSD95/Dlg/ZO-1 (PDZ) domain situated between the adhesion molecule and the actin cytoskeleton. However, PDZ-mediated interactions are characteristically nonspecific, weak, and transient, with multiple binding partners per PDZ domain, micromolar dissociation constants, and bond lifetimes of seconds or less. Here, we demonstrate that the bonds between the PDZ domain of the cytoskeletal adaptor protein afadin and the intracellular domains of the adhesion molecules nectin-1 and JAM-A form molecular catch bonds that reinforce in response to mechanical load. In contrast, the bond between the PDZ3-SH3-GUK (PSG) domain of the cytoskeletal adaptor ZO-1 and the JAM-A intracellular domain becomes dramatically weaker in response to ∼2 pN of load, the amount generated by single molecules of the cytoskeletal motor protein myosin II. Thus, physiologically relevant forces can exert dramatic and opposite effects on the stability of two of the major linkages between cell-cell adhesion proteins and the F-actin cytoskeleton. Our data demonstrate that that PDZ domains can serve as force-responsive mechanical anchors at cell-cell adhesion complexes. More broadly, our findings suggest that mechanical force may serve as a previously unsuspected regulator of the hundreds of PDZ-ligand interactions present in animal cells.

The Energetic Landscape of Catch Bonds in TCR Interfaces

Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.

Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor

The bacterial flagellar motor is the membrane-embedded rotary motor, which turns the flagellum that provides thrust to many bacteria. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels that dynamically bind to the peptidoglycan at the rotor periphery and apply torque. Their dynamic exchange is a function of the viscous load on the flagellum, allowing the bacterium to adapt to its local environment, although the molecular mechanisms of mechanosensitivity remain unknown. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models that recapitulate the asymmetry, finding assembly dynamics to be particularly well described by a two-state catch-bond mechanism.

Stabilization of the Hinge Region of Human E-selectin Enhances Binding Affinity to Ligands Under Force

Introduction

E-selectin is a member of the selectin family of cell adhesion molecules expressed on the plasma membrane of inflamed endothelium and facilitates initial leukocyte tethering and subsequent cell rolling during the early stages of the inflammatory response via binding to glycoproteins expressing sialyl Lewis^X and sialyl Lewis^A (sLe^X/A). Existing crystal structures of the extracellular lectin/EGF-like domain of E-selectin complexed with sLe^X have revealed that E-selectin can exist in two conformation states, a low affinity (bent) conformation, and a high affinity (extended) conformation. The differentiating characteristic of the two conformations is the interdomain angle between the lectin and the EGF-like domain.

Methods

Using molecular dynamics (MD) simulations we observed that in the absence of tensile force E-selectin undergoes spontaneous switching between the two conformational states at equilibrium. A single amino acid substitution at residue 2 (serine to tyrosine) on the lectin domain favors the extended conformation.

Results

Steered molecular dynamics (SMD) simulations of E-selectin and PSGL-1 in conjunction with experimental cell adhesion assays show a longer binding lifetime of E-selectin (S2Y) to PSGL-1 compared to wildtype protein.

Conclusions

The findings in this study advance our understanding into how the structural makeup of E-selectin allosterically influences its adhesive dynamics.

The bioenergetics of integrin-based adhesion, from single molecule dynamics to stability of macromolecular complexes

The forces actively generated by motile cells must be transmitted to their environment in a spatiotemporally regulated manner, in order to produce directional cellular motion. This task is accomplished through integrin-based adhesions, large macromolecular complexes that link the actin-cytoskelton inside the cell to its external environment. Despite their relatively large size, adhesions exhibit rapid dynamics, switching between assembly and disassembly in response to chemical and mechanical cues exerted by cytoplasmic biochemical signals, and intracellular/extracellular forces, respectively. While in material science, force typically disrupts adhesive contact, in this biological system, force has a more nuanced effect, capable of causing assembly or disassembly. This initially puzzled experimentalists and theorists alike, but investigation into the mechanisms regulating adhesion dynamics have progressively elucidated the origin of these phenomena. This review provides an overview of recent studies focused on the theoretical understanding of adhesion assembly and disassembly as well as the experimental studies that motivated them. We first concentrate on the kinetics of integrin receptors, which exhibit a complex response to force, and then investigate how this response manifests itself in macromolecular adhesion complexes. We then turn our attention to studies of adhesion plaque dynamics that link integrins to the actin-cytoskeleton, and explain how force can influence the assembly/disassembly of these macromolecular structure. Subsequently, we analyze the effect of force on integrins populations across lengthscales larger than single adhesions. Finally, we cover some theoretical studies that have considered both integrins and the adhesion plaque and discuss some potential future avenues of research.

Mechanochemistry of von Willebrand factor

Von Willebrand factor (VWF), a blood multimeric protein with a very high molecular weight, plays a crucial role in the primary haemostasis, the physiological process characterized by the adhesion of blood platelets to the injured vessel wall. Hydrodynamic forces are responsible for extensive conformational transitions in the VWF multimers that change their structure from a globular form to a stretched linear conformation. This feature makes this protein particularly prone to be investigated by mechanochemistry, the branch of the biophysical chemistry devoted to investigating the effects of shear forces on protein conformation. This review describes the structural elements of the VWF molecule involved in the biochemical response to shear forces. The stretched VWF conformation favors the interaction with the platelet GpIb and at the same time with ADAMTS-13, the zinc-protease that cleaves VWF in the A2 domain, limiting its prothrombotic capacity. The shear-induced conformational transitions favor also a process of self-aggregation, responsible for the formation of a spider-web like network, particularly efficient in the trapping process of flowing platelets. The investigation of the biophysical effects of shear forces on VWF conformation contributes to unraveling the molecular mechanisms of many types of thrombotic and haemorrhagic syndromes.

Dynamics of Mechanosensitive Nascent Adhesion Formation

Cellular migration is a tightly regulated process that involves actin cytoskeleton, adaptor proteins, and integrin receptors. Forces are transmitted extracellularly through protein complexes of these molecules, called adhesions. Adhesions anchor the cell to its substrate, allowing it to migrate. In Chinese hamster ovary cells, three classes of adhesion can be identified: nascent adhesions (NAs), focal complexes, and focal adhesions, ranked here ascendingly based on size and stability. To understand the dynamics and mechanosensitive properties of NAs, a biophysical model of these NAs as colocalized clusters of integrins and adaptor proteins is developed. The model is then analyzed to characterize the dependence of NA area on biophysical parameters that regulate the number of integrins and adaptor proteins within NAs through a mechanosensitive coaggregation mechanism. Our results reveal that NA formation is triggered beyond a threshold of adaptor protein, integrin, or extracellular ligand densities, with these three factors listed in descending order of their relative influence on NA area. Further analysis of the model also reveals that an increase in coaggregation or reductions in integrin mobility inside the adhesion potentiate NA formation. By extending the model to consider the mechanosensitivity of the integrin bond, we identify mechanical stress, rather than mechanical load, as a permissive mechanical parameter that allows for noise-dependent and independent NA assembly, despite both parameters producing a bistable switch possessing a hysteresis. Stochastic simulations of the model confirm these results computationally. This study thus provides insight into the mechanical conditions defining NA dynamics.

Unraveling the mechanism of the cadherin-catenin-actin catch bond

The adherens junctions between epithelial cells involve a protein complex formed by E-cadherin, β-catenin, α-catenin and F-actin. The stability of this complex was a puzzle for many years, since in vitro studies could reconstitute various stable subsets of the individual proteins, but never the entirety. The missing ingredient turned out to be mechanical tension: a recent experiment that applied physiological forces to the complex with an optical tweezer dramatically increased its lifetime, a phenomenon known as catch bonding. However, in the absence of a crystal structure for the full complex, the microscopic details of the catch bond mechanism remain mysterious. Building on structural clues that point to α-catenin as the force transducer, we present a quantitative theoretical model for how the catch bond arises, fully accounting for the experimental lifetime distributions. The underlying hypothesis is that force induces a rotational transition between two conformations of α-catenin, overcoming a significant energy barrier due to a network of salt bridges. This transition allosterically regulates the energies at the interface between α-catenin and F-actin. The model allows us to predict these energetic changes, as well as highlighting the importance of the salt bridge rotational barrier. By stabilizing one of the α-catenin states, this barrier could play a role in how the complex responds to additional in vivo binding partners like vinculin. Since significant conformational energy barriers are a common feature of other adhesion systems that exhibit catch bonds, our model can be adapted into a general theoretical framework for integrating structure and function in a variety of force-regulated protein complexes.

Tunable seat belt behavior in nanocomposite interfaces inspired from bacterial adhesion pili

A challenging problem in designing nanocomposites is to engineer nanoparticle interfaces that have tunable cohesive strength and rate-responsive behavior, for which inspiration can be taken from biological systems. An exemplary bio-interface is the Chaperone-Usher (CU) pili, such as type 1 expressed by bacteria Escherichia coli. The pili have unique biomechanical properties that enhance the ability of bacteria to sustain attachment to surfaces under large stresses, such as constant force extensibility, logarithmic velocity-uncoiling force dependence, and adhesive tips with catch bond behavior that exhibit longer bond life-times at greater force levels. Although biophysics of the pili under strain or stress is well-studied for anti-infective applications that aim to compromise pili adhesion, utilizing the biomechanical properties of the pili in material design applications is yet to be explored. In this work, we modeled the elongation of a single CU pilus with catch bond tip adhesin and examined its toughness response using Monte Carlo simulations. We showed that the pilus can act as a "molecular seat belt" that exhibits low toughness when pulled slowly and high toughness when pulled rapidly. Furthermore, we found that systematically varying the catch bond and shaft parameters leads to tunable seat belt behavior at the interface, where the sharpness of the transition from the low toughness to the high toughness regime and the velocity at the start of the transition can be dictated by molecular design parameters. Lastly, we tested the performance of CU pilus in slowing down a fast particle, and reveal that pili can effectively stop micron size projectiles with high initial velocities. The molecular seat belt mechanism presented here provides insight into how nanocomposite interfaces can be engineered to create molecular networks with linkers that switch on or off depending on strain rate.

Phenomenological and microscopic theories for catch bonds

Lifetimes of bound states of protein complexes or biomolecule folded states typically decrease when subject to mechanical force. However, a plethora of biological systems exhibit the counter-intuitive phenomenon of catch bonding, where non-covalent bonds become stronger under externally applied forces. The quest to understand the origin of catch-bond behavior has led to the development of phenomenological and microscopic theories that can quantitatively recapitulate experimental data. Here, we assess the successes and limitations of such theories in explaining experimental data. The most widely applied approach is a phenomenological two-state model, which fits all of the available data on a variety of complexes: actomyosin, kinetochore-microtubule, selectin-ligand, and cadherin-catenin binding to filamentous actin. With a primary focus on the selectin family of cell-adhesion complexes, we discuss the positives and negatives of phenomenological models and the importance of evaluating the physical relevance of fitting parameters. We describe a microscopic theory for selectins, which provides a structural basis for catch bonds and predicts a crucial allosteric role for residues Asn82-Glu88. We emphasize the need for new theories and simulations that can mimic experimental conditions, given the complex response of cell adhesion complexes to force and their potential role in a variety of biological contexts.

Measuring Force-Induced Dissociation Kinetics of Protein Complexes Using Single-Molecule Atomic Force Microscopy

Proteins respond to mechanical force by undergoing conformational changes and altering the kinetics of their interactions. However, the biophysical relationship between mechanical force and the lifetime of protein complexes is not completely understood. In this chapter, we provide a step-by-step tutorial on characterizing the force-dependent regulation of protein interactions using in vitro and in vivo single-molecule force clamp measurements with an atomic force microscope (AFM). While we focus on the force-induced dissociation of E-cadherins, a critical cell-cell adhesion protein, the approaches described here can be readily adapted to study other protein complexes. We begin this chapter by providing a brief overview of theoretical models that describe force-dependent kinetics of biomolecular interactions. Next, we present step-by-step methods for measuring the response of single receptor-ligand bonds to tensile force in vitro. Finally, we describe methods for quantifying the mechanical response of single protein complexes on the surface of living cells. We describe general protocols for conducting such measurements, including sample preparation, AFM force clamp measurements, and data analysis. We also highlight critical limitations in current technologies and discuss solutions to these challenges.

Biomechanics of cell adhesion: how force regulates the lifetime of adhesive bonds at the single molecule level

Cell adhesion proteins play critical roles in positioning cells during development, segregating cells into distinct tissue compartments and in maintaining tissue integrity. The principle function of these proteins is to bind cells together and resist mechanical force. Adhesive proteins also enable migrating cells to adhere and roll on surfaces even in the presence of shear forces exerted by fluid flow. Recently, several experimental and theoretical studies have provided quantitative insights into the physical mechanisms by which adhesion proteins modulate their unbinding kinetics in response to tensile force. This perspective reviews these biophysical investigations. We focus on single molecule studies of cadherins, selectins, integrins, the von Willebrand factor and FimH adhesion proteins; the effect of mechanical force on the lifetime of these interactions has been extensively characterized. We review both theoretical models and experimental investigations and discuss future directions in this exciting area of research.

Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme

The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae). The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory.

Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes

Mechanical forces acting on cell adhesion receptor proteins regulate a range of cellular functions by formation and rupture of noncovalent interactions with ligands. Typically, force decreases the lifetimes of intact complexes ("slip bonds"), making the discovery that these lifetimes can also be prolonged ("catch bonds") a surprise. We created a microscopic analytic theory by incorporating the structures of selectin and integrin receptors into a conceptual framework based on the theory of stochastic equations, which quantitatively explains a wide range of experimental data (including catch bonds at low forces and slip bonds at high forces). Catch bonds arise due to force-induced remodeling of hydrogen bond networks, a finding that also accounts for unbinding in structurally unrelated integrin-fibronectin and actomyosin complexes. For the selectin family, remodeling of hydrogen bond networks drives an allosteric transition resulting in the formation of the maximum number of hydrogen bonds determined only by the structure of the receptor and independent of the ligand. A similar transition allows us to predict the increase in the number of hydrogen bonds in a particular allosteric state of α5β1 integrin-fibronectin complex, a conformation which is yet to be crystallized. We also make a testable prediction that a single point mutation (Tyr51Phe) in the ligand associated with selectin should dramatically alter the nature of the catch bond compared with the wild type. Our work suggests that nature uses a ductile network of hydrogen bonds to engineer function over a broad range of forces.

Resolving the molecular mechanism of cadherin catch bond formation

Classical cadherin Ca(2+)-dependent cell-cell adhesion proteins play key roles in embryogenesis and in maintaining tissue integrity. Cadherins mediate robust adhesion by binding in multiple conformations. One of these adhesive states, called an X-dimer, forms catch bonds that strengthen and become longer lived in the presence of mechanical force. Here we use single-molecule force-clamp spectroscopy with an atomic force microscope along with molecular dynamics and steered molecular dynamics simulations to resolve the molecular mechanisms underlying catch bond formation and the role of Ca(2+) ions in this process. Our data suggest that tensile force bends the cadherin extracellular region such that they form long-lived, force-induced hydrogen bonds that lock X-dimers into tighter contact. When Ca(2+) concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated.

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.

Influence of substrate rigidity on primary nucleation of cell adhesion: a thermal fluctuation model

Experimental investigations have demonstrated that cells can actively sense and respond to physical aspects of their environments, such as substrate stiffness of biomaterials, via integrin receptors with the help of stochastic thermal undulations of cell membranes. This paper develops a physical model for the mechanism of integrin-dependent cell-substrate adhesion nucleation in order to investigate the influence of substrate stiffness on primary adhesion formation. In this model, a series of so-called energy potential wells are established to quantitatively describe force-driven conformational changes of integrins on elastic substrates with different rigidities. A concept of nucleation domain is proposed to characterize the necessary condition of integrin-mediated cell-substrate primary adhesion formation. In the framework of classical statistical mechanics, the competitive relationship is investigated between the local thermal undulations of plasma membranes and the conformational conversions of substrate-binding integrins. The quantitative dependence of integrin-mediated adhesion nucleation on substrate rigidities is systematically explored, which shows a reasonable agreement with existing experimental results.

Polymer-based catch-bonds

Catch-bonds refer to the counterintuitive notion that the average lifetime of a bond has a maximum at a nonzero applied force. They have been found in several ligand-receptor pairs and their origin is still a topic of debate. Here, we use coarse-grained simulations and kinetic theory to demonstrate that a multimeric protein, with self-interacting domain pairs, can display catch-bond behavior. Our model is motivated by one of the largest proteins in the human body, the von Willebrand Factor, which has been found to display this behavior. In particular, our model polymer consists of a series of repeating units that self-interact with their nearest neighbors along the chain. Each of the units mimics a domain of the protein. Apart from the short-range specific interaction, we also include a linker chain that will hold the domains together if unbinding occurs. This linker molecule represents the sequence of unfolded amino acids that connect contiguous domains, as is typically found in multidomain proteins. The units also interact with an immobilized ligand, but the interaction is masked by the presence of the self-interacting neighbor along the chain. Our results show that this model displays all the features of catch-bonds because the average lifetime of a binding event between the polymer and the immobilized receptor has a maximum at a nonzero pulling force of the polymer. The effects of the energy barriers for detaching the masking domain and the ligand from the binding domain, as well as the effects of the properties of the polypeptide chain connecting the contiguous domains, are also studied. Our study suggests that multimeric proteins can engage in catch-bonds if their self-interactions are carefully tuned, and this mechanism presumably plays a major role in the mechanics of extracellular proteins that share a multidomain character. Furthermore, our biomimetic design clearly shows how one could build and tune macromolecules that exhibit catch-bond characteristics.

Regulation of catch binding by allosteric transitions

An allosteric model is used to describe changes in lifetimes of biological receptor-ligand bonds subjected to an external force. Force-induced transitions between the two states of the allosteric site lead to changes in the receptor conformation. The ligand bound to the receptor fluctuates between two different potentials formed by the two receptor conformations. The effect of the force on the receptor-ligand interaction potential is described by the Bell mechanism. The probability of detecting the ligand in the bound state is found to depend on the relaxation times of both ligand and allosteric sites. An analytic expression for the bond lifetime is derived as a function of force. The formal theoretical results are used to explain the anomalous force and time dependences of the integrin-fibronectin bond lifetimes measured by atomic force microscopy (Kong, F.; et al J. Cell Biol. 2009, 185, 1275-1284). The analytic expression and model parameters describe very well all anomalous dependences identified in the experiments.

Adhesive organelles of Gram-negative pathogens assembled with the classical chaperone/usher machinery: structure and function from a clinical standpoint

This review summarizes current knowledge on the structure, function, assembly and biomedical applications of the superfamily of adhesive fimbrial organelles exposed on the surface of Gram-negative pathogens with the classical chaperone/usher machinery. High-resolution three-dimensional (3D) structure studies of the minifibers assembling with the FGL (having a long F1-G1 loop) and FGS (having a short F1-G1 loop) chaperones show that they exploit the same principle of donor-strand complementation for polymerization of subunits. The 3D structure of adhesive subunits bound to host-cell receptors and the final architecture of adhesive fimbrial organelles reveal two functional families of the organelles, respectively, possessing polyadhesive and monoadhesive binding. The FGL and FGS chaperone-assembled polyadhesins are encoded exclusively by the gene clusters of the γ3- and κ-monophyletic groups, respectively, while gene clusters belonging to the γ1-, γ2-, γ4-, and π-fimbrial clades exclusively encode FGS chaperone-assembled monoadhesins. Novel approaches are suggested for a rational design of antimicrobials inhibiting the organelle assembly or inhibiting their binding to host-cell receptors. Vaccines are currently under development based on the recombinant subunits of adhesins.