Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy

The Electric Field in Solid State Nanopores Causes Dissociation of Strong Biomolecular Interactions

Electrical sensing with nanopores has become a widely used bioanalytical tool. However, it remains unclear if and how the extremely strong electric field generated inside the pores influences biomolecular interactions. Here we show that the field disrupts the strongest known protein-ligand interaction in biology, namely biotin-avidin bonds. Remarkably, the lifetime of the interaction is decreased by at least 4 orders of magnitude. At hundreds of mV, avidin (from egg-white) starts dissociating from biotin-functionalized nanopores over a time scale of minutes even at the maximum bond valency of four. Streptavidin-coated nanoparticles, which form many more bonds, remain bound but exhibit surface mobility due to the field. These results show that nanopore sensors can give very inaccurate results when used for affinity-based detection or biomolecular interaction analysis and that the pore environment should be regarded as potentially invasive for the molecules inside.

Revealing the location and dynamics of a concealed binding site in the dopamine transporter

The dopamine transporter (DAT) is linked to neuropsychiatric disorders including ADHD, Parkinson's disease, and substance use disorders. Accordingly, DAT is the target of illicit drugs and clinically important medicines. However, the number and function of ligand binding sites in DAT is enigmatic due to conflicting data from available structures and molecular pharmacology. Herein, we design force sensors with DAT ligands and measure their interaction forces with wild-type and mutated DATs, from which two distinct populations of unbinding strengths and off-rates are detected. The high-force population is reduced by V152I and S422A mutations, or by substituting Na+ with K+ or NMDG+. In contrast, several modifications including mutation G386H, acetylation of K92 and K384, mutation K92A, mutation K384A, or protonation of H477 decrease the low-force population. The present data delineate the threshold of binding strength, which may account for certain ligand binding sites to be imperceptible in crystal or cryo-EM structures. Furthermore, the force spectra provide the information on the position and kinetic rates of a herein detected ligand binding site in DAT.

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.

AFM reveals differential effects of acidification on LDL- and oxidized LDL-receptor interactions: biomechanical implications in atherogenesis

The receptor recognition and interaction of plasma lipoproteins (e.g., native low-density lipoproteins (LDL)/oxidized low-density lipoproteins (oxLDL), as well as the influence of microenvironmental/lysosomal acidification, play critical roles in lipoprotein metabolism and diseases (e.g., atherosclerosis) but have been less investigated. Here, the recognition/interaction of LDL or oxLDL with LDL receptor (LDLR) or CD36 (a scavenger receptor) or with living cells at various pHs was evaluated mainly via atomic force microscopy (AFM). To improve force measurement accuracy, a novel, micro-droplet-based method for AFM probe functionalization was developed. We found that solution acidification significantly reduced the LDL-LDLR binding at pH ≤ 6.4, whereas the oxLDL-CD36 binding had no significant change until pH ≤ 4.4. Compared with a traditional immersion method, our micro-droplet method for AFM probe functionalization produced more accurate interaction forces, and revealed that acidification significantly reduced the LDL-LDLR/cell interaction forces, instead of the oxLDL-CD36/cell-specific interaction forces and nonspecific interaction forces. The data imply that the LDL-LDLR/cell recognition and interaction are susceptible to acidification, whereas the oxLDL-CD36/cell recognition and interaction are tolerant of acidification. The results may provide important novel information and biomechanical/pathological implications for understanding lipoprotein metabolism and atherosclerosis.

A biophysical basis for the spreading behavior and limited diffusion of Xist

Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome.

From viral assembly to host interaction: AFM's contributions to virology

Viruses represent a diverse pool of obligate parasites that infect virtually every known organism, as such, their study is incredibly valuable for a range of fields including public health, medicine, agriculture, and ecology, and the development of biomedical technologies. Having evolved over millions of years, each virus has a unique and often complicated biology, that must be characterized on a case-by-case basis, even between strains of the same taxon. Owing to its nanoscale spatial resolution, atomic force microscopy (AFM) represents a powerful tool for exploring virus biology, including structural features, kinetics of binding to host cell ligands, virion self-assembly, and budding behaviors. Through the availability of numerous chemistries and advances in imaging modes, AFM is able to explore the complex web of host-virus interactions and life-cycle at a single virus level, exploring features at the level of individual bonds and molecules. Due to the wide array of techniques developed and data analysis approaches available, AFM can provide information that cannot be furnished by other modalities, especially at a single virus level. Here, we highlight the unique methods and information that can be obtained through the use of AFM, demonstrating both its utility and versatility in the study of viruses. As the technology continues to rapidly evolve, AFM is likely to remain an integral part of research, providing unique and important insight into many aspects of virology.

Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice?

During the last decade, artificial intelligence (AI) was applied to nearly all domains of human activity, including scientific research. It is thus warranted to ask whether AI thinking should be durably involved in biomedical research. This problem was addressed by examining three complementary questions (i) What are the major barriers currently met by biomedical investigators? It is suggested that during the last 2 decades there was a shift towards a growing need to elucidate complex systems, and that this was not sufficiently fulfilled by previously successful methods such as theoretical modeling or computer simulation (ii) What is the potential of AI to meet the aforementioned need? it is suggested that recent AI methods are well-suited to perform classification and prediction tasks on multivariate systems, and possibly help in data interpretation, provided their efficiency is properly validated. (iii) Recent representative results obtained with machine learning suggest that AI efficiency may be comparable to that displayed by human operators. It is concluded that AI should durably play an important role in biomedical practice. Also, as already suggested in other scientific domains such as physics, combining AI with conventional methods might generate further progress and new applications, involving heuristic and data interpretation.

Probing living cell dynamics and molecular interactions using atomic force microscopy

Atomic force microscopy (AFM) has emerged as a powerful tool for studying biological interactions at the single-molecule level, offering unparalleled insights into receptor-ligand dynamics on living cells. This review discusses key developments in the application of AFM, highlighting its ability to capture nanomechanical properties of cellular surfaces and probe dynamic interactions, such as virus-host binding. AFM's versatility in measuring mechanical forces and mapping molecular interactions in near-physiological conditions is explored. The review also emphasizes how AFM provides critical insights into cell surface organization, receptor functionality, and viral entry mechanisms, advancing the understanding of cellular and molecular processes.

Influence of temperature and crack-tip speed on crack propagation in elastic solids

I study the influence of temperature and the crack-tip velocity of bond breaking at the crack tip in rubber-like materials. Bond breaking is considered as a stress-aided thermally activated process and results in an effective crack propagation energy, which increases strongly with decreasing temperature or increasing crack-tip speed. This effect is particularly important for adhesive (interfacial) crack propagation but less important for cohesive (bulk) crack propagation owing to the much larger bond-breaking energies in the latter case. For adhesive cracks, the theory results are consistent with adhesion measurements for silicone rubber polydimethylsiloxane (PDMS) in contact with silica glass surfaces. For cohesive cracks, the theory agrees well with experimental results PDMS films chemically bound to silanized glass.

Measuring interaction force between T lymphocytes and their target cells using live microscopy and laminar shear flow chambers

Understanding the immunological synapse formation and dynamics can be enriched by measuring cell-cell interaction forces and their kinetics. Microscopy imaging reveals structural organization of the synapse, while physical methods detail its mechanical construction. Various techniques have been reported for measuring forces needed to rupture the interface between a T lymphocyte and its target cell but most of them measure one pair at a time. We describe here a laminar shear flow-based method that exerts dragging forces on T cell-target cells pairs immobilized on the surface of a flow chamber. Increasing flow rate allows us to observe the detachment of hundreds of cell conjugates on the wide field of a light transmission microscope. Monitoring precisely the flow rate gradient exerted on T cells readily yields synapse rupture measurements. Dragging forces are measured at the point of rupture as a linear function of the flow speed in minutes from 10pN to 20nN for each cell pair among a statistically representative cell population in the whole field of view of a single experiment. The output cells can be collected in multi-well plate sorted in the increasing order of rupture forces. We used this approach to unveil the involvement of the cytoskeleton regulator adenomatous polyposis coli (APC) in the stability of immunological synapses formed between human cytotoxic T cell and tumor target cells. APC is a polarity regulator and tumor suppressor associated with familial adenomatous polyposis and colorectal cancer. Reduced APC expression impairs T cell adhesion with tumor target cells suggesting an impact of APC mutation in anti-tumor immune defense.

Site-specific sulfations regulate the physicochemical properties of papillomavirus-heparan sulfate interactions for entry

Certain human papillomaviruses (HPVs) are etiological agents for several anogenital and oropharyngeal cancers. During initial infection, HPV16, the most prevalent cancer-causing type, specifically interacts with heparan sulfates (HSs), not only enabling initial cell attachment but also triggering a crucial conformational change in viral capsids termed structural activation. It is unknown, whether these HPV16-HS interactions depend on HS sulfation patterns. Thus, we probed potential roles of HS sulfations using cell-based functional and physicochemical assays, including single-molecule force spectroscopy. Our results demonstrate that N-sulfation of HS is crucial for virus binding and structural activation by providing high-affinity sites, and that additional 6O-sulfation is required to mechanically stabilize the interaction, whereas 2O-sulfation and 3O-sulfation are mostly dispensable. Together, our findings identify the contribution of HS sulfation patterns to HPV16 binding and structural activation and reveal how distinct sulfation groups of HS synergize to facilitate HPV16 entry, which, in turn, likely influences the tropism of HPVs.

Mechanochemical Controlled Radical Polymerization: From Harsh to Mild

Mechanochemistry constitutes a burgeoning field that investigates the chemical and physicochemical alterations of substances under mechanical force. It enables the synthesis of materials which is challenging to obtain via thermal, optical or electrical activation methods. In addition, it diminishes reliance on organic solvents and provides a novel route for green chemistry. Today, as a distinct branch alongside electrochemistry, photochemistry, and thermochemistry, mechanochemistry has emerged as a frontier research domain within chemistry and material science. In recent years, the intersection of mechanochemistry with controlled radical polymerization has witnessed rapid advancements, providing new routes to polymer science. Significantly, we have experienced breakthroughs in methods relying on sonochemistry, piezoelectricity and contact electrification. These methodologies not only facilitate the synthesis of polymers with high molecular weight but also enable precise control over polymer chain length and structure. Transitioning from harsh to mild conditions in mechanochemical routes has facilitated a significant improvement in the controllability of mechanochemical polymerization. From this perspective, we introduce the progress of mechanochemistry in controlled radical polymerization in recent years, aim to clarify the historcial development of this topic.

DNA-based ForceChrono probes for deciphering single-molecule force dynamics in living cells

Understanding cellular force transmission dynamics is crucial in mechanobiology. We developed the DNA-based ForceChrono probe to measure force magnitude, duration, and loading rates at the single-molecule level within living cells. The ForceChrono probe circumvents the limitations of in vitro single-molecule force spectroscopy by enabling direct measurements within the dynamic cellular environment. Our findings reveal integrin force loading rates of 0.5-2 pN/s and durations ranging from tens of seconds in nascent adhesions to approximately 100 s in mature focal adhesions. The probe's robust and reversible design allows for continuous monitoring of these dynamic changes as cells undergo morphological transformations. Additionally, by analyzing how mutations, deletions, or pharmacological interventions affect these parameters, we can deduce the functional roles of specific proteins or domains in cellular mechanotransduction. The ForceChrono probe provides detailed insights into the dynamics of mechanical forces, advancing our understanding of cellular mechanics and the molecular mechanisms of mechanotransduction.

Effects of Contact Surface Shape on Dynamic Lifetime and Strength of Molecular Bond Clusters under Displacement- and Force-Controlled Loading Conditions

Many experimental and theoretical studies have shown that the mechanical properties of cells and the extracellular matrix can significantly affect the lifetime and strength of the adhesion clusters of molecular bonds. However, there are few studies on how the shape of the contact surface affects the lifetime and strength of the adhesion clusters of molecular bonds, especially theoretical studies in this area. An idealized model of focal adhesion is adopted, in which two rigid media are bonded together by an array of receptor-ligand bonds modeled as Hookean springs on a complex surface topography, which is described by three parameters: the surface shape factor β, the length of a single identical surface shape L, and the amplitude of surface shapes w. In this study, systematic Monte Carlo simulations of this model are conducted to study the lifetime of the molecular bond cluster under linear incremental force loading and the strength of the molecular bond cluster under linear incremental displacement loading. We find that both small surface shape amplitudes and large surface shape factors will increase the lifetime and strength of the adhesion cluster, whereas the length of a single surface shape causes oscillations in the lifetime and strength of the cluster, and this oscillation amplitude is affected by the surface shape amplitude and the factor. At the same time, we also find that the pretension in the cluster will play a dominant role in the adhesion strength under large amplitudes and small factors of surface shapes. The physical mechanisms behind these phenomena are that the changes of the length of a single surface shape, the amplitude of surface shapes, and the surface shape factor cause the changes of stress concentration in the adhesion region, bond affinity, and the number of similar affinity bonds.

Polymer time crystal: Mechanical activation of reversible bonds by low-amplitude high frequency excitations

Reversible supramolecular bonds play an important role in materials science and in biological systems. The equilibrium between open and closed bonds and the association rate can be controlled thermally, chemically, by mechanical pulling, by ultrasound, or by catalysts. In practice, these intrinsic equilibrium methods either suffer from a limited range of tunability or may damage the material. Here, we present a nonequilibrium strategy that exploits the dissipative properties of the system to control and change the dynamic properties of sacrificial and reversible networks. We show theoretically and numerically how high-frequency mechanical oscillations of very low amplitude can open or close bonds. This mechanism indicates how reversible bonds could alleviate mechanical fatigue of materials especially at low temperatures where they are fragile. In another area, it suggests that the system can be actively modified by the application of ultrasound to induce gel-fluid transitions and to activate or deactivate adhesion properties.

A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy

Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force-fluorescence spectroscopy apparatus broadly used to investigate various biological processes, in particular, protein:DNA interactions. Such experiments typically involve imaging of fluorescently labeled proteins bound to DNA and force spectroscopy measurements of trapped individual DNA molecules. Here, we present a versatile state-of-the-art toolbox including the preparation of protein:DNA complex samples, design of a microfluidic flow cell incorporated with OT, automation of OT-confocal scanning measurements, and the development and implementation of a streamlined data analysis package for force and fluorescence spectroscopy data processing. Its components can be adapted to any commercialized or home-built dual-beam OT setup equipped with a confocal scanning microscope, which will facilitate single-molecule force-fluorescence spectroscopy studies on a large variety of biological systems.

Improving Pharmacokinetics of Peptides Using Phage Display

Phage display is a versatile method often used in the discovery of peptides that targets disease-related biomarkers. A major advantage of this technology is the ease and cost efficiency of affinity selection, also known as biopanning, to identify novel peptides. While it is relatively straightforward to identify peptides with optimal binding affinity, the pharmacokinetics of the selected peptides often prove to be suboptimal. Therefore, careful consideration of the experimental conditions, including the choice of using in vitro, in situ, or in vivo affinity selections, is essential in generating peptides with high affinity and specificity that also demonstrate desirable pharmacokinetics. Specifically, in vivo biopanning, or the combination of in vitro, in situ, and in vivo affinity selections, has been proven to influence the biodistribution and clearance of peptides and peptide-conjugated nanoparticles. Additionally, the marked difference in properties between peptides and nanoparticles must be considered. While peptide biodistribution depends primarily on physiochemical properties and can be modified by amino acid modifications, the size and shape of nanoparticles also affect both absorption and distribution. Thus, optimization of the desired pharmacokinetic properties should be an important consideration in biopanning strategies to enable the selection of peptides and peptide-conjugated nanoparticles that effectively target biomarkers in vivo.

Reversible Host-Guest Crosslinks in Supramolecular Hydrogels for On-Demand Mechanical Stimulation of Human Mesenchymal Stem Cells

Stem cells are regulated not only by biochemical signals but also by biophysical properties of extracellular matrix (ECM). The ECM is constantly monitored and remodeled because the fate of stem cells can be misdirected when the mechanical interaction between cells and ECM is imbalanced. A well-defined ECM model for bone marrow-derived human mesenchymal stem cells (hMSCs) based on supramolecular hydrogels containing reversible host-guest crosslinks is fabricated. The stiffness (Young's modulus E) of the hydrogels can be switched reversibly by altering the concentration of non-cytotoxic, free guest molecules dissolved in the culture medium. Fine-adjustment of substrate stiffness enables the authors to determine the critical stiffness level E* at which hMSCs turn the mechano-sensory machinery on or off. Next, the substrate stiffness across E* is switched and the dynamic adaptation characteristics such as morphology, traction force, and YAP/TAZ signaling of hMSCs are monitored. These data demonstrate the instantaneous switching of traction force, which is followed by YAP/TAZ signaling and morphological adaptation. Periodical switching of the substrate stiffness across E* proves that frequent applications of mechanical stimuli drastically suppress hMSC proliferation. Mechanical stimulation across E* level using dynamic hydrogels is a promising strategy for the on-demand control of hMSC transcription and proliferation.

Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications

Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.

Mechanochemistry of Pterodactylane

Pterodactylane is a [4]-ladderane with substituents on the central rung. Comparing the mechanochemistry of the [4]-ladderane structure when pulled from the central rung versus the end rung revealed a striking difference in the threshold force of mechanoactivation: the threshold force is dramatically lowered from 1.9 nN when pulled on the end rung to 0.7 nN when pulled on the central rung. We investigated the bicyclic products formed from the mechanochemical activation of pterodactylane experimentally and computationally, which are distinct from the mechanochemical products of ladderanes being activated from the end rung. We compared the products of pterodactylane's mechanochemical and thermal activation to reveal differences and similarities in the mechanochemical and thermal pathways of pterodactylane transformation. Interestingly, we also discovered the presence of elementary steps that are accelerated or suppressed by force within the same mechanochemical reaction of pterodactylane, suggesting rich mechanochemical manifolds of multicyclic structures. We rationalized the greatly enhanced mechanochemical reactivity of the central rung of pterodactylane and discovered force-free ground state bond length to be a good low-cost predictor of the threshold force for cyclobutane-based mechanophores. These findings advance our understanding of mechanochemical reactivities and pathways, and they will guide future designs of mechanophores with low threshold forces to facilitate their applications in force-responsive materials.

Ligand-Mediated Mechanical Enhancement in Protein Complexes at Nano- and Macro-Scale

Protein self-assembly plays a vital role in a myriad of biological functions and in the construction of biomaterials. Although the physical association underlying these assemblies offers high specificity, the advantage often compromises the overall durability of protein complexes. To address this challenge, we propose a novel strategy that reinforces the molecular self-assembly of protein complexes mediated by their ligand. Known for their robust noncovalent interactions with biotin, streptavidin (SAv) tetramers are examined to understand how the ligand influences the mechanical strength of protein complexes at the nanoscale and macroscale, employing atomic force microscopy-based single-molecule force spectroscopy, rheology, and bioerosion analysis. Our study reveals that biotin binding enhances the mechanical strength of individual SAv tetramers at the nanoscale. This enhancement translates into improved shear elasticity and reduced bioerosion rates when SAv tetramers are utilized as cross-linking junctions within hydrogel. This approach, which enhances the mechanical strength of protein-based materials without compromising specificity, is expected to open new avenues for advanced biotechnological applications, including self-assembled, robust biomimetic scaffolds and soft robotics.

Membrane Tubulation with a Biomembrane Force Probe

Tubulation is a common cellular process involving the formation of membrane tubes ranging from 50 nm to 1 µm in diameter. These tubes facilitate intercompartmental connections, material transport within cells and content exchange between cells. The high curvature of these tubes makes them specific targets for proteins that sense local geometry. In vitro, similar tubes have been created by pulling on the membranes of giant unilamellar vesicles. Optical tweezers and micromanipulation are typically used in these experiments, involving the manipulation of a GUV with a micropipette and a streptavidin-coated bead trapped in optical tweezers. The interaction forms streptavidin/biotin bonds, leading to tube formation. Here, we propose a cost-effective alternative using only micromanipulation techniques, replacing optical tweezers with a Biomembrane Force Probe (BFP). The BFP, employing a biotinylated erythrocyte as a nanospring, allows for the controlled measurement of forces ranging from 1 pN to 1 nN. The BFP has been widely used to study molecular interactions in cellular processes, extending beyond its original purpose. We outline the experimental setup, tube formation and characterization of tube dimensions and energetics, and discuss the advantages and limitations of this approach in studying membrane tubulation.

Ligand Presentation Inside Protein Crystal Nanopores: Tunable Interfacial Adhesion Noncovalently Modulates Cell Attachment

Protein crystals with sufficiently large solvent pores can non-covalently adsorb polymers in the pores. In principle, if these polymers contain cell adhesion ligands, the polymer-laden crystals could present ligands to cells with tunable adhesion strength. Moreover, porous protein crystals can store an internal ligand reservoir, so that the surface can be replenished. In this study, we demonstrate that poly(ethylene glycol) terminated with a cyclic cell adhesion ligand peptide (PEG-RGD) can be loaded into porous protein crystals by diffusion. Through atomic force microscopy (AFM), force-distance correlations of the mechanical interactions between activated AFM tips and protein crystals were precisely measured. The activation of AFM tips allows the tips to interact with PEG-RGD that was pre-loaded in the protein crystal nanopores, mimicking how a cell might attach to and pull on the ligand through integrin receptors. The AFM experiments also simultaneously reveal the detailed morphology of the buffer-immersed nanoporous protein crystal surface. We also show that porous protein crystals (without and with loaded PEG-RGD) serve as suitable substrates for attachment and spreading of adipose-derived stem cells. This strategy can be used to design surfaces that non-covalently present multiple different ligands to cells with tunable adhesive strength for each ligand, and with an internal reservoir to replenish the precisely defined crystalline surface.

Non-contact non-resonant atomic force microscopy method for measurements of highly mobile molecules and nanoparticles

Atomic force microscopy (AFM) is nowadays indispensable versatile scanning probe method widely employed for fundamental and applied research in physics, chemistry, biology as well as industrial metrology. Conventional AFM systems can operate in various environments such as ultra-high vacuum, electrolyte solutions, or controlled gas atmosphere. Measurements in ambient air are prevalent due to their technical simplicity; however, there are drawbacks such as formation of water meniscus that greatly increases attractive interaction (adhesion) between the tip and the sample, reduced spatial resolution, and too strong interactions leading to tip and/or sample modifications. Here we show how the attractive forces in AFM under ambient conditions can be used with advantage to probe surface properties in a very sensitive way even on highly mobile molecules and nanoparticles. We introduce a stable non-contact non-resonant (NCNR) AFM method which enables to reliably perform measurements in the attractive force regime even in air by controlling the tip position in the intimate surface vicinity without touching it. We demonstrate proof-of-concept results on helicene-based macrocycles, DNA on mica, and nanodiamonds on SiO2. We compare the results with other conventional AFM regimes, showing NCNR advantages such as higher spatial resolution, reduced tip contamination, and negligible sample modification. We analyze principle physical and chemical mechanisms influencing the measurements, discuss issues of stability and various possible method implementations. We explain how the NCNR method can be applied in any AFM system by a mere software modification. The method thus opens a new research field for measurements of highly sensitive and mobile nanoscale objects under air and other environments.

Biomembrane force probe (BFP): Design, advancements, and recent applications to live-cell mechanobiology

Mechanical forces play a vital role in biological processes at molecular and cellular levels, significantly impacting various diseases such as cancer, cardiovascular disease, and COVID-19. Recent advancements in dynamic force spectroscopy (DFS) techniques have enabled the application and measurement of forces and displacements with high resolutions, providing crucial insights into the mechanical pathways underlying these diseases. Among DFS techniques, the biomembrane force probe (BFP) stands out for its ability to measure bond kinetics and cellular mechanosensing with pico-newton and nano-meter resolutions. Here, a comprehensive overview of the classical BFP-DFS setup is presented and key advancements are emphasized, including the development of dual biomembrane force probe (dBFP) and fluorescence biomembrane force probe (fBFP). BFP-DFS allows us to investigate dynamic bond behaviors on living cells and significantly enhances the understanding of specific ligand-receptor axes mediated cell mechanosensing. The contributions of BFP-DFS to the fields of cancer biology, thrombosis, and inflammation are delved into, exploring its potential to elucidate novel therapeutic discoveries. Furthermore, future BFP upgrades aimed at improving output and feasibility are anticipated, emphasizing its growing importance in the field of cell mechanobiology. Although BFP-DFS remains a niche research modality, its impact on the expanding field of cell mechanobiology is immense.

S373P Mutation Stabilizes the Receptor-Binding Domain of the Spike Protein in Omicron and Promotes Binding

A cluster of several newly occurring mutations on Omicron is found at the β-core region of the spike protein's receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ∼20% compared with the wild type. Molecular dynamics (MD) simulations revealed that Omicron RBD showed more hydrogen bonds in the β-core region due to the closing of the α-helical motif caused primarily by the S373P mutation. In addition to a higher unfolding force, we showed a higher dissociation force between Omicron RBD and ACE2. This work reveals the mechanically stabilizing effect of the conserved mutation S373P for Omicron and the possible evolution trend of the β-core region of RBD.

Engineering Tissue-Scale Properties with Synthetic Cells: Forging One from Many

In metazoans, living cells achieve capabilities beyond individual cell functionality by assembling into multicellular tissue structures. These higher-order structures represent dynamic, heterogeneous, and responsive systems that have evolved to regenerate and coordinate their actions over large distances. Recent advances in constructing micrometer-sized vesicles, or synthetic cells, now point to a future where construction of synthetic tissue can be pursued, a boon to pressing material needs in biomedical implants, drug delivery systems, adhesives, filters, and storage devices, among others. To fully realize the potential of synthetic tissue, inspiration has been and will continue to be drawn from new molecular findings on its natural counterpart. In this review, we describe advances in introducing tissue-scale features into synthetic cell assemblies. Beyond mere complexation, synthetic cells have been fashioned with a variety of natural and engineered molecular components that serve as initial steps toward morphological control and patterning, intercellular communication, replication, and responsiveness in synthetic tissue. Particular attention has been paid to the dynamics, spatial constraints, and mechanical strengths of interactions that drive the synthesis of this next-generation material, describing how multiple synthetic cells can act as one.

Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds

Single-molecule data are of great significance in biology, chemistry, and medicine. However, new experimental tools to characterize, in a multiplexed manner, protein bond rupture under force are still needed. Acoustic force spectroscopy is an emerging manipulation technique which generates acoustic waves to apply force in parallel on multiple microbeads tethered to a surface. We here exploit this configuration in combination with the recently developed modular junctured-DNA scaffold that has been designed to study protein-protein interactions at the single-molecule level. By applying repetitive constant force steps on the FKBP12-rapamycin-FRB complex, we measure its unbinding kinetics under force at the single-bond level. Special efforts are made in analyzing the data to identify potential pitfalls. We propose a calibration method allowing in situ force determination during the course of the unbinding measurement. We compare our results with well-established techniques, such as magnetic tweezers, to ensure their accuracy. We also apply our strategy to study the force-dependent rupture of a single-domain antibody with its antigen. Overall, we get a good agreement with the published parameters that have been obtained at zero force and population level. Thus, our technique offers single-molecule precision for multiplexed measurements of interactions of biotechnological and medical interest.

AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements

Transposon Tn4430 belongs to a widespread family of bacterial transposons, the Tn3 family, which plays a prevalent role in the dissemination of antibiotic resistance among pathogens. Despite recent data on the structural architecture of the transposition complex, the molecular mechanisms underlying the replicative transposition of these elements are still poorly understood. Here, we use force-distance curve-based atomic force microscopy to probe the binding of the TnpA transposase of Tn4430 to DNA molecules containing one or two transposon ends and to extract the thermodynamic and kinetic parameters of transposition complex assembly. Comparing wild-type TnpA with previously isolated deregulated TnpA mutants supports a stepwise pathway for transposition complex formation and activation during which TnpA first binds as a dimer to a single transposon end and then undergoes a structural transition that enables it to bind the second end cooperatively and to become activated for transposition catalysis, the latter step occurring at a much faster rate for the TnpA mutants. Our study thus provides an unprecedented approach to probe the dynamic of a complex DNA processing machinery at the single-particle level.

Catch Bond-Mediated Adhesion Drives Staphylococcus aureus Host Cell Invasion

Various viruses and pathogenic bacteria interact with annexin A2 to invade mammalian cells. Here, we show that Staphylococcus aureus engages in extremely strong catch bonds for host cell invasion. By means of single-molecule atomic force microscopy, we find that bacterial surface-located clumping factors bind annexin A2 with extraordinary strength, indicating that these bonds are extremely resilient to mechanical tension. By determining the lifetimes of the complexes under increasing mechanical stress, we demonstrate that the adhesins form catch bonds with their ligand that are capable to sustain forces of 1500-1700 pN. The force-dependent adhesion mechanism identified here provides a molecular framework to explain how S. aureus pathogens tightly attach to host cells during invasion and shows promise for the design of new therapeutics against intracellular S. aureus.

Anisotropic Friction in a Ligand-Protein Complex

The effect of an externally applied directional force on molecular friction is so far poorly understood. Here, we study the force-driven dissociation of the ligand-protein complex biotin-streptavidin and identify anisotropic friction as a not yet described type of molecular friction. Using AFM-based stereographic single molecule force spectroscopy and targeted molecular dynamics simulations, we find that the rupture force and friction for biotin-streptavidin vary with the pulling angle. This observation holds true for friction extracted from Kramers' rate expression and by dissipation-corrected targeted molecular dynamics simulations based on Jarzynski's identity. We rule out ligand solvation and protein-internal friction as sources of the angle-dependent friction. Instead, we observe a heterogeneity in free energy barriers along an experimentally uncontrolled orientation parameter, which increases the rupture force variance and therefore the overall friction. We anticipate that anisotropic friction needs to be accounted for in a complete understanding of friction in biomolecular dynamics and anisotropic mechanical environments.

Force: A messenger of axon outgrowth

The axon is a sophisticated macromolecular machine composed of interrelated parts that transmit signals like spur gears transfer motion between parallel shafts. The growth cone is a fine sensor that integrates mechanical and chemical cues and transduces these signals through the generation of a traction force that pushes the tip and pulls the axon shaft forward. The axon shaft, in turn, senses this pulling force and transduces this signal in an orchestrated response, coordinating cytoskeleton remodeling and intercalated mass addition to sustain and support the advancing of the tip. Extensive research suggests that the direct application of active force is per se a powerful inducer of axon growth, potentially bypassing the contribution of the growth cone. This review provides a critical perspective on current knowledge of how the force is a messenger of axon growth and its mode of action for controlling navigation, including aspects that remain unclear. It also focuses on novel approaches and tools designed to mechanically manipulate axons, and discusses their implications in terms of potential novel therapies for re-wiring the nervous system.

A Tale of Two Foulants: The Coupling of Organic Fouling and Mineral Scaling in Membrane Desalination

Membrane desalination that enables the harvesting of purified water from unconventional sources such as seawater, brackish groundwater, and wastewater has become indispensable to ensure sustainable freshwater supply in the context of a changing climate. However, the efficiency of membrane desalination is greatly constrained by organic fouling and mineral scaling. Although extensive studies have focused on understanding membrane fouling or scaling separately, organic foulants commonly coexist with inorganic scalants in the feedwaters of membrane desalination. Compared to individual fouling or scaling, combined fouling and scaling often exhibits different behaviors and is governed by foulant-scalant interactions, resembling more complex but practical scenarios than using feedwaters containing only organic foulants or inorganic scalants. In this critical review, we first summarize the performance of membrane desalination under combined fouling and scaling, involving mineral scales formed via both crystallization and polymerization. We then provide the state-of-the-art knowledge and characterization techniques pertaining to the molecular interactions between organic foulants and inorganic scalants, which alter the kinetics and thermodynamics of mineral nucleation as well as the deposition of mineral scales onto membrane surfaces. We further review the current efforts of mitigating combined fouling and scaling via membrane materials development and pretreatment. Finally, we provide prospects for future research needs that guide the design of more effective control strategies for combined fouling and scaling to improve the efficiency and resilience of membrane desalination for the treatment of feedwaters with complex compositions.

Physical biomarkers for human hematopoietic stem and progenitor cells

Adhesion of hematopoietic stem and progenitor cells (HSPCs) to the bone marrow niche plays critical roles in the maintenance of the most primitive HSPCs. The interactions of HSPC-niche interactions are clinically relevant in acute myeloid leukemia (AML), because (i) leukemia-initiating cells adhered to the marrow niche are protected from the cytotoxic effect by chemotherapy and (ii) mobilization of HSPCs from healthy donors' bone marrow is crucial for the effective stem cell transplantation. However, although many clinical agents have been developed for the HSPC mobilization, the effects caused by the extrinsic molecular cues were traditionally evaluated based on phenomenological observations. This review highlights the recent interdisciplinary challenges of hematologists, biophysicists and cell biologists towards the design of defined in vitro niche models and the development of physical biomarkers for quantitative indexing of differential effects of clinical agents on human HSPCs.

Recent advances in the application of atomic force microscopy to structural biology

The application of atomic force microscopy (AFM) for (functional) imaging and manipulating biomolecules at all levels of organization has enabled great progress in the structural biology field over the last decades, contributing to the discovery of novel structural entities of biological significance across many disciplines ranging from biochemistry, biomedicine and biophysics to molecular and cell biology, up to food systems and beyond. AFM has the capability to generate high-resolution topographic images spanning from the submolecular to the (sub)cellular range and can probe biochemical and biophysical sample properties in close to native conditions with excellent temporal resolution. Instrumental developments in the past decade enable dynamical structural and conformational studies of single biomolecules and new techniques for structural and chemical modification of the AFM probe have converted the cantilever into a versatile tool to study different biological phenomena, such as the mechanical stability of biomolecular complexes or the force induced dynamic changes of mechanically stressed proteins at the nanoscopic level. To improve the functionality of AFM and approach dynamic processes of complex biological systems ex vivo, AFM is combined with complementary microscopy, nanoscopy and spectroscopy tools. These multimethodological approaches provide unprecedented possibilities of probing physical, chemical and biological properties of complex cellular systems with high spatio-temporal resolution, leading to novel applications that correlate structural results with functional biochemical, biophysical, immunological, or genetic data on the system under study.

Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain

Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.

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.

Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy

Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.

[Corneal epithelial biomechanics: Resistance to stress and role in healing and remodeling]

The corneal epithelium is one of the first tissue barriers of the eye against the environment. In recent years, many studies provided better knowledge of its healing, its behavior and its essential role in the optical system of the eye. At the crossroads of basic science and clinical medicine, the study of the mechanical stresses applied to the cornea makes it possible to learn the behavior of epithelial cells and better understand ocular surface disease. We describe herein the current knowledge about the adhesion systems of the corneal epithelium and their resistance to mechanical stress. We will also describe the involvement of these mechanisms in corneal healing and their role in epithelial dynamics. Adhesion molecules of the epithelial cells, especially hemidesmosomes, allow the tissue cohesion required to maintain the integrity of the corneal epithelium against the shearing forces of the eyelids as well as external forces. Their regeneration after a corneal injury is mandatory for the restoration of a healthy epithelium. Mechanotransduction plays a significant role in regulating epithelial cell behavior, and the study of the epithelium's response to mechanical forces helps to better understand the evolution of epithelial profiles after refractive surgery. A better understanding of corneal epithelial biomechanics could also help improve future therapies, particularly in the field of tissue engineering.

Resolving Molecular Heterogeneity with Single-Molecule Centrifugation

For many classes of biomolecules, population-level heterogeneity is an essential aspect of biological function─from antibodies produced by the immune system to post-translationally modified proteins that regulate cellular processes. However, heterogeneity is difficult to fully characterize for multiple reasons: (i) single-molecule approaches are needed to avoid information lost by ensemble-level averaging, (ii) sufficient statistics must be gathered on both a per-molecule and per-population level, and (iii) a suitable analysis framework is required to make sense of a potentially limited number of intrinsically noisy measurements. Here, we introduce an approach that overcomes these difficulties by combining three techniques: a DNA nanoswitch construct to repeatedly interrogate the same molecule, a benchtop centrifuge force microscope (CFM) to obtain thousands of statistics in a highly parallel manner, and a Bayesian nonparametric (BNP) inference method to resolve separate subpopulations with distinct kinetics. We apply this approach to characterize commercially available antibodies and find that polyclonal antibody from rabbit serum is well-modeled by a mixture of three subpopulations. Our results show how combining a spatially and temporally multiplexed nanoswitch-CFM assay with BNP analysis can help resolve complex biomolecular interactions in heterogeneous samples.

Few-shot deep learning for AFM force curve characterization of single-molecule interactions

Deep learning (DL)-based analytics has the scope to transform the field of atomic force microscopy (AFM) with regard to fast and bias-free measurement characterization. For example, AFM force-distance curves can help estimate important parameters of binding kinetics, such as the most probable rupture force, binding probability, association, and dissociation constants, as well as receptor density on live cells. Other than the ideal single-rupture event in the force-distance curves, there can be no-rupture, double-rupture, or multiple-rupture events. The current practice is to go through such datasets manually, which can be extremely tedious work for the experimentalists. We address this issue by adopting a few-shot learning approach to build sample-efficient DL models that demonstrate better performance than shallow ML models while matching the performance of moderately trained humans. We also release our AFM force curve dataset and annotations publicly as a benchmark for the research community.

Cell mechanical responses to subcellular perturbations generated by ultrasound and targeted microbubbles

The inherently dynamic and anisotropic microenvironment of cells imposes not only global and slow physical stimulations on cells but also acute and local perturbations. However, cell mechanical responses to transient subcellular physical signals remain unclear. In this study, acoustically activated targeted microbubbles were used to exert mechanical perturbations to single cells. The cellular contractile force was sensed by elastic micropillar arrays, while the pillar deformations were imaged using brightfield high-speed video microscopy at a frame rate of 1k frames per second for the first 10s and then confocal fluorescence microscopy. Cell mechanical responses are accompanied by cell membrane integrity changes. Both processes are determined by the perturbation strength generated by microbubble volumetric oscillations. The instantaneous cellular traction force relaxation exhibits two distinct patterns, correlated with two cell fates (survival or permanent damage). The mathematical modeling unveils that force-induced actomyosin disassembly leads to gradual traction force relaxation in the first few seconds. The perturbation may also influence the far end subcellular regions from the microbubbles and may propagate into connected cells with attenuations and delays. This study carefully characterizes the cell mechanical responses to local perturbations induced by ultrasound and microbubbles, advancing our understanding of the fundamentals of cell mechano-sensing, -responsiveness, and -transduction. STATEMENT OF SIGNIFICANCE: Subcellular physical perturbations commonly exist but haven't been fully explored yet. The subcellular perturbation generated by ultrasound and targeted microbubbles covers a wide range of strength, from mild, intermediate to intense, providing a broad biomedical relevance. With µm² spatial sensing ability and up to 1ms temporal resolution, we present spatiotemporal details of the instantaneous cellular contractile force changes followed by attenuated and delayed global responses. The correlation between the cell mechanical responses and cell fates highlights the important role of the instantaneous mechanical responses in the entire cellular reactive processes. Supported by mathematical modeling, our work provides new insights into the dynamics and mechanisms of cell mechanics.

Interaction Kinetics of Individual mRNA-Containing Lipid Nanoparticles with an Endosomal Membrane Mimic: Dependence on pH, Protein Corona Formation, and Lipoprotein Depletion

Lipid nanoparticles (LNPs) have emerged as potent carriers for mRNA delivery, but several challenges remain before this approach can offer broad clinical translation of mRNA therapeutics. To improve their efficacy, a better understanding is required regarding how LNPs are trapped and processed at the anionic endosomal membrane prior to mRNA release. We used surface-sensitive fluorescence microscopy with single LNP resolution to investigate the pH dependency of the binding kinetics of ionizable lipid-containing LNPs to a supported endosomal model membrane. A sharp increase of LNP binding was observed when the pH was lowered from 6 to 5, accompanied by stepwise large-scale LNP disintegration. For LNPs preincubated in serum, protein corona formation shifted the onset of LNP binding and subsequent disintegration to lower pH, an effect that was less pronounced for lipoprotein-depleted serum. The LNP binding to the endosomal membrane mimic was observed to eventually become severely limited by suppression of the driving force for the formation of multivalent bonds during LNP attachment or, more specifically, by charge neutralization of anionic lipids in the model membrane due to their association with cationic lipids from earlier attached LNPs upon their disintegration. Cell uptake experiments demonstrated marginal differences in LNP uptake in untreated and lipoprotein-depleted serum, whereas lipoprotein-depleted serum increased mRNA-controlled protein (eGFP) production substantially. This complies with model membrane data and suggests that protein corona formation on the surface of the LNPs influences the nature of the interaction between LNPs and endosomal membranes.

Phosphorylation disrupts long-distance electron transport in cytochrome c

It has been recently shown that electron transfer between mitochondrial cytochrome c and the cytochrome c₁ subunit of the cytochrome bc₁ can proceed at long-distance through the aqueous solution. Cytochrome c is thought to adjust its activity by changing the affinity for its partners via Tyr48 phosphorylation, but it is unknown how it impacts the nanoscopic environment, interaction forces, and long-range electron transfer. Here, we constrain the orientation and separation between cytochrome c₁ and cytochrome c or the phosphomimetic Y48pCMF cytochrome c, and deploy an array of single-molecule, bulk, and computational methods to investigate the molecular mechanism of electron transfer regulation by cytochrome c phosphorylation. We demonstrate that phosphorylation impairs long-range electron transfer, shortens the long-distance charge conduit between the partners, strengthens their interaction, and departs it from equilibrium. These results unveil a nanoscopic view of the interaction between redox protein partners in electron transport chains and its mechanisms of regulation.

Low cost and massively parallel force spectroscopy with fluid loading on a chip

Current approaches for single molecule force spectroscopy are typically constrained by low throughput and high instrumentation cost. Herein, a low-cost, high throughput technique is demonstrated using microfluidics for multiplexed mechanical manipulation of up to ~4000 individual molecules via molecular fluid loading on-a-chip (FLO-Chip). The FLO-Chip consists of serially connected microchannels with varying width, allowing for simultaneous testing at multiple loading rates. Molecular force measurements are demonstrated by dissociating Biotin-Streptavidin and Digoxigenin-AntiDigoxigenin interactions along with unzipping of double stranded DNA of varying sequence under different dynamic loading rates and solution conditions. Rupture force results under varying loading rates and solution conditions are in good agreement with prior studies, verifying a versatile approach for single molecule biophysics and molecular mechanobiology. FLO-Chip enables straightforward, rapid, low-cost, and portable mechanical testing of single molecules that can be implemented on a wide range of microscopes to broaden access and may enable new applications of molecular force spectroscopy.

Mechano-Redox Control of Integrins in Thromboinflammation

Significance: How mechanical forces and biochemical cues are coupled remains a miracle for many biological processes. Integrins, well-known adhesion receptors, sense changes in mechanical forces and reduction-oxidation reactions (redox) in their environment to mediate their adhesive function. The coupling of mechanical and redox function is a new area of investigation. Disturbance of normal mechanical forces and the redox balance occurs in thromboinflammatory conditions; atherosclerotic plaques create changes to the mechanical forces in the circulation. Diabetes induces redox changes in the circulation by the production of reactive oxygen species and vascular inflammation. Recent Advances: Integrins sense changes in the blood flow shear stress at the level of focal adhesions and respond to flow and traction forces by increased signaling. Talin, the integrin-actin linker, is a traction force sensor and adaptor. Oxidation and reduction of integrin disulfide bonds regulate their adhesion. A conserved disulfide bond in integrin αlpha IIb beta 3 (αIIbβ3) is directly reduced by the thiol oxidoreductase endoplasmic reticulum protein 5 (ERp5) under shear stress. Critical Issues: The coordination of mechano-redox events between the extracellular and intracellular compartments is an active area of investigation. Another fundamental issue is to determine the spatiotemporal arrangement of key regulators of integrins' mechanical and redox interactions. How thromboinflammatory conditions lead to mechanoredox uncoupling is relatively unexplored. Future Directions: Integrated approaches, involving disulfide bond biochemistry, microfluidic assays, and dynamic force spectroscopy, will aid in showing that cell adhesion constitutes a crossroad of mechano- and redox biology, within the same molecule, the integrin. Antioxid. Redox Signal. 37, 1072-1093.

Interaction of the Staphylococcus aureus Surface Protein FnBPB with Corneodesmosin Involves Two Distinct, Extremely Strong Bonds

Attachment of Staphylococcus aureus to human skin corneocyte cells plays a critical role in exacerbating the severity of atopic dermatitis (AD). Pathogen-skin adhesion is mediated by bacterial cell-surface proteins called adhesins, including fibronectin-binding protein B (FnBPB). FnBPB binds to corneodesmosin (CDSN), a glycoprotein exposed on AD patient corneocytes. Using single-molecule experiments, we demonstrate that CDSN binding by FnBPB relies on a sophisticated two-site mechanism. Both sites form extremely strong bonds with binding forces of ∼1 and ∼2.5 nN albeit with faster dissociation rates than those reported for homologues of the adhesin. This previously unidentified two-binding site interaction in FnBPB illustrates its remarkable variety of adhesive functions and is of biological significance as the high strength and short bond lifetime will favor efficient skin colonization by the pathogen.

The activated ClpP peptidase forcefully grips a protein substrate

ATPases associated with diverse cellular activities (AAA+) proteases power the maintenance of protein homeostasis by coupling ATP hydrolysis to mechanical protein unfolding, translocation, and ultimately degradation. Although ATPase activity drives a large portion of the mechanical work these molecular machines perform, how the peptidase contributes to the forceful denaturation and processive threading of substrates remains unknown. Here, using single-molecule optical trapping, we examine the mechanical activity of the caseinolytic peptidase P (ClpP) from Escherichia coli in the absence of a partner ATPase and in the presence of an activating small-molecule acyldepsipeptide. We demonstrate that ClpP grips protein substrate under mechanical loads exceeding 40 pN, which are greater than those observed for the AAA+ unfoldase ClpX and the AAA+ protease complexes ClpXP and ClpAP. We further characterize substrate-ClpP bond lifetimes and rupture forces under varying loads. We find that the resulting slip bond behavior does not depend on ClpP peptidase activity. In addition, we find that unloaded bond lifetimes between ClpP and protein substrate are on a timescale relevant to unfolding times (up to ∼160 s) for difficult to unfold model substrate proteins. These direct measurements of the substrate-peptidase bond under load define key properties required by AAA+ proteases to mechanically unfold and degrade protein substrates.

Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy

Mechanoactive proteins are essential for a myriad of physiological and pathological processes. Guided by the advances in single-molecule force spectroscopy (SMFS), we have reached a molecular-level understanding of how mechanoactive proteins sense and respond to mechanical forces. However, even SMFS has its limitations, including the lack of detailed structural information during force-loading experiments. That is where molecular dynamics (MD) methods shine, bringing atomistic details with femtosecond time-resolution. However, MD heavily relies on the availability of high-resolution structural data, which is not available for most proteins. For instance, the Protein Data Bank currently has 192K structures deposited, against 231M protein sequences available on Uniprot. But many are betting that this gap might become much smaller soon. Over the past year, the AI-based AlphaFold created a buzz on the structural biology field by being able to predict near-native protein folds from their sequences. For some, AlphaFold is causing the merge of structural biology with bioinformatics. Here, using an in silico SMFS approach pioneered by our group, we investigate how reliable AlphaFold structure predictions are to investigate mechanical properties of Staphylococcus bacteria adhesins proteins. Our results show that AlphaFold produce extremally reliable protein folds, but in many cases is unable to predict high-resolution protein complexes accurately. Nonetheless, the results show that AlphaFold can revolutionize the investigation of these proteins, particularly by allowing high-throughput scanning of protein structures. Meanwhile, we show that the AlphaFold results need to be validated and should not be employed blindly, with the risk of obtaining an erroneous protein mechanism.