Unraveling complex nanoscale lipid dynamics in simple model biomembranes: Insights from fluorescence correlation spectroscopy in super-resolution stimulated emission depletion mode

Pore-Forming Proteins: From Pore Assembly to Structure by Quantitative Single-Molecule Imaging

Pore-forming proteins (PFPs) play a central role in many biological processes related to infection, immunity, cancer, and neurodegeneration. A common feature of PFPs is their ability to form pores that disrupt the membrane permeability barrier and ion homeostasis and generally induce cell death. Some PFPs are part of the genetically encoded machinery of eukaryotic cells that are activated against infection by pathogens or in physiological programs to carry out regulated cell death. PFPs organize into supramolecular transmembrane complexes that perforate membranes through a multistep process involving membrane insertion, protein oligomerization, and finally pore formation. However, the exact mechanism of pore formation varies from PFP to PFP, resulting in different pore structures with different functionalities. Here, we review recent insights into the molecular mechanisms by which PFPs permeabilize membranes and recent methodological advances in their characterization in artificial and cellular membranes. In particular, we focus on single-molecule imaging techniques as powerful tools to unravel the molecular mechanistic details of pore assembly that are often obscured by ensemble measurements, and to determine pore structure and functionality. Uncovering the mechanistic elements of pore formation is critical for understanding the physiological role of PFPs and developing therapeutic approaches.

Modification of bacterial cell membrane dynamics and morphology upon exposure to sub inhibitory concentrations of ciprofloxacin

Ciprofloxacin (CPX), a second generation fluoroquinolone antibiotic, is used as a primary antibiotic for treatment against gastroenteritis, drug-resistant tuberculosis, and malignant otitis externa. CPX is a broad spectrum antibiotic that targets the DNA gyrase of both Gram-positive and Gram-negative bacteria. Irrational and improper usage of CPX results in emergence of CPX resistant organisms emphasizing the importance of using lethal doses of CPX. Here, we have systematically analysed the effect of CPX at sub lethal concentrations on live E. coli membrane and growth dynamics. As a result of CPX interaction at sub-lethal concentrations, we detected filamentation of the bacterial cells during cell division. Although CPX is a DNA targeting antibiotic and did not result in considerable increase of live E. coli cell surface roughness, we observed significant enhancement in the lipid diffusion coefficients possibly due to disrupted lipid packing or altered lipid composition. Interestingly, we seem to observe slightly higher extent of lipid diffusion alteration when bacterial inner membrane specific label FM4-64 was used in comparison to the non-specific membrane dye. Both these results are contrary to that observed in bacterial cells for colistin, a membrane targeting antibiotics. Our work highlights the need for using multiple, complementary surface and depth sensitive techniques to obtain information on the realistic nature of bacterial cell membrane remodelling due to non-membrane targeting antibiotics. Our work could have implications for identification of potential biomembrane markers at sub-lethal concentrations even for antibiotics which are non-membrane targeting that could help in unravelling pathways for emergence of antimicrobial resistance.

Multimodal Investigation into the Interaction of Quinacrine with Microcavity-Supported Lipid Bilayers

Quinacrine is a versatile drug that is widely recognized for its antimalarial action through its inhibition of the phospholipase enzyme. It also has antianthelmintic and antiprotozoan activities and is a strong DNA binder that may be used to combat multidrug resistance in cancer. Despite extensive cell-based studies, a detailed understanding of quinacrine's influence on the cell membrane, including permeability, binding, and rearrangement at the molecular level, is lacking. Herein, we apply microcavity-suspended lipid bilayers (MSLBs) as in vitro models of the cell membrane comprising DOPC, DOPC:Chol(3:1), and DOPC:SM:Chol(2:2:1) to investigate the influence of cholesterol and intrinsic phase heterogeneity induced by mixed-lipid composition on the membrane interactions of quinacrine. Using electrochemical impedance spectroscopy (EIS) and surface-enhanced Raman spectroscopy (SERS) as label-free surface-sensitive techniques, we have studied quinacrine interaction and permeability across the different MSLBs. Our EIS data reveal that the drug is permeable through ternary DOPC:SM:Chol and DOPC-only bilayer compositions. In contrast, the binary cholesterol/DOPC membrane arrested permeation, yet the drug binds or intercalates at this membrane as reflected by an increase in membrane impedance. SERS supported the EIS data, which was utilized to gain structural insights into the drug-membrane interaction. Our SERS data also provides a simple but powerful label-free assessment of drug permeation because a significant SERS enhancement of the drug's Raman signature was observed only if the drug accessed the plasmonic interior of the pore cavity passing through the membrane. Fluorescent lifetime correlation spectroscopy (FLCS) provides further biophysical insight, revealing that quinacrine binding increases the lipid diffusivity of DOPC and the ternary membrane while remarkably decreasing the lipid diffusivity of the DOPC:Chol membrane. Overall, because of its adaptability to multimodal approaches, the MSLB platform provides rich and detailed insights into drug-membrane interactions, making it a powerful tool for in vitro drug screening.

Escherichia coli response to subinhibitory concentrations of colistin: insights from a study of membrane dynamics and morphology

Prevalence of widespread bacterial infections brings forth a critical need to understand the molecular mechanisms of the antibiotics as well as the bacterial response to those antibiotics. Improper use of antibiotics, which can be in sub-lethal concentrations is one among the multiple reasons for acquiring antibiotic resistance which makes it vital to understand the bacterial response towards sub-lethal concentrations of antibiotics. In this work, we have used colistin, a well-known membrane active antibiotic used to treat severe bacterial infections and explored the impact of its sub-minimum inhibitory concentration (MIC) on the lipid membrane dynamics and morphological changes of E. coli. Upon investigation of live cell membrane properties such as lipid dynamics using fluorescence correlation spectroscopy, we observed that colistin disrupts the lipid membrane at sub-MIC by altering the lipid diffusivity. Interestingly, filamentation-like cell elongation was observed upon colistin treatment which led to further exploration of surface morphology with the help of atomic force spectroscopy. The changes in the surface roughness upon colistin treatment provides additional insight on the colistin-membrane interaction corroborating with the altered lipid diffusion. Although altered lipid dynamics could be attributed to an outcome of lipid rearrangement due to direct disruption by antibiotic molecules on the membrane or an indirect consequence of disruptions in lipid biosynthetic pathways, we were able to ascertain that altered bacterial membrane dynamics is due to direct disruptions. Our results provide a broad overview on the consequence of the cyclic polypeptide colistin on membrane-specific lipid dynamics and morphology of a live Gram-negative bacterial cell.

Pore Forming Protein Induced Biomembrane Reorganization and Dynamics: A Focused Review

Pore forming proteins are a broad class of pathogenic proteins secreted by organisms as virulence factors due to their ability to form pores on the target cell membrane. Bacterial pore forming toxins (PFTs) belong to a subclass of pore forming proteins widely implicated in bacterial infections. Although the action of PFTs on target cells have been widely investigated, the underlying membrane response of lipids during membrane binding and pore formation has received less attention. With the advent of superresolution microscopy as well as the ability to carry out molecular dynamics (MD) simulations of the large protein membrane assemblies, novel microscopic insights on the pore forming mechanism have emerged over the last decade. In this review, we focus primarily on results collated in our laboratory which probe dynamic lipid reorganization induced in the plasma membrane during various stages of pore formation by two archetypal bacterial PFTs, cytolysin A (ClyA), an α-toxin and listeriolysin O (LLO), a β-toxin. The extent of lipid perturbation is dependent on both the secondary structure of the membrane inserted motifs of pore complex as well as the topological variations of the pore complex. Using confocal and superresolution stimulated emission depletion (STED) fluorescence correlation spectroscopy (FCS) and MD simulations, lipid diffusion, cholesterol reorganization and deviations from Brownian diffusion are correlated with the oligomeric state of the membrane bound protein as well as the underlying membrane composition. Deviations from free diffusion are typically observed at length scales below ∼130 nm to reveal the presence of local dynamical heterogeneities that emerge at the nanoscale-driven in part by preferential protein binding to cholesterol and domains present in the lipid membrane. Interrogating the lipid dynamics at the nanoscale allows us further differentiate between binding and pore formation of β- and α-PFTs to specific domains in the membrane. The molecular insights gained from the intricate coupling that occurs between proteins and membrane lipids and receptors during pore formation are expected to improve our understanding of the virulent action of PFTs.

Sensing Hydration of Biomimetic Cell Membranes

Biological membranes play a vital role in cell functioning, providing structural integrity, controlling signal transduction, and controlling the transport of various chemical species. Owing to the complex nature of biomembranes, the self-assembly of lipids in aqueous media has been utilized to develop model systems mimicking the lipid bilayer structure, paving the way to elucidate the mechanisms underlying various biological processes, as well as to develop a number of biomedical and technical applications. The hydration properties of lipid bilayers are crucial for their activity in various cellular processes. Of particular interest is the local membrane dehydration, which occurs in membrane fusion events, including neurotransmission, fertilization, and viral entry. The lack of universal technique to evaluate the local hydration state of the membrane components hampers understanding of the molecular-level mechanisms of these processes. Here, we present a new approach to quantify the hydration state of lipid bilayers. It takes advantage of the change in the lateral diffusion of lipids that depends on the number of water molecules hydrating them. Using fluorescence recovery after photobleaching technique, we applied this approach to planar single and multicomponent supported lipid bilayers. The method enables the determination of the hydration level of a biomimetic membrane down to a few water molecules per lipid.

Bacterial protein listeriolysin O induces nonmonotonic dynamics because of lipid ejection and crowding

Membrane-bound protein complexes involving pore forming toxins (PFTs) released by virulent bacteria are known to form transmembrane pores leading to host cell lysis. Developing alternative strategies against PFT mediated bacterial virulence factors requires an understanding of the cellular membrane response. However, membrane disruption and related lipid reorganization events during attack by PFTs remain largely unexplored. We report counterintuitive and nonmonotonic variations in lipid diffusion, measured using confocal fluorescence correlation spectroscopy, due to interplay of lipid ejection and crowding by membrane-bound oligomers of a prototypical cholesterol-dependent cytolysin, listeriolysin O (LLO). The observed dynamical crossover is correlated with concentration dependent transitions of LLO oligomeric state populations from rings to arc-like pore complexes, predicted using a proposed two-state free area-based diffusion model. At low PFT concentrations, a hitherto unexplored regime of increased lipid diffusivity is attributed to lipid ejection events because of a preponderance of ring-like pore states. At higher protein concentrations in which membrane-inserted arc-like pores dominate, lipid ejection is less efficient and the ensuing crowding results in a lowering of lipid diffusion. These variations in lipid dynamics are corroborated by macroscopic rheological response measurements of PFT bound vesicles. Our study correlates PFT oligomeric state transitions, membrane remodeling, and mechanical property variations, providing unique insights into the pore forming mechanisms of cholesterol-dependent cytolysins.

Membrane dynamics during individual and combined abiotic stresses in plants and tools to study the same

The plasma membrane (PM) is possibly the most diverse biological membrane of plant cells; it separates and guards the cell against its external environment. It has an extremely complex structure comprising a mosaic of lipids and proteins. The PM lipids are responsible for maintaining fluidity, permeability and integrity of the membrane and also influence the functioning of membrane proteins. However, the PM is the primary target of environmental stress, which affects its composition, conformation and properties, thereby disturbing the cellular homeostasis. Maintenance of integrity and fluidity of the PM is a prerequisite for ensuring the survival of plants during adverse environmental conditions. The ability of plants to remodel membrane lipid and protein composition plays a crucial role in adaptation towards varying abiotic environmental cues, including high or low temperature, drought, salinity and heavy metals stress. The dynamic changes in lipid composition affect the functioning of membrane transporters and ultimately regulate the physical properties of the membrane. Plant membrane-transport systems play a significant role in stress adaptation by cooperating with the membrane lipidome to maintain the membrane integrity under stressful conditions. The present review provides a holistic view of stress responses and adaptations in plants, especially the changes in the lipidome and proteome of PM under individual or combined abiotic stresses, which cause alterations in the activity of membrane transporters and modifies the fluidity of the PM. The tools to study the varying lipidome and proteome of the PM are also discussed.

Using multiscale molecular dynamics simulations to obtain insights into pore forming toxin mechanisms

Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse-grained MARTINI models and structure-based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.

Mechanistic Insights into Pore Formation by an α-Pore Forming Toxin: Protein and Lipid Bilayer Interactions of Cytolysin A

Pore forming toxins (PFTs) are the largest class of bacterial toxins playing a central role in bacterial pathogenesis. They are proteins specifically designed to form nanochannels in the membranes of target cells, ultimately resulting in cell death and establishing infection. PFTs are broadly classified as α- and β-PFTs, depending on secondary structures that form the transmembrane channel. A unique feature about this class of proteins is the drastic conformational changes and complex oligomerization pathways that occur upon exposure to the plasma membrane. A molecular understanding of pore formation has implications in designing novel intervention strategies to combat rising antimicrobial resistance, targeted-cancer therapy, as well as designing nanopores for specialized technologies. Central to unraveling the pore formation pathway is the availability of high resolution crystal structures. In this regard, β-toxins are better understood, when compared with α-toxins whose pore forming mechanisms are complicated by an incomplete knowledge of the driving forces for amphiphatic membrane-inserted helices to organize into functional pores. With the publication of the first crystal structure for an α-toxin, cytolysin A (ClyA), in 2009 we embarked on an extensive multiscale study to unravel its pore forming mechanism. This Account represents the collective mechanistic knowledge gained in our laboratories using a variety of experimental and theoretical techniques which include large scale molecular dynamics (MD) simulations, kinetic modeling studies, single-molecule fluorescence imaging, and super-resolution spectroscopy. We reported MD simulations of the ClyA protomer, oligomeric intermediates, and full pore complex in a lipid bilayer and mapped the conformational transitions that accompany membrane binding. Using single-molecule fluorescence imaging, the conformational transition was experimentally verified by analysis of various diffusion states of membrane bound ClyA. Importantly, we have uncovered a hitherto unknown putative cholesterol binding motif in the membrane-inserted helix of ClyA. Distinct binding pockets for cholesterol formed by adjacent membrane-inserted helices are revealed in MD simulations. Cholesterol appears to play a dual role by stabilizing both the membrane-inserted protomer as well as oligomeric intermediates. Molecular dynamics simulations and kinetic modeling studies suggest that the membrane-inserted arcs oligomerize reversibly to form the predominant transmembrane oligomeric intermediates during pore formation. We posit that this mechanistic understanding of the complex action of α-PFTs has implications in unraveling pore assembly across the wider family of bacterial toxins. With emerging antimicrobial resistance, alternate therapies may rely on disrupting pore functionality or oligomerization of these pathogenic determinants utilized by bacteria, and our study includes assessing the potential for dendrimers as pore blockers.

Assessing the extent of the structural and dynamic modulation of membrane lipids due to pore forming toxins: insights from molecular dynamics simulations

Infections caused by many virulent bacterial strains are triggered by the release of pore forming toxins (PFTs), which form oligomeric transmembrane pore complexes on the target plasma membrane. The spatial extent of the perturbation to the surrounding lipids during pore formation is relatively unexplored. Using all-atom molecular dynamics simulations, we investigate the changes in the structure and dynamics of lipids in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer in the presence of contrasting PFTs. Cytolysin A (ClyA), an α toxin with its inserted wedge shaped bundle of inserted α helices, induces significant asymmetry across the membrane leaflets in comparison with α hemolysin (AHL), a β toxin. Despite the differences in hydrophobic mismatch and uniquely different topologies of the two oligomers, perturbations to lipid order as reflected in the tilt angle and order parameters and membrane thinning are short ranged, lying within ∼2.5 nm from the periphery of either pore complex, and commensurate with distances typically associated with van der Waals forces. In contrast, the spatial extent of perturbations to the lipid dynamics extends outward to at least 4 nm for both proteins, and the continuous survival probabilities reveal the presence of a tightly bound shell of lipids in this region. Displacement probability distributions show long tails and the distinctly non-Gaussian features reflect the induced dynamic heterogeneity. A detailed profiling of the protein-lipid contacts with tyrosine, tryptophan, lysine and arginine residues shows increased non-polar contacts in the cytoplasmic leaflet for both PFTs, with a higher number of atomic contacts in the case of AHL in the extracellular leaflet due to the mushroom-like topology of the pore complex. The short ranged nature of the perturbations observed in this simple one component membrane suggests inherent plasticity of membrane lipids enabling the recovery of the structure and membrane fluidity even in the presence of these large oligomeric transmembrane protein assemblies. This observation has implications in membrane repair processes such as budding or vesicle fusion events used to mitigate PFT virulence, where the underlying lipid dynamics and fluidity in the vicinity of the pore complex are expected to play an important role.

Dynamic Landscape in Self-Assembled Surfactant Aggregates

A process in which a disordered system of pre-existing molecules generates an organized structure through specific, local interactions among the molecules themselves is termed molecular self-assembly. Micelles, microemulsions, and vesicles are examples of such self-assembled systems where amphiphilic molecules are involved. As the functional properties of these systems (such as wetting and emulsification, release of solubilized drugs, etc.) are dictated by the dynamic behavior of the surfactants at the molecular level, it is of immense interest to investigate these systems for the same. The dynamics in soft matter systems is quite complex, involving different time and length scales. We used a combination of neutron scattering and molecular dynamics simulation studies in probing the dynamic landscape in various self-assembled surfactant aggregates. Neutron scattering experiments were carried out using several spectrometers covering a wide dynamic range to probe motions on different time scales. The interaction between the surfactants can be varied by changing the molecular architecture, counterion concentration, temperature, and so forth. It is important to study the effect of these parameters on the dynamics of surfactants in these aggregates. We have carried out experiments on various ionic (anionic as well as cationic) micelles with varied counterion concentrations, vesicles, and lipid bilayers to unravel the complex dynamic features present in these systems. In this feature article, we will discuss some important results of our recent work on dynamics in these self-assembled surfactant aggregates.

Measuring nanoscale diffusion dynamics in cellular membranes with super-resolution STED-FCS

Super-resolution microscopy techniques enable optical imaging in live cells with unprecedented spatial resolution. They unfortunately lack the temporal resolution required to directly investigate cellular dynamics at scales sufficient to measure molecular diffusion. These fast time scales are, on the other hand, routinely accessible by spectroscopic techniques such as fluorescence correlation spectroscopy (FCS). To enable the direct investigation of fast dynamics at the relevant spatial scales, FCS has been combined with super-resolution stimulated emission depletion (STED) microscopy. STED-FCS has been applied in point or scanning mode to reveal nanoscale diffusion behavior of molecules in live cells. In this protocol, we describe the technical details of performing point STED-FCS (pSTED-FCS) and scanning STED-FCS (sSTED-FCS) measurements, from calibration and sample preparation to data acquisition and analysis. We give particular emphasis to 2D diffusion dynamics in cellular membranes, using molecules tagged with organic fluorophores. These measurements can be accomplished within 4-6 h by those proficient in fluorescence imaging.

Pathways for creation and annihilation of nanoscale biomembrane domains reveal alpha and beta-toxin nanopore formation processes

Raft-like functional domains with putative sizes of 20–200 nm and which are evolving dynamically are believed to be the most crucial regions in cellular membranes which determine cell signaling and various functions of cells.