High force catch bond mechanism of bacterial adhesion in the human gut

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.

Engineering Adhesion of the Probiotic Strain Escherichia coli Nissle to the Fungal Pathogen Candida albicans

Engineering live biotherapeutic products against fungal pathogens such as Candida albicans has been suggested as a means to tackle the increasing threat of fungal infections and the development of resistance to classical antifungal treatments. One important challenge in the design of live therapeutics is to control their localization inside the human body. The specific binding capability to target organisms or tissues would greatly increase their effectiveness by increasing the local concentration of effector molecules at the site of infection. In this study, we utilized surface display of carbohydrate binding domains to enable the probiotic E. coli Nissle 1917 to adhere specifically to the pathogenic yeast Candida albicans. Binding was quantified using a newly developed method based on the automated analysis of microscopic images. In addition to a rationally selected chitin binding domain, a synthetic peptide of identical length but distinct sequence also conferred binding. Efficient binding was specific to fungal hyphae, the invasive form of C. albicans, while the yeast form, as well as abiotic cellulose and PET particles, was only weakly recognized.

De novo DNA-based catch bonds

All primary chemical interactions weaken under mechanical stress, which imposes fundamental mechanical limits on the materials constructed from them. Biological materials combine plasticity with strength, for which nature has evolved a unique solution-catch bonds, supramolecular interactions that strengthen under tension. Biological catch bonds use force-gated conformational switches to convert weak bonds into strong ones. So far, catch bonds remain exclusive to nature, leaving their potential as mechanoadaptive elements in synthetic systems untapped. Here we report the design and realization of artificial catch bonds. Starting from a minimal set of thermodynamic design requirements, we created a molecular motif capable of catch bonding. It consists of a DNA duplex featuring a cryptic domain that unfolds under tension to strengthen the interaction. We show that these catch bonds recreate force-enhanced rolling adhesion, a hallmark feature of biological catch bonds in bacteria and leukocytes. This Article introduces catch bonds into the synthetic domain, and could lead to the creation of artificial catch-bonded materials.

Bidirectional Allostery Mechanism in Catch-Bond Formation of CD44 Mediated Cell Adhesion

Catch-bonds, whereby noncovalent ligand-receptor interactions are counterintuitively reinforced by tensile forces, play a major role in cell adhesion under mechanical stress. A basic prerequisite for catch-bond formation, as implicated in classic catch-bond models, is that force-induced remodeling of the ligand binding interface occurs prior to bond rupture. However, what strategy receptor proteins utilize to meet such specific kinetic control remains elusive. Here we report a bidirectional allostery mechanism of catch-bond formation based on theoretical and molecular dynamics simulation studies. Binding of ligand allosterically reduces the threshold force for unlocking of otherwise stably folded force-sensing element (i.e., forward allostery), so that a much smaller tensile force can trigger the conformational switching of receptor protein to high binding-strength state via backward allosteric coupling before bond rupture. Such bidirectional allostery fulfills the specific kinetic control required by catch-bond formation and is likely to be commonly utilized in cell adhesion. The essential thermodynamic and kinetic features of receptor proteins essential for catch-bond formation were identified.

Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations

Rational design of novel antibody therapeutics against viral infections such as coronavirus relies on surface complementarity and high affinity for their effectiveness. Here, we explore an additional property of protein complexes, the intrinsic mechanical stability, in SARS-CoV-2 variants when complexed with a potent antibody. In this study, we utilized a recent implementation of the GōMartini 3 approach to investigate large conformational changes in protein complexes with a focus on the mechanostability of the receptor-binding domain (RBD) from WT, Alpha, Delta, and XBB.1.5 variants in complex with the H11-H4 nanobody. The analysis revealed moderate differences in mechanical stability among these variants. Also, we identified crucial residues in both the RBD and certain protein segments in the nanobody that contribute to this property. By performing pulling simulations and monitoring the presence of specific native and non-native contacts across the protein complex interface, we provided mechanistic insights into the dissociation process. Force-displacement profiles indicate a tensile force clamp mechanism associated with the type of protein complex. Our computational approach not only highlights the key mechanostable interactions that are necessary to maintain overall stability, but it also paves the way for the rational design of potent antibodies that are mechanostable and effective against emergent SARS-CoV-2 variants.

Bacterial interactions on nutrient-rich surfaces in the gut lumen

The intestinal lumen is a turbulent, semi-fluid landscape where microbial cells and nutrient-rich particles are distributed with high heterogeneity. Major questions regarding the basic physical structure of this dynamic microbial ecosystem remain unanswered. Most gut microbes are non-motile, and it is unclear how they achieve optimum localization relative to concentrated aggregations of dietary glycans that serve as their primary source of energy. In addition, a random spatial arrangement of cells in this environment is predicted to limit sustained interactions that drive co-evolution of microbial genomes. The ecological consequences of random versus organized microbial localization have the potential to control both the metabolic outputs of the microbiota and the propensity for enteric pathogens to participate in proximity-dependent microbial interactions. Here, we review evidence suggesting that several bacterial species adopt organized spatial arrangements in the gut via adhesion. We highlight examples where localization could contribute to antagonism or metabolic interdependency in nutrient degradation, and we discuss imaging- and sequencing-based technologies that have been used to assess the spatial positions of cells within complex microbial communities.

Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions

Understanding binding epitopes involved in protein-protein interactions and accurately determining their structure are long-standing goals with broad applicability in industry and biomedicine. Although various experimental methods for binding epitope determination exist, these approaches are typically low throughput and cost-intensive. Computational methods have potential to accelerate epitope predictions; however, recently developed artificial intelligence (AI)-based methods frequently fail to predict epitopes of synthetic binding domains with few natural homologues. Here we have developed an integrated method employing generalized-correlation-based dynamic network analysis on multiple molecular dynamics (MD) trajectories, initiated from AlphaFold2Multimer structures, to unravel the structure and binding epitope of the therapeutic PD-L1:Affibody complex. Both AlphaFold2 and conventional molecular dynamics trajectory analysis were ineffective in distinguishing between two proposed binding models, parallel and perpendicular. However, our integrated approach, utilizing dynamic network analysis, demonstrated that the perpendicular mode was significantly more stable. These predictions were validated using a suite of experimental epitope mapping protocols, including cross-linking mass spectrometry and next-generation sequencing-based deep mutational scanning. Conversely, AlphaFold3 failed to predict a structure bound in the perpendicular pose, highlighting the necessity for exploratory research in the search for binding epitopes and challenging the notion that AI-generated protein structures can be accepted without scrutiny. Our research underscores the potential of employing dynamic network analysis to enhance AI-based structure predictions for more accurate identification of protein-protein interaction interfaces.

A Handle-Free, All-Protein-Based Optical Tweezers Method to Probe Protein Folding-Unfolding Dynamics

Optical tweezers (OT) have evolved into powerful single molecule force spectroscopy tools to investigate protein folding-unfolding dynamics. To stretch a protein of interest using OT, the protein must be flanked with two double stranded DNA (dsDNA) handles. However, coupling dsDNA handles to the protein is often of low yield, representing a bottleneck in OT experiments. Here, we report a handle-free, all-protein-based OT method for investigating protein folding/unfolding dynamics. In this new method, we employed disordered elastin-like polypeptides (ELPs) as a molecular linker and the mechanically stable cohesin-dockerin (Coh-Doc) pair as the prey-bait system to enable the efficient capture and stretching of individual protein molecules. This novel approach was validated by using model proteins NuG2 and RTX-v, yielding experimental results comparable to those obtained by using the dsDNA handle approach. This new method provides a streamlined and efficient OT approach to investigate the folding-unfolding dynamics of proteins at the single molecule level, thus expanding the toolbox of OT-based single molecule force spectroscopy.

Engineering an artificial catch bond using mechanical anisotropy

Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.

The effects of whole grain cereals on tryptophan metabolism and intestinal barrier function: underlying factors of health impact

This review aims to investigate the relationship between the health impact of whole grains mediated via the interaction with intestinal microbiota and intestinal barrier function with special interest on tryptophan metabolism, focusing on the role of the intestinal microbiota and their impact on barrier function. Consuming various types of whole grains can lead to the growth of different microbiota species, which in turn leads to the production of diverse metabolites, including those derived from tryptophan metabolism, although the impact of whole grains on intestinal microbiota composition results remains inconclusive and vary among different studies. Whole grains can exert an influence on tryptophan metabolism through interactions with the intestinal microbiota, and the presence of fibre in whole grains plays a notable role in establishing this connection. The impact of whole grains on intestinal barrier function is closely related to their effects on the composition and activity of intestinal microbiota, and SCFA and tryptophan metabolites serve as potential links connecting whole grains, intestinal microbiota and the intestinal barrier function. Tryptophan metabolites affect various aspects of the intestinal barrier, such as immune balance, mucus and microbial barrier, tight junction complexes and the differentiation and proliferation of epithelial cells. Despite the encouraging discoveries in this area of research, the evidence regarding the effects of whole grain consumption on intestine-related activity remains limited. Hence, we can conclude that we are just starting to understand the actual complexity of the intestinal factors mediating in part the health impacts of whole grain cereals.

Molecular basis and cellular functions of vinculin-actin directional catch bonding

The ability of cells and tissues to respond differentially to mechanical forces applied in distinct directions is mediated by the ability of load-bearing proteins to preferentially maintain physical linkages in certain directions. However, the molecular basis and biological consequences of directional force-sensitive binding remain unclear. Vinculin (Vcn) is a load-bearing linker protein that exhibits directional catch bonding due to interactions between the Vcn tail domain (Vt) and filamentous (F)-actin. We developed a computational approach to predict Vcn residues involved in directional catch bonding and produced a set of associated Vcn variants with unaltered Vt structure, actin binding, or phospholipid interactions. Incorporation of the variants did not affect Vcn activation but reduced Vcn loading and altered exchange dynamics, consistent with the loss of directional catch bonding. Expression of Vcn variants perturbed the coordination of subcellular structures and cell migration, establishing key cellular functions for Vcn directional catch bonding.

Iterative Machine Learning for Classification and Discovery of Single-Molecule Unfolding Trajectories from Force Spectroscopy Data

We report the application of machine learning techniques to expedite classification and analysis of protein unfolding trajectories from force spectroscopy data. Using kernel methods, logistic regression, and triplet loss, we developed a workflow called Forced Unfolding and Supervised Iterative Online (FUSION) learning where a user classifies a small number of repeatable unfolding patterns encoded as images, and a machine is tasked with identifying similar images to classify the remaining data. We tested the workflow using two case studies on a multidomain XMod-Dockerin/Cohesin complex, validating the approach first using synthetic data generated with a Monte Carlo algorithm and then deploying the method on experimental atomic force spectroscopy data. FUSION efficiently separated traces that passed quality filters from unusable ones, classified curves with high accuracy, and identified unfolding pathways that were undetected by the user. This study demonstrates the potential of machine learning to accelerate data analysis and generate new insights in protein biophysics.

Single-Molecule Force Spectroscopy Reveals Cation-π Interactions in Aqueous Media Are Highly Affected by Cation Dehydration

Cation-π interactions underlie many important processes in biology and materials science. However, experimental investigations of cation-π interactions in aqueous media remain challenging. Here, we studied the cation-π binding strength and mechanism by pulling two hydrophobic polymers with distinct cation binding properties, i.e., poly-pentafluorostyrene and polystyrene, in aqueous media using single-molecule force spectroscopy and nuclear magnetic resonance measurement. We found that the interaction strengths linearly depend on the cation concentrations, following the order of Li^{+}<NH_{4}^{+}<Na^{+}<K^{+}. The binding energies are 0.03-0.23  kJ mol^{-1} M^{-1}. This order is distinct from the strength of cation-π interactions in gas phase and may be caused by the different dehydration ability of the cations. Taken together, our method provides a unique perspective to investigate cation-π interactions under physiologically relevant conditions.

Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator

Yeast surface display is a valuable tool for protein engineering and directed evolution; however, significant variability in the copy number (i.e., avidity) of displayed variants on the yeast cell wall complicates screening and selection campaigns. Here, we report an engineered titratable display platform that modulates the avidity of Aga2-fusion proteins on the yeast cell wall dependent on the concentration of the anhydrotetracycline (aTc) inducer. Our design is based on a genomic Aga1 gene copy and an episomal Aga2-fusion construct both under the control of an aTc-dependent transcriptional regulator that enables stoichiometric and titratable expression, secretion, and display of Aga2-fusion proteins. We demonstrate tunable display levels over 2-3 orders of magnitude for various model proteins, including glucose oxidase enzyme variants, mechanostable dockerin-binding domains, and anti-PDL1 affibody domains. By regulating the copy number of displayed proteins, we demonstrate the effects of titratable avidity levels on several specific phenotypic activities, including enzyme activity and cell adhesion to surfaces under shear flow. Finally, we show that titrating down the display level allows yeast-based binding affinity measurements to be performed in a regime that avoids ligand depletion effects while maintaining small sample volumes, avoiding a well-known artifact in yeast-based binding assays. The ability to titrate the multivalency of proteins on the yeast cell wall through simple inducer control will benefit protein engineering and directed evolution methodology relying on yeast display for broad classes of therapeutic and diagnostic proteins of interest.

May the force be with you: The role of hyper-mechanostability of the bone sialoprotein binding protein during early stages of Staphylococci infections

The bone sialoprotein-binding protein (Bbp) is a mechanoactive MSCRAMM protein expressed on the surface of Staphylococcus aureus that mediates adherence of the bacterium to fibrinogen-α (Fgα), a component of the bone and dentine extracellular matrix of the host cell. Mechanoactive proteins like Bbp have key roles in several physiological and pathological processes. Particularly, the Bbp: Fgα interaction is important in the formation of biofilms, an important virulence factor of pathogenic bacteria. Here, we investigated the mechanostability of the Bbp: Fgα complex using in silico single-molecule force spectroscopy (SMFS), in an approach that combines results from all-atom and coarse-grained steered molecular dynamics (SMD) simulations. Our results show that Bbp is the most mechanostable MSCRAMM investigated thus far, reaching rupture forces beyond the 2 nN range in typical experimental SMFS pulling rates. Our results show that high force-loads, which are common during initial stages of bacterial infection, stabilize the interconnection between the protein's amino acids, making the protein more "rigid". Our data offer new insights that are crucial on the development of novel anti-adhesion strategies.

Understanding the microbial fibre degrading communities & processes in the equine gut

The equine gastrointestinal tract is a self-sufficient fermentation system, housing a complex microbial consortium that acts synergistically and independently to break down complex lignocellulolytic material that enters the equine gut. Despite being strict herbivores, equids such as horses and zebras lack the diversity of enzymes needed to completely break down plant tissue, instead relying on their resident microbes to carry out fibrolysis to yield vital energy sources such as short chain fatty acids. The bulk of equine digestion occurs in the large intestine, where digesta is fermented for 36-48 h through the synergistic activities of bacteria, fungi, and methanogenic archaea. Anaerobic gut dwelling bacteria and fungi break down complex plant polysaccharides through combined mechanical and enzymatic strategies, and notably possess some of the greatest diversity and repertoire of carbohydrate active enzymes among characterized microbes. In addition to the production of enzymes, some equid-isolated anaerobic fungi and bacteria have been shown to possess cellulosomes, powerful multi-enzyme complexes that further enhance break down. The activities of both anaerobic fungi and bacteria are further facilitated by facultatively aerobic yeasts and methanogenic archaea, who maintain an optimal environment for fibrolytic organisms, ultimately leading to increased fibrolytic microbial counts and heightened enzymatic activity. The unique interactions within the equine gut as well as the novel species and powerful mechanisms employed by these microbes makes the equine gut a valuable ecosystem to study fibrolytic functions within complex communities. This review outlines the primary taxa involved in fibre break down within the equine gut and further illuminates the enzymatic strategies and metabolic pathways used by these microbes. We discuss current methods used in analysing fibrolytic functions in complex microbial communities and propose a shift towards the development of functional assays to deepen our understanding of this unique ecosystem.

Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections

The unbinding pathway of a protein complex can vary significantly depending on biochemical and mechanical factors. Under mechanical stress, a complex may dissociate through a mechanism different from that used in simple thermal dissociation, leading to different dissociation rates under shear force and thermal dissociation. This is a well-known phenomenon studied in biomechanics whose molecular and atomic details are still elusive. A particularly interesting case is the complex formed by bacterial adhesins with their human peptide target. These protein interactions have a force resilience equivalent to those of covalent bonds, an order of magnitude stronger than the widely used streptavidin:biotin complex, while having an ordinary affinity, much lower than that of streptavidin:biotin. Here, in an in silico single-molecule force spectroscopy approach, we use molecular dynamics simulations to investigate the dissociation mechanism of adhesin/peptide complexes. We show how the Staphylococcus epidermidis adhesin SdrG uses a catch-bond mechanism to increase complex stability with increasing mechanical stress. While allowing for thermal dissociation in a low-force regime, an entirely different mechanical dissociation path emerges in a high-force regime, revealing an intricate mechanism that does not depend on the peptide's amino acid sequence. Using a dynamic network analysis approach, we identified key amino acid contacts that describe the mechanics of this complex, revealing differences in dynamics that hinder thermal dissociation and establish the mechanical dissociation path. We then validate the information content of the selected amino acid contacts using their dynamics to successfully predict the rupture forces for this complex through a machine learning model.

Extensible membrane nanotubules mediate attachment of Trypanosoma cruzi epimastigotes under flow

Trypanosoma cruzi is the etiological agent of Chagas disease, an important cause of infectious chronic myocardiopathy in Latin America. The life cycle of the parasite involves two main hosts: a triatomine (arthropod hematophagous vector) and a mammal. Epimastigotes are flagellated forms inside the triatomine gut; they mature in its intestine into metacyclic trypomastigotes, the infective form for humans. Parasites attach despite the shear stress generated by fluid flow in the intestines of the host, but little is known about the mechanisms that stabilize attachment in these conditions. Here, we describe the effect of varying levels of shear stress on attached T. cruzi epimastigotes using a parallel plate flow chamber. When flow is applied, parasites are partially dragged but maintain a connection to the surface via ~40 nm wide filaments (nanotubules) and the activity of flagella is reduced. When flow stops, parasites return near their original position and flagellar motion resumes. Nanotubule elongation increases with increasing shear stress and is consistent with a model of membrane tether extension under force. Fluorescent probes used to confirm membrane composition also show micron-wide anchoring pads at the distal end of the nanotubules. Multiple tethering accounts for more resistance to large shear stresses and for reduced flagellar movement when flow is stopped. The formation of membrane nanotubules is a possible mechanism to enhance adherence to host cells under shear stress, favoring the continuity of the parasite´s life cycle.

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.

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.

Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.

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.

Histidine-Specific Bioconjugation for Single-Molecule Force Spectroscopy

Atomic force microscopy (AFM) based single-molecule force spectroscopy (SMFS) is a powerful tool to study the mechanical properties of proteins. In these experiments, site-specific immobilization of proteins is critical, as the tether determines the direction and amplitude of forces applied to the protein of interest. However, existing methods are mainly based on thiol chemistry or specific protein tags, which cannot meet the need of many challenging experiments. Here, we developed a histidine-specific phosphorylation strategy to covalently anchor proteins to an AFM cantilever tip or the substrate via their histidine tag or surface-exposed histidine residues. The formed covalent linkage was mechanically stable with rupture forces of over 1.3 nN. This protein immobilization method considerably improved the pickup rate and data quality of SMFS experiments. We further demonstrated the use of this method to explore the pulling-direction-dependent mechanical stability of green fluorescent protein and the unfolding of the membrane protein archaerhodopsin-3.

Measurement of Interfacial Adhesion Force with a 3D-Printed Fiber-Tip Microforce Sensor

With the current trend of device miniaturization, the measurement and control of interfacial adhesion forces are increasingly important in fields such as biomechanics and cell biology. However, conventional fiber optic force sensors with high Young’s modulus (>70 GPa) are usually unable to measure adhesion forces on the micro- or nano-Newton level on the surface of micro/nanoscale structures. Here, we demonstrate a method for interfacial adhesion force measurement in micro/nanoscale structures using a fiber-tip microforce sensor (FTMS). The FTMS, with microforce sensitivity of 1.05 nm/μN and force resolution of up to 19 nN, is fabricated using femtosecond laser two-photon polymerization nanolithography to program a clamped-beam probe on the end face of a single-mode fiber. As a typical verification test, the micronewton-level contact and noncontact adhesion forces on the surfaces of hydrogels were measured by FTMS. In addition, the noncontact adhesion of human hair was successfully measured with the sensor.

Kinetics and mechanism analysis on self-decay of airborne bacteria:biological and physical decay under different temperature

Bioaerosol as an important medium has aroused widespread concern on its potential hazards in disease transmission and environment biosafety. However, little is known about the duration and self-decay of airborne bacteria in the atmosphere environment. Further, the self-decay process is proposed to include biological-decay and physical-decay. At present, there are many reports on the bacteria apoptosis mechanism and airborne particle migration. However, few studies focus on self-decay during the physical movement of airborne bacteria. The present study investigated self-decay laws and efficiencies of airborne bacteria in the sealed reactor under room temperature (18 ± 2 °C, RT) and low temperature (3 ± 2 °C, LT). The self-decay rate constants of 0.0089, 0.0133, 0.0092, and 0.0122 min^-1 were obtained under RT-E. coli, LT-E. coli, RT-S. aureus and LT-S. aureus, respectively. There was no significant difference between the self-decay efficiency of gram-negative and gram-positive bacteria under the same conditions. Nevertheless, gram-negative bacteria were more sensitive to temperature change compared with gram-positive bacteria, where the self-decay efficiency of gram-negative under LT was 49% higher than that under RT, and the value of gram-positive was 32% at the same condition. Furthermore, the laws of biological-decay and physical-decay conformed to the first-order kinetic model by theoretical derivation. Biological-decay accounted for 59.5% at RT and 88.5% at LT among self-decay, which is mainly caused by energy absorption, environmental stress, and bacterial structure changes. Physical-decay mainly caused by gravity settlement accounting for 40% at RT and 10% at LT among self-decay, approximately. Meanwhile, the influence of environmental factors on self-decay was mainly reflected in the biological-decay process. Overall, it is of great significance for clarifying the changing laws of bioaerosol and controlling the transmission of airborne bacteria.

Intramolecular covalent bonds in Gram-positive bacterial surface proteins

Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.

Optimal Sacrificial Domains in Mechanical Polyproteins: S. epidermidis Adhesins Are Tuned for Work Dissipation

The opportunistic pathogen Staphylococcus epidermidis utilizes a multidomain surface adhesin protein to bind host components and adhere to tissues. While it is known that the interaction between the SdrG receptor and its fibrinopeptide target (FgB) is exceptionally mechanostable (∼2 nN), the influence of downstream B domains (B1 and B2) is unclear. Here, we studied the mechanical relationships between folded B domains and the SdrG receptor bound to FgB. We used protein engineering, single-molecule force spectroscopy (SMFS) with an atomic force microscope (AFM), and Monte Carlo simulations to understand how the mechanical properties of folded sacrificial domains, in general, can be optimally tuned to match the stability of a receptor-ligand complex. Analogous to macroscopic suspension systems, sacrificial shock absorber domains should neither be too weak nor too strong to optimally dissipate mechanical energy. We built artificial molecular shock absorber systems based on the nanobody (VHH) scaffold and studied the competition between domain unfolding and receptor unbinding. We quantitatively determined the optimal stability of shock absorbers that maximizes work dissipation on average for a given receptor and found that natural sacrificial domains from pathogenic S. epidermidis and Clostridium perfringens adhesins exhibit stabilities at or near this optimum within a specific range of loading rates. These findings demonstrate how tuning the stability of sacrificial domains in adhesive polyproteins can be used to maximize mechanical work dissipation and serve as an adhesion strategy by bacteria.

Recombinant FimH Adhesin Demonstrates How the Allosteric Catch Bond Mechanism Can Support Fast and Strong Bacterial Attachment in the Absence of Shear

The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an 'inactive' conformation with fast binding to mannose to an 'active' conformation with slow detachment from mannose. Because mechanical tensile force favors separation of the domains and, thus, FimH activation, it has been thought that the catch bonds can only be manifested in a fluidic shear-dependent mode of adhesion. Here, we used recombinant FimH variants with a weakened inter-domain interaction and show that a fast and sustained allosteric activation of FimH can also occur under static, non-shear conditions. Moreover, it appears that lectin domain conformational activation happens intrinsically at a constant rate, independently from its ability to interact with the pilin domain or mannose. However, the latter two factors control the rate of FimH deactivation. Thus, the allosteric catch bond mechanism can be a much broader phenomenon involved in both fast and strong cell-pathogen attachments under a broad range of hydrodynamic conditions. This concept that allostery can enable more effective receptor-ligand interactions is fundamentally different from the conventional wisdom that allostery provides a mechanism to turn binding off under specific conditions.

Single-Chain Mechanical Properties of Gelatin: A Single-Molecule Study

Gelatin is an important natural biological resource with a wide range of applications in the pharmaceutical, industrial and food industries. We investigated the single-chain behaviors of gelatin by atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS), and found that gelatin exists as long chains by fitting with the M-FJC model. By comparing the single-chain elasticity in a nonpolar organic solvent (nonane) and DI water, it was surprising to find that there was almost no difference in the single-chain elasticity of gelatin in nonane and DI water. Considering the specificity of gelatin solubility and the solvent size effect of nonane molecules, when a single gelatin chain is pulled into loose nonane, dehydration does not occur due to strong binding water interactions. Gelatin chains can only interact with water molecules at high temperatures; therefore, no further interaction of single gelatin chains with water molecules occurred at the experimental temperature. This eventually led to almost no difference in the single-chain F-E curves under the two conditions. It is expected that our study will enable the deep exploration of the interaction between water molecules and gelatin and provide a theoretical basis and experimental foundation for the design of gelatin-based materials with more functionalities.

Role of Cel5H protein surface amino acids in binding with clay minerals and measurements of its forces

Our previous study on the binding activity between Cel5H and clay minerals showed highest binding efficiency among other cellulase enzymes cloned. Here, based on previous studies, we hypothesized that the positive amino acids on the surface of Cel5H protein may play an important role in binding to clay surfaces. To examine this, protein sequences of Bacillus licheniformis Cel5H (BlCel5H) and Paenibacillus polymyxa Cel5A (PpCel5A) were analyzed and then selected amino acids were mutated. These mutated proteins were investigated for binding activity and force measurement via atomic force microscopy (AFM). A total of seven amino acids which are only present in BlCel5H but not in PpCel5A were selected for mutational studies and the positive residues which are present in both were omitted. Of the seven selected surface lysine residues, only three mutants K196A(M2), K54A(M3) and K157T(M4) showed 12%, 7% and 8% less clay mineral binding ability, respectively compared with wild-type. The probable reason why other mutants did not show altered binding efficiency might be due to relative location of amino acids on the protein surface. Meanwhile, measurement of adhesion forces on mica sheets showed a well-defined maximum at 69 ± 19 pN for wild-type, 58 ± 19 pN for M2, 53 ± 19 pN for M3, and 49 ± 19 pN for M4 proteins. Hence, our results demonstrated that relative location of surface amino acids of Cel5H protein especially positive charged amino acids are important in the process of clay mineral-protein binding interaction through electrostatic exchange of charges.

Enzymatic Protein-Protein Conjugation through Internal Site Verified at the Single-Molecule Level

Enzymes are widely used for protein ligation because of their efficient and site-specific connections under mild conditions. However, many enzymatic ligations are restricted to connections between protein termini while protein-protein conjugation at a specific internal site is limited. Previous work has found that Sortase A (SrtA) conjugates small molecules/peptides to a pilin protein at an internal lysine site via an isopeptide bond. Herein, we apply this noncanonical ligation property of SrtA for protein-protein conjugation at a designed YPKH site. Both a small protein domain, I27, and a large protein, GFP, were ligated at the designed internal site. Moreover, besides characterization by classic methods at the ensemble level, the specific ligation site at the interior YPKH motif is unambiguously verified by atomic force microscopy-based single-molecule force spectroscopy, showing the characteristic unfolding signature at the single-molecule level. Finally, steered molecular dynamics simulations also agreed with the results.

An ester bond underlies the mechanical strength of a pathogen surface protein

Gram-positive bacteria can resist large mechanical perturbations during their invasion and colonization by secreting various surface proteins with intramolecular isopeptide or ester bonds. Compared to isopeptide bonds, ester bonds are prone to hydrolysis. It remains elusive whether ester bonds can completely block mechanical extension similarly to isopeptide bonds, or whether ester bonds dissipate mechanical energy by bond rupture. Here, we show that an ester-bond containing stalk domain of Cpe0147 is inextensible even at forces > 2 nN. The ester bond locks the structure to a partially unfolded conformation, in which the ester bond remains largely water inaccessible. This allows the ester bond to withstand considerable mechanical forces and in turn prevent complete protein unfolding. However, the protecting effect might be reduced at non-physiological basic pHs or low calcium concentrations due to destabilizing the protein structures. Inspired by this design principle, we engineer a disulfide mutant resistant to mechanical unfolding under reducing conditions.

Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.

Biophysical determinants of biofilm formation in the gut

The gastrointestinal (GI) tract harbors the most complex microbial ecosystem in the human body. The mucosal layer that covers the GI tract serves as a polymer-based defensive barrier that prevents the microbiome from reaching the epithelium and disseminating inside the body. Colonization of the mucus may result in the formation of structured polymicrobial communities or biofilms, a hallmark in pathologies such as colorectal cancer, inflammatory bowel disease, and chronic gut wounds. However, the mechanisms by which multispecies biofilms establish on the gut mucosa is unknown. Whether mucus-associated biofilms exist as part of a healthy mucosal barrier is still debated. Here, we discuss the impact that diet and microbial-derived polymers has on mucus structure and microcolony formation and highlight relevant biophysical forces that further shape nascent biofilms.

Peak force tapping atomic force microscopy for advancing cell and molecular biology

The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.

AFM in cellular and molecular microbiology

The unique capabilities of the atomic force microscope (AFM), including super-resolution imaging, piconewton force-sensitivity, nanomanipulation and ability to work under physiological conditions, have offered exciting avenues for cellular and molecular biology research. AFM imaging has helped unravel the fine architectures of microbial cell envelopes at the nanoscale, and how these are altered by antimicrobial treatment. Nanomechanical measurements have shed new light on the elasticity, tensile strength and turgor pressure of single cells. Single-molecule and single-cell force spectroscopy experiments have revealed the forces and dynamics of receptor-ligand interactions, the nanoscale distribution of receptors on the cell surface and the elasticity and adhesiveness of bacterial pili. Importantly, recent force spectroscopy studies have demonstrated that extremely stable bonds are formed between bacterial adhesins and their cognate ligands, originating from a catch bond behaviour allowing the pathogen to reinforce adhesion under shear or tensile stress. Here, we survey how the versatility of AFM has enabled addressing crucial questions in microbiology, with emphasis on bacterial pathogens. TAKE AWAYS: AFM topographic imaging unravels the ultrastructure of bacterial envelopes. Nanomechanical mapping shows what makes cell envelopes stiff and resistant to drugs. Force spectroscopy characterises the molecular forces in pathogen adhesion. Stretching pili reveals a wealth of mechanical and adhesive responses.

Stress-Induced Catch-Bonds to Enhance Bacterial Adhesion

Physical forces have a profound influence on bacterial cell physiology and disease. A striking example is the formation of catch-bonds that reinforce under mechanical stress. While mannose-binding by the Escherichia coli FimH adhesin has long been the only thoroughly studied microbial catch-bond, it has recently become clear that proteins from other species, such as staphylococci, are also engaged in such stress-dependent interactions.

Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex

We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.