Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations

Effect of Exogenous Glucose on Molecular Transport through Bacterial Membranes Studied by Second Harmonic Light Scattering

Recent studies revealed that exogenous glucose increases the efficacy of aminoglycosides in eliminating bacterial persister cells. It was speculated that this increased antimicrobial efficacy is induced by glucose-facilitated uptake of the antibiotics. Here, we examine this hypothesis by using second-harmonic light scattering to time-resolve the transport of an antimicrobial quaternary ammonium compound (QAC), malachite green, across the membranes of living Escherichia coli (E. coli) in the presence of glucose. The results show that when the glucose concentration increased from 0 to 100 μM, the QAC transport rate constant across the cytoplasmic membrane of E. coli increased by 3.6 times. Further increase of glucose concentration into the millimolar range, however, does not further enhance the transport rate constant. Conversely, a study of QAC transport across the protein-free membrane of liposomes (constructed from the polar lipid extract of E. coli) indicates that the glucose-induced enhancement in membrane transport in E. coli is mediated by protein transporters. Cell viability experiments show that low concentration of exogenous glucose enhances the QAC efficacy in eliminating E. coli. The loss of viability of the bacterial cells in the presence of the QAC at minimum inhibitory concentration increased dramatically when glucose concentration increased from 0 to 100 μM but increasing the glucose concentration up to 1 mM did not further enhance the antimicrobial efficacy. This behavior coincides with the observed increase in QAC transport rate constant as a function of glucose concentration. These observations reveal a novel antimicrobial strategy in which low concentration glucose enhances the uptake of antimicrobials into the bacteria, thereby improving antimicrobial efficacy.

Thicket and Mesh: How the Outer Membrane Can Resist Tension Imposed by the Cell Wall

The cell envelope of Gram-negative bacteria is composed of an outer membrane (OM) and an inner membrane (IM) and a peptidoglycan cell wall (CW) between them. Combined with Braun's lipoprotein (Lpp), which connects the OM and the CW, and numerous membrane proteins that exist in both OM and IM, the cell envelope creates a mechanically stable environment that resists various physical and chemical perturbations to the cell, including turgor pressure caused by the solute concentration difference between the cytoplasm of the cell and the extracellular environment. Previous computational studies have explored how individual components (OM, IM, and CW) can resist turgor pressure although combinations of them have been less well studied. To that end, we constructed multiple OM-CW systems, including the Lpp connections with the CW under increasing degrees of strain. The results show that the OM can effectively resist the tension imposed by the CW, shrinking by only 3-5% in area even when the CW is stretched to 2.5× its relaxed area. The area expansion modulus of the system increases with increasing CW strain, although the OM remains a significant contributor to the envelope's mechanical stability. Additionally, we find that when the protein TolC is embedded in the OM, its stiffness increases.

Determining the Young's Modulus of the Bacterial Cell Envelope

Bacteria experience substantial physical forces in their natural environment, including forces caused by osmotic pressure, growth in constrained spaces, and fluid shear. The cell envelope is the primary load-carrying structure of bacteria, but the mechanical properties of the cell envelope are poorly understood; reports of Young's modulus of the cell envelope of Escherichia coli range from 2 to 18 MPa. We developed a microfluidic system to apply mechanical loads to hundreds of bacteria at once and demonstrated the utility of the approach for evaluating whole-cell stiffness. Here, we extend this technique to determine Young's modulus of the cell envelope of E. coli and of the pathogens Vibrio cholerae and Staphylococcus aureus. An optimization-based inverse finite element analysis was used to determine the cell envelope Young's modulus from observed deformations. The Young's modulus values of the cell envelope were 2.06 ± 0.04 MPa for E. coli, 0.84 ± 0.02 MPa for E. coli treated with a chemical (A22) known to reduce cell stiffness, 0.12 ± 0.03 MPa for V. cholerae, and 1.52 ± 0.06 MPa for S. aureus (mean ± SD). The microfluidic approach allows examination of hundreds of cells at once and is readily applied to Gram-negative and Gram-positive organisms as well as rod-shaped and cocci cells, allowing further examination of the structural causes behind differences in cell envelope Young's modulus among bacterial species and strains.

Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations

Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.

Insights into the molecular mechanism of yellow cuticle coloration by a chitin-binding carotenoprotein in gregarious locusts

Carotenoids are hydrophobic pigments binding to diverse carotenoproteins, many of which remain unexplored. Focusing on yellow gregarious locusts accumulating cuticular carotenoids, here we use engineered Escherichia coli cells to reconstitute a functional water-soluble β-carotene-binding protein, BBP. HPLC and Raman spectroscopy confirmed that recombinant BBP avidly binds β-carotene, inducing the unusual vibronic structure of its absorbance spectrum, just like native BBP extracted from the locust cuticles. Bound to recombinant BBP, β-carotene exhibits pronounced circular dichroism and allows BBP to withstand heating (T0.5 = 68 °C), detergents and pH variations. Using bacteria producing distinct xanthophylls we demonstrate that, while β-carotene is the preferred carotenoid, BBP can also extract from membranes ketocarotenoids and, very poorly, hydroxycarotenoids. We show that BBP-carotenoid complex reversibly binds to chitin, but not to chitosan, implying the role for chitin acetyl groups in cuticular BBP deposition. Reconstructing such locust coloration mechanism in vitro paves the way for structural studies and BBP applications.

Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli

The outer lipopolysaccharide (LPS) membrane of Gram-negative bacteria forms the main barrier for transport of antimicrobial molecules into the bacterial cell. In this study we develop coarse-grained models for the outer membrane of Escherichia coli in the Martini-3 framework. The coarse-grained model force field was parametrized and validated using all-atom simulations of symmetric membranes of lipid A and rough LPS as well as a complete asymmetric membrane of LPS with the O-antigen. The bonded parameters were obtained using an iterative refinement procedure with target bonded distributions obtained from all-atom simulations. The membrane thickness, area of the LPS, and density distributions for the different regions as well as the water and ion densities in Martini-3 simulations show excellent agreement with the all-atom data. Additionally the solvent accessible surface area for individual molecules in water was found to be in good agreement. The binding of calcium ions with phosphate and carboxylate moieties of LPS is accurately captured in the Martini-3 model, indicative of the integrity of the highly negatively charged LPS molecules in the outer membranes of Gram-negative bacteria. The melting transition of the coarse-grained lipid A membrane model was found to occur between 300 and 310 K, and the model captured variations in area per LPS, order parameter, and membrane thickness across the melting transition. Our study reveals that the proposed Martini-3 models for LPS are able to capture the physicochemical balance of the complex sugar architecture of the outer membrane of Escherichia coli. The coarse-grained models developed in this study would be useful for determining membrane protein interactions and permeation of potential antimicrobials through bacterial membranes at mesoscopic spatial and temporal scales.

Bacillus subtilis YisK possesses oxaloacetate decarboxylase activity and exhibits Mbl-dependent localization

YisK is an uncharacterized protein in Bacillus subtilis previously shown to interact genetically with the elongasome protein Mbl. YisK overexpression leads to cell widening and lysis, phenotypes that are dependent on mbl and suppressed by mbl mutations. In the present work, we characterize YisK's localization, structure, and enzymatic activity. We show that YisK localizes as puncta that depend on Mbl. YisK belongs to the fumarylacetoacetate hydrolase (FAH) superfamily, and crystal structures revealed close structural similarity to two oxaloacetate (OAA) decarboxylases: human mitochondrial FAHD1 and Corynebacterium glutamicum Cg1458. We demonstrate that YisK can also catalyze the decarboxylation of OAA (K m = 134 µM, K cat = 31 min-1). A catalytic dead variant (YisK E148A, E150A) retains wild-type localization and still widens cells following overexpression, indicating these activities are not dependent on YisK catalysis. Conversely, a non-localizing variant (YisK E30A) retains wild-type enzymatic activity in vitro but localizes diffusely and no longer widens cells following overexpression. Together, these results suggest that YisK may be subject to spatial regulation that depends on the cell envelope synthesis machinery. IMPORTANCE The elongasome is a multiprotein complex that guides lengthwise growth in some bacteria. We previously showed that, in B. subtilis, overexpression of an uncharacterized putative enzyme (YisK) perturbed function of the actin-like elongasome protein Mbl. Here, we show that YisK exhibits Mbl-dependent localization. Through biochemical and structural characterization, we demonstrate that, like its mitochondrial homolog FAHD1, YisK can catalyze the decarboxylation of the oxaloacetate to pyruvate and CO2. YisK is the first example of an enzyme implicated in central carbon metabolism with subcellular localization that depends on Mbl.

Molecular Modeling and Simulation of the Mycobacterial Cell Envelope: From Individual Components to Cell Envelope Assemblies

Unlike typical Gram-positive bacteria, the cell envelope of mycobacteria is unique and composed of a mycobacterial outer membrane, also known as the mycomembrane, a peptidoglycan layer, and a mycobacterial inner membrane, which is analogous to that of Gram-negative bacteria. Despite its importance, however, our understanding of this complex cell envelope is rudimentary at best. Thus, molecular modeling and simulation of such an envelope can benefit the scientific community by proposing new hypotheses about the biophysical properties of its different layers. In this Perspective, we present recent advances in molecular modeling and simulation of the mycobacterial cell envelope from individual components to cell envelope assemblies. We also show how modeling other types of cell envelopes, such as that of Escherichia coli, may help modeling part of the mycobacterial envelopes. We hope that the studies presented here are just the beginning of the road and more and more new modeling and simulation studies help us to understand crucial questions related to mycobacteria such as antibiotic resistance or bacterial survival in the host.

Computational microbiology of bacteria: Advancements in molecular dynamics simulations

Microbiology is traditionally considered within the context of wet laboratory methodologies. Computational techniques have a great potential to contribute to microbiology. Here, we describe our loose definition of "computational microbiology" and provide a short survey focused on molecular dynamics simulations of bacterial systems that fall within this definition. It is our contention that increased compositional complexity and realistic levels of molecular crowding within simulated systems are key for bridging the divide between experimental and computational microbiology.

Relationship between the Rod complex and peptidoglycan structure in Escherichia coli

Peptidoglycan for elongation in Escherichia coli is synthesized by the Rod complex, which includes RodZ. Although various mutant strains of the Rod complex have been isolated, the relationship between the activity of the Rod complex and the overall physical and chemical structures of the peptidoglycan have not been reported. We constructed a RodZ mutant, termed RMR, and analyzed the growth rate, morphology, and other characteristics of cells producing the Rod complexes containing RMR. The growth and morphology of RMR cells were abnormal, and we isolated suppressor mutants from RMR cells. Most of the suppressor mutations were found in components of the Rod complex, suggesting that these suppressor mutations increase the integrity and/or the activity of the Rod complex. We purified peptidoglycan from wild-type, RMR, and suppressor mutant cells and observed their structures in detail. We found that the peptidoglycan purified from RMR cells had many large holes and different compositions of muropeptides from those of WT cells. The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure to support the mechanical strength of the cell wall.

Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding

The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.

Molecular Imaging of Isolated Escherichia coli DH5α Peptidoglycan Sacculi Identifies the Mechanism of Action of Cell Wall-Inhibiting Antibiotics

Antibiotic resistance of pathogenic bacteria needs to be urgently addressed by the development of new antibacterial entities. Although the prokaryotic cell wall comprises a valuable target for this purpose, development of novel cell wall-active antibiotics is mostly missing today. This is mainly caused by hindrances in the assessment of isolated enzymes of the co-dependent murein synthesis machineries, e.g., the elongasome and divisome. We therefore present imaging methodologies to evaluate inhibitors of bacterial cell wall synthesis by high-resolution atomic force microscopy on isolated Escherichia coli murein sacculi. With the ability to elucidate the peptidoglycan ultrastructure of E. coli cells, unprecedented molecular insights into the mechanisms of antibiotics were established. The nanoscopic impairments introduced by ampicillin, amoxicillin, and fosfomycin were not only identified by AFM but readily correlated with their known mechanism of action. These valuable in vitro capabilities will facilitate the identification and evaluation of new antibiotic leads in the future.

Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches

The increase of antibiotic-resistant bacterial pathogens has created challenges in treatment and warranted the design of antibiotics against comparatively less exploited targets. The peptidoglycan (PG) biosynthesis delineates unique pathways for the design and development of a novel class of drugs. Mur ligases are an essential component of bacterial cell wall synthesis that play a pivotal role in PG biosynthesis to maintain internal osmotic pressure and cell shape. Inhibition of these enzymes can interrupt bacterial replication and hence, form attractive targets for drug discovery. In the present work, we focused on the PG biosynthesis pathway enzyme, UDP-N-acetylpyruvylglucosamine reductase, from Salmonella enterica serovar Typhi (stMurB). Biophysical characterization of purified StMurB was performed to gauge the molecular interactions and estimate thermodynamic stability for determination of attributes for possible therapeutic intervention. The thermal melting profile of MurB was monitored by circular dichroism and validated through differential scanning calorimetry experiment. Frequently used chemical denaturants, GdmCl and urea, were employed to study the chemical-induced denaturation of stMurB. In the search for natural compound-based inhibitors, against this important drug target, an in silico virtual screening based investigation was conducted with modeled stMurB structure. The three top hits (quercetin, berberine, and scopoletin) returned were validated for complex stability through molecular dynamics simulation. Further, fluorescence binding studies were undertaken for the selected natural compounds with stMurB alone and with NADPH bound form. The compounds scopoletin and berberine, displayed lesser binding to stMurB whereas quercetin exhibited stronger binding affinity than NADPH. This study suggests that quercetin can be evolved as an inhibitor of stMurB enzyme.

A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses

Both Gram-positive and Gram-negative bacteria release nanosized extracellular vesicles called membrane vesicles (MVs, 20-400 nm), which have great potential in various biomedical applications due to their abilities to deliver effector molecules and induce therapeutic responses. To fully utilize bacterial MVs for therapeutic purposes, regulated and enhanced production of MVs would be highly advantageous. In this study, we developed a universal method to enhance MV yields in both G+/G- bacteria through an autonomous controlled peptidoglycan hydrolase (PGase) expression system. A significant increase (9.37-fold) of MV concentration was observed in engineered E. coli Nissle 1917 compared to the wild-type. With the help of this autonomous system, for the first time we experimentally confirmed horizontal gene transfer and nutrient acquisition in a cocultured bacterial consortium. Furthermore, the engineered probiotic E. coli strains with high yield of MVs showed higher activation of the innate immune responses in human embryonic kidney 293T (HEK293T) and human colorectal carcinoma cells (HCT116), thereby demonstrating the great potential of engineering probiotics in immunology and further living therapeutics in humans.

Interactions of Surfactants with the Bacterial Cell Wall and Inner Membrane: Revealing the Link between Aggregation and Antimicrobial Activity

Surfactants with their intrinsic ability to solubilize lipid membranes are widely used as antibacterial agents, and their interactions with the bacterial cell envelope are complicated by their differential aggregation tendencies. We present a combined experimental and molecular dynamics investigation to unravel the molecular basis for the superior antimicrobial activity and faster kill kinetics of shorter-chain fatty acid surfactant, laurate, when compared with the longer-chain surfactants studied in contact time assays with live Escherichia coli (E. coli). From all-atom molecular dynamics simulations, translocation events across peptidoglycan were the highest for laurate followed by sodium dodecyl sulfate, myristate, palmitate, oleate, and stearate. The translocation kinetics were positively correlated with the critical micellar concentration, which determined the free monomer surfactant concentration available for translocation across peptidoglycan. Interestingly, aggregates showed a lower propensity to translocate across the peptidoglycan layer and longer translocation times were observed for oleate, thereby revealing an intrinsic sieving property of the bacterial cell wall. Molecular dynamics simulations with surfactant-incorporated bacterial inner membranes revealed the greatest hydrophobic mismatch and membrane thinning in the presence of laurate when compared with the other surfactants. The enhanced antimicrobial efficacy of laurate over oleate was further verified by experiments with giant unilamellar vesicles, and electroporation molecular dynamics simulations revealed greater inner membrane poration tendency in the presence of laurate when compared with the longer-chain surfactants. Our study provides molecular insights into surfactant translocation across peptidoglycan and chain length-induced structural disruption of the inner membrane, which correlate with contact time kill efficacies observed as a function of chain length with E. coli. The insights gained from our study uncover unexplored barrier properties of the bacterial cell envelope to rationalize the development of antimicrobial formulations and therapeutics.

Differentiating interactions of antimicrobials with Gram-negative and Gram-positive bacterial cell walls using molecular dynamics simulations

Developing molecular models to capture the complex physicochemical architecture of the bacterial cell wall and to study the interaction with antibacterial molecules is an important aspect of assessing and developing novel antimicrobial molecules. We carried out molecular dynamics simulations using an atomistic model of peptidoglycan to represent the architecture for Gram-positive S. aureus. The model is developed to capture various structural features of the Staphylococcal cell wall, such as the peptide orientation, area per disaccharide, glycan length distribution, cross-linking, and pore size. A comparison of the cell wall density and electrostatic potentials is made with a previously developed cell wall model of Gram-negative bacteria, E. coli, and properties for both single and multilayered structures of the Staphylococcal cell wall are studied. We investigated the interactions of the antimicrobial peptide melittin with peptidoglycan structures. The depth of melittin binding to peptidoglycan is more pronounced in E. coli than in S. aureus, and consequently, melittin has greater contacts with glycan units of E. coli. Contacts of melittin with the amino acids of peptidoglycan are comparable across both the strains, and the D-Ala residues, which are sites for transpeptidation, show enhanced interactions with melittin. A low energetic barrier is observed for translocation of a naturally occurring antimicrobial thymol with the four-layered peptidoglycan model. The molecular model developed for Gram-positive peptidoglycan allows us to compare and contrast the cell wall penetrating properties with Gram-negative strains and assess for the first time binding and translocation of antimicrobial molecules for Gram-positive cell walls.

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.

Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus

The peptidoglycan (PG) layer is a vital component of the bacterial cell wall that protects the cell from rupturing due to internal pressure. Its ubiquity across the bacterial kingdom but not animals has made it the target of drug discovery efforts. The PG layer composed of cross-linked PG strands is porous enough to allow the diffusion of molecules through the PG mesh and into the cell. The lack of an accurate atomistic model of the PG mesh has limited the computational investigations of drug diffusion in Gram-positive bacteria, which lack the outer membrane but consist of a much thicker PG layer compared to Gram-negative bacteria. In this work, we built an atomistic model of the Staphylococcus aureus PG layer architecture with horizontally aligned PG strands and performed molecular dynamics simulations of the diffusion of curcumin molecules through the PG mesh. An accurate model of the Gram-positive bacterial cell wall may aid in developing novel antibiotics to tackle the threat posed by antibiotic resistance.

Bi-based photocatalysts for bacterial inactivation in water: Inactivation mechanisms, challenges, and strategies to improve the photocatalytic activity

Bi-based photocatalysts have been considered suitable materials for water disinfection under natural solar light due to their outstanding optical and electronic properties. However, until now, there are not extensive reviews about the development of Bi-based materials and their application in bacterial inactivation in aqueous solutions. For this reason, this work has focused on summarizing the state of the art related to the inactivation of Gram- and Gram + pathogenic bacteria under visible light irradiation using different Bi-based micro and nano structures. In this sense, the photocatalytic bacterial inactivation mechanisms are analyzed, considering several modifications. The factors that can affect the photocatalytic performance of these materials in real conditions and at a large scale (e.g., water characteristics, pH, light intensity, photocatalyst dosage, and bacteria level) have been studied. Furthermore, current alternatives for improving the photocatalytic antibacterial activity and reuse of Bi-based materials (e.g., surface engineering, crystal facet engineering, doping, noble metal coupling, heterojunctions, Z-scheme junctions, coupling with graphene derivatives, magnetic composites, immobilization) have been explored. According to several reports, inactivation rate values higher than 90% can be achieved by using the modified Bi-based micro/nano structures, which become them excellent candidates for photocatalytic water disinfection. However, these innovative photocatalytic materials bring a variety of future difficulties and opportunities in water disinfection.

Cavitation bubble interaction with compliant structures on a microscale: A contribution to the understanding of bacterial cell lysis by cavitation treatment

Numerous studies have already shown that the process of cavitation can be successfully used for water treatment and eradication of bacteria. However, most of the relevant studies are being conducted on a macro scale, so the understanding of the processes at a fundamental level remains poor. In attempt to further elucidate the process of cavitation-assisted water treatment on a scale of a single bubble, the present paper numerically addresses interaction between a collapsing microbubble and a nearby compliant structure, that mechanically and structurally resembles a bacterial cell. A fluid-structure interaction methodology is employed, where compressible multiphase flow is considered and the bacterial cell wall is modeled as a multi-layered shell structure. Simulations are performed for two selected model structures, each resembling the main structural features of Gram-negative and Gram-positive bacterial cell envelopes. The contribution of two independent dimensionless geometric parameters is investigated, namely the bubble-cell distance δ and their size ratio ς. Three characteristic modes of bubble collapse dynamics and four modes of spatiotemporal occurrence of peak local stresses in the bacterial cell membrane are identified throughout the parameter space considered. The former range from the development of a weak and thin jet away from the cell to spherical bubble collapses. The results show that local stresses arising from bubble-induced loads can exceed poration thresholds of cell membranes and that bacterial cell damage could be explained solely by mechanical effects in absence of thermal and chemical ones. Based on this, the damage potential of a single microbubble for bacteria eradication is estimated, showing a higher resistance of the Gram-positive model organism to the nearby bubble collapse. Microstreaming is identified as the primary mechanical mechanism of bacterial cell damage, which in certain cases may be enhanced by the occurrence of shock waves during bubble collapse. The results are also discussed in the scope of bacteria eradication by cavitation treatment on a macro scale, where processes of hydrodynamic and ultrasonic cavitation are being employed.

An Updated Model of the Divisome: Regulation of the Septal Peptidoglycan Synthesis Machinery by the Divisome

The synthesis of a peptidoglycan septum is a fundamental part of bacterial fission and is driven by a multiprotein dynamic complex called the divisome. FtsW and FtsI are essential proteins that synthesize the peptidoglycan septum and are controlled by the regulatory FtsBLQ subcomplex and the activator FtsN. However, their mode of regulation has not yet been uncovered in detail. Understanding this process in detail may enable the development of new compounds to combat the rise in antibiotic resistance. In this review, recent data on the regulation of septal peptidoglycan synthesis is summarized and discussed. Based on structural models and the collected data, multiple putative interactions within FtsWI and with regulators are uncovered. This elaborates on and supports an earlier proposed model that describes active and inactive conformations of the septal peptidoglycan synthesis complex that are stabilized by these interactions. Furthermore, a new model on the spatial organization of the newly synthesized peptidoglycan and the synthesis complex is presented. Overall, the updated model proposes a balance between several allosteric interactions that determine the state of septal peptidoglycan synthesis.

Antibacterial and Anticancer Potentials of Presynthesized Photosensitive Plectranthus cylindraceus Oil/TiO2/Polyethylene Glycol Polymeric Bionanocomposite

The present study is concerned with the fabrication of the bifunctional Plectranthus cylindraceus oil/TiO2/polyethylene glycol polymeric film for antibacterial and anticancer activities. The suggested film is based on the utility of naturally extracted P. cylindraceus oil in the formation of the polymeric bionanocomposite film decorated with TiO2 nanoparticles. The bionanocomposite film was fabricated by incorporating 15 w% of P. cylindraceus oil with 10 w% polyethylene glycol and 5 w% TiO2 nanoparticles. The active components of P. cylindraceus oil were verified using gas chromatography coupled with mass spectrometry (GC-MS). The surface morphology of the resulted bionanocomposite film was characterized by various spectroscopic and microscopic techniques. The antibacterial potential of the fabricated bionanocomposite film was investigated against four pathogenic strains. The obtained results revealed excellent sensitivity against the bacterial strains, particularly E. coli and S. aureus, with minimum inhibitory concentration 320 µg mL-1 and minimum bactericidal concentration 640 and 1280 µg mL-1 for E. coli and S. aureus, respectively. Polymeric bionanocomposite exerted significant cytotoxicity against human lung carcinoma cell lines in a concentration-dependent manner with an IC50 value of 42.7 ± 0.25 μg mL-1. Safety assessment test against peripheral blood mononuclear cells (PBMCs) demonstrated that the bionanocomposite is nontoxic in nature. Bionanocomposite also showed potent photocatalytic effects. Overall, the results concluded that the bionanocomposite has expressed scope for multifaceted biomedical applications.

Adhesion heterogeneity of individual bacterial cells in an axenic culture studied by atomic force microscopy

The evaluation of bacterial adhesive properties at a single-cell level is critical for under standing the role of phenotypic heterogeneity in bacterial attachment and community formation. Bacterial population exhibits a wide variety of adhesive properties at the single-cell level, suggesting that bacterial adhesion is a rather complex process and some bacteria are prone to phenotypic heterogeneity. This heterogeneity was more pronounced for Escherichia coli, where two subpopulations were detected. Subpopulations exhibiting higher adhesion forces may be better adapted to colonize a new surface, especially during sudden changes in environmental conditions. Escherichia coli was characterized by a higher adhesion force, a stronger ability to form biofilm and larger heterogeneity index calculated in comparison with Bacillus subtilis. Higher adhesion forces are associated with a more efficient attachment of bacteria observed in an adhesion assay and might provide a basis for successful colonization, survival and multiplications in changing environment. The atomic force microscopy provides a platform for investigation of the adhesion heterogeneity of individual cells within a population, which may be expected to underpin further elucidation of the adaptive significance of phenotypic heterogeneity in a natural environment.

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump

The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun's lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.

Nanocapsule designs for antimicrobial resistance

The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections. The recent coronavirus pandemic has dramatically highlighted the necessity of effective antibacterial and antiviral protection. This work explores at the molecular level the mechanism of action of antibacterial nanocapsules assembled in virus-like particles, their stability and their interaction with mammal and antimicrobial model membranes. We use Molecular Dynamics with force-fields of different granularity and protein design strategies to study the stability, self-assembly and membrane poration properties of these nanocapsules.

Mg(OH)2 nanoparticles enhance the antibacterial activities of macrophages by activating the reactive oxygen species

Infection often causes disastrous consequences in all fields of clinical medicine, especially orthopedics. Hence, critical efforts are being made to engineer novel nanomaterials for the treatment of orthopedic infections due to the high biocompatibility and antibacterial properties they possess. The purpose of this study was to investigate the antibacterial effects of magnesium hydroxide (Mg(OH)₂ ) nanoparticles (NPs) in vitro and determine their possible mechanisms of action. In this study, Escherichia coli was selected as the pathogenic bacteria and it was found that Mg(OH)₂ NPs significantly inhibited the growth of E. coli by promoting nucleic acid leakage, inhibiting protein synthesis, and suppressing the metabolic activity. The minimum inhibitory concentration for these bacteria was determined to be 4.4 μg/ml. In vitro flow cytometry and immunofluorescence tests indicated that Mg(OH)₂ NPs induced the macrophages to generate reactive oxygen species to kill the bacteria. To understand the mechanisms involved in this process, western blotting was performed and it was found that Mg(OH)₂ NPs activated the phosphatidylinositol-3-kinase/serine-threonine kinase (PI3K/Akt) signaling pathway of macrophages to enhance their phagocytosis with no obvious cytotoxicity. Thus, Mg(OH)₂ NPs are a suitable choice to develop promising agents or coating materials for the treatment of clinically widespread infections in view of their safety, biocompatibility, and powerful antibacterial properties.

Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison

Halogen atoms are widely used in drug molecules to improve their binding affinity for the receptor proteins. Many of the examples involve "halogen bonding" between the molecule and the binding site, which is a directional interaction between a halogen atom and a nucleophilic atom. Such an interaction is induced by an electron cloud shift of the halogen atom toward its covalently bonded neighbor to form the σ-bond, leaving a small electrostatic positive region opposite to the bond called the "σ-hole." To mimic the effect of the σ-hole in the CHARMM non-polarizable force field, recently CGenFF added a positively charged massless particle to halogen atoms, positioned at the opposite side of the carbon-halogen bond. This particle is referred to as a lone pair (LP) particle because it uses the lone pair implementation in the CHARMM force field. Here, we have added support for LP particles to ffTK, an automated force field parameterization toolkit widely distributed as a plugin to the molecular visualization software VMD. We demonstrate the updated optimization process using an example halogenated drug molecule, AT130, which is a capsid assembly modulator targeting the hepatitis B virus. Our results indicate that parameterization with the LP particle significantly improves the accuracy of the electrostatic response of the molecule, especially around the halogen atom. Although the inclusion of the LP particle does not produce a prominent effect on the interactions between the molecule and its target protein, the protein-ligand binding performance is greatly improved by optimization of the parameters.

An updated toolkit for exploring bacterial cell wall structure and dynamics

The bacterial cell wall is made primarily from peptidoglycan, a complex biomolecule which forms a bag-like exoskeleton that envelops the cell. As it is unique to bacteria and typically essential for their growth and survival, it represents one of the most successful targets for antibiotics. Although peptidoglycan has been studied intensively for over 50 years, the past decade has seen major steps in our understanding of this molecule because of the advent of new analytical and imaging methods. Here, we outline the most recent developments in tools that have helped to elucidate peptidoglycan structure and dynamics.

Precision Design of Antimicrobial Surfaces

The overall expectation from an antimicrobial surface has been high considering the need for efficiency in preventing the attachment and growth of pathogenic microbes, durability, safety to both humans and environment as well as cost-effectiveness. To date, antimicrobial surface design has been mostly conducted liberally, without rigorous consideration of establishing robust structure-activity relationships for each design strategy or of the use intended for a specific antimicrobial material. However, the variability among the domain bacteria, which is the most diverse of all, alongside the highly dynamic nature of the bacteria-surface interface have taught us that the likelihood of finding universal antimicrobial surfaces is low. In this perspective we discuss some of the current hurdles faced by research in this promising field, emphasizing the relevance and complexity of probing the bacteria-surface interface, and explain why we feel it would greatly benefit from a more streamlined ad-hoc approach.

Molecular Machinery Responsible for Graphene Oxide's Distinct Inhibitory Effects towards Pseudomonas aeruginosa and Staphylococcus aureus Pathogens

Graphene oxide flakes are considered as potential inhibitors for different pathogenic bacteria. However, the efficacy of inhibition changes for different types and strains of bacteria. In this work, we examine Pseudomonas aeruginosa and Staphylococcus aureus, two common hospital-acquired infections, which react quite differently to graphene oxide flakes. The minimum inhibitory tests yield two distinct outcomes: stopped proliferation for S. aureus versus almost no effect for P. aeruginosa. Integrating our experimental evidence with molecular dynamics simulations, we elucidate the molecular machinery involved, explaining the behavior we see in scanning electron microscopy images. According to our simulations, the peptidoglycan network, the outermost layer of S. aureus, is completely entangled with the flakes, acting as a hunting ground, which consequently results in the inhibition of the pathogen itself. Lipopolysaccharides, the outermost layer of P. aeruginosa, on the other hand, resist interacting with the flakes. Lipopolysaccharides make no effective contacts, and thus no effective inhibition of the pathogen takes place. Likewise, the electron microscopy images show complete coverage and wrapping of S. aureus. In contrast, for P. aeruginosa, barely any bacteria are spotted with any flakes on top except for some loosely half-covered cases. As we did not observe any damaged bacteria in our images, we exclude the knife-cutting inhibition mechanism and suggest the wrapping and trapping mechanism for S. aureus for our flakes' rather large size (average area of 0.05 μm2). The molecular machinery suggested in this work can be used for molecular engineering and functionalizing graphene flakes to inhibit different pathogens.

Peptidoglycan binding by a pocket on the accessory NTF2-domain of Pgp2 directs helical cell shape of Campylobacter jejuni

The helical morphology of Campylobacter jejuni, a bacterium involved in host gut colonization and pathogenesis in humans, is determined by the structure of the peptidoglycan (PG) layer. This structure is dictated by trimming of peptide stems by the LD-carboxypeptidase Pgp2 within the periplasm. The interaction interface between Pgp2 and PG to select sites for peptide trimming is unknown. We determined a 1.6 Å resolution crystal structure of Pgp2, which contains a conserved LD-carboxypeptidase domain and a previously uncharacterized domain with an NTF2-like fold (NTF2). We identified a pocket in the NTF2 domain formed by conserved residues and located ∼40 Å from the LD-carboxypeptidase active site. Expression of pgp2 in trans with substitutions of charged (Lys257, Lys307, Glu324) and hydrophobic residues (Phe242 and Tyr233) within the pocket did not restore helical morphology to a pgp2 deletion strain. Muropeptide analysis indicated a decrease of murotripeptides in the deletion strain expressing these mutants, suggesting reduced Pgp2 catalytic activity. Pgp2 but not the K307A mutant was pulled down by C. jejuni Δpgp2 PG sacculi, supporting a role for the pocket in PG binding. NMR spectroscopy was used to define the interaction interfaces of Pgp2 with several PG fragments, which bound to the active site within the LD-carboxypeptidase domain and the pocket of the NTF2 domain. We propose a model for Pgp2 binding to PG strands involving both the LD-carboxypeptidase domain and the accessory NTF2 domain to induce a helical cell shape.

Structural Determinants and Their Role in Cyanobacterial Morphogenesis

Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called cytoskeleton and its associated proteins. In bacteria, FtsZ and MreB, the bacterial homologs to tubulin and actin, respectively, as well as coiled-coil-rich proteins of intermediate filament (IF)-like function to fulfil these tasks. Despite generally being characterized as Gram-negative, cyanobacteria have a remarkably thick peptidoglycan layer and possess Gram-positive-specific cell division proteins such as SepF and DivIVA-like proteins, besides Gram-negative and cyanobacterial-specific cell division proteins like MinE, SepI, ZipN (Ftn2) and ZipS (Ftn6). The diversity of cellular morphologies and cell growth strategies in cyanobacteria could therefore be the result of additional unidentified structural determinants such as cytoskeletal proteins. In this article, we review the current advances in the understanding of the cyanobacterial cell shape, cell division and cell growth.

Mechanics of Bacterial Interaction and Death on Nanopatterned Surfaces

Nanopatterned surfaces are believed to kill bacteria through physical deformation, a mechanism that has immense potential against biochemical resistance. Because of its elusive nature, this mechanism is mostly understood through biophysical modeling. Problematically, accurate descriptions of the contact mechanics and various boundary conditions involved in the bacteria-nanopattern interaction remain to be seen. This may underpin conflicting predictions, found throughout the literature, regarding two important aspects of the mechanism-that is, its critical action site and relationship with geometry. Herein, a robust computational analysis of bacteria-nanopattern interaction is performed using a three-dimensional finite element modeling that incorporates relevant continuum mechanical properties, multilayered envelope structure, and adhesion interaction conditions. The model is applied to more accurately study the elusory mechanism and its enhancement via nanopattern geometry. Additionally, micrographs of bacteria adhered on a nanopatterned cicada wing are examined to further inform and verify the major modeling predictions. Together, the results indicate that nanopatterned surfaces do not kill bacteria predominantly by rupture in between protruding pillars as previously thought. Instead, nondevelopable deformation about pillar tips is more likely to create a critical site at the pillar apex, which delivers significant in-plane strains and may locally rupture and penetrate the cell. The computational analysis also demonstrates that envelope deformation is increased by adhesion to nanopatterns with smaller pillar radii and spacing. These results further progress understanding of the mechanism of nanopatterned surfaces and help guide their design for enhanced bactericidal efficiency.

β-Barrel proteins tether the outer membrane in many Gram-negative bacteria

Gram-negative bacteria have a cell envelope that comprises an outer membrane (OM), a peptidoglycan (PG) layer and an inner membrane (IM)¹. The OM and PG are load-bearing, selectively permeable structures that are stabilized by cooperative interactions between IM and OM proteins^2,3. In E. coli, Braun’s lipoprotein (Lpp) forms the only covalent tether between the OM and PG and is crucial for cell envelope stability⁴ but most other Gram-negative bacteria lack Lpp so it has been assumed that alternative mechanisms of OM stabilization are present⁵. We use a glycoproteomic analysis of PG to show that β-barrel OM proteins are covalently attached to PG in several Gram-negative species, including Coxiella burnetii, Agrobacterium tumefaciens and Legionella pneumophila. In C. burnetii, we found that four different types of covalent attachments occur between OM proteins and PG, with tethering of the β-barrel OM protein BbpA becoming most abundant in stationary phase and tethering of the lipoprotein LimB similar throughout the cell-cycle. Using a genetic approach, we demonstrate that the cell-cycle dependent tethering of BbpA is partly dependent on a developmentally regulated L,D transpeptidase (Ldt). We use our findings to propose a model of Gram-negative cell envelope stabilization that includes cell-cycle control and an expanded role for Ldts in covalently attaching surface proteins to PG.

Membrane thinning and lateral gating are consistent features of BamA across multiple species

In Gram-negative bacteria, the folding and insertion of β-barrel outer membrane proteins (OMPs) to the outer membrane are mediated by the β-barrel assembly machinery (BAM) complex. Two leading models of this process have been put forth: the hybrid barrel model, which claims that a lateral gate in BamA’s β-barrel can serve as a template for incoming OMPs, and the passive model, which claims that a thinned membrane near the lateral gate of BamA accelerates spontaneous OMP insertion. To examine the key elements of these two models, we have carried out 45.5 μs of equilibrium molecular dynamics simulations of BamA with and without POTRA domains from Escherichia coli, Salmonella enterica, Haemophilus ducreyi and Neisseria gonorrhoeae, together with BamA’s homolog, TamA from E. coli, in their native, species-specific outer membranes. In these equilibrium simulations, we consistently observe membrane thinning near the lateral gate for all proteins. We also see occasional spontaneous lateral gate opening and sliding of the β-strands at the gate interface for N. gonorrhoeae, indicating that the gate is dynamic. An additional 14 μs of free-energy calculations shows that the energy necessary to open the lateral gate in BamA/TamA varies by species, but is always lower than the Omp85 homolog, FhaC. Our combined results suggest OMP insertion utilizes aspects of both the hybrid barrel and passive models.

Gram-negative bacteria such as Escherichia coli have a second, outer membrane surrounding them. This outer membrane provides an additional layer of protection, but also presents an additional challenge in its construction, exacerbated by the lack of chemical energy in this region of the bacterial cell. For example, proteins in the outer membrane are inserted via BamA, itself an integral membrane protein. The precise mechanisms by which BamA assists in the insertion process are still unclear. Here, we use extensive simulations in atomistic detail of BamA from multiple species in its native outer membrane environment to shed light on this process. We find that the lateral gate of BamA, a proposed pathway into the membrane, is dynamic, although to a degree varying by species. On the other hand, thinning of the outer membrane near BamA’s lateral gate is observed consistently across all simulations. We conclude that multiple features of BamA contribute to protein insertion into the outer membrane.

Ultrafast physical bacterial inactivation and photocatalytic self-cleaning of ZnO nanoarrays for rapid and sustainable bactericidal applications

Various nanostructured surfaces have been developed recently to physically inactivate bacteria, for reducing the rapidly spreading threat of pathogenic bacteria. However, it generally takes several hours for these surfaces to inactivate most of the bacteria, which greatly limits their application in the fields favoring rapid bactericidal performance. Besides, the accumulated bacteria debris left on these surfaces is rarely discussed in the previous reports. Herein we report the nanotip-engineered ZnO nanoarrays (NAs) with ultrafast physical bactericidal rate and the ability to photocatalytically remove the bacteria debris. Neither chemical (Zn2+ or reactive oxygen species) nor photocatalytic effect leads to the ultrafast bactericidal rate, where 97.5% of E. coli and 94.9% of S. aureus are inactivated within only 1 min. The simulation analysis further supported our proposed mechanism attributing the ultrafast bactericidal activity to the great stress enabled by the uneven topography. Moreover, the re-exposure of the ZnO NAs nanotips can be achieved in only 10 min under a mild UV light source. This study not only presents an ultrafast physical bactericidal activity, but also demonstrates the potential of the recyclable and photocatalytic self-cleaning functions of theses surfaces for applications that desire rapid and sustainable bactericidal performance.

Live Cell Electron Microscopy Using Graphene Veils

As a promising tool over the optical resolution limits, liquid electron microscopy is practically utilized to visualize the structural information on wet biological specimens, such as cells, proteins, and nucleic acids. However, the functionality of biomolecules during their observation is still controversial. Here we show the feasibility of live-cell electron microscopy using graphene veils. We demonstrate that the electron dose resistivity of live bacterial cells increases to 100-fold in graphene veils, and thus they maintain their structures and functions after electron microscopy experiments. Our results provide the guidelines and show possibilities for the electron microscopy imaging of live cells and functional biomolecules.

Structural basis of peptidoglycan endopeptidase regulation

Most bacteria surround themselves with a cell wall, a strong meshwork consisting primarily of the polymerized aminosugar peptidoglycan (PG). PG is essential for structural maintenance of bacterial cells, and thus for viability. PG is also constantly synthesized and turned over; the latter process is mediated by PG cleavage enzymes, for example, the endopeptidases (EPs). EPs themselves are essential for growth but also promote lethal cell wall degradation after exposure to antibiotics that inhibit PG synthases (e.g., β-lactams). Thus, EPs are attractive targets for novel antibiotics and their adjuvants. However, we have a poor understanding of how these enzymes are regulated in vivo, depriving us of novel pathways for the development of such antibiotics. Here, we have solved crystal structures of the LysM/M23 family peptidase ShyA, the primary EP of the cholera pathogen Vibrio cholerae Our data suggest that ShyA assumes two drastically different conformations: a more open form that allows for substrate binding and a closed form, which we predicted to be catalytically inactive. Mutations expected to promote the open conformation caused enhanced activity in vitro and in vivo, and these results were recapitulated in EPs from the divergent pathogens Neisseria gonorrheae and Escherichia coli Our results suggest that LysM/M23 EPs are regulated via release of the inhibitory Domain 1 from the M23 active site, likely through conformational rearrangement in vivo.

Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age

Gram-negative bacteria are protected by a multicompartmental molecular architecture known as the cell envelope that contains two membranes and a thin cell wall. As the cell envelope controls influx and efflux of molecular species, in recent years both experimental and computational studies of such architectures have seen a resurgence due to the implications for antibiotic development. In this article we review recent progress in molecular simulations of bacterial membranes. We show that enormous progress has been made in terms of the lipidic and protein compositions of bacterial systems. The simulations have moved away from the traditional setup of one protein surrounded by a large patch of the same lipid type toward a more bio-logically representative viewpoint. Simulations with multiple cell envelope components are also emerging. We review some of the key method developments that have facilitated recent progress, discuss some current limitations, and offer a perspective on future directions.

Mechanism of pH-induced conformational changes in MurE ligase obtained from Salmonella enterica serovar Typhi

Communicated by Ramaswamy H. Sarma.

A Theoretical Framework for Evolutionary Cell Biology

One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologies at the structural and functional levels, the potential for rapid progress is great. The primary challenge for theory development is the establishment of a quantitative framework that transcends species boundaries. Two approaches to the problem are presented here: establishing the long-term steady-state distribution of mean phenotypes under specific regimes of mutation, selection, and drift and evaluating the energetic costs of cellular structures and functions. Although not meant to be the final word, these theoretical platforms harbor potential for generating insight into a diversity of unsolved problems, ranging from genome structure to cellular architecture to aspects of motility in organisms across the Tree of Life.

Importance of being cross-linked for the bacterial cell wall

The bacterial cell wall is primarily composed of a mesh of glycan strands cross-linked by peptide bridges and is essential for safeguarding the cell. The structure of the cell wall has to be stiff enough to bear the high turgor pressure and sufficiently tough to ensure protection against failure. Here we explore the role of various design features of the cell in enhancing the toughness of the cell wall. We explain how the glycan strand length distribution, the degree of cross-linking and the placement of the cross-links on the glycan strands can act in tandem to ensure that the cell wall offers sufficient resistance to propagation of cracks. Further, we suggest a possible mechanism by which peptide bond hydrolysis, via judicious cleaving of peptide cross-links, can act to mitigate this risk of failure. We also study the reinforcing effect of MreB cytoskeleton, which can offer a degree of safety to the cell wall. However, we show that the cross-linked structure of the cell wall is its primary line of defense against mechanical failure.

Antibacterial Activities of Aliphatic Polyester Nanocomposites with Silver Nanoparticles and/or Graphene Oxide Sheets

Aliphatic polyesters such as poly(lactic acid) (PLA), polycaprolactone (PCL) and poly(lactic-co-glycolic) acid (PLGA) copolymers have been widely used as biomaterials for tissue engineering applications including: bone fixation devices, bone scaffolds, and wound dressings in orthopedics. However, biodegradable aliphatic polyesters are prone to bacterial infections due to the lack of antibacterial moieties in their macromolecular chains. In this respect, silver nanoparticles (AgNPs), graphene oxide (GO) sheets and AgNPs-GO hybrids can be used as reinforcing nanofillers for aliphatic polyesters in forming antimicrobial nanocomposites. However, polymeric matrix materials immobilize nanofillers to a large extent so that they cannot penetrate bacterial membrane into cytoplasm as in the case of colloidal nanoparticles or nanosheets. Accordingly, loaded GO sheets of aliphatic polyester nanocomposites have lost their antibacterial functions such as nanoknife cutting, blanket wrapping and membrane phospholipid extraction. In contrast, AgNPs fillers of polyester nanocomposites can release silver ions for destroying bacterial cells. Thus, AgNPs fillers are more effective than loaded GO sheets of polyester nanocomposiites in inhibiting bacterial infections. Aliphatic polyester nanocomposites with AgNPs and AgNPs-GO fillers are effective to kill multi-drug resistant bacteria that cause medical device-related infections.

Simulations suggest a constrictive force is required for Gram-negative bacterial cell division

To divide, Gram-negative bacterial cells must remodel cell wall at the division site. It remains debated, however, whether this cell wall remodeling alone can drive membrane constriction, or if a constrictive force from the tubulin homolog FtsZ is required. Previously, we constructed software (REMODELER 1) to simulate cell wall remodeling during growth. Here, we expanded this software to explore cell wall division (REMODELER 2). We found that simply organizing cell wall synthesis complexes at the midcell is not sufficient to cause invagination, even with the implementation of a make-before-break mechanism, in which new hoops of cell wall are made inside the existing hoops before bonds are cleaved. Division can occur, however, when a constrictive force brings the midcell into a compressed state before new hoops of relaxed cell wall are incorporated between existing hoops. Adding a make-before-break mechanism drives division with a smaller constrictive force sufficient to bring the midcell into a relaxed, but not necessarily compressed, state.

Melittin-Induced Permeabilization, Re-sealing, and Re-permeabilization of E. coli Membranes

The permeabilization of model lipid bilayers by cationic peptides has been studied extensively over decades, with the bee-sting toxin melittin perhaps serving as the canonical example. However, the relevance of these studies to the permeabilization of real bacterial membranes by antimicrobial peptides remains uncertain. Here, we employ single-cell fluorescence microscopy in a detailed study of the interactions of melittin with the outer membrane (OM) and the cytoplasmic membrane (CM) of live Escherichia coli. Using periplasmic green fluorescent protein (GFP) as a probe, we find that melittin at twice the minimum inhibitory concentration first induces abrupt cell shrinkage and permeabilization of the OM to GFP. Within ∼4 s of OM permeabilization, the CM invaginates to form inward facing "periplasmic bubbles." Seconds later the bubbles begin to leak periplasmic GFP into the cytoplasm. Permeabilization is localized, consistent with possible formation of toroidal pores. Within ∼20 s, first the OM and then the CM re-seals to GFP. Some 2-20 min later, both CM and OM are re-permeabilized to GFP. We invoke a mechanism based on curvature stress concepts derived from model bilayer studies. The permeabilization and re-sealing events involve sequential, time-dependent build-up of melittin density within the outer and inner leaflets of each bilayer. We also propose a mechanical explanation for the early cell shrinkage event induced by melittin and a variety of other cationic peptides. As peptides gain access to the periplasm, they bind to the anionic peptido-crosslinks of the lipopolysaccharide layer, increasing its longitudinal elastic modulus. The cell wall shrinks because it can withstand the same turgor pressure with smaller overall extension. Shrinkage in turn induces invagination of the CM, preserving its surface area. We conclude by comparing the behavior of different peptides.