Lipidic Mesophases Research Articles

Characterizing the Self-Assembly Properties of Monoolein Lipid Isosteres.

Living cells feature lipid compartments which exhibit a variety of shapes and structures that assist essential cellular processes. Many natural cell compartments frequently adopt convoluted nonlamellar lipid architectures that facilitate specific biological reactions. Improved methods for controlling the structural organization of artificial model membranes would facilitate investigations into how membrane morphology affects biological functions. Monoolein (MO) is a single-chain amphiphile which forms nonlamellar lipid phases in aqueous solution and has wide applications in nanomaterial development, the food industry, drug delivery, and protein crystallization. However, even if MO has been extensively studied, simple isosteres of MO, while readily accessible, have seen limited characterization. An improved understanding of how relatively minor changes in lipid chemical structure affect self-assembly and membrane topology could instruct the construction of artificial cells and organelles for modeling biological structures and facilitate nanomaterial-based applications. Here, we investigate the differences in self-assembly and large-scale organization between MO and two MO lipid isosteres. We show that replacing the ester linkage between the hydrophilic headgroup and hydrophobic hydrocarbon chain with a thioesther or amide functional group results in the assembly of lipid structures with different phases not resembling those formed by MO. Using light and cryo-electron microscopy, small-angle X-ray scattering, and infrared spectroscopy, we demonstrate differences in the molecular ordering and large-scale architectures of the self-assembled structures made from MO and its isosteric analogues. These results improve our understanding of the molecular underpinnings of lipid mesophase assembly and may facilitate the development of MO-based materials for biomedicine and as model lipid compartments.

Interplay of Hydropathy and Heterogeneous Diffusion in the Molecular Transport within Lamellar Lipid Mesophases

Lipid mesophases are being intensively studied as potential candidates for drug-delivery purposes. Extensive experimental characterization has unveiled a wide palette of release features depending on the nature of the host lipids and of the guest molecule, as well as on the environmental conditions. However, only a few simulation works have addressed the matter, which hampers a solid rationalization of the richness of outcomes observed in experiments. Particularly, to date, there are no theoretical works addressing the impact of hydropathy on the transport of a molecule within lipid mesophases, despite the significant fraction of hydrophobic molecules among currently-available drugs. Similarly, the high heterogeneity of water mobility in the nanoscopic channels within lipid mesophases has also been neglected. To fill this gap, we introduce here a minimal model to account for these features in a lamellar geometry, and systematically study the role played by hydropathy and water-mobility heterogeneity by Brownian-dynamics simulations. We unveil a fine interplay between the presence of free-energy barriers, the affinity of the drug for the lipids, and the reduced mobility of water in determining the net molecular transport. More in general, our work is an instance of how multiscale simulations can be fruitfully employed to assist experiments in release systems based on lipid mesophases.

Xia2.multiplex: a multi-crystal data-analysis pipeline.

In macromolecular crystallography, radiation damage limits the amount of data that can be collected from a single crystal. It is often necessary to merge data sets from multiple crystals; for example, small-wedge data collections from micro-crystals, in situ room-temperature data collections and data collection from membrane proteins in lipidic mesophases. Whilst the indexing and integration of individual data sets may be relatively straightforward with existing software, merging multiple data sets from small wedges presents new challenges. The identification of a consensus symmetry can be problematic, particularly in the presence of a potential indexing ambiguity. Furthermore, the presence of non-isomorphous or poor-quality data sets may reduce the overall quality of the final merged data set. To facilitate and help to optimize the scaling and merging of multiple data sets, a new program, xia2.multiplex, has been developed which takes data sets individually integrated with DIALS and performs symmetry analysis, scaling and merging of multi-crystal data sets. xia2.multiplex also performs analysis of various pathologies that typically affect multi-crystal data sets, including non-isomorphism, radiation damage and preferential orientation. After the description of a number of use cases, the benefit of xia2.multiplex is demonstrated within a wider autoprocessing framework in facilitating a multi-crystal experiment collected as part of in situ room-temperature fragment-screening experiments on the SARS-CoV-2 main protease.

A lipidic mesophase with tunable release properties for the local delivery of macromolecules: the apoferritin nanocage, a case study.

Lipid mesophases are able to incorporate and release a plethora of molecules, spanning from hydrophobic drugs to small hydrophilic proteins and therefore they have been widely used as drug delivery systems. However, their 3-5 nm water channels do not allow the release of large hydrophilic molecules such as monoclonal antibodies and therapeutic proteins. To overcome this major geometrical constraint, we designed a gel by mixing monoacylglycerol lipids, generally recognized as safe for human and/or animal use by FDA, and phospholipids, to obtain a material with swollen water channels suitable to host and further release macromolecules. Apoferritin, a 12 nm nanocage protein with intrinsic tumor-targeting properties able to incorporate several molecules, was selected here as the hydrophilic model protein to be embedded in the biocompatible gel. When immersed completely in the release media, mesophases with a swollen water channel of 22 nm, composed of monoolein and doped with 5 mole% of DOPS and 10 mole% of Chol allowed us to achieve a protein release of 60%, which is 120 times higher with respect to that obtained by employing non swollen-LMPs composed only of monoolein. Thus, the formulation can be administered locally to the rectal or vaginal mucosa, reducing the drawbacks often associated with the parenteral administration of bio-therapeutics. This approach would pave the way for the local application of other biomacromolecules (including human ferritin, monoclonal antibodies and antibody drug-conjugates) in those diseases easily reachable by a local application such as rectal or vaginal cancer.

Crystallization of Microbial Rhodopsins.

Microbial rhodopsins are light-sensitive transmembrane proteins, evolutionary adapted by various organisms like archaea, bacteria, simple eukaryote, and viruses to utilize solar energy for their survival. A complete understanding of functional mechanisms of these proteins is not possible without the knowledge of their high-resolution structures, which can be primarily obtained by X-ray crystallography. This technique, however, requires high-quality crystals, growing of which is a great challenge especially in case of membrane proteins. In this chapter, we summarize methods applied for crystallization of microbial rhodopsins with the emphasis on crystallization in lipidic mesophases, also known as in meso approach. In particular, we describe in detail the methods of crystallization using lipidic cubic phase to grow both large crystals optimized for traditional crystallographic data collection and microcrystals for serial crystallography.

High-pressure SAXS, deep life, and extreme biophysics.

The biological relevance of hydrostatic pressure is becoming much more widely understood and appreciated as discoveries of new niches for extreme life continue to emerge. The unusual chemistry and physiological adaptations of organisms under extreme pressure promises to be a rich source of new insights in the years ahead if structural information can be obtained at the molecular level. Fortunately, recent advances in instrumentation are making structural biology techniques easier to perform at extreme pressures and more widely available. In addition to biological applications, hydrostatic pressure is a useful biophysical tool that can perturb systems in ways directly connected to the presence of atomic-level voids, cavities, and other volumetric properties. Under pressure, individual molecular complexes can dissociate, and monomers can unfold; transitions can occur in lipid mesophases, and liquid phases can dissolve and re-form. Small angle X-ray solution scattering (SAXS) can detect and characterize pressure-induced changes in all these situations. This chapter reviews what is known about pressure effects in a wide variety of biomolecular systems and how those effects display in X-ray scattering data. The influence of hydrostatic pressure on solution scattering is discussed, and the most widely used data processing methods are re-examined considering pressure effects. The chapter concludes with an overview of the high-pressure SAXS instrument design followed by recommended data collection protocol.

Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX.

CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open-close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono-acyl-glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy-droxy-propyl methyl-cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.

Probing Water State during Lipidic Mesophases Phase Transitions.

We investigate the static and dynamic states of water network during the phase transitions from double gyroid (Ia3‾d ) to double diamond (Pn3‾m ) bicontinuous cubic phases and from the latter to the reverse hexagonal (H II) phase in monolinolein based lipidic mesophases by combining FTIR and broadband dielectric spectroscopy (BDS). In both cubic(s) and H II phase, two dynamically different fractions of water are detected and attributed to bound and interstitial free water. The dynamics of the two water fractions are all slower than bulk water due to the hydrogen‐bonds between water molecules and the lipid's polar headgroups and to nanoconfinement. Both FTIR and BDS results suggest that a larger fraction of water is hydrogen‐bonded to the headgroup of lipids in the H II phase at higher temperature than in the cubic phase at lower temperature via H‐bonds, which is different from the common expectation that the number of H‐bonds should decrease with increase of temperature. These findings are rationalized by considering the topological ratio of interface/volume of the two mesophases.

Probing Water State during Lipidic Mesophases Phase Transitions

AbstractWe investigate the static and dynamic states of water network during the phase transitions from double gyroid ( ) to double diamond ( ) bicontinuous cubic phases and from the latter to the reverse hexagonal (HII) phase in monolinolein based lipidic mesophases by combining FTIR and broadband dielectric spectroscopy (BDS). In both cubic(s) and HII phase, two dynamically different fractions of water are detected and attributed to bound and interstitial free water. The dynamics of the two water fractions are all slower than bulk water due to the hydrogen‐bonds between water molecules and the lipid's polar headgroups and to nanoconfinement. Both FTIR and BDS results suggest that a larger fraction of water is hydrogen‐bonded to the headgroup of lipids in the HII phase at higher temperature than in the cubic phase at lower temperature via H‐bonds, which is different from the common expectation that the number of H‐bonds should decrease with increase of temperature. These findings are rationalized by considering the topological ratio of interface/volume of the two mesophases.

Cubic and Hexagonal Mesophases for Protein Encapsulation: Structural Effects of Insulin Confinement

Monoolein-based cubic and hexagonal mesophases were investigated as matrices for insulin loading, at low pH, as a function of temperature and in the presence of increasing amounts of oleic acid, as a structural stabilizer for the hexagonal phase. Synchrotron small angle X-ray diffraction, rheological measurements, and attenuated total reflection-Fourier transform infrared spectroscopy were used to study the effects of insulin loading on the lipid mesophases and of the effect of protein confinement in the 2D- and 3D-lipid matrix water channels on its stability and unfolding behavior. We found that insulin encapsulation has only little effects both on the mesophase structures and on the viscoelastic properties of lipid systems, whereas protein confinement affects the response of the secondary structure of insulin to thermal changes in a different manner according to the specific mesophase: in the cubic structure, the unfolding toward an unordered structure is favored, while the prevalence of parallel β-sheets, and nuclei for fibril formation, is observed in hexagonal structures.

Flavin-Helicene Amphiphilic Hybrids: Synthesis, Characterization, and Preparation of Surface-Supported Films.

This work reports on the preparation and structural characterization of flavo[7]helicene 1 (flavin-[7]helicene conjugate), which was subsequently characterized at the molecular level in either an aqueous environment or an organic phase, at the supramolecular level in the form of polymeric layers, and also embedded in a lipidic mesophase environment to study the resulting properties of such a hybrid relative to its parent molecules. The flavin benzo[g]pteridin-2,4-dione (isoalloxazine) was selected for conjugation because of its photoactivity and reversible redox behavior. Compound 1 was prepared from 2-nitroso[6]helicene and 6-methylamino-3-methyluracil, and characterized using common structural and spectroscopic tools: circular dichroism (CD), circularly polarized luminescence (CPL) spectroscopy, cyclic voltammetry (CV), and DFT quantum calculations. In addition, a methodology that allows the loading of 1 enantiomers into an internally nanostructured lipid (1-monoolein) matrix was developed.

Designing cryo-enzymatic reactions in subzero liquid water by lipidic mesophase nanoconfinement.

Cryo-enzymology provides the possibility to develop unconventional biological reactions and detect intermediates in ultrafast enzymatic catalysis processes, but also illuminates the understanding of life principles in extremely cold environments. The scarcity of biological or biomimetic host systems that provide liquid water at subzero temperatures inhibits the prosperity of cryo-enzymology. Here we introduce cryo-enzymatic reactions in subzero water nanoconfined within lipid mesophases formed by conventional lipids. We show that the enzymatic reactions that ensue outperform the homologue catalytic processes run at standard temperatures. We use phytantriol-based lipidic mesophases (LMPs), within which water remains in the liquid state down to -120 °C, and combine crystallization and dynamic studies of the confined water to provide a fundamental understanding of the physical status of water at subzero temperatures, which sets the stage for cryo-enzymatic reactions in these environments. In the model horseradish peroxidase oxidization, the cation free-radical product is stabilized in LMPs at -20 °C, in contrast to the fast-consuming reactions at temperatures above 0 °C. Furthermore, the LMP system also supports the cascade reaction and lipase reaction at subzero temperatures, at which enzymatic reactions with both hydrophilic and hydrophobic substrates are successfully carried out. Our designed LMP system opens access to the nature of confined water in the biomimetic environment and provides a platform for low-temperature biomacromolecule reconstitution and the cryogenic control of enzymatic reactions in bionanotechnology.

Structural basis for the catalysis and inhibition of human steroid 5α‐reductase 2

Human steroid 5α-reductases (SRD5As) are membrane-embedded NADPH-dependent steroid and lipid reductases with diverse physiological and pathological roles. Among them, SRD5A2 is a critical enzyme in steroid metabolism that catalyzes testosterone to dihydrotestosterone. Mutations on its gene have been linked to 5α-reductase deficiency and prostate cancer. Finasteride and dutasteride as SRD5A2 inhibitors are widely used anti-androgen drugs for benign prostate hyperplasia and androgenic alopecia, which have recently been indicated in the treatment of COVID-19. The molecular mechanisms underlying enzyme catalysis and inhibition had remained elusive for SRD5A2 and other eukaryotic integral membrane steroid reductases due to a lack of structural information. We recently solved a crystal structure of human SRD5A2 at 2.8 Å with finasteride using the lipid mesophase (or LCP) crystallization method. The structure reveals a unique structural topology of 7-transmembrane helices and an intermediate adduct of finasteride and NADPH as NADP-dihydrofinasteride, which binds in a largely enclosed binding cavity inside the membrane. To our knowledge, similar NADPH adducts have not been reported previously. Structural analysis together with computational and mutagenesis studies reveals molecular mechanisms for the 5α-reduction of testosterone and the semi-irreversible finasteride inhibition involving residues E57 and Y91 of SRD5A2. Molecular dynamics simulation results indicate high conformational dynamics of the cytosolic region of SRD5A2 including three cytosolic loops regulating the NADPH/NADP+ exchange and their entry into the transmembrane region of SRD5A2. Mapping disease-causing mutations of SRD5A2 to our structure suggests molecular mechanisms for their pathological effects. In summary, our results offer critical and unprecedented structural insights into the function of integral membrane steroid reductases and will facilitate drug development.

Macromolecular crystallography using microcrystal electron diffraction.

Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.

Cryogenic activity and stability of benzaldehyde lyase enzyme in lipidic mesophases-nanoconfined water.

Phytantriol-based lipidic mesophases (LMs) are introduced as a platform for cryoenzymology, which relies on the presence of liquid water in LMs at subzero temperatures. After incorporation into LMs, the model enzyme Benzaldehyde lyase (BAL) shows high cryogenic stability and activity. In contrast, BAL in bulk solution undergoes significant secondary structural transitions caused by low temperatures (cold denaturation), demonstrating the potential of this approach to enable in meso cryoenzymology.

Lipids from algal biomass provide new (nonlamellar) nanovectors with high carrier potentiality for natural antioxidants

Lipid mesophases are lyotropic liquid crystalline systems which differ from liposomes and other globular aggregates in dilute regimes due to their inner ordering. It is known that natural lipids enable to obtain a rich variety of nanosystems and many of them have been proposed as delivery agents for bioactive compounds. Due to their packing parameters, several classes of lipids found in natural sources are able to self-assemble into nonlamellar structures. Among lipids occurring in plants and algae, triglycerides display this tendency. In the present study we examine new nanosystems built with lipids extracted from the marine microalga Nannochloropsis sp and their use as carriers for lipophilic antioxidants. The antioxidants studied, curcumin and tocopherol were encapsulated with high rate in the carriers. The physico-chemical characterization of plain and loaded vectors showed their structure and localization site, as well as the structure-functionality relationship related to potential drug delivery. The results show that the cargo molecules play an active role in driving the interactions which characterize the overall structure of the aggregates. The systems studied showed several coexisting mesophases, the most predominant structure being of cubic symmetry.

Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures.

Electron crystallography of sub-micrometre-sized 3D protein crystals has emerged recently as a valuable field of structural biology. In meso crystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realizing 3D electron crystallography of MP crystals, grown in meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix that surrounds the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can be used to remove excess host lipidic mesophase matrix is experimentally verified, and then the crystals are thinned to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic cubic mesophase of monoolein were used as a model system. LCP from a part of a hexagon-shaped plate-like BR crystal (∼10 µm in thickness and ∼70 µm in the longest dimension), which was flash-frozen in liquid nitro-gen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210 nm-thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope, and a nanovolume of ∼1400 × 1400 × 210 nm of the BR lamella was exposed to 200 kV electrons at a fluence of ∼0.06 e Å-2. The resulting electron diffraction peaks were detected beyond 2.7 Å resolution (with an average peak height to background ratio of >2) by a CMOS-based Ceta 16M camera. The results demonstrate that cryo-FIB milling produces high-quality lamellae from crystals grown in lipidic mesophases and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.

Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center.

With the recent developments in the field of free-electron-laser-based serial femtosecond crystallography, the necessity to obtain a large number of high-quality crystals has emerged. In this work crystallization techniques were selected, tested and optimized for the lipid mesophase crystallization of the Rhodobacter sphaeroides membrane pigment-protein complex, known as the photosynthetic reaction center (RC). Novel approaches for lipid sponge phase crystallization in comparatively large volumes using Hamilton gas-tight glass syringes and plastic pipetting tips are described. An analysis of RC crystal structures obtained by lipid mesophase crystallization revealed non-native ligands that displaced the native electron-transfer cofactors (carotenoid sphero-idene and a ubi-quinone molecule) from their binding pockets. These ligands were identified and were found to be lipids that are major mesophase components. The selection of distinct co-crystallization conditions with the missing cofactors facilitated the restoration of sphero-idene in its binding site.

Controlling the Kinetics of an Enzymatic Reaction through Enzyme or Substrate Confinement into Lipid Mesophases with Tunable Structural Parameters.

Lipid liquid crystalline mesophases, resulting from the self-assembly of polymorphic lipids in water, have been widely explored as biocompatible drug delivery systems. In this respect, non-lamellar structures are particularly attractive: they are characterized by complex 3D architectures, with the coexistence of hydrophobic and hydrophilic regions that can conveniently host drugs of different polarities. The fine tunability of the structural parameters is nontrivial, but of paramount relevance, in order to control the diffusive properties of encapsulated active principles and, ultimately, their pharmacokinetics and release. In this work, we investigate the reaction kinetics of p-nitrophenyl phosphate conversion into p-nitrophenol, catalysed by the enzyme Alkaline Phosphatase, upon alternative confinement of the substrate and of the enzyme into liquid crystalline mesophases of phytantriol/H2O containing variable amounts of an additive, sucrose stearate, able to swell the mesophase. A structural investigation through Small-Angle X-ray Scattering, revealed the possibility to finely control the structure/size of the mesophases with the amount of the included additive. A UV–vis spectroscopy study highlighted that the enzymatic reaction kinetics could be controlled by tuning the structural parameters of the mesophase, opening new perspectives for the exploitation of non-lamellar mesophases for confinement and controlled release of therapeutics.

The physics of lipidic mesophase delivery systems

Effectively releasing drugs in the body depends on the physical and chemical traits of a special class of liquid crystals.