All Subdomains of the Talin Rod Are Mechanically Vulnerable and May Contribute To Cellular Mechanosensing

Mechanical Factors Regulate Annulus Fibrosus (AF) Injury Repair and Remodeling: A Review

Low back pain is a common chronic disease that can severely affect the patient's work and daily life. The breakdown of spinal mechanical homeostasis caused by intervertebral disc (IVD) degeneration is a leading cause of low back pain. Annulus fibrosus (AF), as the outer layer structure of the IVD, is often the first affected part. AF injury caused by consistent stress overload will further accelerate IVD degeneration. Therefore, regulating AF injury repair and remodeling should be the primary goal of the IVD repair strategy. Mechanical stimulation has been shown to promote AF regeneration and repair, but most studies only focus on the effect of single stress on AF, and lack realistic models and methods that can mimic the actual mechanical environment of AF. In this article, we review the effects of different types of stress stimulation on AF injury repair and remodeling, suggest possible beneficial load combinations, and explore the underlying molecular mechanisms. It will provide the theoretical basis for designing better tissue engineering therapy using mechanical factors to regulate AF injury repair and remodeling in the future.

Decoding Biomechanical Cues Based on DNA Sensors

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin

Force transmission at integrin-based adhesions is important for cell migration and mechanosensing. Talin is an essential focal adhesion (FA) protein that links F-actin to integrins. F-actin constantly moves on FAs, yet how Talin simultaneously maintains the connection to F-actin and transmits forces to integrins remains unclear. Here we show a critical role of dynamic Talin unfolding in force transmission. Using single-molecule speckle microscopy, we found that the majority of Talin are bound only to either F-actin or the substrate, whereas 4.1% of Talin is linked to both structures via elastic transient clutch. By reconstituting Talin knockdown cells with Talin chimeric mutants, in which the Talin rod subdomains are replaced with the stretchable β-spectrin repeats, we show that the stretchable property is critical for force transmission. Simulations suggest that unfolding of the Talin rod subdomains increases in the linkage duration and work at FAs. This study elucidates a force transmission mechanism, in which stochastic molecular stretching bridges two cellular structures moving at different speeds.

Force transmission by retrograde actin flow-induced dynamic molecular stretching of Talin

Force transmission at integrin-based adhesions is important for cell migration and mechanosensing. Talin is an essential focal adhesion (FA) protein that links F-actin to integrins. F-actin constantly moves on FAs, yet how Talin simultaneously maintains the connection to F-actin and transmits forces to integrins remains unclear. Here we show a critical role of dynamic Talin unfolding in force transmission. Using single-molecule speckle microscopy, we found that the majority of Talin are bound only to either F-actin or the substrate, whereas 4.1% of Talin is linked to both structures via elastic transient clutch. By reconstituting Talin knockdown cells with Talin chimeric mutants, in which the Talin rod subdomains are replaced with the stretchable β-spectrin repeats, we show that the stretchable property is critical for force transmission. Simulations suggest that unfolding of the Talin rod subdomains increases in the linkage duration and work at FAs. This study reveals a new mode of force transmission, in which stochastic molecular stretching bridges two cellular structures moving at different speeds.

Microfluidics-Based Force Spectroscopy Enables High-Throughput Force Experiments with Sub-Nanometer Resolution and Sub-Piconewton Sensitivity

Several techniques have been established to quantify the mechanicals of single molecules. However, most of them show only limited capabilities of parallelizing the measurement by performing many individual measurements simultaneously. Herein, a microfluidics-based single-molecule force spectroscopy method, which achieves sub-nanometer spatial resolution and sub-piconewton sensitivity and is capable of simultaneously quantifying hundreds of single-molecule targets in parallel, is presented. It relies on a combination of total internal reflection microscopy and microfluidics, in which monodisperse fluorescent beads are immobilized on the bottom of a microfluidic channel by macromolecular linkers. Application of a flow generates a well-defined shear force acting on the beads, whereas the nanomechanical linker response is quantified based on the force-induced displacement of individual beads. To handle the high amount of data generated, a cluster analysis which is capable of a semi-automatic identification of measurement artifacts and molecular populations is implemented. The method is validated by probing the mechanical response polyethylene glycol linkers and binding strength of biotin-NeutrAvidin complexes. Two energy barriers (at 3 and 5.7 Å, respectively) in the biotin-NeutrAvidin interaction are resolved and the unfolding behavior of talin's rod domain R3 in the force range between 1 to ≈10 pN is probed.

The role of single protein elasticity in mechanobiology

In addition to biochemical signals and genetic considerations, mechanical forces are rapidly emerging as a master regulator of human physiology. Yet the molecular mechanisms that regulate force-induced functionalities across a wide range of scales, encompassing the cell, tissue or organ levels, are comparatively not so well understood. With the advent, development and refining of single molecule nanomechanical techniques, enabling to exquisitely probe the conformational dynamics of individual proteins under the effect of a calibrated force, we have begun to acquire a comprehensive knowledge on the rich plethora of physicochemical principles that regulate the elasticity of single proteins. Here we review the major advances underpinning our current understanding of how the elasticity of single proteins regulates mechanosensing and mechanotransduction. We discuss the present limitations and future challenges of such a prolific and burgeoning field.

The mechanical cell - the role of force dependencies in synchronising protein interaction networks

The role of mechanical signals in the proper functioning of organisms is increasingly recognised, and every cell senses physical forces and responds to them. These forces are generated both from outside the cell or via the sophisticated force-generation machinery of the cell, the cytoskeleton. All regions of the cell are connected via mechanical linkages, enabling the whole cell to function as a mechanical system. In this Review, we define some of the key concepts of how this machinery functions, highlighting the critical requirement for mechanosensory proteins, and conceptualise the coupling of mechanical linkages to mechanochemical switches that enables forces to be converted into biological signals. These mechanical couplings provide a mechanism for how mechanical crosstalk might coordinate the entire cell, its neighbours, extending into whole collections of cells, in tissues and in organs, and ultimately in the coordination and operation of entire organisms. Consequently, many diseases manifest through defects in this machinery, which we map onto schematics of the mechanical linkages within a cell. This mapping approach paves the way for the identification of additional linkages between mechanosignalling pathways and so might identify treatments for diseases, where mechanical connections are affected by mutations or where individual force-regulated components are defective.

Challenges of Periodontal Tissue Engineering: Increasing Biomimicry through 3D Printing and Controlled Dynamic Environment

In recent years, tissue engineering studies have proposed several approaches to regenerate periodontium based on the use of three-dimensional (3D) tissue scaffolds alone or in association with periodontal ligament stem cells (PDLSCs). The rapid evolution of bioprinting has sped up classic regenerative medicine, making the fabrication of multilayered scaffolds-which are essential in targeting the periodontal ligament (PDL)-conceivable. Physiological mechanical loading is fundamental to generate this complex anatomical structure ex vivo. Indeed, loading induces the correct orientation of the fibers forming the PDL and maintains tissue homeostasis, whereas overloading or a failure to adapt to mechanical load can be at least in part responsible for a wrong tissue regeneration using PDLSCs. This review provides a brief overview of the most recent achievements in periodontal tissue engineering, with a particular focus on the use of PDLSCs, which are the best choice for regenerating PDL as well as alveolar bone and cementum. Different scaffolds associated with various manufacturing methods and data derived from the application of different mechanical loading protocols have been analyzed, demonstrating that periodontal tissue engineering represents a proof of concept with high potential for innovative therapies in the near future.

Mechanical regulation of talin through binding and history-dependent unfolding

Talin is a force-sensing multidomain protein and a major player in cellular mechanotransduction. Here, we use single-molecule magnetic tweezers to investigate the mechanical response of the R8 rod domain of talin. We find that under various force cycles, the R8 domain of talin can display a memory-dependent behavior: At the same low force (<10 pN), the same protein molecule shows vastly different unfolding kinetics. This history-dependent behavior indicates the evolution of a unique force-induced native state. We measure through mechanical unfolding that talin R8 domain binds one of its ligands, DLC1, with much higher affinity than previously reported. This strong interaction can explain the antitumor response of DLC1 by regulating inside-out activation of integrins. Together, our results paint a complex picture for the mechanical unfolding of talin in the physiological range and a new mechanism of function of DLC1 to regulate inside-out activation of integrins.

Direct observation of chaperone-modulated talin mechanics with single-molecule resolution

Talin as a critical focal adhesion mechanosensor exhibits force-dependent folding dynamics and concurrent interactions. Being a cytoplasmic protein, talin also might interact with several cytosolic chaperones; however, the roles of chaperones in talin mechanics remain elusive. To address this question, we investigated the force response of a mechanically stable talin domain with a set of well-known unfoldase (DnaJ, DnaK) and foldase (DnaKJE, DsbA) chaperones, using single-molecule magnetic tweezers. Our findings demonstrate that chaperones could affect adhesion proteins’ stability by changing their folding mechanics; while unfoldases reduce their unfolding force from ~11 pN to ~6 pN, foldase shifts it upto ~15 pN. Since talin is mechanically synced within 2 pN force ranges, these changes are significant in cellular conditions. Furthermore, we determined that chaperones directly reshape the energy landscape of talin: unfoldases decrease the unfolding barrier height from 26.8 to 21.7 k_BT, while foldases increase it to 33.5 k_BT. We reconciled our observations with eukaryotic Hsp70 and Hsp40 and observed their similar function of decreasing the talin unfolding barrier. Quantitative mapping of this chaperone-induced talin folding landscape directly illustrates that chaperones perturb the adhesion protein stability under physiological force, thereby, influencing their force-dependent interactions and adhesion dynamics.

Chakraborty et al. uses single-molecule magnetic tweezers to investigate the chaperone-modulated talin protein mechanics. The results showed that chaperones are involved in the regulation of talin folding/unfolding under mechanical force with some chaperones stabilizing talin and increasing the force, whereas others destabilize it and reduce the force.

Nonexponential kinetics in captured in sequential unfolding of polyproteins over a range of loads

While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L₈ under varying loads, specifically high (150, 100 ​pN) and moderate-low (45, 30, 20 ​pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality.

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Poly-L₈ unfolding shows nonexponential kinetics at forces ranging from 150 to 20 ​pN.

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Different phenomenological trends are observed for the dwell-time distributions.

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The unfolding events were shown to be dependent and not identically distributed.

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Free energy analysis reveals elastic impact and hierarchy in the unfolding barriers.

Integrin Regulated Autoimmune Disorders: Understanding the Role of Mechanical Force in Autoimmunity

The pathophysiology of autoimmune disorders is multifactorial, where immune cell migration, adhesion, and lymphocyte activation play crucial roles in its progression. These immune processes are majorly regulated by adhesion molecules at cell–extracellular matrix (ECM) and cell–cell junctions. Integrin, a transmembrane focal adhesion protein, plays an indispensable role in these immune cell mechanisms. Notably, integrin is regulated by mechanical force and exhibit bidirectional force transmission from both the ECM and cytosol, regulating the immune processes. Recently, integrin mechanosensitivity has been reported in different immune cell processes; however, the underlying mechanics of these integrin-mediated mechanical processes in autoimmunity still remains elusive. In this review, we have discussed how integrin-mediated mechanotransduction could be a linchpin factor in the causation and progression of autoimmune disorders. We have provided an insight into how tissue stiffness exhibits a positive correlation with the autoimmune diseases’ prevalence. This provides a plausible connection between mechanical load and autoimmunity. Overall, gaining insight into the role of mechanical force in diverse immune cell processes and their dysregulation during autoimmune disorders will open a new horizon to understand this physiological anomaly.

Protein nanomechanics in biological context

How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.

Nanomechanical Phenotypes in Cardiac Myosin-Binding Protein C Mutants That Cause Hypertrophic Cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is a disease of the myocardium caused by mutations in sarcomeric proteins with mechanical roles, such as the molecular motor myosin. Around half of the HCM-causing genetic variants target contraction modulator cardiac myosin-binding protein C (cMyBP-C), although the underlying pathogenic mechanisms remain unclear since many of these mutations cause no alterations in protein structure and stability. As an alternative pathomechanism, here we have examined whether pathogenic mutations perturb the nanomechanics of cMyBP-C, which would compromise its modulatory mechanical tethers across sliding actomyosin filaments. Using single-molecule atomic force spectroscopy, we have quantified mechanical folding and unfolding transitions in cMyBP-C domains targeted by HCM mutations that do not induce RNA splicing alterations or protein thermodynamic destabilization. Our results show that domains containing mutation R495W are mechanically weaker than wild-type at forces below 40 pN and that R502Q mutant domains fold faster than wild-type. None of these alterations are found in control, nonpathogenic variants, suggesting that nanomechanical phenotypes induced by pathogenic cMyBP-C mutations contribute to HCM development. We propose that mutation-induced nanomechanical alterations may be common in mechanical proteins involved in human pathologies.

An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

The alpha-helix coiled-coils within talin's rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb's law shows a simulated force interaction within the physiological relevant range of 5-40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2-3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.

Molecular Fluctuations as a Ruler of Force-Induced Protein Conformations

Molecular fluctuations directly reflect the underlying energy landscape. Variance analysis examines protein dynamics in several biochemistry-driven approaches, yet measurement of probe-independent fluctuations in proteins exposed to mechanical forces remains only accessible through steered molecular dynamics simulations. Using single molecule magnetic tweezers, here we conduct variance analysis to show that individual unfolding and refolding transitions occurring in dynamic equilibrium in a single protein under force are hallmarked by a change in the protein's end-to-end fluctuations, revealing a change in protein stiffness. By unfolding and refolding three structurally distinct proteins under a wide range of constant forces, we demonstrate that the associated change in protein compliance to reach force-induced thermodynamically stable states scales with the protein's contour length increment, in agreement with the sequence-independent freely jointed chain model of polymer physics. Our findings will help elucidate the conformational dynamics of proteins exposed to mechanical force at high resolution which are of central importance in mechanosensing and mechanotransduction.

Molecular Force Measurement with Tension Sensors

The ability of cells to generate mechanical forces, but also to sense, adapt to, and respond to mechanical signals, is crucial for many developmental, postnatal homeostatic, and pathophysiological processes. However, the molecular mechanisms underlying cellular mechanotransduction have remained elusive for many decades, as techniques to visualize and quantify molecular forces across individual proteins in cells were missing. The development of genetically encoded molecular tension sensors now allows the quantification of piconewton-scale forces that act upon distinct molecules in living cells and even whole organisms. In this review, we discuss the physical principles, advantages, and limitations of this increasingly popular method. By highlighting current examples from the literature, we demonstrate how molecular tension sensors can be utilized to obtain access to previously unappreciated biophysical parameters that define the propagation of mechanical forces on molecular scales. We discuss how the methodology can be further developed and provide a perspective on how the technique could be applied to uncover entirely novel aspects of mechanobiology in the future.

Talin folding as the tuning fork of cellular mechanotransduction

Cells continually sample their mechanical environment using exquisite force sensors such as talin, whose folding status triggers mechanotransduction pathways by recruiting binding partners. Mechanical signals in biology change quickly over time and are often embedded in noise; however, the mechanics of force-sensing proteins have only been tested using simple force protocols, such as constant or ramped forces. Here, using our magnetic tape head tweezers design, we measure the folding dynamics of single talin proteins in response to external mechanical noise and cyclic force perturbations. Our experiments demonstrate that talin filters out external mechanical noise but detects periodic force signals over a finely tuned frequency range. Hence, talin operates as a mechanical band-pass filter, able to read and interpret frequency-dependent mechanical information through its folding dynamics. We describe our observations in the context of stochastic resonance, which we propose as a mechanism by which mechanosensing proteins could respond accurately to force signals in the naturally noisy biological environment.

Does protein unfolding play a functional role in vivo?

Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.

Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study

Mechanical signals regulate functions of mechanosensitive proteins by inducing structural changes that are determinant for force-dependent interactions. Talin is a focal adhesion protein that is known to extend under mechanical load, and it has been shown to unfold via intermediate states. Here, we compared different nonequilibrium molecular dynamics (MD) simulations to study unfolding of the talin rod. We combined boxed MD (BXD), steered MD, and umbrella sampling (US) techniques and provide free energy profiles for unfolding of talin rod subdomains. We conducted BXD, steered MD, and US simulations at different detail levels and demonstrate how these different techniques can be used to study protein unfolding under tension. Unfolding free energy profiles determined by BXD suggest that the intermediate states in talin rod subdomains are stabilized by force during unfolding, and US confirmed these results.

Talin dissociates from RIAM and associates to vinculin sequentially in response to the actomyosin force

Cells reinforce adhesion strength and cytoskeleton anchoring in response to the actomyosin force. The mechanical stretching of talin, which exposes cryptic vinculin-binding sites, triggers this process. The binding of RIAM to talin could regulate this mechanism. However, the mechanosensitivity of the talin-RIAM complex has never been tested. It is also not known whether RIAM controls the mechanosensitivity of the talin-vinculin complex. To address these issues, we designed an in vitro microscopy assay with purified proteins in which the actomyosin force controls RIAM and vinculin-binding to talin. We demonstrate that actomyosin triggers RIAM dissociation from several talin domains. Actomyosin also provokes the sequential exchange of RIAM for vinculin on talin. The effect of RIAM on this force-dependent binding of vinculin to talin varies from one talin domain to another. This mechanism could allow talin to biochemically code a wide range of forces by selecting different combinations of partners.

Force-dependent formation of the talin-vinculin complex reinforces actin anchoring to focal adhesions, but how different talin-binding proteins respond to force is unclear. Here authors use an in vitro microscopy assay and show that the actomyosin force triggers the dissociation of RIAM from several talin domains.

The Importance of Mechanical Forces for in vitro Endothelial Cell Biology

Blood and lymphatic vessels are lined by endothelial cells which constantly interact with their luminal and abluminal extracellular environments. These interactions confer physical forces on the endothelium, such as shear stress, stretch and stiffness, to mediate biological responses. These physical forces are often altered during disease, driving abnormal endothelial cell behavior and pathology. Therefore, it is critical that we understand the mechanisms by which endothelial cells respond to physical forces. Traditionally, endothelial cells in culture are grown in the absence of flow on stiff substrates such as plastic or glass. These cells are not subjected to the physical forces that endothelial cells endure in vivo, thus the results of these experiments often do not mimic those observed in the body. The field of vascular biology now realize that an intricate analysis of endothelial signaling mechanisms requires complex in vitro systems to mimic in vivo conditions. Here, we will review what is known about the mechanical forces that guide endothelial cell behavior and then discuss the advancements in endothelial cell culture models designed to better mimic the in vivo vascular microenvironment. A wider application of these technologies will provide more biologically relevant information from cultured cells which will be reproducible to conditions found in the body.

Direct observation of a coil-to-helix contraction triggered by vinculin binding to talin

Vinculin binds unfolded talin domains in focal adhesions, which recruits actin filaments to reinforce the mechanical coupling of this organelle. However, it remains unknown how this interaction is regulated and its impact on the force transmission properties of this mechanotransduction pathway. Here, we use magnetic tweezers to measure the interaction between vinculin head and the talin R3 domain under physiological forces. For the first time, we resolve individual binding events as a short contraction of the unfolded talin polypeptide caused by the reformation of the vinculin-binding site helices, which dictates a biphasic mechanism that regulates this interaction. Force favors vinculin binding by unfolding talin and exposing the vinculin-binding sites; however, the coil-to-helix contraction introduces an energy penalty that increases with force, defining an optimal binding regime. This mechanism implies that the talin-vinculin-actin association could operate as a negative feedback mechanism to stabilize force on focal adhesions.

A HaloTag-TEV genetic cassette for mechanical phenotyping of proteins from tissues

Single-molecule methods using recombinant proteins have generated transformative hypotheses on how mechanical forces are generated and sensed in biological tissues. However, testing these mechanical hypotheses on proteins in their natural environment remains inaccesible to conventional tools. To address this limitation, here we demonstrate a mouse model carrying a HaloTag-TEV insertion in the protein titin, the main determinant of myocyte stiffness. Using our system, we specifically sever titin by digestion with TEV protease, and find that the response of muscle fibers to length changes requires mechanical transduction through titin's intact polypeptide chain. In addition, HaloTag-based covalent tethering enables examination of titin dynamics under force using magnetic tweezers. At pulling forces < 10 pN, titin domains are recruited to the unfolded state, and produce 41.5 zJ mechanical work during refolding. Insertion of the HaloTag-TEV cassette in mechanical proteins opens opportunities to explore the molecular basis of cellular force generation, mechanosensing and mechanotransduction.

Different Vinculin Binding Sites Use the Same Mechanism to Regulate Directional Force Transduction

Vinculin is a universal adaptor protein that transiently reinforces the mechanical stability of adhesion complexes. It stabilizes mechanical connections that cells establish between the actomyosin cytoskeleton and the extracellular matrix via integrins or to neighboring cells via cadherins, yet little is known regarding its mechanical design. Vinculin binding sites (VBSs) from different nonhomologous actin-binding proteins use conserved helical motifs to associate with the vinculin head domain. We studied the mechanical stability of such complexes by pulling VBS peptides derived from talin, α-actinin, and Shigella IpaA out of the vinculin head domain. Experimental data from atomic force microscopy single-molecule force spectroscopy and steered molecular dynamics (SMD) simulations both revealed greater mechanical stability of the complex for shear-like than for zipper-like pulling configurations. This suggests that reinforcement occurs along preferential force directions, thus stabilizing those cytoskeletal filament architectures that result in shear-like pulling geometries. Large force-induced conformational changes in the vinculin head domain, as well as protein-specific fine-tuning of the VBS sequence, including sequence inversion, allow for an even more nuanced force response.

Interfering with the Folding of Group A Streptococcal pili Proteins

Gram-positive bacteria use their adhesive pili to attach to host cells during early stages of a bacterial infection. These extracellular hair-like appendages experience mechanical stresses of hundreds of picoNewtons; however, the presence of an internal isopeptide bond prevents the pilus protein from unfolding. Here, we describe a method to interfere with nascent pili proteins through a peptide that mimics one of the β-strands of the molecule. By using AFM-based force spectroscopy, we study the isopeptide bond formation and the effect of the peptide in the elasticity of the pilus protein. This method could be used to afford a new strategy for mechanically targeted antibiotics by simply blocking the folding of the bacterial pilus protein.

The nanomechanics of individual proteins

This tutorial review provides an overview of the single protein force spectroscopy field, including the main techniques and the basic tools for analysing the data obtained from the single molecule experiments.

Biophysics of Cell-Substrate Interactions Under Shear

Cells adhere to substrates through mechanosensitive focal adhesion complexes. Measurements that probe how cells detach from substrates when they experience an applied force connect molecular-scale aspects of cell adhesion with the biophysical properties of adherent cells. Such forces can be applied through shear devices that flow fluid in a controlled manner across cells. The signaling pathways associated with focal adhesions, in particular those that involve integrins and receptor tyrosine kinases, are complex, receiving mechano-chemical feedback from the sensing of substrate stiffness as well as of external forces. This article reviews the signaling processes involved in mechanosensing and mechanotransduction during cell-substrate interactions, describing the role such signaling plays in cancer metastasis. We examine some recent progress in quantifying the strength of these interactions, describing a novel fluid shear device that allows for the visualization of the cell and its sub-cellular structures under a shear flow. We also summarize related results from a biophysical model for cellular de-adhesion induced by applied forces. Quantifying cell-substrate adhesions under shear should aid in the development of mechano-diagnostic techniques for diseases in which cell-adhesion is mis-regulated, such as cancers.

Augmenting cancer cell proteomics with cellular images - A semantic approach to understand focal adhesion

If monolayers of cancer cells are exposed to microgravity, some of the cells cease adhering to the bottom of a culture flask and join three-dimensional aggregates floating in the culture medium. Searching reasons for this change in phenotype, we performed proteome analyses and learnt that accumulation and posttranslational modification of proteins involved in cell-matrix and cell-cell adhesion are affected. To further investigate these proteins, we developed a methodology to find histological images about focal adhesion complex (FA) proteins. Selecting proteins expressed by human FTC-133 and MCF-7 cancer cells and known to be incorporated in FA, we transformed the experimental data to RDF to establish a core semantic knowledgebase. Applying iterative SPARQL queries to Linked Open Databases, we augmented these data with additional functional, transformation- and aggregation-related relationships. Using reasoning, we retrieved publications with images about the spatial arrangement of proteins incorporated in FA. Contextualizing those images enabled us to gain insights about FA of cells changing their site of growth, and to independently validate our experimental results. This new way to link experimental proteome data to biomedical knowledge from various sources via searching images may generally be applied in science when images are a tool of knowledge dissemination.

Engineering the cellular mechanical microenvironment - from bulk mechanics to the nanoscale

The field of mechanobiology studies how mechanical properties of the extracellular matrix (ECM), such as stiffness, and other mechanical stimuli regulate cell behaviour. Recent advancements in the field and the development of novel biomaterials and nanofabrication techniques have enabled researchers to recapitulate the mechanical properties of the microenvironment with an increasing degree of complexity on more biologically relevant dimensions and time scales. In this Review, we discuss different strategies to engineer substrates that mimic the mechanical properties of the ECM and outline how these substrates have been applied to gain further insight into the biomechanical interaction between the cell and its microenvironment.

Talin-mediated force transmission and talin rod domain unfolding independently regulate adhesion signaling

Talin protein is one of the key components in integrin-mediated adhesion complexes. Talins transmit mechanical forces between β-integrin and actin, and regulate adhesion complex composition and signaling through the force-regulated unfolding of talin rod domain. Using modified talin proteins, we demonstrate that these functions contribute to different cellular processes and can be dissected. The transmission of mechanical forces regulates adhesion complex composition and phosphotyrosine signaling even in the absence of the mechanically regulated talin rod subdomains. However, the presence of the rod subdomains and their mechanical activation are required for the reinforcement of the adhesion complex, cell polarization and migration. Talin rod domain unfolding was also found to be essential for the generation of cellular signaling anisotropy, since both insufficient and excess activity of the rod domain severely inhibited cell polarization. Utilizing proteomics tools, we identified adhesome components that are recruited and activated either in a talin rod-dependent manner or independently of the rod subdomains. This study clarifies the division of roles between the force-regulated unfolding of a talin protein (talin 1) and its function as a physical linker between integrins and the cytoskeleton.

Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome

Most natural proteins fold into a native folded conformation stabilized by noncovalent interactions. The free-energy difference between the folded and unfolded conformations of a protein (“thermodynamic folding stability”) establishes the fraction of its population that is in a folded conformation at equilibrium. Here, we used a mass spectrometry-based approach to measure the stabilities of ∼10,000 unique domains within ∼3,000 proteins in human cell extracts. Our data provide a global census of the magnitudes of folding stabilities within the human proteome and identify specific subsets of the proteome that are enriched in stable and unstable domains. We also show that the stability of proteins impacts their tendency to become oxidized and is globally altered by the chemical chaperone trimethylamine N-oxide (TMAO).

The stability of proteins influences their tendency to aggregate, undergo degradation, or become modified in cells. Despite their significance to understanding protein folding and function, quantitative analyses of thermodynamic stabilities have been mostly limited to soluble proteins in purified systems. We have used a highly multiplexed proteomics approach, based on analyses of methionine oxidation rates, to quantify stabilities of ∼10,000 unique regions within ∼3,000 proteins in human cell extracts. The data identify lysosomal and extracellular proteins as the most stable ontological subsets of the proteome. We show that the stability of proteins impacts their tendency to become oxidized and is globally altered by the osmolyte trimethylamine N-oxide (TMAO). We also show that most proteins designated as intrinsically disordered retain their unfolded structure in the complex environment of the cell. Together, the data provide a census of the stability of the human proteome and validate a methodology for global quantitation of folding thermodynamics.

Kindlin Is Mechanosensitive: Force-Induced Conformational Switch Mediates Cross-Talk among Integrins

Mechanical stresses directly regulate the function of several proteins of the integrin-mediated focal adhesion complex as they experience intra- and extracellular forces. Kindlin is a largely overlooked member of the focal adhesion complex whose roles in cellular mechanotransduction are only recently being identified. Recent crystallographic experiments have revealed that kindlins can form dimers that bind simultaneously to two integrins, providing a mechanistic explanation of how kindlins may promote integrin activation and clustering. In this study, using the newly identified molecular structure, we modeled the response of the kindlin2 dimer in complex with integrin β1 to mechanical cytoskeletal forces on integrins. Using molecular dynamics simulations, we show that forces on integrins are directly transmitted to the kindlin2 dimerization site, resulting in a shift in an R577-S550/E553 interaction network at this site. Under force, R577 on one protomer switches from interacting with S550 to forming new hydrogen bonds with E553 on the neighboring protomer, resulting in the strengthening of the kindlin2 dimer in complex with integrin β1. This force-induced strengthening is similar to the catch-bond mechanisms that have previously been observed in other adhesion molecules. Based on our results, we propose that the kindlin2 dimer is mechanosensitive and can strengthen integrin-mediated focal adhesions under force by shifting the interactions at its dimerization sites.

Visualizing the ‘backbone’ of focal adhesions

To understand how complex machines perform their functions, it is essential to map out the ‘blueprints’ of how their internal components are organized. Focal adhesions (FAs) are complex mechanobiological structures involved in a plethora of cell biological processes. The application of super-resolution microscopy in concert with protein engineering offers one approach to unravel the complexity of how individual proteins are organized within FAs. In our recent application, the FA protein talin was found to form a direct structural and physical link between integrin and actin. Interestingly, engineered talin constructs with alternate lengths rescaled the FA nanostructure accordingly. This helped establish that talin could be analogous to the backbone of FAs, serving as the mechanosensitive master coordinator of FA structural organization.

The emergence of solid stress as a potent biomechanical marker of tumour progression

Cancer is a disease of dysregulated mechanics which alters cell behaviour, compromises tissue structure, and promotes tumour growth and metastasis. In the context of tumour progression, the most widely studied of biomechanical markers is matrix stiffness as tumour tissue is typically stiffer than healthy tissue. However, solid stress has recently been identified as another marker of tumour growth, with findings strongly suggesting that its role in cancer is distinct from that of stiffness. Owing to the relative infancy of the field which draws from diverse disciplines, a comprehensive knowledge of the relationships between solid stress, tumorigenesis, and metastasis is likely to provide new and valuable insights. In this review, we discuss the micro- and macro-scale biomechanical interactions that give rise to solid stresses, and also examine the techniques developed to quantify solid stress within the tumour environment. Moreover, by reviewing the effects of solid stress on tissues, cancer and stromal cells, and signalling pathways, we also detail its mode of action at each level of the cancer cascade.

Talin: a protein designed for mechanotransduction

Mechanotransduction, the topic of this volume, has become a major area of cell biological research. That cells respond to their external environments has been known for decades; however, research was largely confined to studying how cells respond to soluble factors and not mechanical forces. Here, I will use talin, a canonical mechanosensitive protein, to illustrate certain emerging concepts.

The extracellular matrix-myosin pathway in mechanotransduction: from molecule to tissue

Mechanotransduction via the extracellular matrix (ECM)–myosin pathway is involved in determining cell morphology during development and in coupling external transient mechanical stimuli to the reorganization of the cytoskeleton. Here, we present a review on the molecular mechanisms involved in this pathway and how they influence cellular development and organization. We investigate key proteins involved in the ECM–myosin pathway and discuss how specific binding events and conformational changes under force are related to mechanical signaling. We connect these molecular mechanisms with observed morphological changes at the cellular and organism level. Finally, we propose a model encompassing the biomechanical signals along the ECM–myosin pathway and how it could be involved in cell adhesion, cell migration, and tissue architecture.

Where No Hand Has Gone Before: Probing Mechanobiology at the Cellular Level

Physical forces and other mechanical stimuli are fundamental regulators of cell behavior and function. Cells are also biomechanically competent: they generate forces to migrate, contract, remodel, and sense their environment. As the knowledge of the mechanisms of mechanobiology increases, the need to resolve and probe increasingly small scales calls for novel technologies to mechanically manipulate cells, examine forces exerted by cells, and characterize cellular biomechanics. Here, we review novel methods to quantify cellular force generation, measure cell mechanical properties, and exert localized piconewton and nanonewton forces on cells, receptors, and proteins. The combination of these technologies will provide further insight on the effect of mechanical stimuli on cells and the mechanisms that convert these stimuli into biochemical and biomechanical activity.

A DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by an electric field

Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA. The motion of the gold nanoparticle and thus the conformational changes of the DNA under varying electric field were analyzed by dark field spectroscopy. After this basic characterization, another actuator was built utilizing hairpin-DNA coated gold nanoparticles, where the hairpin-DNA induced discrete transitions between two specific open-loop and folded-loop states. These two states and the transition dynamics between them were clearly visible in the actuator behavior. The demonstrated nanoactuator concept could be readily extended to inspection of conformational changes of other biomolecules as well. Besides, this concept enables other possibilities in applications like surface-enhanced Raman spectroscopy and fluorescence enhancement, since the specific wavelength of the plasmon resonance of the actuator can be tuned by the external voltage.

Modeling Protein-Based Hydrogels under Force

Hydrogels made from structured polyprotein domains combine the properties of cross-linked polymers with the unfolding phase transition. The use of protein hydrogels as an ensemble approach to study the physics of domain unfolding is limited by the lack of scaling tools and by the complexity of the system. Here we propose a model to describe the biomechanical response of protein hydrogels based on the unfolding and extension of protein domains under force. Our model considers the contributions of the network dynamics of the molecules inside the gels, which have random cross-linking points and random topology. This model reproduces reported macroscopic viscoelastic effects and constitutes an important step toward using rheometry on protein hydrogels to scale down to the average mechanical response of protein molecules.

Role of Extracellular Matrix in Development and Cancer Progression

The immense diversity of extracellular matrix (ECM) proteins confers distinct biochemical and biophysical properties that influence cell phenotype. The ECM is highly dynamic as it is constantly deposited, remodelled, and degraded during development until maturity to maintain tissue homeostasis. The ECM’s composition and organization are spatiotemporally regulated to control cell behaviour and differentiation, but dysregulation of ECM dynamics leads to the development of diseases such as cancer. The chemical cues presented by the ECM have been appreciated as key drivers for both development and cancer progression. However, the mechanical forces present due to the ECM have been largely ignored but recently recognized to play critical roles in disease progression and malignant cell behaviour. Here, we review the ways in which biophysical forces of the microenvironment influence biochemical regulation and cell phenotype during key stages of human development and cancer progression.

Cellular Mechanotransduction: From Tension to Function

Living cells are constantly exposed to mechanical stimuli arising from the surrounding extracellular matrix (ECM) or from neighboring cells. The intracellular molecular processes through which such physical cues are transformed into a biological response are collectively dubbed as mechanotransduction and are of fundamental importance to help the cell timely adapt to the continuous dynamic modifications of the microenvironment. Local changes in ECM composition and mechanics are driven by a feed forward interplay between the cell and the matrix itself, with the first depositing ECM proteins that in turn will impact on the surrounding cells. As such, these changes occur regularly during tissue development and are a hallmark of the pathologies of aging. Only lately, though, the importance of mechanical cues in controlling cell function (e.g., proliferation, differentiation, migration) has been acknowledged. Here we provide a critical review of the recent insights into the molecular basis of cellular mechanotransduction, by analyzing how mechanical stimuli get transformed into a given biological response through the activation of a peculiar genetic program. Specifically, by recapitulating the processes involved in the interpretation of ECM remodeling by Focal Adhesions at cell-matrix interphase, we revise the role of cytoskeleton tension as the second messenger of the mechanotransduction process and the action of mechano-responsive shuttling proteins converging on stage and cell-specific transcription factors. Finally, we give few paradigmatic examples highlighting the emerging role of malfunctions in cell mechanosensing apparatus in the onset and progression of pathologies.

Mechanotransduction in talin through the interaction of the R8 domain with DLC1

The mechanical unfolding of proteins is a cellular mechanism for force transduction with potentially broad implications in cell fate. Despite this, the mechanism by which protein unfolding elicits differential downstream signalling pathways remains poorly understood. Here, we used protein engineering, atomic force microscopy, and biophysical tools to delineate how protein unfolding controls cell mechanics. Deleted in liver cancer 1 (DLC1) is a negative regulator of Ras homolog family member A (RhoA) and cell contractility that regulates cell behaviour when localised to focal adhesions bound to folded talin. Using a talin mutant resistant to force-induced unfolding of R8 domain, we show that talin unfolding determines DLC1 downstream signalling and, consequently, cell mechanics. We propose that this new mechanism of mechanotransduction may have implications for a wide variety of associated cellular processes.

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

Nanoscale mechanobiology of cell adhesions

Proper physiological functions of cells and tissues depend upon their abilities to sense, transduce, integrate, and generate mechanical and biochemical signals. Although such mechanobiological phenomena are widely observed, the molecular mechanisms driving these outcomes are still not fully understood. Cell adhesions formed by integrins and cadherins receptors are key structures that process diverse sources of signals to elicit complex mechanobiological responses. Since the nanoscale is the length scale at which molecules interact to relay force and information, the understanding of cell adhesions at the nanoscale level is important for grasping the inner logics of cellular decision making. Until recently, the study of the biological nanoscale has been restricted by available molecular and imaging tools. Fortunately, rapid technological advances have increasingly opened up the nanoscale realm to systematic investigations. In this review, we discuss current insights and key open questions regarding the nanoscale structure and function relationship of cell adhesions, focusing on recent progresses in characterizing their composition, spatial organization, and cytomechanical operation.

Mechanical stability of talin rod controls cell migration and substrate sensing

Cells adhere to the surrounding tissue and probe its mechanical properties by forming cell-matrix adhesions. Talin is a critical adhesion protein and participates in the transmission of mechanical signals between extracellular matrix and cell cytoskeleton. Force induced unfolding of talin rod subdomains has been proposed to act as a cellular mechanosensor, but so far evidence linking their mechanical stability and cellular response has been lacking. Here, by utilizing computationally designed mutations, we demonstrate that stepwise destabilization of the talin rod R3 subdomain decreases cellular traction force generation, which affects talin and vinculin dynamics in cell-matrix adhesions and results in the formation of talin-rich but unstable adhesions. We observed a connection between talin stability and the rate of cell migration and also found that talin destabilization affects the usage of different integrin subtypes and sensing of extracellular matrix proteins. Experiments with truncated forms of talin confirm the mechanosensory role of the talin R3 subdomain and exclude the possibility that the observed effects are caused by the release of talin head-rod autoinhibition. In conclusion, this study provides evidence into how the controlled talin rod domain unfolding acts as a key regulator of adhesion structure and function and consequently controls central cellular processes such as cell migration and substrate sensing.

Nano-mechanical characterization of tension-sensitive helix bundles in talin rod

Tension-induced exposure of a cryptic signaling binding site is one of the most fundamental mechanisms in molecular mechanotransduction. Helix bundles in rod domains of talin, a tension-sensing protein at focal adhesions, unfurl under tension to expose cryptic vinculin binding sites. Although the difference in their mechanical stabilities would determine which helix bundle is tension-sensitive, their respective mechanical behaviors under tension have not been characterized. In this study, we evaluated the mechanical behaviors of residues 486-654 and 754-889 of talin, which form helix bundles with low and high tension-sensitivity, by employing AFM nano-tensile testing. As a result, residues 754-889 exhibited lower unfolding energy for complete unfolding than residues 486-654. In addition, we found that residues 754-889 transition into intermediate conformations under lower tension than residues 486-654. Furthermore, residues 754-889 showed shorter persistence length in the intermediate conformation than residues 486-654, suggesting that residues 754-889 under tension exhibit separated α-helices, while residues 486-654 assume a compact conformation with inter-helix interactions. Therefore, we suggest that residues 754-889 of talin work as a tension-sensitive domain to recruit vinculin at the early stage of focal adhesion development, while residues 486-654 contribute to rather robust tension-sensitivity by recruiting vinculin under high tension.