Phosphoinositide-containing polymerized liposomes: stable membrane-mimetic vesicles for protein-lipid binding analysis

HIV-1 Gag MA domain binds to cardiolipin in a binding mode distinct from virus assemble mediator PI(4,5)P2

The human immunodeficiency virus type 1 (HIV-1) Gag protein is responsible for facilitating HIV-1 virion assembly and budding. Our study demonstrates that cardiolipin (CL), a component found in the inner mitochondrial membrane, exhibits the highest binding affinity to the N-terminal MA domain of the HIV-1 Gag protein within the lipid group of host cells. To assess this binding interaction, we synthesized short acyl chain derivatives of CL and employed surface plasmon resonance (SPR) analysis to determine the dissociation constants (Kd) for CL and the MA domain. Simultaneously, we examined the Kd of D-myo-phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2 ) derivatives, known to play a crucial role in virion formation. Among all the derivatives, Tetra-C7 -CL exhibited the lowest Kd value (Kd = 30.8 ± 6.9 μM) for MA binding on the CL analog-immobilized sensorchip, indicating a higher affinity. Similarly, the Kd value of Di-C7 -PIP2 (Kd = 36.6 ± 4.7 μM) was the lowest on the PI(4,5)P2 analog-immobilized sensorchip. Thus, Tetra-C7 -CL binds to the MA domain using a distinct binding mode while displaying a comparable binding affinity to Di-C7 -PIP2. This discovery holds significant implications for comprehending the virological importance of CL-MA domain binding, such as its subcellular distribution, including mitochondrial translocation, and involvement in viral particle formation in concert with PI(4,5)P2 . Furthermore, this study has the potential to contribute to the development of drugs in the future.

Structures and strategies for enhanced sensitivity of polydiacetylene(PDA) based biosensor platforms

Polydiacetylene (PDA) is a versatile polymer that has been studied in numerous fields because of its unique optical properties derived from alternating multiple bonds in the polymer backbone. The conjugated structure in the polymer backbone enables PDA to possess the ability of blue-red colorimetric transition when π-π interactions in the PDA backbone chain are disturbed by the external environment. The chromatic property of PDA disturbed by external stimuli can also emit fluorescence in the red region. Owing to the unique characteristics of PDA, it has been widely studied in facile and label-free sensing applications based on colorimetric or fluorescence signals for several decades. Among the various PDA structures, membrane structures assembled by amphiphilic molecules are widely used as a versatile platform because facile modification of the synthetic membrane provides extensive applications, such as receptor-ligand interactions, resulting in potent biosensors. To use PDA as a sensory material, several methods have been studied to endow the specificity to PDA molecules and to amplify the signal from PDA supramolecules. This is because selective and sensitive detection of target materials is required at an appropriate level corresponding to each material for applicable sensor applications. This review focuses on factors that affect the sensitivity of PDA composites and several strategies to enhance the sensitivity of the PDA sensor to various structures. Owing to these strategies, the PDA sensor system has achieved a higher level of sensitivity and selectivity, enabling it to detect multiple target materials for a full field of application.

Inhalable hybrid nanocarriers for respiratory disorders

Rapid advancements in the field of drug delivery lead to increased use of inhalable formulations as they are cost effective, noninvasive, and targeted and have less systemic side effects and above all better patient compliance. Development of inhalable hybrid systems has offered manifold advantages to this area of drug delivery. Inclusion of polymer and lipid, inorganic and organic substances, and metallic nanoparticles all of them aim to achieve codelivery of drugs which are incompatible in single phase systems. The recent progress in nanotechnology has gained momentum toward delivery of siRNA and miRNA and vaccines to the targeted site. The present work is an attempt to compile all the hybrid and inhalable systems to give readers an overview toward this delivery system as much more work is needed in this field to achieve better resolution of inflammatory disorders.

Clusters of Nanoscale Liposomes Modulate the Release of Encapsulated Species and Mimic the Compartmentalization Intrinsic in Cell Structures

We report the ability to place a high concentration of liposomes in a confined volume as a multicompartment cluster that mimics biological cells and allows for the modulation of release of encapsulated species. The formation of these coated multicompartmental structures is achieved by first binding liposomes into clusters before encapsulating them within a two-dimensional metal-organic framework composed of tannic acid coordinated with a metal ion. The essential feature is a molecularly thin skin over a ssystem of clustered liposomes in a pouch. The structural features of these pouches are revealed by small-angle scattering and electron microscopy. Through cryogenic electron microscopy, clusters with intact liposomes are observed that appear to be encapsulated within a pouch. Small-angle X-ray scattering shows the emergence of a relatively weak Bragg peak at q = 0.125 Å^-1, possibly indicating the attachment of the bilayers of adjacent liposomes. The metal-phenolic network (MPN) forms a nanosized conformal coating around liposome clusters, resulting in the reduced release rate of the encapsulated rhodamine B dye. We further show the possibility of communication between the adjacent nanocompartments in the cluster by demonstrating enhanced energy transfer using fluorescence resonance energy transfer (FRET) experiments where the lipophilic donor dye 3,3'-dioctadecyloxacarbocyanine perchlorate (DiO) incorporated within one liposomal compartment transfers energy upon excitation to the lipophilic acceptor dye 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) in a neighboring liposomal compartment due to their close proximity within the multicompartmental cluster. These observations have significance in adapting these multicompartmental structures that mimic biological cells for cascade reactions and as new depot drug delivery systems.

Quantitative Evaluation of Viral Protein Binding to Phosphoinositide Receptors and Pharmacological Inhibition

There is significant interest in developing analytical methods to characterize molecular recognition events between proteins and phosphoinositides, which are a medically important class of carbohydrate-functionalized lipids. Within this scope, one area of high priority involves quantitatively evaluating drug candidates that pharmacologically inhibit protein-phosphoinositide interactions. As full-length proteins are often difficult to produce, establishing methods to study these interactions with shorter, bioactive peptides would be advantageous. Herein, we report an atomic force microscopy (AFM)-based force spectroscopic approach to detect the specific interaction between an amphipathic, α-helical (AH) peptide derived from the hepatitis C virus NS5A protein and its biological target, the phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P₂] phosphoinositide receptor. After optimization of the peptide tethering strategy and measurement parameters, the binding specificity of AH peptide for PI(4,5)P₂ receptors was comparatively evaluated across a panel of phosphoinositides and the influence of ionic strength on AH-PI(4,5)P₂ binding strength was tested. Importantly, these capabilities were translated into the development of a novel experimental methodology to determine the inhibitory activity of a small-molecule drug candidate acting against the AH-PI(4,5)P₂ interaction, and extracted kinetic parameters agree well with literature values obtained by conventional biochemical methods. Taken together, our findings provide a nanomechanical basis for explaining the high binding specificity of the NS5A AH to PI(4,5)P₂ receptors, in turn establishing an analytical framework to study phosphoinositide-binding viral peptides and proteins as well as a broadly applicable approach to evaluate candidate inhibitors of protein-phosphoinositide interactions.

Structure and dynamics of cetyltrimethylammonium chloride-sodium dodecylsulfate (CTAC-SDS) catanionic vesicles: High-value nano-vehicles from low-cost surfactants

HYPOTHESIS

Catanionic vesicles based on large-scale produced surfactants represent a promising platform for the design of innovative, effective and relatively inexpensive nano-vehicles for a variety of actives. Structural, dynamic and functional behavior of these aggregates is finely tuned by the molecular features of their components and can be opportunely tailored for their applications as drug carriers.

EXPERIMENTS

Here we investigate the aggregates formed by CTAC and SDS, two of the most diffused surfactants, by means of Dynamic Light Scattering, Small Angle Neutron Scattering and Electron Paramagnetic Resonance spectroscopy (EPR). The exploitation of these aggregates as nano-vehicles is explored using the poorly water-soluble antioxidant trans-resveratrol (t-RESV), testing t-RESV solubility and antioxidant activity by means of UV, fluorescence spectroscopy and EPR.

FINDINGS

The presence of a large stability region of catanionic vesicles on the CTAC-rich side of the phase diagram is highlighted and interpreted in terms of the mismatch between the lengths of the surfactant tails and of first reported effects of the chloride counterions. CTAC-SDS vesicles massively solubilize t-RESV, which in catanionic vesicles exerts a potent antioxidant and radical-scavenging activity. This behavior arises from the positioning of the active at the surface of the vesicular aggregates thus being sufficiently exposed to the external medium.

Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2

To be incorporated into progeny virions, the viral genome must be transported to the inner leaflet of the plasma membrane (PM) and accumulate there. Some viruses utilize lipid components to assemble at the PM. For example, simian virus 40 (SV40) targets the ganglioside GM1 and human immunodeficiency virus type 1 (HIV-1) utilizes phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2]. Recent studies clearly indicate that Rab11-mediated recycling endosomes are required for influenza A virus (IAV) trafficking of vRNPs to the PM but it remains unclear how IAV vRNP localized or accumulate underneath the PM for viral genome incorporation into progeny virions. In this study, we found that the second intrinsically disordered region (IDR2) of NP regulates two binding steps involved in viral genome packaging. First, IDR2 facilitates NP oligomer binding to viral RNA to form vRNP. Secondly, vRNP assemble by interacting with PI(4,5)P2 at the PM via IDR2. These findings suggest that PI(4,5)P2 functions as the determinant of vRNP accumulation at the PM.

Single-Molecule Analysis of Lipid-Protein Interactions in Crude Cell Lysates

Recognition of signaling phospholipids by proteins is a critical requirement for the targeting and initiation of many signaling cascades. Most biophysical methods for measuring protein interactions with signaling phospholipids use purified proteins, which do not take into account the effect of post-translational modifications and other cellular components on these interactions. To potentially circumvent these problems, we have developed a single-molecule fluorescence approach to analyzing lipid-protein interactions in crude cell extracts. As a proof of principle for this assay, we show that a variety of lipid-binding domains (LBDs) can be recruited from cell lysates specifically onto their target phospholipids. With single-molecule analysis in real-time, our assay allows direct determination of binding kinetics for transient lipid-protein interactions and has revealed unique assembly properties and multiple binding modes of different LBDs. Whereas single-copy LBDs display transient interaction with lipid vesicles, tandem-repeat LBDs, often used as lipid biosensors, tend to form stable interactions that accumulate over time. We have extended the assay to study a cellular protein, Akt, and discovered marked differences in the lipid binding properties of the full-length protein compared to its PH domain. Importantly, we have found that phosphorylation of Akt at T308 and S473 does not affect the lipid binding behaviors of Akt, contrary to the long-standing model of Akt regulation. Overall, this work establishes the single-molecule lipid pulldown assay as a simple and highly sensitive approach to interrogating lipid-protein interactions in a setting that at least partly mimics the cellular environment.

Phosphatidylinositol phosphate kinase PIPKIγ and phosphatase INPP5E coordinate initiation of ciliogenesis

Defective primary cilia are causative to a wide spectrum of human genetic disorders, termed ciliopathies. Although the regulation of ciliogenesis is intensively studied, how it is initiated remains unclear. Here we show that type Iγ phosphatidylinositol 4-phosphate (PtdIns(4)P) 5-kinase (PIPKIγ) and inositol polyphosphate-5-phosphatase E (INPP5E), a Joubert syndrome protein, localize to the centrosome and coordinate the initiation of ciliogenesis. PIPKIγ counteracts INPP5E in regulating tau-tubulin kinase-2 (TTBK2) recruitment to the basal body, which promotes the removal of microtubule capping protein CP110 and the subsequent axoneme elongation. Interestingly, INPP5E and its product—PtdIns(4)P—accumulate at the centrosome/basal body in non-ciliated, but not ciliated, cells. PtdIns(4)P binding to TTBK2 and the distal appendage protein CEP164 compromises the TTBK2-CEP164 interaction and inhibits the recruitment of TTBK2. Our results reveal that PtdIns(4)P homoeostasis, coordinated by PIPKIγ and INPP5E at the centrosome/ciliary base, is vital for ciliogenesis by regulating the CEP164-dependent recruitment of TTBK2.

The primary cilium is essential for embryonic development and tissue pattern formation. Here the authors show that PIPKIγ localizes to the basal body of the primary cilium and cooperates with the Joubert Syndrome associated protein INPP5E to regulate the initiation of ciliogenesis.

A strategy for analyzing bond strength and interaction kinetics between Pleckstrin homology domains and PI(4,5)P2 phospholipids using force distance spectroscopy and surface plasmon resonance

Phospholipids are important membrane components involved in diverse biological activities ranging from cell signaling to infection by viral particles. A thorough understanding of protein-phospholipid interaction dynamics is thus crucial for deciphering basic cellular processes as well as for targeted drug discovery. For any specific phospholipid-protein binding experiment, various groups have reported different binding constants, which are strongly dependent on applied conditions of interactions. Here, we report a method for accurate determination of the binding affinity and specificity between proteins and phospholipids using a model interaction between PLC-δ1/PH and phosphoinositide phospholipid PtdIns(4,5)P2. We developed an accurate Force Distance Spectroscopy (FDS)-based assay and have attempted to resolve the problem of variation in the observed binding constant by directly measuring the bond force. We confirm the FDS findings of a high bond strength of ∼0.19 ± 0.04 nN by Surface Plasmon Resonance (SPR) data analysis, segregating non-specific interactions, which show a significantly lower K(D) suggesting tight binding.

Specificity of Collybistin-Phosphoinositide Interactions: IMPACT OF THE INDIVIDUAL PROTEIN DOMAINS

The regulatory protein collybistin (CB) recruits the receptor-scaffolding protein gephyrin to mammalian inhibitory glycinergic and GABAergic postsynaptic membranes in nerve cells. CB is tethered to the membrane via phosphoinositides. We developed an in vitro assay based on solid-supported 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membranes doped with different phosphoinositides on silicon/silicon dioxide substrates to quantify the binding of various CB2 constructs using reflectometric interference spectroscopy. Based on adsorption isotherms, we obtained dissociation constants and binding capacities of the membranes. Our results show that full-length CB2 harboring the N-terminal Src homology 3 (SH3) domain (CB2SH3+) adopts a closed and autoinhibited conformation that largely prevents membrane binding. This autoinhibition is relieved upon introduction of the W24A/E262A mutation, which conformationally "opens" CB2SH3+ and allows the pleckstrin homology domain to properly bind lipids depending on the phosphoinositide species with a preference for phosphatidylinositol 3-monophosphate and phosphatidylinositol 4-monophosphate. This type of membrane tethering under the control of the release of the SH3 domain of CB is essential for regulating gephyrin clustering.

Phosphatidylinositol 4,5-bisphosphate is an HCV NS5A ligand and mediates replication of the viral genome

BACKGROUND & AIMS

Phosphoinositides (PIs) bind and regulate localization of proteins via a variety of structural motifs. PI 4,5-bisphosphate (PI[4,5]P2) interacts with and modulates the function of several proteins involved in intracellular vesicular membrane trafficking. We investigated interactions between PI(4,5)P2 and hepatitis C virus (HCV) nonstructural protein 5A (NS5A) and effects on the viral life cycle.

METHODS

We used a combination of quartz crystal microbalance, circular dichroism, molecular genetics, and immunofluorescence to study specific binding of PI(4,5)P2 by the HCV NS5A protein. We evaluated the effects of PI(4,5)P2 on the function of NS5A by expressing wild-type or mutant forms of Bart79I or FL-J6/JFH-5'C19Rluc2AUbi21 RNA in Huh7 cells. We also studied the effects of strategies designed to inhibit PI(4,5)P2 on HCV replication in these cells.

RESULTS

The N-terminal amphipathic helix of NS5A bound specifically to PI(4,5)P2, inducing a conformational change that stabilized the interaction between NS5A and TBC1D20, which is required for HCV replication. A pair of positively charged residues within the amphipathic helix (the basic amino acid PI(4,5)P2 pincer domain) was required for PI(4,5)P2 binding and replication of the HCV-RNA genome. A similar motif was found to be conserved across all HCV isolates, as well as amphipathic helices of many pathogens and apolipoproteins.

CONCLUSIONS

PI(4,5)P2 binds to HCV NS5A to promote replication of the viral RNA genome in hepatocytes. Strategies to disrupt this interaction might be developed to inhibit replication of HCV and other viruses.

Catanionic vesicles and DNA complexes: a strategy towards novel gene delivery systems

Catanionic vesicles and DNA form complexes, the structure and composition of which depend on the DNA content. The DNA undergoes a reversible compaction process and its release can be triggered by adding an anionic surfactant to the complexes.

Characterization and stability of catanionic vesicles formed by pseudo-tetraalkyl surfactant mixtures

The phase behavior of an ad hoc synthesized surfactant, sodium 8-hexadecylsulfate (8-SHS), and its mixtures with didecyldimethylammonium bromide (DiDAB) in water is reported. We dealt with dilute concentration regimes, at a total surfactant content of <30 mmol kg(-1) where vesicular aggregates may be formed. The high synergistic behavior of such catanionic mixtures is concomitant with strongly negative interaction parameters, β (≈-18 kBT), significant gain in the free energy of association, ΔGagg, and much lower association concentration compared to the pure surfactants. Vesicle size and ζ-potential depend on the mixture composition. Hydrodynamic diameters increase by progressive addition of oppositely charged surfactants to the one in excess. Counter-intuitively, the ζ-potential becomes more negative at DiDAB molar fractions close to 0.2. The same holds in the reverse case, the ζ-potential becomes more positive after small additions of 8-SHS; anyhow, the effect is more significant in anionic-rich mixtures. This phenomenon was explained by assuming a significant release of counterions and an asymmetric distribution of the two surfactants in the inner and outer vesicle leaflets. The equimolar mixtures form a cubic phase rather than the expected lamellar one. The effect of NaBr concentration on the stability of catanionic vesicles was also investigated. At high NaBr concentrations, all systems are destabilized. For DiDAB-rich vesicles, flocculation is observed, while for 8-SHS-rich ones, lamellar domains are formed at the bottom of the samples. The role played by NaBr depends on whether it is added before or after mixing the surfactants. In particular, preformed catanionic vesicles show a great kinetic stability towards addition of NaBr compared to those obtained by other procedures.

Compositional redistribution and dynamic heterogeneity in mixed lipid membrane induced by polyelectrolyte adsorption: effects of chain rigidity

Monte Carlo simulation is employed to investigate the interaction between a polyelectrolyte and a fluid mixed membrane containing neutral (phosphatidyl-choline, PC), monovalent anionic (phosphatidylserine, PS), and multivalent anionic (phosphatidylinositol, PIP2) lipids. The effects of the intrinsic polyelectrolyte rigidity and solution ionic strength on the lateral rearrangement and dynamics of different anionic lipid species are systematically studied. Our results show that, the increase of polyelectrolyte chain rigidity reduces the loss of polyelectrolyte conformational entropy and the energy gains in electrostatic interaction, but raises the demixing entropy loss of the segregated anionic lipids. Therefore, the polyelectrolyte/membrane adsorption strength exhibits a non-monotonic dependence on the polyelectrolyte rigid parameter k ang, and there exists a certain optimal k ang for which the adsorption strength is maximal. Because the less loss of chain conformational entropy dominates the increase of the demixing entropy loss of the segregated anionic lipids and the decreases of the electrostatic energy gains, the semiflexible polyelectrolyte adsorbs onto the membrane more firmly than the flexible one. Whereas, for the adsorption of rigid polyelectrolyte, larger anionic lipid demixing entropy loss and less energy gain in the electrostatic interaction dominate over the decrease of the polyelectrolyte conformation entropy loss, leading to the desorption of the chain from the membrane. By decreasing the ionic concentration of the salt solution, the certain optimal k ang shifts to larger values. The cooperative effects of the adsorbing polyelectrolyte beads determine the concentration gradients and hierarchical mobility of the bound anionic lipids, as well as the polyelectrolyte dynamics.

Interaction of protein phosphatase inhibitors with membrane lipids assessed by surface plasmon resonance based binding technique

The interaction of okadaic acid (OA), tautomycin (TM), microcystin-LR (MC-LR), cantharidin (CA), epigallocatechin-gallate (EGCG) and cyclosporin A (CsA), inhibitors of protein phosphatases, with liposome covered surfaces prepared from the lipid extracts of bovine brain, heart and liver was investigated by surface plasmon resonance (SPR) based binding technique. The SPR sensorgrams indicated reversible association or partial intercalation of the inhibitors with liposomes at 20°C or 37°C, respectively. Distinct lipid composition specificities were reflected in different saturation values of inhibitor binding in a decreasing order of liver>heart>>brain lipids. Assaying the effect of OA, TM, MC-LR, CA and EGCG on the activity of protein phosphatases in neuroblastoma B50, cardiomyoblast H9C2 and hepatocarcinoma HepG2 cells implied that the cell type specific association of phosphatase inhibitors with membrane lipids may influence their inhibitory potencies exerted on intact cells.

Design and synthesis of lipid-coupled inositol 1,2,3,4,5,6-hexakisphosphate derivatives exhibiting high-affinity binding for the HIV-1 MA domain

Lipid-coupled inositol 1,2,3,4,5,6-hexakisphosphate binds to HIV-1 MA tightly through both electrostatic and hydrophobic interactions.

Autoreactivity and exceptional CDR plasticity (but not unusual polyspecificity) hinder elicitation of the anti-HIV antibody 4E10

The broadly-neutralizing anti-HIV antibody 4E10 recognizes an epitope in the membrane-proximal external region of the HIV envelope protein gp41. Previous attempts to elicit 4E10 by vaccination with envelope-derived or reverse-engineered immunogens have failed. It was presumed that the ontogeny of 4E10-equivalent responses was blocked by inherent autoreactivity and exceptional polyreactivity. We generated 4E10 heavy-chain knock-in mice, which displayed significant B cell dysregulation, consistent with recognition of autoantigen/s by 4E10 and the presumption that tolerance mechanisms may hinder the elicitation of 4E10 or 4E10-equivalent responses. Previously proposed candidate 4E10 autoantigens include the mitochondrial lipid cardiolipin and a nuclear splicing factor, 3B3. However, using carefully-controlled assays, 4E10 bound only weakly to cardiolipin-containing liposomes, but also bound negatively-charged, non-cardiolipin-containing liposomes comparably poorly. 4E10/liposome binding was predominantly mediated by electrostatic interactions rather than presumed hydrophobic interactions. The crystal structure of 4E10 free of bound ligands showed a dramatic restructuring of the combining site, occluding the HIV epitope binding site and revealing profound flexibility, but creating an electropositive pocket consistent with non-specific binding of phospholipid headgroups. These results strongly suggested that antigens other than cardiolipin mediate 4E10 autoreactivity. Using a synthetic peptide library spanning the human proteome, we determined that 4E10 displays limited and focused, but unexceptional, polyspecificity. We also identified a novel autoepitope shared by three ER-resident inositol trisphosphate receptors, validated through binding studies and immunohistochemistry. Tissue staining with 4E10 demonstrated reactivity consistent with the type 1 inositol trisphosphate receptor as the most likely candidate autoantigen, but is inconsistent with splicing factor 3B3. These results demonstrate that 4E10 recognition of liposomes competes with MPER recognition and that HIV antigen and autoepitope recognition may be distinct enough to permit eliciting 4E10-like antibodies, evading autoimmunity through directed engineering. However, 4E10 combining site flexibility, exceptional for a highly-matured antibody, may preclude eliciting 4E10 by conventional immunization strategies.

Selective and ATP-driven transport of ions across supported membranes into nanoporous carriers using gramicidin A and ATP synthase

We report a robust and versatile membrane protein based system for selective uptake and release of ions from nanoporous particles sealed with ion-tight lipid bilayers of various compositions that is driven by the addition of ATP or a chemical potential gradient. We have successfully incorporated both a passive ion channel-type peptide (gramicidin A) and a more complex primary sodium ion transporter (ATP synthase) into the supported lipid bilayers on solid nanoporous silica particles. Protein-mediated controlled release/uptake of sodium ions across the ion-tight lipid bilayer seal from or into the nanoporous silica carrier was imaged in real time using a confocal laser scanning microscope and the intensity changes were quantified. ATP-driven transport of sodium ions across the supported lipid bilayer against a chemical gradient was demonstrated. The possibility of designing durable carriers with tight lipid membranes, containing membrane proteins for selective ion uptake and release, offers new possibilities for functional studies of single or cascading membrane protein systems and could also be used as biomimetic microreactors for controlled synthesis of inorganic multicomponent materials.

Microarray analysis of Akt PH domain binding employing synthetic biotinylated analogs of all seven phosphoinositide headgroup isomers

Signaling lipids control many of the most important biological pathways, typically by recruiting cognate protein binding targets to cell surfaces, thereby regulating both their function and subcellular localization. A critical family of signaling lipids is that of the phosphatidylinositol polyphosphates (PIP(n)s), which is composed of seven isomers that vary based on phosphorylation pattern. A key protein that is activated upon PIP(n) binding is Akt, which then plays important roles in regulating the cell cycle, and is thus aberrant in disease. Characterization of protein-PIP(n) binding interactions is hindered by the complexity of the membrane environment and of the PIP(n) structures. Herein, we describe two rapid assays of use for characterizing protein-PIP(n) binding interactions. First, a microplate-based binding assay was devised to characterize the binding of effectors to immobilized synthetic PIP(n) headgroup-biotin conjugates corresponding to all seven isomers. The assay was implemented for simultaneous analysis of Akt-PH domain, indicating PI(3,4,5)P(3) and PI(3,4)P(2) as the primary ligands. In addition, density-dependant studies indicated that the amount of ligand immobilized on the surface affected the amplitude of protein binding, but not the affinity, for Akt-PH. Since the PIP(n) ligand motifs used in this analysis lack the membrane environment and glycerolipid backbone, yet still exhibit high-affinity protein binding, these results narrow down the structural requirements for Akt recognition. Additionally, binding detection was also achieved through microarray analysis via the robotic pin printing of ligands onto glass slides in a miniaturized format. Here, fluorescence-based detection provided sensitive detection of binding using minimal amounts of materials. Due to their high-throughput and versatile attributes, these assays provide invaluable tools for probing and perturbing protein-membrane binding interactions.

Quantitative detection of glyphosate by simultaneous analysis of UV spectroscopy and fluorescence using DNA-labeled gold nanoparticles

A sandwich-type immunosensor composed of antigen-double target/probe DNA-coated gold nanoparticles (NPs) was developed for the measurement of fluorescence intensity and quantitative analysis of single-stranded DNA based on the concentration of free glyphosate. The reaction between the antigen-double DNA-gold NPs and immobilized antibody on the substrate was carried out for 2 h. The results of the antigen-antibody reaction were measured on the basis of the fluorescence intensity obtained from comparison with the free antigens at concentrations of 0.01-100 μg mL(-1) for the detection of immobilized antigen-double DNA-gold NPs. For the quantitative analysis based on the concentration of glyphosate(0.01-100 μg mL(-1)), the immunosensor response also revealed the same detection range of glyphosate using DNA detection.

High affinity binding to profilin by a covalently constrained, soluble mimic of phosphatidylinositol-4,5-bisphosphate micelles

Phosphoinositide (PI) lipids are essential regulators of a wide variety of cellular functions. We present here the preparation of a multivalent analogue of a phosphatidylinositol-4,5-bisphosphate (PIP(2)) micelle containing only the polar headgroup portion of this lipid. We show that this dendrimer binds to the cytoskeletal protein profilin with an affinity indistinguishable from that of PIP(2), despite the fact that profilin discriminates between PIP(2) and its monomeric hydrolysis product inositol-1,4,5-triphosphate (IP(3)) under physiological conditions. These data demonstrate that the diacylglycerol (DAG) moiety of PIP(2) is not required for high-affinity binding and suggest that profilin uses multivalency as a key means to distinguish between the intact lipid and IP(3). The class of soluble membrane analogues described here is likely to have broad applicability in the study of protein.PI interactions.

Fabrication of fracture-free nanoglassified substrates by layer-by-layer deposition with a paint gun technique for real-time monitoring of protein-lipid interactions

New sensing materials that are robust, biocompatible, and amenable to array fabrication are vital to the development of novel bioassays. Herein we report the fabrication of ultrathin (ca. 5-8 nm) glass (silicate) layers on top of a gold surface for surface plasmon resonance (SPR) biosensing applications. The nanoglass layers are fabricated by layer-by-layer (LbL) deposition of poly(allylamine) hydrochloride (PAH) and sodium silicate (SiO(x)), followed by calcination at high temperature. To deposit these layers in a uniform and reproducible manner, we employed a high-volume, low-pressure (HVLP) paint gun technique that offers high precision and better control through pressurized nitrogen gas. The new substrates are stable in solution for a long period of time, and scanning electron microscopy (SEM) images confirm that these films are nearly fracture-free. In addition, atomic force microscopy (AFM) indicates that the surface roughness of the silicate layers is low (rms = 2 to 3 nm), similar to that of bare glass slides. By tuning the experimental parameters such as HVLP gun pressure and layers deposited, different surface morphology could be obtained as revealed by fluorescence microscopy and SEM images. To demonstrate the utility of these ultrathin, fracture-free substrates, lipid bilayer membranes composed of phosphorylated derivatives of phosphoinositides (PIs) were deposited on the new substrates for biosensing applications. Fluorescence recovery after photobleaching (FRAP) data indicated that these lipid components in the membranes were highly mobile. Furthermore, interactions of PtdIns(4,5)P2 and PtdIns(4)P lipids with their respective binding proteins were detected with high sensitivity by using SPR spectroscopy. This method of glass deposition can be combined with already well-developed surface chemistry for a range of planar glass assay applications, and the process is amenable to automation for mass production of nanometer thick silicate chips in a highly reproducible manner for label-free measurements.

Live cell imaging of phosphoinositides with expressed inositide binding protein domains

Inositol lipids and calcium signaling has been inseparable twins during the 1980s when the molecular details of phospholipase C-mediated generation of inositol 1,4,5-trisphosphate (InsP3) and its Ca2+ mobilizing action were discovered. Since then, both the Ca2+ and inositol lipid signaling fields have hugely expanded and the tools allowing dissection of the finest details of their molecular organization also followed closely. Although phosphoinositides regulate many cell functions unrelated to Ca2+ signaling there are still many open questions even in the Ca2+ field that would benefit from single cell monitoring of PtdIns(4,5)P2 or InsP3 changes during agonist stimulation. This chapter is designed to provide practical guidance as well as some theoretical background on measurements of phosphoinositides in live cells using protein domain-GFP chimeras that could be also useful for people working on calcium signaling.

Protein binding onto surfactant-based synthetic vesicles

Synthetic vesicles were prepared by mixing anionic and cationic surfactants, aqueous sodium dodecylsulfate with didodecyltrimethylammonium or cetyltrimethylammonium bromide. The overall surfactant content and the (anionic/cationic) mole ratios allow one to obtain negatively charged vesicles. In the phase diagram, the vesicular region is located between a solution phase, a lamellar liquid crystalline dispersion, and a precipitate area. Characterization of the vesicles was performed by electrophoretic mobility, NMR, TEM, and DLS and we determined their uni-lamellar character, size, stability, and charge density. Negatively charged vesicular dispersions, made of sodium dodecylsulfate/didodecyltrimethylammonium bromide or sodium dodecylsulfate/cetyltrimethylammonium bromide, were mixed with lysozyme, to form lipoplexes. Depending on the protein/vesicle charge ratio, binding, surface saturation, and lipoplexes flocculation, or precipitation, occurs. The free protein in excess remains in solution, after binding saturation. The systems were investigated by thermodynamic (surface tension and solution calorimetry), DLS, CD, TEM, 1H NMR, transport properties, electrophoretic mobility, and dielectric relaxation. The latter two methods give information on the vesicle charge neutralization by adsorbed protein. Binding is concomitant to modifications in the double layer thickness of vesicles and in the surface charge density of the resulting lipoplexes. This is also confirmed by developing the electrophoretic mobility results in terms of a Langmuir-like adsorption isotherm. Charges in excess with respect to the amount required to neutralize the vesicle surface promote lipoplexes clustering and/or flocculation. Protein-vesicle interactions were observed by DLS, indicating changes in particle size (and in their distribution functions) upon addition of LYSO. According to CD, the bound protein retains its native conformation, at least in the SDS/CTAB vesicular system. In fact, changes in the alpha-helix and beta-sheet conformations are moderate, if any. Calorimetric methods indicate that the maximum heat effect for LYSO binding occurs at charge neutralization. They also indicate that enthalpic are by far the dominant contributions to the system stability. Accordingly, energy effects associated with charge neutralization and double-layer contributions are much higher than counterion exchange and dehydration terms.

Synthesis and Characterization of Covalent Mimics of Phosphatidylinositol-4,5-bisphosphate Micelles

There is increasing evidence that multivalency plays an important role in protein-lipid recognition and membrane targeting in biological systems. We describe here the preparation and characterization of multivalent analogues of the signaling lipid phosphatidylinositol-4,5-bisphosphate (PIP2). Tetherable analogues of the PIP2 headgroup were appended to polyamidoamine dendrimers via a squarate linker to afford polymers displaying four or eight headgroup moieties. This class of molecules should provide a powerful tool for the study of protein-lipid interactions.

Analyzing phosphoinositides and their interacting proteins

Phosphorylated derivatives of phosphatidylinositol (PtdIns), known as phosphoinositides (PIs), are essential regulators of nuclear functions, cytoskeletal dynamics, cell signaling and membrane trafficking. These lipids are found on the cytosolic face of intracellular membranes but can also be detected in membrane-free regions of the nucleoplasm. Their downstream effectors include several proteins that contain various PI-specific domains. Because impaired PI metabolism is associated with disorders such as cancer, cardiovascular disease and immune dysfunction, there is currently great interest in studying PIs and their metabolic enzymes. Here we describe strategies and techniques for quantitative and qualitative measurement of PIs, for characterization of specific PI-binding proteins and for determination of PI kinase and phosphatase activities in vitro and in vivo.

Survey of the year 2005 commercial optical biosensor literature

We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.