Assessment of membrane lipid state at the natural killer cell immunological synapse.

The plasma membrane is a fluid structure that protects cells as one of their first barriers and actively participates in numerous biological processes in many ways including through distinct membrane sub-regions. For immunological cells, highly organized sub-compartments of plasma membranes are vital for them to sense and react to environmental changes. This includes a varying spectrum of lipid ordering in the plasma membrane which signifies or enables cellular functions. Thus, comprehensive analyses of the plasma membrane can facilitate understanding of important cell biological elements which include insights into immune cells. Here, we describe two methods that can be used to assess membrane lipid state at the natural killer cell immunological synapse via high-resolution live cell imaging techniques.

The Origin of Lipid Rafts.

The time-averaged lateral organization of the lipids and proteins that make up mammalian cell membranes continues to be the subject of intense interest and debate. Since the introduction of the fluid mosaic model almost 50 years ago, the "lipid raft hypothesis" has emerged as a popular concept that has captured the imagination of a large segment of the biomembrane community. In particular, the notion that lipid rafts play a pivotal role in cellular processes such as signal transduction and membrane protein trafficking is now favored by many investigators. Despite the attractiveness of lipid rafts, their composition, size, lifetime, biological function, and even the very existence remain controversial. The central tenet that underlies this hypothesis is that cholesterol and high-melting lipids have favorable interactions (i.e., they pull together), which lead to transient domains. Recent nearest-neighbor recognition (NNR) studies have expanded the lipid raft hypothesis to include the influence that low-melting lipids have on the organization of lipid membranes. Specifically, it has been found that mimics of cholesterol and high-melting lipids are repelled (i.e., pushed away) by low-melting lipids in fluid bilayers. The picture that has emerged from our NNR studies is that lipid mixing is governed by a balance of these "push and pull" forces, which maximizes the number of hydrocarbon contacts and attractive van der Waals interactions within the membrane. The power of the NNR methodology is that it allows one to probe these push/pull interaction energies that are measured in tens of calories per mole.

Interaction of semiochemicals with model lipid membranes: A biophysical approach.

Unravelling the chemical language of insects has been the subject of intense research in the field of chemical ecology for the past five decades. Insect communication is mainly based on chemosensation due to the small body size of insects, which limits their ability to produce or perceive auditory and visual signals, especially over large distances. Chemicals involved in insect communication are called semiochemicals. These volatiles and semivolatiles compounds allow to Insects to find a mate, besides the oviposition site in reproduction and food sources. Actually, insect olfaction mechanism is subject to study, but systematic analyses of the role of neural membranes are scarce. In the present work we evaluated the interactions of α-pinene, benzaldehyde, eugenol, and grandlure, among others, with a lipid membrane model using surface pressure experiments and Monte Carlo computational analysis. This allowed us to propose a plausible membranotropic mechanism of interaction between semiochemicals and insect neural membrane.

Prediction of transition from ultra-high risk to first-episode psychosis using a probabilistic model combining history, clinical assessment and fatty-acid biomarkers.

Current criteria identifying patients with ultra-high risk of psychosis (UHR) have low specificity, and less than one-third of UHR cases experience transition to psychosis within 3 years of initial assessment. We explored whether a Bayesian probabilistic multimodal model, combining baseline historical and clinical risk factors with biomarkers (oxidative stress, cell membrane fatty acids, resting quantitative electroencephalography (qEEG)), could improve this specificity. We analyzed data of a UHR cohort (n=40) with a 1-year transition rate of 28%. Positive and negative likelihood ratios were calculated for predictor variables with statistically significant receiver operating characteristic curves (ROCs), which excluded oxidative stress markers and qEEG parameters as significant predictors of transition. We clustered significant variables into historical (history of drug use), clinical (Positive and Negative Symptoms Scale positive, negative and general scores and Global Assessment of Function) and biomarker (total omega-3, nervonic acid) groups, and calculated the post-test probability of transition for each group and for group combinations using the odds ratio form of Bayes' rule. Combination of the three variable groups vastly improved the specificity of prediction (area under ROC=0.919, sensitivity=72.73%, specificity=96.43%). In this sample, our model identified over 70% of UHR patients who transitioned within 1 year, compared with 28% identified by standard UHR criteria. The model classified 77% of cases as very high or low risk (P>0.9, <0.1) based on history and clinical assessment, suggesting that a staged approach could be most efficient, reserving fatty-acid markers for 23% of cases remaining at intermediate probability following bedside interview.

MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models.

A large number of modular domains that exhibit specific lipid binding properties are present in many membrane proteins involved in trafficking and signal transduction. These domains are present in either eukaryotic peripheral membrane or transmembrane proteins and are responsible for the non-covalent interactions of these proteins with membrane lipids. Here we report a profile Hidden Markov Model based method capable of detecting Membrane Binding Proteins (MBPs) from information encoded in their amino acid sequence, called MBPpred. The method identifies MBPs that contain one or more of the Membrane Binding Domains (MBDs) that have been described to date, and further classifies these proteins based on their position in respect to the membrane, either as peripheral or transmembrane. MBPpred is available online at http://bioinformatics.biol.uoa.gr/MBPpred. This method was applied in selected eukaryotic proteomes, in order to examine the characteristics they exhibit in various eukaryotic kingdoms and phyla.

Nanomedicine for Infectious Disease Applications: Innovation towards Broad-Spectrum Treatment of Viral Infections.

Nanomedicine enables unique diagnostic and therapeutic capabilities to tackle problems in clinical medicine. As multifunctional agents with programmable properties, nanomedicines are poised to revolutionize treatment strategies. This promise is especially evident for infectious disease applications, for which the continual emergence, re-emergence, and evolution of pathogens has proven difficult to counter by conventional approaches. Herein, a conceptual framework is presented that envisions possible routes for the development of nanomedicines as superior broad-spectrum antiviral agents against enveloped viruses. With lipid membranes playing a critical role in the life cycle of medically important enveloped viruses including HIV, influenza, and Ebola, cellular and viral membrane interfaces are ideal elements to incorporate into broad-spectrum antiviral strategies. Examples are presented that demonstrate how nanomedicine strategies inspired by lipid membranes enable a wide range of targeting opportunities to gain control of critical stages in the virus life cycle through either direct or indirect approaches involving membrane interfaces. The capabilities can be realized by enabling new inhibitory functions or improving the function of existing drugs through nanotechnology-enabled solutions. With these exciting opportunities, due attention is also given to the clinical translation of nanomedicines for infectious disease applications, especially as pharmaceutical drug-discovery pipelines demand new routes of innovation.

Structural and functional assessment of perilipin 2 lipid binding domain(s).

Although perilipin 2 (Plin2) has been shown to bind lipids with high affinity, the Plin2 lipid binding site has yet to be defined. This is of interest since Plin2's affinity for lipids has been suggested to be important for lipid droplet biogenesis and intracellular triacylglycerol accumulation. To define these regions, mouse Plin2 and several deletion mutants expressed as recombinant proteins and in mammalian cells were assessed by molecular modeling, fluorescence binding, circular dichroic, and fluorescence resonance energy transfer techniques to identify the structural and functional requirements for lipid binding. Major findings of this study indicate (1) the N-terminal PAT domain does not bind cholesterol or stearic acid; (2) Plin2 residues 119-251, containing helix α4, the α-ß domain, and part of helix α6 form a Plin3-like cleft found to be important for highest affinity lipid binding; (3) both stearic acid and cholesterol interact favorably with the Plin2 cleft formed by conserved residues in helix α6 and adjacent strands, which is common to all the active lipid-binding constructs; and (4) discrete targeting of the Plin2 mutants to lipid droplets supports Plin2 containing two independent, nonoverlapping lipid droplet targeting domains in its central and C-terminal sequences. Thus, the current work reveals specific domains responsible for Plin2-lipid interactions that involves the protein's lipid binding and targeting functions.

A cost-benefit analysis of the physical mechanisms of membrane curvature.

Many cellular membrane-bound structures exhibit distinct curvature that is driven by the physical properties of their lipid and protein constituents. Here we review how cells manipulate and control this curvature in the context of dynamic events such as vesicle-mediated membrane traffic. Lipids and cargo proteins each contribute energy barriers that must be overcome during vesicle formation. In contrast, protein coats and their associated accessory proteins drive membrane bending using a variety of interdependent physical mechanisms. We survey the energy costs and drivers involved in membrane curvature, and draw a contrast between the stochastic contributions of molecular crowding and the deterministic assembly of protein coats. These basic principles also apply to other cellular examples of membrane bending events, including important disease-related problems such as viral egress.

Nucleation in mesoscopic systems under transient conditions: peptide-induced pore formation in vesicles.

Attachment of lytic peptides to the lipid membrane of virions or bacteria is often accompanied by their aggregation and pore formation, resulting eventually in membrane rupture and pathogen neutralization. The membrane rupture may occur gradually via formation of many pores or abruptly after the formation of the first pore. In academic studies, this process is observed during interaction of peptides with lipid vesicles. We present an analytical model and the corresponding Monte Carlo simulations focused on the pore formation in such situations. Specifically, we calculate the time of the first nucleation-limited pore-formation event and show the distribution of this time in the regime when the fluctuations of the number of peptides attached to a vesicle are appreciable. The results obtained are used to clarify the mechanism of the pore formation and membrane destabilization observed recently during interaction of highly active α-helical peptide with sub-100-nm lipid vesicles that mimic enveloped viruses with nanoscale membrane curvature. The model proposed and the analysis presented are generic and may be applicable to other meso- and nanosystems.

Monte Carlo simulation of protein-induced lipid demixing in a membrane with interactions derived from experiment.

Lipid domain formation induced by annexin was investigated in mixtures of phosphatidylcholine (PC), phosphatidylserine (PS), and cholesterol (Chol), which were selected to mimic the inner leaflet of a eukaryotic plasma membrane. Annexins are ubiquitous and abundant cytoplasmic, peripheral proteins, which bind to membranes containing PS in the presence of calcium ions (Ca(2+)), but whose function is unknown. Prompted by indications of interplay between the presence of cholesterol in PS/PC mixtures and the binding of annexins, we used Monte Carlo simulations to investigate protein and lipid domain formation in these mixtures. The set of interaction parameters between lipids and proteins was assigned by matching experimental observables to corresponding variables in the calculations. In the case of monounsaturated phospholipids, the PS-PC and PC-Chol interactions are weakly repulsive. The interaction between protein and PS was determined based on experiments of annexin binding to PC/PS mixtures in the presence of Ca(2+). Based on the proposal that PS and cholesterol form a complex in model membranes, a favorable PS-Chol interaction was postulated. Finally, protein-protein favorable interactions were also included, which are consistent with observations of large, two-dimensional, regular arrays of annexins on membranes. Those net interactions between pairs of lipids, proteins and lipids, and between proteins are all small, of the order of the average kinetic energy. We found that annexin a5 can induce formation of large PS domains, coincident with protein domains, but only if cholesterol is present.

Assessment of two thawing processes of cryopreserved human sperm in pellets.

In this study, we evaluated the effects of the thawing methodology on sperm function after cryopreservation in pellets. We compared the use of two thawing procedures: method (1) maintaining pellet for 10 min in air at room temperature, then another 10-min period in air at 37°C followed by dilution in a thawing medium; and method (2) immersing the pellets directly in thawing medium at 37°C for 20 min. This procedure leads to a higher rate of temperature increase and a dilution of the glycerol present in the freezing medium. We analyzed the effect of the thawing procedure on sperm motility, viability, membrane lipid packing disorder, acrosome status, reactive oxygen species (ROS) level and sperm chromatin condensation. This study revealed a positive effect of the M2 thawing methodology on sperm parameters. The percentage of spermatozoa with fast-linear movement is increased (M1: 17.26% vs. M2: 28.05%, p<0.01), with higher viability (M1: 37.81% vs. M2: 40.15%, p<0.01) and less acrosome damage (M1: 40.44% vs. M2: 35.45%, p=0.02). We also detected an increase in the percentage of viable spermatozoa with low membrane lipid disorder (M1: 31.36% vs. M2: 33.17%, p=0.03) and a reduction in chromatin condensation (44.62 vs. 46.62 arbitrary units, p=0.02). Further studies will be necessary to evaluate the possible clinical applications.

Stochastic simulations of mixed-lipid compartments: from self-assembling vesicles to self-producing protocells.

The computational platform ENVIRONMENT, developed to simulate stochastically reaction systems in varying compartmentalized conditions [Mavelli and Ruiz-Mirazo: Philos Trans R Soc Lond B Biol Sci 362:1789-1802, 2007; Physical Biology 7(3): 036002, 2010], is here applied to study the dynamic properties and stability of model protocells that start producing their own lipid molecules (e.g., phospholipids), which get inserted in previously self-assembled vesicles, made of precursor amphiphiles (e.g., fatty acids). Attention is mainly focused on the changes that this may provoke in the permeability of the compartment, as well as in its eventual osmotic robustness.

Lipid-modulated sequence-specific association of glycophorin A in membranes.

Protein association in lipid membranes is a complex process with thermodynamics directed by a multitude of different factors. Amino-acid sequence is a molecular parameter that affects dimerization as shown by limited directed mutations along the transmembrane domains. Membrane-mediated interactions are also important although details of such contributions remain largely unclear. In this study, we probe directly the free energy of association of Glycophorin A by means of extensive parallel Monte Carlo simulations with recently developed methods and a model that accounts for sequence-specificity while representing lipid membranes faithfully. We find that lipid-induced interactions are significant both at short and intermediate separations. The ability of molecules to tilt in a specific hydrophobic environment extends their accessible interfaces, leading to intermittent contacts during protein recognition. The dimer with the lowest free energy is largely determined by the favorable lipid-induced attractive interactions at the closest distance. Finally, the coarse-grained model employed herein, together with the extensive sampling performed, provides estimates of the free energy of association that are in excellent agreement with existing data.

Activation of Bax by joint action of tBid and mitochondrial outer membrane: Monte Carlo simulations.

The mitochondrial pathway of apoptosis proceeds when molecules, such as cytochrome c, sequestered between the outer and inner mitochondrial membranes are released to the cytosol by mitochondrial outer membrane (MOM) permeabilization. Bax, a member of the Bcl-2 protein family, plays a pivotal role in mitochondrion-mediated apoptosis. In response to apoptotic stimuli, Bax integrates into the MOM, where it mediates the release of cytochrome c from the intermembrane space into the cytosol, leading to caspase activation and cell death. The pro-death action of Bax is regulated by interactions with both other prosurvival proteins, such as tBid, and the MOM, but the exact mechanisms remain largely unclear. Here, the mechanisms of integration of Bax into a model membrane mimicking the MOM were studied by Monte Carlo simulations preceded by a computer prediction of the docking of tBid with Bax. A novel model of Bax activation by tBid was predicted by the simulations. In this model, tBid binds to Bax at an interaction site formed by Bax helices alpha1, alpha2, alpha3 and alpha5 leading, due to interaction of the positively charged N-terminal fragment of tBid with anionic lipid headgroups, to Bax reorientation such that a hydrogen-bonded pair of residues, Asp98 and Ser184, is brought into close proximity with negatively charged lipid headgroups. The interaction with these headgroups destabilizes the hydrogen bond which results in the release of helix alpha9 from the Bax-binding groove, its insertion into the membrane, followed by insertion into the membrane of the alpha5-alpha6 helical hairpin.

Comparison of blood-brain barrier permeability assays: in situ brain perfusion, MDR1-MDCKII and PAMPA-BBB.

Permeability data from MDR1-MDCKII and PAMPA-BBB assays were compared to data from in situ brain perfusion to evaluate the accuracy of in vitro assays in predicting in vivo blood-brain barrier (BBB) permeability. PAMPA-BBB significantly correlated to in situ brain perfusion, however, MDR1-MDCKII had no correlation with in situ brain perfusion. PAMPA-BBB also significantly correlated with MDR1-MDCKII. The differential correlation of PAMPA-BBB and MDR1-MDCKII to in situ brain perfusion appears to be mainly due to the difference in membrane characteristics rather than binding to brain tissue. The MDR1-MDCKII cell membrane has lower ratios of: phospholipid to cholesterol, unsaturated to saturated acyl chains, and phosphatidyl-choline (PC) to sphingomyelin (SM) than brain endothelial cells, making it a poor passive permeability model for BBB. The BBB is more hydrophobic, rigid, and less fluidic than MDR1-MDCKII cell membrane. PAMPA-BBB more closely matches the BBB membrane in these characteristics and is a more accurate passive diffusion permeability model for BBB than MDR1-MDCKII. PAMPA-BBB is high throughput, low cost and has good prediction of in vivo BBB permeability, and therefore, it is a valuable tool in drug discovery to screen compounds for the rate of brain penetration.

Formation of irreversibly bound annexin A1 protein domains on POPC/POPS solid supported membranes.

The specific interaction of annexin A1 with phospholipid bilayers is scrutinized by means of scanning force and fluorescence microscopy, quartz crystal microbalance, ellipsometry, and modeled by dynamic Monte Carlo simulations. It was found that POPC/POPS bilayers exhibit phase separation in POPC- and POPS-enriched domains as a function of Ca2+ concentration. Annexin A1 interacts with POPC/POPS bilayers by forming irreversibly bound protein domains with monolayer thickness on POPS-enriched nanodomains, while the attachment of proteins to the POPC-enriched regions is fully reversible. A thorough kinetic analysis of the process reveals that both, the binding constant of annexin A1 at the POPC-rich areas as well as the irreversible adsorption rate to the POPS-rich domains increases with calcium ion concentration. Based on the thermodynamic and kinetic data, a possible mechanism of the annexin A1 membrane interaction can be proposed.

Oocyte cryopreservation: oocyte assessment and strategies for improving survival.

Despite significant progress in cryopreservation of mammalian oocytes and embryos, many ofthe molecular and biochemical events that underlie this technology are poorly understood. In recent years, researchers have focused on obtaining viable oocytes that are developmentally competent. Even under the most favourable conditions, experimental approaches have achieved only limited success compared with fresh oocytes used in routine in vitro embryo production. Chilling injuries and toxic effects of the cryoprotectants are the major adverse consequences following cryoprocedures. To overcome these problems, different strategies have been developed for improving cryopreservation results. These strategies include reducing container volumes, increasing the thermal gradient, changing the cell surface/volume ratio, enhancing cryotolerance by supplementation with various additives or modifying the lipid composition of the oocyte membrane. In order to develop new strategies for reducing the various forms of stress associated with oocyte cryopreservation, it is fundamental to gain a better understanding of the major changes responsible for poor post-thaw survival. With this knowledge, we hope that oocyte cryostorage will become a fully reliable reproductive technique in the near future.

The "bioeffect assessment index" (BAI). A concept for the quantification of effects of marine pollution by an integrated biomarker approach.

The "bioeffect assessment index" (BAI) is based on the integration of several pathological endpoints measured in the liver of European flounder (Platichthys flesus (L.)) during a long term study of biological effects of pollution in the German Bight. The BAI represents a modification of the "health assessment index" since it includes solely validated biomarkers reflecting toxically induced alterations at different levels of biological organisation in order to quantify the effects of environmental pollution. The concept of the BAI is based on the observation of progressive deleterious effects from early responses to late effects. Specific "key events" were detected, representing progressive stages of functional deterioration. The biomarkers selected from a whole battery of cellular markers for the BAI calculation reflect deleterious effects of various classes of contaminants such as heavy metals, organochlorines, pesticides, PAHs, and therefore reflect general toxicity in an integrative manner. Selected biomarkers were: lysosomal perturbations (reduced membrane stability), storage disorders (lipid accumulation) as early markers for toxic effects of liver cells, and the size of macrophage aggregates and their acid phosphatase activity. The latter two markers are indicative for the modulation of non-specific immune response which represents longer time scale responses after chronic exposure.

Mitochondrial function, energy expenditure, aging and insulin resistance.

Mitochondria are the cells' powerhouse that produce the ubiquitous energy currency (ATP) by consuming oxygen, producing water and building up the proton motive force. Oxygen consumption is a classical means of assessing energy expenditure, one component of energy balance. When energy balance is positive, weight increases. This is observed during the dynamic phase of obesity, and during body composition changes associated with aging. Whether intrinsic defaults in mitochondria occur is the matter of this review. Indeed, the ratio of ATP over oxygen consumed, which is not fixed, is one way of regulating heat release and ATP flux, but can also be the consequence of environmental conditions of mitochondrial work. For example, various hormones (T3, glucocorticoids), changes in lipid membrane composition, changes in food intake and exercise, and various drugs, can modify the ratio of ATP over oxygen consumed. Aging and insulin resistance are other regulators of this ratio. Finally there is a rising body of evidence linking diabetes to mitochondrial functions.

Lipid modulation of protein-induced membrane domains as a mechanism for controlling signal transduction.

The reason for the enormous lipid variety present in eukaryotic membranes remains largely an enigma. We suggest that its role is to provide an on-off switch for a signaling event at the membrane level. This is achieved through lipid-lipid interactions that convert membrane protein binding and association events into very cooperative processes while maintaining reversibility. We have previously shown [Hinderliter, A., at al. (2001) Biochemistry 40, 4181-4191] that thermodynamic linkage between an intrinsic tendency for lipid demixing and a preferential interaction of a protein with a specific lipid within the mixture leads to dramatic changes in lipid and protein domain formation. Here, we tested the hypothesis that small alterations in lipid chemical structure alter the magnitude of the net interaction free energy (omega(AB)) between unlike lipids in a predictable manner, and that even very small changes in omega(AB) lead to dramatic changes in bilayer organization when coupled with protein binding. We systematically varied the chemical structure of phosphatidylcholine (PC), in mixtures with a fixed phosphatidylserine (PS), by changing the PC acyl chain length and the degree of unsaturation, and examined domain formation upon addition of a peripheral protein, the synaptotagmin I C2A motif. Experimental excimer/monomer ratios (E/M) of pyrene-substituted lipids mimicking the PS were interpreted using Monte Carlo computer simulations. E/M is larger if the PC melting temperature is lower, suggesting that domain formation is a thermodynamic consequence of weak interactions between PC and PS. Consistent with our hypothesis, only very small changes in omega(AB) were required for prediction of large changes in lipid and protein domain formation.