Lipid-mediated Interactions Research Articles

The membrane phase transition drives tunable assembly and function of B cell receptor signaling domains.

Clustering the B cell receptor (BCR) leads to assembly of a signaling platform with a distinct protein and lipid composition, creating a local membrane environment that facilitates interactions between signaling proteins and influences downstream responses. While many studies have linked BCR activation to “lipid rafts”, the lack of a structural correlate measured in intact cells impedes using these observations in a predictive model of the immune response. We systematically compared membrane organization in cells and plasma membrane vesicles using quantitative super-resolution imaging of a panel of fluorescent membrane anchor probes. We observed agreement between probe enrichment in BCR clusters and ordered phase partitioning in membrane vesicles, indicating that membrane phase separation is an underlying mechanism for assembly of functional domains. We showed that an ordered membrane domain emerges upon BCR clustering in which lipid-mediated interactions are sufficient to alter local membrane composition. To connect domain formation back to BCR activation, we employed two strategies to modulate the contrast between the composition of BCR proximal domains and the surrounding membrane. We altered the protein composition of BCR clusters by co-ligating BCR with engineered minimal “co-receptors” that favor or oppose ordered domain formation. We also used chemical treatments that enhance or suppress membrane phase separation overall. We found that not only is the contrast of BCR cluster domains variable and influenced by the nature of the stimulus and thermodynamics of the membrane, but the extent of BCR phosphorylation also varies with domain contrast. This dependence of activation on domain contrast extends to downstream signaling events as well as to other immune receptor systems. Together, these data suggest that domain formation at BCR clusters driven by membrane phase separation provides a mechanism to produce a tunable activation response.

Aggregation and mobility of membrane proteins interplay with local lipid order in the plasma membrane of T cells.

To disentangle the elusive lipid-protein interactions in T-cell activation, we investigate how externally imposed variations in mobility of key membrane proteins (T-cell receptor [TCR], kinase Lck, and phosphatase CD45) affect the local lipid order and protein colocalisation. Using spectral imaging with polarity-sensitive membrane probes in model membranes and live Jurkat T cells, we find that partial immobilisation of proteins (including TCR) by aggregation or ligand binding changes their preference towards a more ordered lipid environment, which can recruit Lck. Our data suggest that the cellular membrane is poised to modulate the frequency of protein encounters upon alterations of their mobility, for example in ligand binding, which offers new mechanistic insight into the involvement of lipid-mediated interactions in membrane-hosted signalling events.

Antimicrobial peptides: mechanism of action and lipid-mediated synergistic interactions within membranes.

Biophysical and structural studies of peptide-lipid interactions, peptide topology and dynamics have changed our view of how antimicrobial peptides insert and interact with membranes. Clearly, both peptides and lipids are highly dynamic, and change and mutually adapt their conformation, membrane penetration and detailed morphology on a local and a global level. As a consequence, peptides and lipids can form a wide variety of supramolecular assemblies in which the more hydrophobic sequences preferentially, but not exclusively, adopt transmembrane alignments and have the potential to form oligomeric structures similar to those suggested by the transmembrane helical bundle model. In contrast, charged amphipathic sequences tend to stay intercalated at the membrane interface. Although the membranes are soft and can adapt, at increasing peptide density they cause pronounced disruptions of the phospholipid fatty acyl packing. At even higher local or global concentrations the peptides cause transient membrane openings, rupture and ultimately lysis. Interestingly, mixtures of peptides such as magainin 2 and PGLa, which are stored and secreted naturally as a cocktail, exhibit considerably enhanced antimicrobial activities when investigated together in antimicrobial assays and also in pore forming experiments applied to biophysical model systems. Our most recent investigations reveal that these peptides do not form stable complexes but act by specific lipid-mediated interactions and the nanoscale properties of phospholipid bilayers.

Contribution of allosteric disulfide in the structural regulation of membrane-bound tissue factor–factor VIIa binary complex

Two distinct populations, active and cryptic forms of tissue factor (TF), reside on the cell surface. Apart from phospholipid contribution, various models have been introduced to explain decryption/encryption of TF. The proposed model, the switching of Cys186–Cys209 bond of TF, has become the matter of controversy. However, it is well accepted that this disulfide has an immense influence upon ligand factor VIIa (FVIIa) for its binding. However, molecular level understanding for this remains unveiled due to lack of detailed structural information. In this regard, we have performed the molecular dynamic study of membrane-bound TF/TF–FVIIa in both the forms (±Cys186–Cys209 allosteric disulfide bond), individually. Dynamic study depicts that disulfide bond provides structural rigidity of TF in both free and ligand-bound forms. This disulfide bond also governs the conformation of FVIIa structure as well as the binding affinity of FVIIa toward TF. Significant differences in lipid–protein interaction profiles of both the forms of TF in the complex were observed. Two forms of TF, oxidized and reduced, have different structural conformation and behave differentially toward its ligand FVIIa. This disulfide bond not only alters the conformation of GLA domain of FVIIa in the vicinity but allosterically regulates the conformation of the distantly located FVIIa protease domain. We suggest that the redox status of the disulfide bond also governs the lipid-mediated interactions with both TF and FVIIa.Communicated by Ramaswamy H. Sarma

Lipid-Mediated Interactions between the Antimicrobial Peptides Magainin 2 and PGLa in Bilayers

A synergistic enhancement of activities has been described for the amphipathic cationic antimicrobial peptides magainin 2 and PGLa when tested in antimicrobial assays or in biophysical experiments using model membranes. In the presence of magainin 2, PGLa changes from an in-planar alignment parallel to the membrane surface to a more transmembrane orientation when investigated in membranes made from fully saturated PC or PC/PG, but not when one of the fatty acyl chains is unsaturated. Such lipid-mediated changes in the membrane topology of polypeptide domains could provide an interesting mechanism for the regulation of membrane proteins. Here we investigated the PGLa topology in a wide variety of membranes made of saturated or unsaturated PE, PC, and/or PG using 15N solid-state NMR spectroscopy. In contrast to predictions made by previous models the data show that membrane curvature has only a minor effect on PGLa realignment. Furthermore, using 2H solid-state NMR spectroscopy of deuterated phospholipid fatty acyl chains the order parameters of the lipids were investigated in the presence of PGLa, magainin, or equimolar peptide mixtures. Both peptides cause a pronounced decrease in the order parameters when oriented parallel to the membrane surface, an effect that reverts when PGLa flips into transmembrane alignments. Taken together, these data are suggestive that the magainin-induced disordering of fatty acyl chains provides an important driving force for PGLa realignment.

Pore formation by dimeric Bak and Bax: an unusual pore?

Apoptotic cell death via the mitochondrial pathway occurs in all vertebrate cells and requires the formation of pores in the mitochondrial outer membrane. Two Bcl-2 protein family members, Bak and Bax, form these pores during apoptosis, and how they do so has been investigated for the last two decades. Many of the conformation changes that occur during their transition to pore-forming proteins have now been delineated. Notably, biochemical, biophysical and structural studies indicate that symmetric homodimers are the basic unit of pore formation. Each dimer contains an extended hydrophobic surface that lies on the outer membrane, and is anchored at either end by a transmembrane domain. Membrane-remodelling events such as positive membrane curvature have been reported to accompany apoptotic pore formation, suggesting Bak and Bax form lipidic pores rather than proteinaceous pores. However, it remains unclear how symmetric dimers assemble to porate the membrane. Here, we review how clusters of dimers and their lipid-mediated interactions provide a molecular explanation for the heterogeneous assemblies of Bak and Bax observed during apoptosis.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

Magainin 2-PGLa Interactions in Membranes - Two Peptides that Exhibit Synergistic Enhancement of Antimicrobial Activity.

The structural requirements for the synergistic enhancement of antimicrobial activities of the cationic linear peptides PGLa and magainin 2 were investigated. In a first step the antimicrobial activities were evaluated for a number of modifications of the sequences and equimolar mixtures thereof. In particular fluorophore labelled peptides maintain a high degree of antimicrobial activity and considerable synergism when tested conjointly. Thereafter, circular dichroism spectroscopy indicated that these extended sequences adopt helical conformations in the presence of model membranes similar to the unmodified sequences. Energy transfer between the fluorophores suggested that the peptides reside in close proximity to each other when bound to the membrane surface at high concentrations. The fluorophore interactions quickly diminish at lower peptide-to-lipid ratios indicating that the peptide-peptide interactions are weak. Furthermore, (15)N solid-state NMR measurements of the membrane topology of [(15)N-Ala14]-PGLa and of its fluorophorecarrying analogue reconstituted into supported 1, 2-didecanoyl-sn-glycero-3-phosphocholine bilayers were performed. These experiments revealed no correlation between the topological state of PGLa and the observed synergistic enhancement of antimicrobial activities due to the presence of magainins. These results suggest that lipid mediated interactions rather than the formation of tight peptide-peptide complexes in the membrane are responsible for synergistic activities of the mixtures.

Lipid-Mediated Polypeptide Interactions in Membranes: Case Study on the Synergism Between Linear Cationic Antimicrobial Peptides

Biophysical investigations, that aim to explain the antimicrobial activities of cationic linear peptides will be presented (1,2). In particular we aim to understand how some mixtures of these peptides exhibit synergistic activities. Therefore, the structure, topology and dynamics of PGLa and magainin 2 were investigated in oriented phospholipid bilayers using solid-state NMR in the presence or absence of the other peptide and as a function of the membrane lipid composition (2,3). Furthermore, fluorescence spectroscopy was used to investigate how the peptides interact with each other within the lipid bilayer environment.Whereas, magainin 2 exhibits stable in-planar alignments under all conditions investigated PGLa adopts a number of different membrane topologies with considerable tilt angle variations (2,3). Notably, the hydrophobic thickness modulates the alignment of PGLa (1). In equimolar mixtures of PGLa and magainin 2 the former adopts transmembrane orientations in DMPC when at the same time magainin 2 remains associated with the surface (1). In contrast in bilayers, which represents better the natural membrane composition (1-palmitoyl-2-oleoyl-phospholipids), both peptides adopt a surface oriented topology. Therefore, lipid-mediated interactions play a fundamental role in determining the topology of membrane peptides and proteins (3) and thereby potentially also the regulation of their activities. These results have important consequences for the mechanistic models explaining synergistic activities of the peptide mixtures and will be discussed in the context of unpublished data where membrane structure and interactions are correlated with biological activities. Furthermore, recent results obtained with DNP enhanced solid-state NMR spectroscopy of supported lipid bilayer samples using prototype equipment will be presented.

Lateral organization of biological membranes

The lateral organization of biological membranes is of great importance in many biological processes, both for the formation of specific structures such as super-complexes and for function as observed in signal transduction systems. Over the last years, AFM studies, particularly of bacterial photosynthetic membranes, have revealed that certain proteins are able to segregate into functional domains with a specific organization. Furthermore, the extended non-random nature of the organization has been suggested to be important for the energy and redox transport properties of these specialized membranes. In the work reported here, using a coarse-grained Monte Carlo approach, we have investigated the nature of interaction potentials able to drive the formation and segregation of specialized membrane domains from the rest of the membrane and furthermore how the internal organization of the segregated domains can be modulated by the interaction potentials. These simulations show that long-range interactions are necessary to allow formation of membrane domains of realistic structure. We suggest that such possibly non-specific interactions may be of great importance in the lateral organization of biological membranes in general and in photosynthetic systems in particular. Finally, we consider the possible molecular origins of such interactions and suggest a fundamental role for lipid-mediated interactions in driving the formation of specialized photosynthetic membrane domains. We call these lipid-mediated interactions a 'lipophobic effect.'

Interplay of cytoskeletal activity and lipid phase stability in dynamic protein recruitment and clustering

Recent experiments have revealed that some membrane proteins aggregate to form clusters. This type of process has been proven to be dynamic and to be actively maintained by external kinetics. Additionally, this dynamic recruiting is cholesterol- and actin-dependent, suggesting that raft organization and cytoskeleton rearrangement play a crucial role. In the present study, we propose a simple model that provides a general framework to describe the dynamical behavior of lipid-protein assemblies. Our results suggest that lipid-mediated interactions and cytoskeleton-anchored proteins contribute to the modulation of such behavior. In particular, we find a resonant condition between the membrane protein and cytoskeleton dynamics that results in the invariance of the ratio of clustered proteins that is found in in vivo experimental observations.

Determination of binding curves via protein micropatterning in vitro and in living cells

Quantification of protein interactions in living cells is of key relevance for understanding cellular signaling. With current techniques, however, it is difficult to determine binding affinities and stoichiometries of protein complexes in the plasma membrane. We introduce here protein micropatterning as a convenient and versatile method for such investigations. Cells are grown on surfaces containing micropatterns of capture antibody to a bait protein, so that the bait gets rearranged in the live cell plasma membrane. Upon interaction with the bait, the fluorescent prey follows the micropatterns, which can be readout with fluorescence microscopy. In this study, we addressed the interaction between Lck and CD4, two central proteins in early T-cell signaling. Binding curves were recorded using the natural fluctuations in the Lck expression levels. Surprisingly, the binding was not saturable up to the highest Lck expression levels: on average, a single CD4 molecule recruited more than nine Lck molecules. We discuss the data in view of protein- and lipid-mediated interactions.

Shape as a determinant of membrane protein cluster formation

Cluster formation of membrane proteins is a crucial event in many vital cellular processes. Here, we present a thorough examination of the oligomerisation ability of membrane proteins with different geometries. By means of mesoscopic membrane simulations we show that lipid-mediated interactions between proteins depend both on the shape of the hydrophobic domain of the proteins and on their hydrophobic mismatch. Based on that, we find that protein interactions can be either attractive or repulsive, depending on the characteristic bilayer perturbations induced by the proteins. The influence of these perturbations is quantified via the associated potential of mean force. Such geometry-dependent interactions are likely to fine-tune protein oligomerization events during cellular processes, for example signal transduction or protein sorting.

Interaction of C70 fullerene with the Kv1.2 potassium channel

Fullerene C(70) is known to partition into lipid membranes and change their physical properties. Together with gallic acid (GA), C(70) induces cell contraction and cell death. How C(70) and GA-induced perturbations of lipid membranes affect cellular function and membrane protein activity is not understood, though. Meanwhile, fullerene is also known to interfere with the activity of potassium channel proteins, but the mechanisms of protein inhibition are not known. Here we consider the possibility that membrane protein function would be inhibited by C(70) and/or GA through direct contact or through lipid-mediated interactions. To this end, we use microsecond time scale atomistic simulations to explore (a) modifications of membrane properties in the presence of C(70) and/or GA, and (b) the possible conformational changes in Kv1.2, a voltage-gated potassium channel, upon exposure to C(70), or GA, or both. C(70) is found to have an observable effect on structural and elastic properties of protein-free membranes, while the effects of GA on the membrane are less evident. Fullerene–GA interaction is strong and affects significantly the partitioning of C(70) in the membrane, stabilizing C(70) in the aqueous phase. When Kv1.2 is exposed to the solutes, only small conformational changes are observed on the microsecond time scale – comparable to the fluctuations observed in the absence of any solute. Blocking of the channel entrance is not observed, as fullerene binds mainly to hydrophobic residues, both in the water-exposed loops and in the transmembrane helices. The tilt angle of transmembrane helices in the voltage-sensing domain appears to be affected by direct contact with fullerene, but a generic effect due to the small increase in membrane thickness might also play a role. A small rotation of the S3 and S4 helices in the voltage-sensing domain is noticed when C(70) is embedded in the membrane. The interpretation of the observed conformational changes is not straightforward due to the associated time scales, which are difficult to sample with state-of-the-art computing resources. We cannot exclude that both membrane-mediated interactions and specific protein–solute interactions affect the conformation of the protein.

Lipid-Controlled Peptide Topology and Interactions in Bilayers: Structural Insights into the Synergistic Enhancement of the Antimicrobial Activities of PGLa and Magainin 2

To gain further insight into the antimicrobial activities of cationic linear peptides, we investigated the topology of each of two peptides, PGLa and magainin 2, in oriented phospholipid bilayers in the presence and absence of the other peptide and as a function of the membrane lipid composition. Whereas proton-decoupled 15N solid-state NMR spectroscopy indicates that magainin 2 exhibits stable in-plane alignments under all conditions investigated, PGLa adopts a number of different membrane topologies with considerable variations in tilt angle. Hydrophobic thickness is an important parameter that modulates the alignment of PGLa. In equimolar mixtures of PGLa and magainin 2, the former adopts transmembrane orientations in dimyristoyl-, but not 1-palmitoyl-2-oleoyl-, phospholipid bilayers, whereas magainin 2 remains associated with the surface in all cases. These results have important consequences for the mechanistic models explaining synergistic activities of the peptide mixtures and will be discussed. The ensemble of data suggests that the thinning of the dimyristoyl membranes caused by magainin 2 tips the topological equilibrium of PGLa toward a membrane-inserted configuration. Therefore, lipid-mediated interactions play a fundamental role in determining the topology of membrane peptides and proteins and thereby, possibly, in regulating their activities as well.

Molecular Simulation of the Effect of Cholesterol on Lipid-Mediated Protein-Protein Interactions

Experiments and molecular simulations have shown that the hydrophobic mismatch between proteins and membranes contributes significantly to lipid-mediated protein-protein interactions. In this article, we discuss the effect of cholesterol on lipid-mediated protein-protein interactions as function of hydrophobic mismatch, protein diameter and protein cluster size, lipid tail length, and temperature. To do so, we study a mesoscopic model of a hydrated bilayer containing lipids and cholesterol in which proteins are embedded, with a hybrid dissipative particle dynamics-Monte Carlo method. We propose a mechanism by which cholesterol affects protein interactions: protein-induced, cholesterol-enriched, or cholesterol-depleted lipid shells surrounding the proteins affect the lipid-mediated protein-protein interactions. Our calculations of the potential of mean force between proteins and protein clusters show that the addition of cholesterol dramatically reduces repulsive lipid-mediated interactions between proteins (protein clusters) with positive mismatch, but does not affect attractive interactions between proteins with negative mismatch. Cholesterol has only a modest effect on the repulsive interactions between proteins with different mismatch.

Molecular modeling of proteinlike inclusions in lipid bilayers: Lipid-mediated interactions

We investigated the insertion of transmembrane structures in a lipid bilayer and their interactions using self-consistent field theory. The lipids are coarse-grained on a united-atom level and consist of a phosphatidylcholinelike headgroup and two hydrophobic tails. The inclusions, acting as simple models for proteins that span biological membranes, are rigid rods (radius R ) with a hydrophobic surface and hydrophilic end caps. The insertion free energy Omega of an individual rod is strongly regulated by the affinity between its hydrophobic surface and the lipid tails. This affinity also controls the best match of the hydrophobic length of the rod with that of the bilayer. The line tension tau(=Omega/2piR) is practically independent of R . The perturbations in the bilayer as a function of distance from the inclusion, have the shape of a damped oscillation. The wavelength and decay length are related to the elastic properties of the bilayer and do not depend on R . These results are used to analyze how the lipid matrix affects the interaction between transmembrane objects, for computational reasons considering the limit of R-->infinity . Contributions on different length scales can be distinguished: (i) a long-range elastic interaction, which is an exponentially decaying oscillation; (ii) an exponentially decaying repulsion on an intermediate length scale, resulting from the loss of conformational entropy of the lipid tails; and (iii) a short-range interaction due to the finite compressibility of the lipid tails, which manifests either as a depletion attraction if there is no affinity between the tails and the inclusions' surface or, otherwise, as an oscillatory structural force.

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes

The specific and non-specific driving forces of helix association within membranes are still poorly understood. Here, we use coarse-grain molecular dynamics simulations to study the association behavior of glycophorin A and two disruptive mutants, T87F and a triple mutant of the GxxxG motif (G79LG83LG86L), embedded in a lipid membrane. Self-assembly simulations and the association free-energy profile confirm an energetically-favorable dimerized state for both the wild type and the mutants. The reduced association of the mutants compared to the wild type, as observed in experiments, can be justified from comparisons of the free energy profiles. Less-favorable protein-protein interactions as well as disruption of lipid packing around the mutant dimers is responsible for their reduced association. The role of the non-specific "lipid-phobic" contribution appears to be as important as the specific "helix-helix" contribution. However, the differences between the wild type and mutants are subtle and our simulations predict a dimerization state not only for the wild-type glycophorin A, but also for these 'disruptive' mutants. Our results highlight the importance of both specific as well as non-specific driving forces in the association of transmembrane helices, and point to the need of more careful interpretation of experimental measurements.

Targeting of the GTPase Irgm1 to the phagosomal membrane via PtdIns(3,4)P2 and PtdIns(3,4,5)P3 promotes immunity to mycobacteria

Vertebrate immunity to infection enlists a new family of 47 kDa immunity-related GTPases (IRGs). One IRG in particular - Irgm1 - is essential for macrophage host defense against phagosomal pathogens including Mycobacterium tuberculosis (Mtb). Here we show Irgm1 targets the mycobacterial phagosome (PG) via lipid-mediated interactions with phosphoinositide-3,4-bisphosphate (PtdIns[3,4]P2) and PtdIns(3,4,5)P3. An isolated Irgm1 amphipathic helix conferred lipid binding in vitro and in vivo. Mutations in this region blocked PG recruitment and failed to complement the antimicrobial defect in Irgm1-/- macrophages. PtdIns(3,4,5)P3 removal or class I phosphoinositide-3-OH kinase (PI(3)K) inhibition mimicked this effect in wild-type cells. Irgm1-PI(3)K co-operation further facilitated Irgm1 engaging its fusogenic effectors at the site of infection, thereby ensuring pathogen-directed responses during innate immunity.

Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers

We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: direct interactions; lipid-induced depletion interactions; lipid bridging; lipid packing; and a smooth long-range contribution. The mechanisms leading to hydrophobic mismatch interactions are critically analyzed.

Modeling and Molecular Dynamics Simulation of the Human Gonadotropin-Releasing Hormone Receptor in a Lipid Bilayer

In the present study, a model for the human gonadotropin-releasing hormone receptor embedded in an explicit lipid bilayer was developed. The final conformation was obtained by extensive molecular dynamics simulations of a homology model based on the bovine rhodopsin crystal structure. The analysis of the receptor structure allowed us to detect a number of specific contacts between different amino acid residues, as well as water- and lipid-mediated interactions. These interactions were stable in six additional independent 35 ns long simulations at 310 and 323 K, which used the refined model as the starting structure. All loops, particularly the extracellular loop 2 and the intracellular loop 3, exhibited high fluctuations, whereas the transmembrane helices were more static. Although other models of this receptor have been previously developed, none of them have been subjected to extensive molecular dynamics simulations, and no other three-dimensional structure is publicly available. Our results suggest that the presence of ions as well as explicit solvent and lipid molecules are critical for the structure of membrane protein models, and that molecular dynamics simulations are certainly useful for their refinement.