Formation and characterization of planar lipid bilayer membranes from synthetic phytanyl-chained glycolipids

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.

Semisynthetic Amides of Amphotericin B and Nystatin A1: A Comparative Study of In Vitro Activity/Toxicity Ratio in Relation to Selectivity to Ergosterol Membranes

Polyene antifungal amphotericin B (AmB) has been used for over 60 years, and remains a valuable clinical treatment for systemic mycoses, due to its broad antifungal activity and low rate of emerging resistance. There is no consensus on how exactly it kills fungal cells but it is certain that AmB and the closely-related nystatin (Nys) can form pores in membranes and have a higher affinity towards ergosterol than cholesterol. Notably, the high nephro- and hemolytic toxicity of polyenes and their low solubility in water have led to efforts to improve their properties. We present the synthesis of new amphotericin and nystatin amides and a comparative study of the effects of identical modifications of AmB and Nys on the relationship between their structure and properties. Generally, increases in the activity/toxicity ratio were in good agreement with increasing ratios of selective permeabilization of ergosterol- vs. cholesterol-containing membranes. We also show that the introduced modifications had an effect on the sensitivity of mutant yeast strains with alterations in ergosterol biosynthesis to the studied polyenes, suggesting a varying affinity towards intermediate ergosterol precursors. Three new water-soluble nystatin derivatives showed a prominent improvement in safety and were selected as promising candidates for drug development.

Impact of cholesterol and sphingomyelin on intrinsic membrane permeability

Transwell experiments with Caco-2 or MDCK cells are the gold standard for determining the intestinal permeability of chemicals. The intrinsic membrane permeability (P₀), that can be extracted from these experiments, might be comparable to P₀ measured in black lipid membrane (BLM) experiments and P₀ predicted by the solubility-diffusion model. Unfortunately, the overlap between experimental P_{0,Caco-2/MDCK} and P_0,BLM data is very small. So far, differences between both approaches have been attributed to the cholesterol and sphingomyelin content of cell membranes, but the database is too sparse to thoroughly test this theory. To create a diverse dataset, we measured P_0,BLM of ten chemicals in BLM experiments using DPhPC and DPhPC/cholesterol/sphingomyelin membranes. The results were compared to predicted BLM data and experimental Caco-2/MDCK data obtained from literature. While P_0,BLM of all chemicals was well predicted by the solubility-diffusion model, P_{0,Caco-2/MDCK} was only predictable for rather hydrophilic compounds with logarithmic hexadecane/water partition coefficients below -0.5. The effect of cholesterol and sphingomyelin on P_0,BLM was negligibly small.

Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication

To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants.

The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales

One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.

Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

Microbes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the lipid core composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the lipid core composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea. This article is protected by copyright. All rights reserved.

Characterisation of cell membrane interaction mechanisms of antimicrobial peptides by electrical bilayer recording

Many antimicrobial peptides (AMPs) are cationic host defence peptides (HDPs) that interact with microbial membranes. This ability may lead to implementation of AMPs as therapeutics to overcome the wide-spread antibiotic resistance problem as the affected bacteria may not be able to recover from membrane lysis types of attack. AMP interactions with lipid bilayer membranes are typically explained through three mechanisms, i.e., barrel-stave pore, toroidal pore and carpet models. Electrical bilayer recording is a relatively simple and sensitive technique that is able to capture the nanoscale perturbations caused by the AMPs in the bilayer membranes. Molecular-level understanding of the behaviour of AMPs in relation to lipid bilayers mimicking bacterial and human cell membranes is essential for their development as novel therapeutic agents that are capable of targeted action against disease causing micro-organisms. The effects of four AMPs (aurein 1.2, caerin 1.1, citropin 1.1 and maculatin 1.1 from the skin secretions of Australian tree frogs) and the toxin melittin (found in the venom of honeybees) on two different phospholipid membranes were studied using the electrical bilayer recording technique. Bilayers composed of zwitterionic (DPhPC) and anionic (DPhPC/POPG) lipids were used to mimic the charge of eukaryotic and prokaryotic cell membranes, respectively, so as to determine the corresponding interaction mechanisms for different concentrations of the peptide. Analysis of the dataset corresponding to the four frog AMPs, as well as the resulting dataset corresponding to the bee toxin, confirms the proposed peptide-bilayer interaction models in existing publications and demonstrates the importance of using appropriate bilayer compositions and peptide concentrations for AMP studies.

Acid Hydrolysis for the Extraction of Archaeal Core Lipids and HPLC-MS Analysis

Lipid membranes are essential cellular elements as they provide cellular integrity and selective permeability under a broad range of environmental settings upon cell growth. In particular, Archaea are commonly recognized for their tolerance to extreme conditions, which is now widely accepted to stem from the unique structure of their lipids. While enhancing the stability of the archaeal cell membrane, the exceptional properties of archaeal lipids also hinder their extraction using regular procedures initially developed for bacterial and eukaryotic lipids. The protocol described here circumvents these issues by directly hydrolyzing the polar head group(s) of archaeal lipids and extracting the resulting core lipids. Although leading to a loss of information on the nature of polar heads, this procedure allows the quantitative extraction of core lipids for most types of archaeal cells in an efficient, reproducible, and rapid manner.

Novel Intact Polar and Core Lipid Compositions in the Pyrococcus Model Species, P. furiosus and P. yayanosii, Reveal the Largest Lipid Diversity Amongst Thermococcales

Elucidating the lipidome of Archaea is essential to understand their tolerance to extreme environmental conditions. Previous characterizations of the lipid composition of Pyrococcus species, a model genus of hyperthermophilic archaea belonging to the Thermococcales order, led to conflicting results, which hindered the comprehension of their membrane structure and the putative adaptive role of their lipids. In an effort to clarify the lipid composition data of the Pyrococcus genus, we thoroughly investigated the distribution of both the core lipids (CL) and intact polar lipids (IPL) of the model Pyrococcus furiosus and, for the first time, of Pyrococcus yayanosii, the sole obligate piezophilic hyperthermophilic archaeon known to date. We showed a low diversity of IPL in the lipid extract of P. furiosus, which nonetheless allowed the first report of phosphatidyl inositol-based glycerol mono- and trialkyl glycerol tetraethers. With up to 13 different CL structures identified, the acid methanolysis of Pyrococcus furiosus revealed an unprecedented CL diversity and showed strong discrepancies with the IPL compositions reported here and in previous studies. By contrast, P. yayanosii displayed fewer CL structures but a much wider variety of polar heads. Our results showed severe inconsistencies between IPL and CL relative abundances. Such differences highlight the diversity and complexity of the Pyrococcus plasma membrane composition and demonstrate that a large part of its lipids remains uncharacterized. Reassessing the lipid composition of model archaea should lead to a better understanding of the structural diversity of their lipidome and of their physiological and adaptive functions.

Cyclopentane rings in hydrophobic chains of a phospholipid enhance the bilayer stability to electric breakdown

Archaeal lipids ensure unprecedented stability of archaea membranes in extreme environments. Here, we incorporate a characteristic structural feature of an archaeal lipid, the cyclopentane ring, into hydrocarbon chains of a short-chain (C12) phosphatidylcholine to explore whether the insertion would allow such a lipid (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, diC12cp-PC) to form stable bilayers at room temperature. According to fluorescence-based assays, in water diC12cp-PC formed liquid-crystalline bilayers at room temperature. Liposomes produced from diC12cp-PC retained calcein for over a week when stored at +4 °C. diC12cp-PC could also form model bilayer lipid membranes that were by an order of magnitude more stable to electrical breakdown than egg PC membranes. Molecular dynamics simulation showed that the cyclopentane fragment fixes five carbon atoms (or four C-C bonds), which is compensated by the higher mobility of the rest of the chain. This was found to be the reason for the remarkable stability of the diC12cp-PC bilayer: restricted conformational mobility of a chain segment increases the membrane bending modulus (compared to a normal hydrocarbon chain of the same length). Here, higher stiffness practically does not affect the line tension of a membrane pore edge. Rather it makes it more difficult for diC12cp-PC to rearrange in order to line the edge of a hydrophilic pore; therefore, fewer pores are formed.

Functionalized Membrane Domains: An Ancestral Feature of Archaea?

Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. A novel membrane ultrastructure predicts that monolayer and bilayer domains would be laterally segregated in the hyperthermophilic archaeon Thermococcus barophilus. With very different physico-chemical parameters of the mono- and bilayer, each domain type would thus allow the docking of different membrane proteins and express different biological functions in the membrane. To estimate the ubiquity of this putative membrane ultrastructure in and out of the order Thermococcales, we re-analyzed the core lipid composition of all the Thermococcales type species and collected all the literature data available for isolated archaea. We show that all species of Thermococcales synthesize a mixture of diether bilayer forming and tetraether monolayer forming lipids, in various ratio from 10 to 80% diether in Pyrococcus horikoshii and Thermococcus gorgonarius, respectively. Since the domain formation prediction rests only on the coexistence of di- and tetraether lipids, we show that all Thermococcales have the ability for domain formation, i.e., differential functionalization of their membrane. Extrapolating this view to the whole Archaea domain, we show that almost all archaea also have the ability to synthesize di- and tetraether lipids, which supports the view that functionalized membrane domains may be shared between all Archaea. Hence domain formation and membrane compartmentalization may have predated the separation of the three domains of life and be essential for the cell cycle.

Structural Characterization of an Archaeal Lipid Bilayer as a Function of Hydration and Temperature

Archaea, the most extremophilic domain of life, contain ether and branched lipids which provide extraordinary bilayer properties. We determined the structural characteristics of diether archaeal-like phospholipids as functions of hydration and temperature by neutron diffraction. Hydration and temperature are both crucial parameters for the self-assembly and physicochemical properties of lipid bilayers. In this study, we detected non-lamellar phases of archaeal-like lipids at low hydration levels, and lamellar phases at levels of 90% relative humidity or more exclusively. Moreover, at 90% relative humidity, a phase transition between two lamellar phases was discernible. At full hydration, lamellar phases were present up to 70ᵒC and no phase transition was observed within the temperature range studied (from 25 °C to 70 °C). In addition, we determined the neutron scattering length density and the bilayer's structural parameters from different hydration and temperature conditions. At the highest levels of hydration, the system exhibited rearrangements on its corresponding hydrophobic region. Furthermore, the water uptake of the lipids examined was remarkably high. We discuss the effect of ether linkages and branched lipids on the exceptional characteristics of archaeal phospholipids.

Contribution of headgroup and chain length of glycerophospholipids to thermal stability and permeability of liposomes loaded with calcein

Biological membranes are complex systems that are composed of lipids, proteins and carbohydrates. They are difficult to study, so it is established practice to use lipid vesicles that consist of closed 'shells' of phospholipid bilayers as model systems to study various functional and structural aspects of lipid organisation. To define the effects of the structural properties of lipid vesicles on their phase behaviour, we investigated their headgroup and chain length, and the chemical bonds by which their acyl chains are attached to the glycerol moiety of glycerophospholipid species, in terms of phase transition temperature, enthalpy change and calcein permeability. We used differential scanning calorimetry to measure the temperature and enthalpy changes of phase transition, and fluorescence to follow calcein release through the bilayer structure. Our data show that longer acyl chains increase the stability of the lipid bilayers, whereas higher salt concentrations decrease the thermal stability and widen the phase transitions of these lipid bilayers. We discuss the possible reasons for the observed phase transition behaviour.

Intrinsic Membrane Permeability to Small Molecules

Spontaneous solute and solvent permeation through membranes is of vital importance to human life, be it gas exchange in red blood cells, metabolite excretion, drug/toxin uptake, or water homeostasis. Knowledge of the underlying molecular mechanisms is the sine qua non of every functional assignment to membrane transporters. The basis of our current solubility diffusion model was laid by Meyer and Overton. It correlates the solubility of a substance in an organic phase with its membrane permeability. Since then, a wide range of studies challenging this rule have appeared. Commonly, the discrepancies have their origin in ill-used measurement approaches, as we demonstrate on the example of membrane CO₂ transport. On the basis of the insight that scanning electrochemical microscopy offered into solute concentration distributions in immediate membrane vicinity of planar membranes, we analyzed the interplay between chemical reactions and diffusion for solvent transport, weak acid permeation, and enzymatic reactions adjacent to membranes. We conclude that buffer reactions must also be considered in spectroscopic investigations of weak acid transport in vesicular suspensions. The evaluation of energetic contributions to membrane translocation of charged species demonstrates the compatibility of the resulting membrane current with the solubility diffusion model. A local partition coefficient that depends on membrane penetration depth governs spontaneous membrane translocation of both charged and uncharged molecules. It is determined not only by the solubility in an organic phase but also by other factors like cholesterol concentration and intrinsic electric membrane potentials.

Tuning the photoexcitation response of cyanobacterial Photosystem I via reconstitution into Proteoliposomes

The role of natural thylakoid membrane housing of Photosystem I (PSI), the transmembrane photosynthetic protein, in its robust photoactivated charge separation with near unity quantum efficiency is not fundamentally understood. To this end, incorporation of suitable protein scaffolds for PSI incorporation is of great scientific and device manufacturing interest. Areas of interest include solid state bioelectronics, and photoelectrochemical devices that require bio-abio interfaces that do not compromise the photoactivity and photostability of PSI. Therefore, the surfactant-induced membrane solubilization of a negatively charged phospholipid (DPhPG) with the motivation of creating biomimetic reconstructs of PSI reconstitution in DPhPG liposomes is studied. Specifically, a simple yet elegant method for incorporation of PSI trimeric complexes into DPhPG bilayer membranes that mimic the natural thylakoid membrane housing of PSI is introduced. The efficacy of this method is demonstrated via absorption and fluorescence spectroscopy measurements as well as direct visualization using atomic force microscopy. This study provides direct evidence that PSI confinements in synthetic lipid scaffolds can be used for tuning the photoexcitation characteristics of PSI. Hence, it paves the way for development of fundamental understanding of microenvironment alterations on photochemical response of light activated membrane proteins.

Specific electrical capacitance and voltage breakdown as a function of temperature for different planar lipid bilayers

The breakdown voltage and specific electrical capacitance of planar lipid bilayers formed from lipids isolated from the membrane of archaeon Aeropyrum pernix K1 as a function of temperature were studied and compared with data obtained previously in MD simulation studies. Temperature dependence of breakdown voltage and specific electrical capacitance was measured also for dipalmitoylphosphatidylcholine (DPPC) bilayers and bilayers formed from mixture of diphytanoylphosphocholine (DPhPC) and DPPC in ratio 80:20. The breakdown voltage of archaeal lipids planar lipid bilayers is more or less constant until 50°C, while at higher temperatures a considerable drop is observed, which is in line with the results from MD simulations. The breakdown voltage of DPPC planar lipid bilayer at melting temperature is considerably higher than in the gel phase. Specific electrical capacitance of planar lipid bilayers formed from archaeal lipids is approximately constant for temperatures up to 40°C and then gradually decreases. The difference with MD simulation predictions is discussed. Specific electrical capacitance of DPPC planar lipid bilayers in fluid phase is 1.75 times larger than that of the gel phase and it follows intermediated phases before phase transition. Increase in specific electrical capacitance while approaching melting point of DPPC is visible also for DPhPC:DPPC mixture.

Control of membrane permeability in air-stable droplet interface bilayers

Air-stable droplet interface bilayers (airDIBs) on oil-infused surfaces are versatile model membranes for synthetic biology applications, including biosensing of airborne species. However, airDIBs are subject to evaporation, which can, over time, destabilize them and reduce their useful lifetime compared to traditional DIBs that are fully submerged in oil. Here, we show that the lifetimes of airDIBs can be extended by as much as an order of magnitude by maintaining the temperature just above the dew point. We find that raising the temperature from near the dew point (which was 7 °C at 38.5% relative humidity and 22 °C air temperature) to 20 °C results in the loss of hydrated water molecules from the polar headgroups of the lipid bilayer membrane due to evaporation, resulting in a phase transition with increased disorder. This dehydration transition primarily affects the bilayer electrical resistance by increasing the permeability through an increasingly disordered polar headgroup region of the bilayer. Temperature and relative humidity are conveniently tunable parameters for controlling the stability and composition of airDIB membranes while still allowing for operation in ambient environments.

Ether- versus ester-linked phospholipid bilayers containing either linear or branched apolar chains

We studied the properties of bilayers formed by ether-and ester-containing phospholipids, whose hydrocarbon chains can be either linear or branched, using sn-1,2 dipalmitoyl, dihexadecyl, diphytanoyl, and diphytanyl phosphatidylcholines (DPPC, DHPC, DPhoPC, and DPhPC, respectively) either pure or in binary mixtures. Differential scanning calorimetry and confocal fluorescence microscopy of giant unilamellar vesicles concurred in showing that equimolar mixtures of linear and branched lipids gave rise to gel/fluid phase coexistence at room temperature. Mixtures containing DHPC evolved in time (0.5 h) from initial reticulated domains to extended solid ones when an equilibrium was achieved. The nanomechanical properties of supported planar bilayers formed by each of the four lipids studied by atomic force microscopy revealed average breakdown forces Fb decreasing in the order DHPC ≥ DPPC > DPhoPC >> DPhPC. Moreover, except for DPPC, two different Fb values were found for each lipid. Atomic force microscopy imaging of DHPC was peculiar in showing two coexisting phases of different heights, probably corresponding to an interdigitated gel phase that gradually transformed, over a period of 0.5 h, into a regular tilted gel phase. Permeability to nonelectrolytes showed that linear-chain phospholipids allowed a higher rate of solute + water diffusion than branched-chain phospholipids, yet the former supported a smaller extent of swelling of the corresponding vesicles. Ether or ester bonds appeared to have only a minor effect on permeability.

Heating-enabled formation of droplet interface bilayers using Escherichia coli total lipid extract

Droplet interface bilayers (DIBs) serve as a convenient platform to study interactions between synthetic lipid membranes and proteins. However, a majority of DIBs have been assembled using a single lipid type, diphytanoylphosphatidylcholine (DPhPC). The work described herein establishes a new method to assemble DIBs using total lipid extract from Escherichia coli (eTLE); it is found that incubating oil-submerged aqueous droplets containing eTLE liposomes at a temperature above the gel-fluid phase transition temperature (Tg) promotes monolayer self-assembly that does not occur below Tg. Once monolayers are properly assembled via heating, droplets can be directly connected or cooled below Tg and then connected to initiate bilayer formation. This outcome contrasts immediate droplet coalescence observed upon contact between nonheated eTLE-infused droplets. Specific capacitance measurements confirm that the interface between droplets containing eTLE lipids is a lipid bilayer with thickness of 29.6 Å at 25 °C in hexadecane. We observe that bilayers formed from eTLE or DPhPC survive cooling and heating between 25 and 50 °C and demonstrate gigaohm (GΩ) membrane resistances at all temperatures tested. Additionally, we study the insertion of alamethicin peptides into both eTLE and DPhPC membranes to understand how lipid composition, temperature, and membrane phase influence ion channel formation. Like in DPhPC bilayers, alamethicin peptides in eTLE exhibit discrete, voltage-dependent gating characterized by multiple open channel conductance levels, though at significantly lower applied voltages. Cyclic voltammetry measurements of macroscopic channel currents confirm that the voltage-dependent conductance of alamethicin channels in eTLE bilayers occurs at lower voltages than in DPhPC bilayers at equivalent peptide concentrations. This result suggests that eTLE membranes, via composition, fluidity, or the presence of subdomains, offer an environment that enhances alamethicin insertion. For both membrane compositions, increasing temperature reduces the lifetimes of single channel gating events and increases the voltage required to cause an exponential increase in channel current. However, the fact that alamethicin insertion in eTLE exhibits significantly greater sensitivity to temperature changes through its Tg suggests that membrane phase plays an important role in channel formation. These effects are much less severe in DPhPC, where heating from 25 to 50 °C does not induce a phase change. The described technique for heating-assisted monolayer formation permits the use of other high transition temperature lipids in aqueous droplets for DIB formation, thereby increasing the types of lipids that can be considered for assembling model membranes.

Challenges in the Development of Functional Assays of Membrane Proteins

Lipid bilayers are natural barriers of biological cells and cellular compartments. Membrane proteins integrated in biological membranes enable vital cell functions such as signal transduction and the transport of ions or small molecules. In order to determine the activity of a protein of interest at defined conditions, the membrane protein has to be integrated into artificial lipid bilayers immobilized on a surface. For the fabrication of such biosensors expertise is required in material science, surface and analytical chemistry, molecular biology and biotechnology. Specifically, techniques are needed for structuring surfaces in the micro- and nanometer scale, chemical modification and analysis, lipid bilayer formation, protein expression, purification and solubilization, and most importantly, protein integration into engineered lipid bilayers. Electrochemical and optical methods are suitable to detect membrane activity-related signals. The importance of structural knowledge to understand membrane protein function is obvious. Presently only a few structures of membrane proteins are solved at atomic resolution. Functional assays together with known structures of individual membrane proteins will contribute to a better understanding of vital biological processes occurring at biological membranes. Such assays will be utilized in the discovery of drugs, since membrane proteins are major drug targets.

Handling of artificial membranes using electrowetting-actuated droplets on a microfluidic device combined with integrated pA-measurements

Artificial membranes, as a controllable environment, are an essential tool to study membrane proteins. Electrophysiology provides information about the ion transport mechanism across a membrane at the single-protein level. Unfortunately, high-throughput studies and screening are not accessible to electrophysiology because it is a set of not automated and technically delicate methods. Therefore, it is necessary to automate and parallelize electrophysiology measurement in artificial membranes. Here, we present a first step toward this goal: the fabrication and characterization of a microfluidic device integrating electrophysiology measurements and the handling of an artificial membrane which includes its formation, its displacement and the separation of its leaflets using electrowetting actuation of sub-μL droplets. To validate this device, we recorded the insertion of a model porin, α-hemolysin.

Polymerized planar suspended lipid bilayers for single ion channel recordings: comparison of several dienoyl lipids

The stabilization of suspended planar lipid membranes, or black lipid membranes (BLMs), through polymerization of mono- and bis-functionalized dienoyl lipids was investigated. Electrical properties, including capacitance, conductance, and dielectric breakdown voltage, were determined for BLMs composed of mono-DenPC, bis-DenPC, mono-SorbPC, and bis-SorbPC both prior to and following photopolymerization, with diphytanoyl phosphocholine (DPhPC) serving as a control. Poly(lipid) BLMs exhibited significantly longer lifetimes and increased the stability of air-water transfers. BLM stability followed the order bis-DenPC > mono-DenPC ≈ mono-SorbPC > bis-SorbPC. The conductance of bis-SorbPC BLMs was significantly higher than that of the other lipids, which is attributed to a high density of hydrophilic pores, resulting in relatively unstable membranes. The use of poly(lipid) BLMs as matrices for supporting the activity of an ion channel protein (IC) was explored using α-hemolysin (α-HL), a model IC. Characteristic i-V plots of α-HL were maintained following photopolymerization of bis-DenPC, mono-DenPC, and mono-SorbPC, demonstrating the utility of these materials for preparing more durable BLMs for single-channel recordings of reconstituted ICs.

Structure and stability of the spinach aquaporin SoPIP2;1 in detergent micelles and lipid membranes

Background

SoPIP2;1 constitutes one of the major integral proteins in spinach leaf plasma membranes and belongs to the aquaporin family. SoPIP2;1 is a highly permeable and selective water channel that has been successfully overexpressed and purified with high yields. In order to optimize reconstitution of the purified protein into biomimetic systems, we have here for the first time characterized the structural stability of SoPIP2;1.

Methodology/Principal Finding

We have characterized the protein structural stability after purification and after reconstitution into detergent micelles and proteoliposomes using circular dichroism and fluorescence spectroscopy techniques. The structure of SoPIP2;1 was analyzed either with the protein solubilized with octyl-β-D-glucopyranoside (OG) or reconstituted into lipid membranes formed by E. coli lipids, diphytanoylphosphatidylcholine (DPhPC), or reconstituted into lipid membranes formed from mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE), 1-palmitoyl-2oleoyl-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-phosphatidylserine (POPS), and ergosterol. Generally, SoPIP2;1 secondary structure was found to be predominantly α-helical in accordance with crystallographic data. The protein has a high thermal structural stability in detergent solutions, with an irreversible thermal unfolding occurring at a melting temperature of 58°C. Incorporation of the protein into lipid membranes increases the structural stability as evidenced by an increased melting temperature of up to 70°C.

Conclusion/Significance

The results of this study provide insights into SoPIP2;1 stability in various host membranes and suggest suitable choices of detergent and lipid composition for reconstitution of SoPIP2;1 into biomimetic membranes for biotechnological applications.

Regulated attachment method for reconstituting lipid bilayers of prescribed size within flexible substrates

A new method called the regulated attachment method (RAM) for reproducibly forming lipid bilayers within flexible substrates has been developed that enables precise control over the size of the bilayer. This technique uses a deformable flexible substrate to open and close an aperture that subdivides aqueous volumes submersed in an organic solvent. Phospholipids incorporated as vesicles in the aqueous phase self-assemble at the oil/water interface to form lipid monolayers that encapsulate each aqueous volume. Controlled attachment of opposing lipid monolayers is achieved by regulating the dimensions of the aperture in the substrate that separates the adjacent aqueous volumes. In this manner, the size of a lipid bilayer formed within a flexible substrate is a function of the substrate and aperture dimensions, and not determined by the sizes or shapes of the aqueous volumes. Lipid bilayers formed within the prototype flexible substrate exhibit DC resistances consistently higher than 10 GOmega and can survive 20-30x changes in area without rupture. Furthermore, RAM permits lipid bilayers to be completely unzipped after thinning by applying sufficient force to fully close the dividing aperture and even allows the introduction of species, such as alamethicin channels, into preformed lipid bilayers via controlled injection through an intersecting channel within the substrate. Controlling the size of the interface through indirect interactions with the supporting substrate offers a new platform for assembling durable lipid bilayers. We envision that this technology can be scaled to higher dimensions consisting of multiple apertures required for creating aqueous networks partitioned by functional lipid bilayers and to smaller length scales to produce very small lipid bilayers capable of hosting single proteins.

Physical encapsulation of droplet interface bilayers for durable, portable biomolecular networks

Physically-encapsulated droplet interface bilayers are formed by confining aqueous droplets encased in lipid monolayers within connected compartments of a solid substrate. Each droplet resides within an individual compartment and is positioned on a fixed electrode built into the solid substrate. Full encapsulation of the network is achieved with a solid cap that inserts into the substrate to form a closed volume. Encapsulated networks provide increased portability over unencapsulated networks by limiting droplet movement and through the integration of fixed electrodes into the supporting fixture. The formation of encapsulated droplet interface bilayers constructed from diphytanoyl phosphocoline (DPhPC) phospholipids is confirmed with electrical impedance spectroscopy, and cyclic voltammetry is used to measure the effect of alamethicin channels incorporated into the resulting lipid bilayers. The durability of the networks is quantified using a mechanical shaker to oscillate the bilayer in a direction transverse to the plane of the membrane and the results show that single droplet interface bilayers can withstand 1-10g of acceleration prior to bilayer failure. Observed failure modes include both droplet separation and bilayer rupturing, where the geometry of the supporting substrate and the presence of integrated electrodes are key contributors. Physically-encapsulated DIBs can be shaken, moved, and inverted without bilayer failure, enabling the creation of a new class of lab-on-chip devices.

Influence of an electric field on oriented films of DMPC/gramicidin bilayers: a circular dichroism study

A film of oriented bilayers containing a mixture of gramicidin and dimyristoylphosphatidylcholine (DMPC) has been deposited on a fused-silica window coated with a 10 nm thick gold layer. The thin layer of gold allows the application of an electric potential across the film and the study of its influence on the structure and integrity of the bilayers. Electrochemical measurements, ellipsometry, and far-UV circular dichroism (CD) were employed to characterize the properties of the film of bilayers as a function of the potential applied to the gold electrode. For potentials across the film that are within the range approximately +300 to -150 mV the oriented film of bilayers is stable, and no change in the CD spectra of gramicidin molecule is observed. At more negative potentials, an increase in the film thickness and water content measured by ellipsometry indicated that the film swells and incorporates water, which causes a change in the circular dichroism spectrum of gramicidin molecules in the film. This transformation was interpreted as a change in the average orientation of gramicidin molecules within the film due to a decrease in the ordering of the molecules upon swelling.

Are S-layers exoskeletons? The basic function of protein surface layers revisited

Surface protein or glycoprotein layers (S-layers) are common structures of the prokaryotic cell envelope. They are either associated with the peptidoglycan or outer membrane of bacteria, and constitute the only cell wall component of many archaea. Despite their occurrence in most of the phylogenetic branches of microorganisms, the functional significance of S-layers is assumed to be specific for genera or groups of organisms in the same environment rather than common to all prokaryotes. Functional aspects have usually been investigated with isolated S-layer sheets or proteins, which disregards the interactions between S-layers and the underlying cell envelope components. This study discusses the synergistic effects in cell envelope assemblies, the hypothetical role of S-layers for cell shape formation, and the existence of a common function in view of new insights.

Mechanism of osmoprotection by archaeal S-layers: a theoretical study

Many Archaea possess protein surface layers (S-layers) as the sole cell wall component. S-layers must therefore integrate the basic functions of mechanical and osmotic cell stabilisation. While the necessity is intuitively clear, the mechanism of structural osmoprotection by S-layers has not been elucidated yet. The theoretical analysis of a model S-layer-membrane assembly, derived from the typical cell envelope of Crenarchaeota, explains how S-layers impart lipid membranes with increased resistance to internal osmotic pressure and offers a quantitative assessment of S-layer stability. These considerations reveal the functional significance of S-layer symmetry and unit cell size and shed light on the rationale of S-layer architectures.

Molecular dynamics study of bipolar tetraether lipid membranes

Membranes composed of bipolar tetraether lipids have been studied by a series of 25-ns molecular dynamics simulations to understand the microscopic structure and dynamics as well as membrane area elasticity. By comparing macrocyclic and acyclic tetraether and diether archaeal lipids, the effect of tail linkage of the two phytanyl-chained lipids on the membrane properties is elucidated. Tetraether lipids show smaller molecular area and lateral mobility. For the latter, calculated diffusion coefficients are indeed one order-of-magnitude smaller than that of the diether lipid. These two tetraether membranes are alike in many physical properties except for membrane area elasticity. The macrocyclic tetraether membrane shows a higher elastic area expansion modulus than its acyclic counterpart by a factor of three. Free energy profiles of a water molecule crossing the membranes show no major difference in barrier height; however, a significant difference is observed near the membrane center due to the lack of the slip-plane in tetraether membranes.

Local anesthetics facilitate ion transport across lipid planar bilayer membranes under an electric field: Dependence on type of lipid bilayer

In order to elucidate the role of structural change of lipid membrane bilayer in the mode of action of local anesthetic, we studied the effects of local anesthetics, charged tetracaine and uncharged benzocaine, on ion permeability across various lipid planar bilayers (PC, mixed PC/PS (4/1, mol/mol); mixed PC/PE (1/1, mol/mol); mixed PC/SM (4/1, mol/mol)) under a constant applied voltage. The membrane conductances increased in the order of PC<<PC/PS<or=PC/SM<<PC/PE. When the constant voltage of -100 or -70 mV was applied through the lipid bilayer membranes in the presence of positively charged tetracaine, the fluctuating current pulses with the large amplitude generated, but not appeared in the absence of tetracaine. The addition of uncharged benzocaine generated the fluctuating currents with the small amplitude. Both charged tetracaine and uncharged benzocaine facilitated electrophoretically the transport of small ions such as KCl in the buffer solution through the fluctuating pores in the lipid bilayer membranes formed by interaction with the local anesthetic under the negative applied membrane potential. The current pulses also contained actual transport of charged tetracaine together with the transport of the small ions. The amplitude and the duration time of the electrical current generated by adding the local anesthetics were dependent on the type of the lipid, the applied voltage and its voltage polarity.

Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers

The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester linked straight chains. In order to elucidate the influence of the ether linkage, instead of an ester one, on the physical properties of the lipid bilayers, we have carried out comparative 10 ns molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data.

Bilayer thickness modulates the conductance of the BK channel in model membranes

The conductance of the BK channel was evaluated in reconstituted bilayers made of POPE/POPS (3.3:1), or POPE/POPS with an added 20% of either SPM (3.3:1:1), CER (3.3:1:1), or CHL (3.3:1:1). The presence of SPM, which is known to increase bilayer thickness, significantly reduced the conductance of the BK channel. To directly test the role of membrane thickness, the conductance of the BK channel was measured in bilayers formed from PCs with acyl chains of increasing length (C14:1-C24:1), all in the absence of SPM. Slope conductance was maximal at a chain length of (C18:1) and much reduced for both thinner (C14:1) and thicker (C24:1) bilayers, indicating that membrane thickness alone can modify slope conductance. Further, in a simplified binary mixture of DOPE/SPM that forms a confined, phase-separated bilayer, the measured conductance of BK channels shows a clear bimodal distribution. In contrast, the addition of CER, which has an acyl chain structure similar to SPM but without its bulky polar head group to POPE/POPS, was without effect, as was the addition of CHL. The surface structure of membranes made from these same lipid mixtures was examined with AFM. Incorporation of both SPM and CER resulted in the formation of microdomains in POPE/POPS monolayers, but only SPM promoted a substantial increase in the amount of the high phase observed for the corresponding bilayers. The addition of CHL to POPE/POPS eliminated the phase separation observed in the POPE/POPS bilayer. The decrease in channel conductance observed with the incorporation of SPM into POPE/POPS membranes was, therefore, attributed to larger SPM-rich domains that appear thicker than the neighboring bilayer.

Hydration and molecular motions in synthetic phytanyl-chained glycolipid vesicle membranes

Proton permeation rates across membranes of a synthetic branch-chained glycolipid, 1,3-di-O-phytanyl-2-O-(beta-D-maltotriosyl)glycerol (Mal3(Phyt)2) as well as a branch-chained phospholipid, diphytanoylphosphatidylcholine (DPhPC) were lower than those of straight-chained lipids such as egg yolk phosphatidylcholine (EPC) by a factor of approximately 4 at pH 7.0 and 25 degrees C. To examine whether degrees of water penetration and molecular motions in Mal3(Phyt)2 membranes can account for the lower permeability, nanosecond time-resolved fluorescence spectroscopy was applied to various membranes of branch-chained lipids (Mal3(Phyt)2, DPhPC, and a tetraether lipid from an extremely thermoacidophilic archaeon Thermoplasma acidophilum), as well as straight-chained lipids (EPC, 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC), and digalactosyldiacylglycerol (DGDG)) using several fluorescent lipids. Degrees of hydration of glycolipids, Mal3(Phyt)2, and DGDG were lower than those of phospholipids, EPC, POPC, and DPhPC at the membrane-water interfaces. DPhPC showed the highest hydration among the lipids examined. Meanwhile, rotational and lateral diffusive motions of the fluorescent phospholipid in branch-chained lipid membranes were more restricted than those in straight-chained ones. The results suggest that the restricted motion of chain segments rather than the lower hydration accounts for the lower proton permeability of branch-chained lipid membranes.

Synthetic phytanyl-chained glycolipid vesicle membrane as a novel matrix for functional reconstitution of cyanobacterial photosystem II complex

The vesicles composed of synthetic phytanyl-chained glycolipid and natural sulfoquinovosyldiacylglycerol at 9:1 molar ratio were successfully applied to functional reconstitution of photosystem II complex (PS II) from a thermophilic cyanobacterium. The synthetic glycolipid employed was one of our model archaeal diether lipids, 1, 3-di-O-phytanyl-2-O-(beta-D-maltotriosyl)glycerol. The light-induced oxygen-evolving activity of PS II reconstituted in the glycolipid vesicles was approximately 6-fold higher than that reconstituted in several phosphatidylcholine vesicles. The present results reveal the first evidence that a well-designed synthetic glycolipid is effective for the functional reconstitution of complicated and labile membrane protein complexes, such as PS II.