Steady-state compartmentalization of lipid membranes by active proteins

Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling

One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.

The excitable fluid mosaic

The Fluid Mosaic Model by Singer & Nicolson proposes that biological membranes consist of a fluid lipid layer into which integral proteins are embedded. The lipid membrane acts as a two-dimensional liquid in which the proteins can diffuse and interact. Until today, this view seems very reasonable and is the predominant picture in the literature. However, there exist broad melting transitions in biomembranes some 10-20 degrees below physiological temperatures that reach up to body temperature. Since they are found below body temperature, Singer & Nicolson did not pay any further attention to the melting process. But this is a valid view only as long as nothing happens. The transition temperature can be influenced by membrane tension, pH, ionic strength and other variables. Therefore, it is not generally correct that the physiological temperature is above this transition. The control over the membrane state by changing the intensive variables renders the membrane as a whole excitable. One expects phase behavior and domain formation that leads to protein sorting and changes in membrane function. Thus, the lipids become an active ingredient of the biological membrane. The melting transition affects the elastic constants of the membrane. This allows for the generation of propagating pulses in nerves and the formation of ion-channel-like pores in the lipid membranes. Here we show that on top of the fluid mosaic concept there exists a wealth of excitable phenomena that go beyond the original picture of Singer & Nicolson.¹.

Regulation of membrane proteins through local heterogeneity in lipid bilayer thickness

Cell membranes show an intricate organization of lipids and membrane proteins into domains with distinct composition and hydrophobic thickness. Using mechanosensitive ion channels as a model system, we employ the membrane elasticity theory of lipid-protein interactions together with the Landau-Ginzburg theory of lipid domain formation to quantify protein-induced lipid bilayer thickness deformations in lipid bilayers with heterogeneous hydrophobic thickness. We show that protein-induced lipid bilayer thickness deformations yield, without any assumptions about preferential interactions between particular lipid and protein species, organization of lipids and membrane proteins according to their preferred hydrophobic thickness, and couple the conformational states of membrane proteins to the local membrane composition. Our calculations suggest that protein-induced lipid bilayer thickness deformations endow proteins in cell membranes with diverse and controlled mechanical environments that, in turn, allow targeted regulation of membrane proteins.

Ion channels can be allosterically regulated by membrane domains near a de-mixing critical point

Ion channels are embedded in the plasma membrane, a compositionally diverse two-dimensional liquid that has the potential to exert profound influence on their function. Recent experiments suggest that this membrane is poised close to an Ising critical point, below which cell-derived plasma membrane vesicles phase separate into coexisting liquid phases. Related critical points have long been the focus of study in simplified physical systems, but their potential roles in biological function have been underexplored. Here we apply both exact and stochastic techniques to the lattice Ising model to study several ramifications of proximity to criticality for idealized lattice channels, whose function is coupled through boundary interactions to critical fluctuations of membrane composition. Because of diverging susceptibilities of system properties to thermodynamic parameters near a critical point, such a lattice channel's activity becomes strongly influenced by perturbations that affect the critical temperature of the underlying Ising model. In addition, its kinetics acquire a range of time scales from its surrounding membrane, naturally leading to non-Markovian dynamics. Our model may help to unify existing experimental results relating the effects of small-molecule perturbations on membrane properties and ion channel function. We also suggest ways in which the role of this mechanism in regulating real ion channels and other membrane-bound proteins could be tested in the future.

A Rationale for Mesoscopic Domain Formation in Biomembranes

Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we especially focus on the many mechanisms that dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e., due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.

Dynamic Scaling of Exosome Sizes

A model is proposed for characterizing exosome size distributions based on dynamic scaling of domain growth on the limiting membrane of multivesicular bodies in the established exosome biogenesis pathway. The scaling exponent in this model captures the asymmetry of exosome size distributions, which are notably right-skewed to larger vesicles, independent of the minimum detectable vesicle size. Analyses of exosome size distributions obtained by cryogenic transmission electron microscopy imaging and nanoparticle tracking show, respectively, that the scaling exponent is sensitive to the state of the cell source for exosomes in cell culture supernatants and can distinguish exosome size distributions in serum samples taken from cancer patients relative to those from healthy donors. Finally, we comment on mechanistic differences between our dynamic scaling model and random fragmentation models used to describe size distributions of synthetic vesicles.

Where Biology Meets Physics--A Converging View on Membrane Microdomain Dynamics

For several decades, the phenomenon of membrane component segregation into microdomains has been a well-known and highly debated subject, and varying concepts including the raft hypothesis, the fence-and-picket model, hydrophobic-mismatch, and specific protein-protein interactions have been offered as explanations. Here, we review the level of insight into the molecular architecture of membrane domains one is capable of obtaining through biological experimentation. Using SNARE proteins as a paradigm, comprehensive data suggest that several dozens of molecules crowd together into almost circular spots smaller than 100 nm. Such clusters are highly dynamical as they constantly capture and lose molecules. The organization has a strong influence on the functional availability of proteins and likely provides a molecular scaffold for more complex protein networks. Despite this high level of insight, fundamental open questions remain, applying not only to SNARE protein domains but more generally to all types of membrane domains. In this context, we explain the view of physical models and how they are beneficial in advancing our concept of micropatterning. While biological models generally remain qualitative and descriptive, physics aims towards making them quantitative and providing reproducible numbers, in order to discriminate between different mechanisms which have been proposed to account for experimental observations. Despite the fundamental differences in biological and physical approaches as far as cell membrane microdomains are concerned, we are able to show that convergence on common points of views is in reach.

Lipid domains in model membranes: a brief historical perspective

All biological membranes consist of a complex composite of macromolecules and macromolecular assemblies, of which the fluid lipid-bilayer component is a core element with regard to cell encapsulation and barrier properties. The fluid lipid bilayer also supports the functional machinery of receptors, channels and pumps that are associated with the membrane. This bilayer is stabilized by weak physical and colloidal forces, and its nature is that of a self-assembled system of amphiphiles in water. Being only approximately 5 nm in thickness and still encapsulating a cell that is three orders of magnitude larger in diameter, the lipid bilayer as a material has very unusual physical properties, both in terms of structure and dynamics. Although the lipid bilayer is a fluid, it has a distinct and structured trans-bilayer profile, and in the plane of the bilayer the various molecular components, viz different lipid species and membrane proteins, have the capacity to organize laterally in terms of differentiated domains on different length and time scales. These elements of small-scale structure and order are crucial for the functioning of the membrane. It has turned out to be difficult to quantitatively study the small-scale structure of biological membranes. A major part of the insight into membrane micro- and nano-domains and the concepts used to describe them have hence come from studies of simple lipid bilayers as models of membranes, by use of a wide range of theoretical, experimental and simulational approaches. Many questions remain to be answered as to which extent the result from model studies can carry over to real biological membranes.

Structure of archaerhodopsin-2 at 1.8 Å resolution

Archaerhodopsin-2 (aR2), the sole protein found in the claret membrane of Halorubrum sp. Aus-2, functions as a light-driven proton pump. In this study, structural analysis of aR2 was performed using a novel three-dimensional crystal prepared by the successive fusion of claret membranes. The crystal is made up of stacked membranes, in each of which aR2 trimers are arranged on a hexagonal lattice. This lattice structure resembles that found in the purple membrane of H. salinarum, except that lipid molecules trapped within the trimeric structure are not distributed with perfect threefold symmetry. Nonetheless, diffraction data at 1.8 Å resolution provide accurate structural information about functionally important residues. It is shown that two glutamates in the proton-release channel form a paired structure that is maintained by a low-barrier hydrogen bond. Although the structure of the proton-release pathway is highly conserved among proton-pumping archaeal rhodopsins, aR2 possesses the following peculiar structural features: (i) the motional freedom of the tryptophan residue that makes contact with the C13 methyl group of retinal is restricted, affecting the formation/decay kinetics of the L state, and (ii) the N-terminal polypeptide folds into an Ω-loop, which may play a role in organizing the higher-order structure.

Is the fluid mosaic (and the accompanying raft hypothesis) a suitable model to describe fundamental features of biological membranes? What may be missing?

The structure, dynamics, and stability of lipid bilayers are controlled by thermodynamic forces, leading to overall tensionless membranes with a distinct lateral organization and a conspicuous lateral pressure profile. Bilayers are also subject to built-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes leading to the formation of non-lamellar and curved structures. A key controller of the bilayer's propensity to form curved structures is the average molecular shape of the different lipid molecules. Via the curvature stress, molecular shape mediates a coupling to membrane-protein function and provides a set of physical mechanisms for formation of lipid domains and laterally differentiated regions in the plane of the membrane. Unfortunately, these relevant physical features of membranes are often ignored in the most popular models for biological membranes. Results from a number of experimental and theoretical studies emphasize the significance of these fundamental physical properties and call for a refinement of the fluid mosaic model (and the accompanying raft hypothesis).

Model answers to lipid membrane questions

Ever since it was discovered that biological membranes have a core of a bimolecular sheet of lipid molecules, lipid bilayers have been a model laboratory for investigating physicochemical and functional properties of biological membranes. Experimental and theoretical models help the experimental scientist to plan experiments and interpret data. Theoretical models are the theoretical scientist's preferred toys to make contact between membrane theory and experiments. Most importantly, models serve to shape our intuition about which membrane questions are the more fundamental and relevant ones to pursue. Here we review some membrane models for lipid self-assembly, monolayers, bilayers, liposomes, and lipid-protein interactions and illustrate how such models can help answering questions in modern lipid cell biology.

Lipids, curvature, and nano-medicine

The physical properties of the lamellar lipid-bilayer component of biological membranes are controlled by a host of thermodynamic forces leading to overall tensionless bilayers with a conspicuous lateral pressure profile and build-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes. In particular, the average molecular shape and the propensity of the different lipid and protein species for forming non-lamellar and curved structures are a source of structural transitions and control of biological function. The effects of different lipids, sterols, and proteins on membrane structure are discussed and it is shown how one can take advantage of the curvature-stress modulations brought about by specific molecular agents, such as fatty acids, lysolipids, and other amphiphilic solutes, to construct intelligent drug-delivery systems that function by enzymatic triggering via curvature.Practical applications: The simple concept of lipid molecular shape and how it impacts on the structure of lipid aggregates, in particular the curvature and curvature stress in lipid bilayers and liposomes, can be exploited to construct liposome-based drug-delivery systems, e.g., for use as nano-medicine in cancer therapy. Non-lamellar-forming lysolipids and fatty acids, some of which may be designed to be prodrugs, can be created by phospholipase action in diseased tissues thereby providing for targeted drug release and proliferation of molecular entities with conical shape that break down the permeability barrier of the target cells and may hence enhance efficacy.

Near-critical fluctuations and cytoskeleton-assisted phase separation lead to subdiffusion in cell membranes

We address the relationship between membrane microheterogeneity and anomalous subdiffusion in cell membranes by carrying out Monte Carlo simulations of two-component lipid membranes. We find that near-critical fluctuations in the membrane lead to transient subdiffusion, while membrane-cytoskeleton interaction strongly affects phase separation, enhances subdiffusion, and eventually leads to hop diffusion of lipids. Thus, we present a minimum realistic model for membrane rafts showing the features of both microscopic phase separation and subdiffusion.

Effect of integral proteins in the phase stability of a lipid bilayer: application to raft formation in cell membranes

The existence of lipid rafts is a controversial issue. The affinity of cholesterol for saturated lipids is manifested in macroscopic phase separation in model membranes, and is believed to be the thermodynamic driving force for raft formation. However, there is no clear reason to explain the small (nanometric) size of raft domains in cell membranes. In a recent paper Yethiraj and Weisshaar [Biophys. J. 93, 3113 (2007)] proposed that the effect of neutral integral membrane proteins may prevent from the formation of large lipid domains. In this paper we extend this approach by studying the effect of the protein size, as well as the lipid-protein interaction. Depending on these factors, two different mechanisms for nanodomain stabilization are shown to be possible for static proteins. The application of these results to a biological context is discussed.

Monosodium urate crystals in inflammation and immunity

Uric acid crystals [monosodium urate (MSU)] have emerged as an important factor for both gouty arthritis and immune regulation. This simple crystalline structure appears to activate innate host defense mechanisms in multiple ways and triggers robust inflammation and immune activation. The recognition mechanisms of MSU following its phase change from soluble uric acid are diverse, involving both protein receptors and non-specific plasma membrane attachment. Upon contact with host cells, MSU induces a set of membrane events that trigger Syk and PI3K activation, phagocytosis, and cytokine production. Having entered the cell, MSU further triggers NALP3 inflammasome activation and induces the production of IL-1 beta, likely inducing a full spectrum of inflammation. This review describes the recognition mechanisms and activation pathways involved in MSU-mediated inflammation and adjuvanticity and hypothesizes that direct membrane binding by solid surfaces, such as MSU, may function as a generic mechanism in tissue responses to particulate and crystalline structures.

Effect of energy metabolism on protein motility in the bacterial outer membrane

We demonstrate the energy dependence of the motion of a porin, the lambda-receptor, in the outer membrane of living Escherichia coli by single molecule investigations. By poisoning the bacteria with arsenate and azide, the bacterial energy metabolism was stopped. The motility of individual lambda-receptors significantly and rapidly decreased upon energy depletion. We suggest two different causes for the ceased motility upon comprised energy metabolism: One possible cause is that the cell uses energy to actively wiggle its proteins, this energy being one order-of-magnitude larger than thermal energy. Another possible cause is an induced change in the connection between the lambda-receptor and the membrane structure, for instance by a stiffening of part of the membrane structure. Treatment of the cells with ampicillin, which directly targets the bacterial cell wall by inhibiting cross-linking of the peptidoglycan layer, had an effect similar to energy depletion and the motility of the lambda-receptor significantly decreased. Since the lambda-receptor is closely linked to the peptidoglycan layer, we propose that lambda-receptor motility is directly coupled to the constant and dynamic energy-consuming reconstruction of the peptidoglycan layer. The result of this motion could be to facilitate transport of maltose-dextrins through the porin.

Nonequilibrium patterns in phase-separating ternary membranes

We present a nonequilibrium approach for the study of a two-dimensional phase-separating ternary mixture. When the component that promotes phase separation is dynamically exchanged with the medium, the separation process is halted and actively maintained finite-size segregation domains appear in the system. In addition to this effect, already reported in our earlier work [J. Gómez, F. Sagués, and R. Reigada, Phys. Rev. E 77, 021907 (2008)], the use of a generic Ginzburg-Landau formalism and the inclusion of thermal fluctuations provide a more dynamic description of the resulting domain organization. Its size, shape, and stability properties are studied. Larger and more circular and stable domains are formed when decreasing the recycling rate, increasing the mobility of the exchanged component, and the mixture is quenched deeper. We expect this outcome to be of applicability in raft phenomenology in plasmatic cell membranes.

Electrostatic and electrokinetic contributions to the elastic moduli of a driven membrane

We discuss the electrostatic contribution to the elastic moduli of a cell or artificial membrane placed in an electrolyte and driven by a DC electric field. The field drives ion currents across the membrane, through specific channels, pumps or natural pores. In steady state, charges accumulate in the Debye layers close to the membrane, modifying the membrane elastic moduli. We first study a model of a membrane of zero thickness, later generalizing this treatment to allow for a finite thickness and finite dielectric constant. Our results clarify and extend the results presented by D. Lacoste, M. Cosentino Lagomarsino, and J.F. Joanny (EPL 77, 18006 (2007)), by providing a physical explanation for a destabilizing term proportional to [see formula in text] in the fluctuation spectrum, which we relate to a nonlinear (E(2)) electrokinetic effect called induced-charge electro-osmosis (ICEO). Recent studies of ICEO have focused on electrodes and polarizable particles, where an applied bulk field is perturbed by capacitive charging of the double layer and drives the flow along the field axis toward surface protrusions; in contrast, we predict "reverse" ICEO flows around driven membranes, due to curvature-induced tangential fields within a nonequilibrium double layer, which hydrodynamically enhance protrusions. We also consider the effect of incorporating the dynamics of a spatially dependent concentration field for the ion channels.

What do diffusion measurements tell us about membrane compartmentalisation? Emergence of the role of interprotein interactions

The techniques of diffusion analysis based on optical microscopy approaches have revealed a great diversity of the dynamic organisation of cell membranes. For a long period, two frameworks have dominated the way of representing the membrane structure: the membrane skeleton fences and the lipid raft models. Progresses in the methods of data analysis have shed light on the features and consequently the possible origin of membrane domains: Inter-protein interactions play a role in confinement. Innovative developments pushing forward the spatiotemporal resolution limits are currently emerging, which are likely to provide in the future a detailed understanding of the intimate functional dynamic organisation of the cell membrane.

Protein-promoted membrane domains

The current notion of biological membranes encompasses a very complex structure, made of dynamically changing compartments or domains where different membrane components partition. These domains have been related to important cellular functions such as membrane sorting, signal transduction, membrane fusion, neuronal maturation, and protein activation. Many reviews have dealt with membrane domains where lipid-lipid interactions direct their formation, especially in the case of raft domains, so in this review we considered domains induced by integral membrane proteins. The nature of the interactions involved and the different mechanisms through which membrane proteins segregate lipid domains are presented, in particular with regard to those induced by the nAChR. It may be concluded that coupling of favourable lipid-lipid and lipid-protein interactions is a general condition for this phenomenon to occur.

Lipid rafts: at a crossroad between cell biology and physics

Membrane lateral heterogeneity is accepted as a requirement for the function of biological membranes and the notion of lipid rafts gives specificity to this broad concept. However, the lipid raft field is now at a technical impasse because the physical tools to study biological membranes as a liquid that is ordered in space and time are still being developed. This has lead to a disconnection between the concept of lipid rafts as derived from biochemical and biophysical assays and their existence in the cell. Here, we compare the concept of lipid rafts as it has emerged from the study of synthetic membranes with the reality of lateral heterogeneity in biological membranes. Further application of existing tools and the development of new tools are needed to understand the dynamic heterogeneity of biological membranes.

Finite-size domains in membranes with active two-state inclusions

The distribution of inclusion-rich domains in membranes with active two-state inclusions is studied by simulations. Our study shows that typical size of inclusion-rich domains (L) can be controlled by inclusion activities in several ways. When there is effective attraction between state-1 inclusions, we find: (i) Small domains with only several inclusions are observed for inclusions with time scales (approximately 10(-3)s) and interaction energy [approximately Omicron(kBT)] comparable to motor proteins. (ii) L scales as 13 power of the lifetime of state-1 for a wide range of parameters. (iii) L shows a switch-like dependence on state-2 lifetime k12(-1). That is, L depends weakly on k12 when k12<k12* but increases rapidly with k12 when k12>k12*, the crossover k12* occurs when the diffusion length of a typical state-2 inclusion within its lifetime is comparable to L. (iv) Inclusion-curvature coupling provides another length scale that competes with the effects of transition rates.

Adhesion of membranes via switchable molecules

Biomimetic membranes that adhere to a solid substrate or another interface via switchable crosslinker molecules are studied theoretically using analytical methods and Monte Carlo simulations. The flexible crosslinkers exhibit two conformations which have a different end-to-end distance and, thus, lead to different local separations of the membrane from the substrate surface. Transitions between the molecular conformations can be induced by light, electric potential, or changes in pH and lead to active shape fluctuations of the membrane and, thus, to an increased membrane roughness. The forward and backward transitions are characterized by two transition rates, omega(+) and omega(-), respectively, which define the average fraction X=omega(+) /(omega(+) + omega(-)) of + (or on) states and the mean switching rate omega = (omega(+) + omega(-)) / 2. The membrane roughness is explicitly calculated as a function of X and omega. It is shown that the interplay of active and thermal fluctuations is subtle and that it is, in general, not possible to describe the active fluctuations in terms of an effective temperature.

Adhesion of membranes with active stickers

We consider a theoretical model for membranes with adhesive receptors, or stickers, that are actively switched between two conformational states. In their "on" state, the stickers bind to ligands in an apposing membrane, whereas they do not interact with the ligands in their "off" state. We show that the adhesiveness of the membranes depends sensitively on the rates of the conformational switching process. This dependence is reflected in a resonance at intermediate switching rates, which can lead to large membrane separations and unbinding. Our results may provide insights into novel mechanisms for the controlled adhesion of biological or biomimetic membranes.

Passive or active fluctuations in membranes containing proteins

We have experimentally investigated the effect of a transmembrane protein, the Ca2+-ATPase, on shape fluctuations of giant vesicles. By using the micropipette method, we have measured a substantial renormalization of the bending modulus due to the presence of proteins in the membrane. Moreover, we have produced the first quantitative measurement of the active force dipole associated with the amplification of the fluctuations when the proteins are activated by adenosine 5'-triphosphate (ATP).

Lipids do influence protein function-the hydrophobic matching hypothesis revisited

A topical review of the current state of lipid-protein interactions is given with focus on the physical interactions between lipids and integral proteins in lipid-bilayer membranes. The concepts of hydrophobic matching and curvature stress are revisited in light of recent data obtained from experimental and theoretical studies which demonstrate that not only do integral proteins perturb the lipids, but the physical state of the lipids does also actively influence protein function. The case of the trans-membrane water-channel protein aquaporin GlpF from E. coli imbedded in lipid-bilayer membranes is discussed in some detail. Numerical data obtained from Molecular Dynamics simulations show on the one side that the lipid bilayer adapts to the channel by a hydrophobic matching condition which reflects the propensity of the lipid molecules for forming curved structures. On the other side, it is demonstrated that the transport function of the channel is modulated by the matching condition and/or the curvature stress in a lipid-specific manner.

Internal states of active inclusions and the dynamics of an active membrane

A theoretical model of a two-component fluid membrane containing lipids and two-state active inclusions is presented. This model predicts several nonequilibrium morphology transitions. (i) Active pumping of the inclusions can drive a long-wavelength undulation instability. (ii) Active excitation of the inclusions can induce aggregation of high-curvature excited inclusions. (iii) Active inclusion conformation changes can produce finite-size domains. The resulting steady state domain size depends on inclusion activities. For a stable membrane the height fluctuation spectrum in the long-wavelength limit is similar to previous studies which neglected the inclusion internal states.

Analysis of resonance energy transfer in model membranes: role of orientational effects

The model of resonance energy transfer (RET) in membrane systems containing donors randomly distributed over two parallel planes separated by fixed distance and acceptors confined to a single plane is presented. Factors determining energy transfer rate are considered with special attention being given to the contribution from orientational heterogeneity of the donor emission and acceptor absorption transition dipoles. Analysis of simulated data suggests that RET in membranes, as compared to intramolecular energy transfer, is substantially less sensitive to the degree of reorientational freedom of chromophores due to averaging over multiple donor-acceptor pairs. The uncertainties in the distance estimation resulting from the unknown mutual orientation of the donor and acceptor are analyzed.

Domain formation in a fluid mixed lipid bilayer modulated through binding of the C2 protein motif

The role and mechanism of formation of lipid domains in a functional membrane have generally received limited attention. Our approach, based on the hypothesis that thermodynamic coupling between lipid-lipid and protein-lipid interactions can lead to domain formation, uses a combination of an experimental lipid bilayer model system and Monte Carlo computer simulations of a simple model of that system. The experimental system is a fluid bilayer composed of a binary mixture of phosphatidylcholine (PC) and phosphatidylserine (PS), containing 4% of a pyrene-labeled anionic phospholipid. Addition of the C2 protein motif (a structural domain found in proteins implicated in eukaryotic signal transduction and cellular trafficking processes) to the bilayer first increases and then decreases the excimer/monomer ratio of the pyrene fluorescence. We interpret this to mean that protein binding induces anionic lipid domain formation until the anionic lipid becomes saturated with protein. Monte Carlo simulations were performed on a lattice representing the lipid bilayer to which proteins were added. The important parameters are an unlike lipid-lipid interaction term and an experimentally derived preferential protein-lipid interaction term. The simulations support the experimental conclusion and indicate the existence of a maximum in PS domain size as a function of protein concentration. Thus, lipid-protein coupling is a possible mechanism for both lipid and protein clustering on a fluid bilayer. Such domains could be precursors of larger lipid-protein clusters ('rafts'), which could be important in various biological processes such as signal transduction at the level of the cell membrane.

A computational model of membrane lipid electronic properties in relation to neural signaling

We present a computational model of a transiently-organized neural membrane molecular system with possible information-processing capacity. The model examines field-induced dipole and quadrupole moments and polarizability in monomeric, dimeric, and trimeric ethenes. Polarization of the ethenes is strongly indicated. This result is interpreted as a significant electronic feature of a molecular computing system based on organization of membrane lipids into a transient ( approximately 10(-4) s) crystalline state due to lipid-protein hydrophobic mismatch at the membrane-ion-channel interface. Predictive implications of the model's electronic features are briefly discussed.

A macroscopic description of lipid bilayer phase transitions of mixed-chain phosphatidylcholines: chain-length and chain-asymmetry dependence

A macroscopic model is presented to quantitatively describe lipid bilayer gel to fluid phase transitions. In this model, the Gibbs potential of the lipid bilayer is expressed in terms of a single order parameter q, the average chain orientational order parameter. The Gibbs potential is based on molecular mean-field and statistical mechanical calculations of inter and intrachain interactions. Chain-length and chain-asymmetry are incorporated into the Gibbs potential so that one equation provides an accurate description of mixed-chain phosphatidylcholines of a single class. Two general classes of lipids are studied in this work: lipid bilayers of partially or noninterdigitated gel phases, and bilayers of mixed interdigitated gel phases. The model parameters are obtained by fitting the transition temperature and enthalpy data of phosphatidylcholines to the model. The proposed model provides estimates for the transition temperature and enthalpy, van der Waals energy, number of gauche bonds, chain orientational order parameter, and bond rotational and excluded volume entropies, achieving excellent agreement with existing data obtained with various techniques.

PMP1 18-38, a yeast plasma membrane protein fragment, binds phosphatidylserine from bilayer mixtures with phosphatidylcholine: a (2)H-NMR study

PMP1 is a 38-residue plasma membrane protein of the yeast Saccharomyces cerevisiae that regulates the activity of the H(+)-ATPase. The cytoplasmic domain conformation results in a specific interfacial distribution of five basic side chains, thought to strongly interact with anionic phospholipids. We have used the PMP1 18-38 fragment to carry out a deuterium nuclear magnetic resonance ((2)H-NMR) study for investigating the interactions between the PMP1 cytoplasmic domain and phosphatidylserines. For this purpose, mixed bilayers of 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphoserine (POPS) were used as model membranes (POPC/POPS 5:1, m/m). Spectra of headgroup- and chain-deuterated POPC and POPS phospholipids, POPC-d4, POPC-d31, POPS-d3, and POPS-d31, were recorded at different temperatures and for various concentrations of the PMP1 fragment. Data obtained from POPS deuterons revealed the formation of specific peptide-POPS complexes giving rise to a slow exchange between free and bound PS lipids, scarcely observed in solid-state NMR studies of lipid-peptide/protein interactions. The stoichiometry of the complex (8 POPS per peptide) was determined and its significance is discussed. The data obtained with headgroup-deuterated POPC were rationalized with a model that integrates the electrostatic perturbation induced by the cationic peptide on the negatively charged membrane interface, and a "spacer" effect due to the intercalation of POPS/PMP1f complexes between choline headgroups.

Phase transitions and steady-state microstructures in a two-temperature lattice-gas model with mobile active impurities

The nonequilibrium, steady-state phase transitions and the structure of the different phases of a two-dimensional system with two thermodynamic temperatures are studied via a simple lattice-gas model with mobile active impurities ("hot/cold spots") whose activity is controlled by an external drive. The properties of the model are calculated by Monte Carlo computer-simulation techniques. The two temperatures and the external drive on the system lead to a rich phase diagram including regions of microstructured phases in addition to macroscopically ordered (phase-separated) and disordered phases. Depending on the temperatures, microstructured phases of both lamellar and droplet symmetry arise, described by a length scale that is determined by the characteristic temperature controlling the diffusive motion of the active impurities.

Lipid-protein interactions in rat renal subcellular membranes: a biophysical and biochemical study

The phase behavior of plasma membrane (PM), endoplasmic reticulum (ER), and nuclear membranes (NM) isolated from adult rat papillary cells was studied using the molecular probe Laurdan. The steady-state fluorescence data analysis was correlated with the lipid composition obtained by biochemical assays. The comparison between intact membranes and protein-free reconstituted vesicles using the whole lipid extract shows the essential role of proteins on the temperature response of natural membranes. The phospholipid (PL) and cholesterol (Cho) content was measured in the three membrane fractions, the PL/Cho molar ratio being between 1.5 and 1.9. However, Laurdan's parameters in NM show a fluid phase state pattern even at low temperature (5 degrees C), with a restricted dipole relaxation in comparison with that displayed in liquid crystalline phase state lipid model membranes. PM and ER are in a gel-like state at temperatures below 20 degrees C, showing increasing dipole relaxation with temperature. The curved fits obtained are characteristic of cholesterol-enriched membranes. The distinctive phase behavior of nuclear membranes vanishes when proteins are extracted. However, relaxation is still faster in this fraction, which correlates with the native lipid composition. NM has the lowest percentage of phosphatidylinositol and sphingomyelin-the latter being a highly saturated phospholipid- and the highest percentage of phosphatidylcholine and phosphatidylethanolamine (PE), nuclear PE being enriched in arachidonic acid. All these changes agree with the higher fluidity of NM compared with ER or PM in the conditions assayed.

A model for membrane patchiness: lateral diffusion in the presence of barriers and vesicle traffic

Patches (lateral heterogeneities) of cell surface membrane proteins and lipids have been imaged by a number of different microscopy techniques. This patchiness has been taken as evidence for the organization of membranes into domains whose composition differs from the average for the entire membrane. However, the mechanism and specificity of patch formation are not understood. Here we show how vesicle traffic to and from a cell surface membrane can create patches of molecules of the size observed experimentally. Our computer model takes into account lateral diffusion, barriers to lateral diffusion, and vesicle traffic to and from the plasma membrane. Neither barriers nor vesicle traffic alone create and maintain patches. Only the combination of these produces a dynamic but persistent patchiness of membrane proteins and lipids.

Electromagnetic-field-induced oscillations of the lipid domain structures in the mixed membranes

The effect of external electromagnetic field (EMF) on a percolation structure formed during phase separation in the mixed phospholipid membranes was studied by computer simulation. Decay of the percolation structure under electromagnetic radiation was detected. It was shown that oscillation regime can be realized in this system: periodic alternation of formation and decay of the percolation cluster was observed under 10 kHz EMF. The decay of the lipid domain structure in the EMF results from anomalous increase of the permittivity of the continuous fluid lipid phase in the percolation threshold region. It is proposed that detected EMF effect can influence the signal and transport processes associated with percolation properties of biomembranes.

Theoretical analysis of protein organization in lipid membranes

The fundamental physical principles of the lateral organization of trans-membrane proteins and peptides as well as peripheral membrane proteins and enzymes are considered from the point of view of the lipid-bilayer membrane, its structure, dynamics, and cooperative phenomena. Based on a variety of theoretical considerations and model calculations, the nature of lipid-protein interactions is considered both for a single protein and an assembly of proteins that can lead to aggregation and protein crystallization in the plane of the membrane. Phenomena discussed include lipid sorting and selectivity at protein surfaces, protein-lipid phase equilibria, lipid-mediated protein-protein interactions, wetting and capillary condensation as means of protein organization, mechanisms of two-dimensional protein crystallization, as well as non-equilibrium organization of active proteins in membranes. The theoretical findings are compared with a variety of experimental data.