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.

The biophysics of bacterial infections: Adhesion events in the light of force spectroscopy

Bacterial infections are the most eminent public health challenge of the 21st century. The primary step leading to infection is bacterial adhesion to the surface of host cells or medical devices, which is mediated by a multitude of molecular interactions. At the interface of life sciences and physics, last years advances in atomic force microscopy (AFM)-based force spectroscopy techniques have made possible to measure the forces driving bacteria-cell and bacteria-materials interactions on a single molecule/cell basis (single molecule/cell force spectroscopy). Among the bacteria-(bio)materials surface interactions, the life-threatening infections associated to medical devices involving Staphylococcus aureus and Escherichia coli are the most eminent. On the other hand, Pseudomonas aeruginosa binding to the pulmonary and urinary tract or the Helicobacter pylori binding to the gastric mucosa, are classical examples of bacteria-host cell interactions that end in serious infections. As we approach the end of the antibiotic era, acquisition of a deeper knowledge of the fundamental forces involved in bacteria - host cells/(bio)materials surface adhesion is crucial for the identification of new ligand-binding events and its assessment as novel targets for alternative anti-infective therapies. This article aims to highlight the potential of AFM-based force spectroscopy for new targeted therapies development against bacterial infections in which adhesion plays a pivotal role and does not aim to be an extensive overview on the AFM technical capabilities and theory of single molecule force spectroscopy.

Bacterial adhesion to collagens: implications for biofilm formation and disease progression in the oral cavity

Collagen is the most abundant structural protein in the body and the main component of the extracellular matrix of most tissues, including dentine and periodontal tissues. Despite the well-characterized role of collagen and specifically type-I collagen, as a ligand for host cells, its role as a substrate for bacterial adhesion and biofilm formation is less explored. Therefore, the purpose of this review is to discuss recent findings regarding the adhesion of oral bacteria to collagen surfaces and its role in the progression and severity of oral and systemic diseases. Initial oral colonizers such as streptococci have evolved collagen-binding proteins (cbp) that are important for the colonization of dentine and periodontal tissues. Also, periodontal pathogens such as Porphyromonas gingivalis and Tannerella forsythia utilise cbps for tissue sensing and subsequent invasion. The implications of bacteria-collagen coupling in the context of collagen biomaterials and regenerative dentistry approaches are also addressed. Furthermore, the importance of interdisciplinary techniques such as atomic force microscopy for the nanocharacterization of bacteria-collagen interactions is also considered. Overall, understanding the process of oral bacterial adhesion onto collagen is important for developing future therapeutic approaches against oral and systemic diseases, by modulating the early stages of biofilm formation.

Surface Proteins of Staphylococcus epidermidis

Staphylococcus epidermidis is a ubiquitous commensal of human skin. The widespread use of indwelling medical devices in modern medicine provides an opportunity for it to cause infections. Disease causing isolates can come from many different genetic backgrounds. Multiply antibiotic resistant strains have spread globally. S. epidermidis has a smaller repertoire of cell wall anchored (CWA) surface proteins than Staphylococcus aureus. Nevertheless, these CWA proteins promote adhesion to components of the extracellular matrix including collagen, fibrinogen, and fibronectin and contribute to the formation of biofilm. The A domain of the accumulation associated protein Aap can promote adhesion to unconditioned biomaterial but must be removed proteolytically to allow accumulation to proceed by homophilic Zn²⁺-dependent interactions. Mature biofilm contains amyloid structures formed by Aap and the small basic protein (Sbp). The latter contributes to the integrity of both protein and polysaccharide biofilm matrices. Several other CWA proteins can also promote S. epidermidis biofilm formation.

Binding Strength of Gram-Positive Bacterial Adhesins

Bacterial pathogens are equipped with specialized surface-exposed proteins that bind strongly to ligands on host tissues and biomaterials. These adhesins play critical roles during infection, especially during the early step of adhesion where the cells are exposed to physical stress. Recent single-molecule experiments have shown that staphylococci interact with their ligands through a wide diversity of mechanosensitive molecular mechanisms. Adhesin-ligand interactions are activated by tensile force and can be ten times stronger than classical non-covalent biological bonds. Overall these studies demonstrate that Gram-positive adhesins feature unusual stress-dependent molecular interactions, which play essential roles during bacterial colonization and dissemination. With an increasing prevalence of multidrug resistant infections caused by Staphylococcus aureus and Staphylococcus epidermidis, chemotherapeutic targeting of adhesins offers an innovative alternative to antibiotics.

Microbial adhesion and ultrastructure from the single-molecule to the single-cell levels by Atomic Force Microscopy

In the last decades, atomic force microscopy (AFM) has evolved towards an accurate and lasting tool to study the surface of living cells in physiological conditions. Through imaging, single-molecule force spectroscopy and single-cell force spectroscopy modes, AFM allows to decipher at multiple scales the morphology and the molecular interactions taking place at the cell surface. Applied to microbiology, these approaches have been used to elucidate biophysical properties of biomolecules and to directly link the molecular structures to their function. In this review, we describe the main methods developed for AFM-based microbial surface analysis that we illustrate with examples of molecular mechanisms unravelled with unprecedented resolution.

The MSCRAMM Family of Cell-Wall-Anchored Surface Proteins of Gram-Positive Cocci

The microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) are a family of proteins that are defined by the presence of two adjacent IgG-like folded subdomains. These promote binding to ligands by mechanisms that involve major conformational changes exemplified by the binding to fibrinogen by the 'dock-lock-latch' mechanism or to collagen by the 'collagen hug'. Clumping factors A and B are two such MSCRAMMs that have several important roles in the pathogenesis of Staphylococcus aureus infections. MSCRAMM architecture, ligand binding, and roles in infection and colonization are examined with a focus on recent developments with clumping factors.

Surface Proteins of Staphylococcus aureus

The surface of Staphylococcus aureus is decorated with over 20 proteins that are covalently anchored to peptidoglycan by the action of sortase A. These cell wall-anchored (CWA) proteins can be classified into several structural and functional groups. The largest is the MSCRAMM family, which is characterized by tandemly repeated IgG-like folded domains that bind peptide ligands by the dock lock latch mechanism or the collagen triple helix by the collagen hug. Several CWA proteins comprise modules that have different functions, and some individual domains can bind different ligands, sometimes by different mechanisms. For example, the N-terminus of the fibronectin binding proteins comprises an MSCRAMM domain which binds several ligands, while the C-terminus is composed of tandem fibronectin binding repeats. Surface proteins promote adhesion to host cells and tissue, including components of the extracellular matrix, contribute to biofilm formation by stimulating attachment to the host or indwelling medical devices followed by cell-cell accumulation via homophilic interactions between proteins on neighboring cells, help bacteria evade host innate immune responses, participate in iron acquisition from host hemoglobin, and trigger invasion of bacteria into cells that are not normally phagocytic. The study of genetically manipulated strains using animal infection models has shown that many CWA proteins contribute to pathogenesis. Fragments of CWA proteins have the potential to be used in multicomponent vaccines to prevent S. aureus infections.

Polymers and biopolymers at interfaces

This review updates recent progress in the understanding of the behaviour of polymers at surfaces and interfaces, highlighting examples in the areas of wetting, dewetting, crystallization, and 'smart' materials. Recent developments in analysis tools have yielded a large increase in the study of biological systems, and some of these will also be discussed, focussing on areas where surfaces are important. These areas include molecular binding events and protein adsorption as well as the mapping of the surfaces of cells. Important techniques commonly used for the analysis of surfaces and interfaces are discussed separately to aid the understanding of their application.

The Surface Protein SdrF Mediates Staphylococcus epidermidis Adherence to Keratin

Background

Staphylococcus epidermidis, a major component of skin flora, is an opportunist, often causing prosthetic device infections. A family of structurally related proteins mediates staphylococcal attachment to host tissues, contributing to the success of S. epidermidis as a pathogen. We examined the ability of the surface protein SdrF to adhere to keratin, a major molecule expressed on the skin surface.

Methods

A heterologous Lactococcus lactis expression system was used to express SdrF and its ligand-binding domains. Adherence to keratin types 1 and 10, human foreskin keratinocytes, and nasal epithelial cells was examined.

Results

SdrF bound human keratins 1 and 10 and adhered to keratinocytes and epithelial cells. Binding involved both the A and B domains. Anti-SdrF antibodies reduced adherence of S. epidermidis to keratin and keratinocytes. RNA interference reduced keratin synthesis in keratinocytes and, as a result, SdrF adherence. Direct force measurements using atomic force microscopy showed that SdrF mediates bacterial adhesion to keratin 10 through strong and weak bonds involving the A and B regions; strong adhesion was primarily mediated by the A region.

Conclusions

These studies demonstrate that SdrF mediates adherence to human keratin and suggest that SdrF may facilitate S. epidermidis colonization of the skin.

Gelatin- and starch-based hydrogels. Part A: Hydrogel development, characterization and coating

The present work aims at constructing the ideal scaffold matrix of which the physico-chemical properties can be altered according to the targeted tissue regeneration application. Ideally, this scaffold should resemble the natural extracellular matrix (ECM) as close as possible both in terms of chemical composition and mechanical properties. Therefore, hydrogel films were developed consisting of methacrylamide-modified gelatin and starch-pentenoate building blocks because the ECM can be considered as a crosslinked hydrogel network consisting of both polysaccharides and structural, signaling and cell-adhesive proteins. For the gelatin hydrogels, three different substitution degrees were evaluated including 31%, 72% and 95%. A substitution degree of 32% was applied for the starch-pentenoate building block. Pure gelatin hydrogels films as well as interpenetrating networks with gelatin and starch were developed. Subsequently, these films were characterized using gel fraction and swelling experiments, high resolution-magic angle spinning (1)H NMR spectroscopy, rheology, infrared mapping and atomic force microscopy. The results indicate that both the mechanical properties and the swelling extent of the developed hydrogel films can be controlled by varying the chemical composition and the degree of substitution of the methacrylamide-modified gelatin applied. The storage moduli of the developed materials ranged between 14 and 63kPa. Phase separation was observed for the IPNs for which separated starch domains could be distinguished located in the surrounding gelatin matrix. Furthermore, we evaluated the affinity of aggrecan for gelatin by atomic force microscopy and radiolabeling experiments. We found that aggrecan can be applied as a bioactive coating for gelatin hydrogels by a straightforward physisorption procedure. Thus, we achieved distinct fine-tuning of the physico-chemical properties of these hydrogels which render them promising candidates for tissue engineering approaches.

Optical and force nanoscopy in microbiology

Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.

Mechanical Strength and Inhibition of the Staphylococcus aureus Collagen-Binding Protein Cna

The bacterial pathogen Staphylococcus aureus expresses a variety of cell surface adhesion proteins that bind to host extracellular matrix proteins. Among these, the collagen (Cn)-binding protein Cna plays important roles in bacterium-host adherence and in immune evasion. While it is well established that the A region of Cna mediates ligand binding, whether the repetitive B region has a dedicated function is not known. Here, we report the direct measurement of the mechanical strength of Cna-Cn bonds on living bacteria, and we quantify the antiadhesion activity of monoclonal antibodies (MAbs) targeting this interaction. We demonstrate that the strength of Cna-Cn bonds in vivo is very strong (~1.2 nN), consistent with the high-affinity "collagen hug" mechanism. The B region is required for strong ligand binding and has been found to function as a spring capable of sustaining high forces. This previously undescribed mechanical response of the B region is of biological significance as it provides a means to project the A region away from the bacterial surface and to maintain bacterial adhesion under conditions of high forces. We further quantified the antiadhesion activity of MAbs raised against the A region of Cna directly on living bacteria without the need for labeling or purification. Some MAbs are more efficient in blocking single-cell adhesion, suggesting that they act as competitive inhibitors that bind Cna residues directly involved in ligand binding. This report highlights the role of protein mechanics in activating the function of staphylococcal adhesion proteins and emphasizes the potential of antibodies to prevent staphylococcal adhesion and biofilm formation.

IMPORTANCE

Cna is a collagen (Cn)-binding protein from Staphylococcus aureus that is involved in pathogenesis. Currently, we know little about the functional role of the repetitive B region of the protein. Here, we unravel the mechanical strength of Cna in living bacteria. We show that single Cna-Cn bonds are very strong, reflecting high-affinity binding by the collagen hug mechanism. We discovered that the B region behaves as a nanospring capable of sustaining high forces. This unanticipated mechanical response, not previously described for any staphylococcal adhesin, favors a model in which the B region has a mechanical function that is essential for strong ligand binding. Finally, we assess the antiadhesion activity of monoclonal antibodies against Cna, suggesting that they could be used to inhibit S. aureus adhesion.

Forces between Staphylococcus aureus and human skin

Characterization of the molecular interactions between microbial cells and the human skin is essential to understand the functions of the skin microbiome, and to gain insight into the molecular basis of skin disorders. Although various molecular approaches have been used to study microbe-skin interactions, the underlying molecular forces were not accessible to study. Here we present a novel atomic force microscopy approach to localize and quantify the nanoscale interaction forces between the bacterial pathogen Staphylococcus aureus and human skin. A method combining nanoscale multiparametric imaging with single bacterial probes is developed to map simultaneously the topography and bacterial-binding properties of corneocytes at high spatiotemporal resolution. Further quantification of the forces between bacteria and corneocytes is achieved using single-cell force spectroscopy. The results show that the S. aureus-skin adhesion is strong (∼500 pN) and originates from multiple specific bonds between adhesins on the bacterial cell surface and target ligands on the corneocyte surface. Applicable to a wide variety of microbes and skin cells, our methodology offers exciting prospects for understanding the molecular details of skin colonization and infection.