Structure Of Biological Membranes Research Articles

Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir.

Molecular dynamics (MD) simulations based on detailed all-atom models offer a powerful approach to study the structure and dynamics of biological membranes. However, the complexity of biological membranes in terms of chemical diversity presents an outstanding challenge. Particularly, difficulties are encountered when a given lipid type is present at very low abundance. While considering a very large simulation system with a small number of the low abundance lipid may offer a practical solution in some cases, resorting to increasingly large system rapidly becomes computationally costly and impractical. More fundamentally, an additional issue may be encountered if the low abundance lipid displays a high affinity for some protein in the simulation system. What is needed is to treat the simulation box as an open system in which the number of lipids can naturally fluctuate, as in the Grand Canonical Monte Carlo (MC) algorithm. However, this approach, in which a whole lipid molecule needs to be inserted or annihilated, is essentially impractical in the context of an all-atom simulation. To enforce equilibrium between a simulated system and an infinite surrounding bath, we propose a hybrid non-equilibrium (neMD)-MC algorithm, in which a randomly chosen lipid molecule in the simulated system is swapped with a lipid picked in a separate system standing as a thermodynamic "reservoir" with the desired mole fraction for all lipid components. The neMD/MC algorithm consists in driving the system via short non-equilibrium trajectories to generate a new state of the system that are subsequently accepted or rejected via a Metropolis MC step. The probability of exchanges in the context of an infinite reservoir with the desired mole fraction for all lipid components is derived and tested with a few illustrative systems for phosphatidylcholine and phosphatidylglycerol lipid mixtures.

Structural and Spectroscopic Characterization of Supported Sarcoplasmic Reticulum Membranes on Solid Substrates.

Sarcoplasmic reticulum (SR) membranes from rabbit muscle were deposited on silicon substrates and characterized by the combination of spectral ellipsometry (SE), high energy specular X-ray reflectivity (XRR), specular neutron reflectivity (NR), and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. Following the optimization of the preparative conditions by SE, the detailed structures in the direction perpendicular to the membrane were probed by XRR. ATR-FTIR data showed strong signals from amide I and amide II bands of the native SR membranes containing a large amount of Ca2+-ATPase, which could not be achieved by the reconstitution in artificial lipid membranes. The treatment with protease led to a significant decrease in the amide peaks, and the XRR data confirmed the modulation of the membrane structures. The obtained data show the potential of the in situ combination of reflectivity and vibrational spectroscopy of native supported membranes in order to unravel both structure and dynamics of complex biological membranes.

Nanoconfined Strategy Optimizing Hard Carbon for Robust Sodium Storage

AbstractDeveloping non‐graphitic carbons with unique microstructure is a popular strategy to enhance the significant potential in practical applications of sodium‐ion batteries (SIB), while the electrochemical performance imbalances arising from their intricate active surface and porous structure pose significant challenges to its commercialization. Inspired by the structure of biological cell membranes, N/P co‐doped hard carbon nanospheres (NPCS) anodes with abundant ultramicropores (≈0.6 nm) are proposed and synthesized as robust sodium anodes. Based on density functional theory calculations, optimizing ultramicropores can enable small Na+ to be well confined within the pores and hinder large solvent molecules from invading and reacting, introducing N/P species contributes to the rapid adsorption/diffusion of Na+. In situ XRD and Raman analysis suggest that the nanoconfinement strategy induced by abundant ultramicropores and N/P co‐doping enables highly reversible electrochemical reactions. Electrochemical test confirms that the nanoconfinement strategy endows the NPCS anode with high reversible capacity (376.3 mAh g−1 at 0.1 A g−1), superior initial coulombic efficiency (87.3% at 1.0 A g−1), remarkable rate capability (155.6 mAh g−1 at 50.0 A g−1) and excellent cycling stability (with capacity retention of ≈94.6% after 10 000 cycles), lightening a promising avenue for developing SIB with robust durability.

Configurational Sampling of All-Atom Solvated Membranes Using Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations.

All-atom simulations are a powerful approach to study the structure and dynamics of biological membranes. However, sampling the atomic configurations of inhomogeneous membranes can be challenging due to the slow lateral diffusion of the various constituents. To address this issue, a hybrid nonequilibrium molecular dynamics Monte Carlo (neMD/MC) simulation method is proposed in which randomly chosen lipid molecules are swapped to generate configurations that are subsequently accepted or rejected according to a Metropolis criterion based on the alchemical work for the attempted swap calculated via a short trajectory. A dual-topology framework constraining the common atoms of the exchanging molecules yields a good acceptance probability using switching trajectories as short as 10 ps. The performance of the hybrid neMD/MC algorithm and its ability to sample the distribution of lipids near a transmembrane helix carrying a net charge are illustrated for a binary mixture of charged and zwitterionic lipids.

Phase separation in model lipid membranes investigated with cryogenic electron microscopy.

We describe a method for investigating lateral membrane heterogeneity using cryogenic electron microscopy (cryo-EM) images of liposomes. The method takes advantage of differences in the thickness and molecular density of ordered and disordered phases that are resolvable in phase contrast cryo-EM. Compared to biophysical techniques like FRET or neutron scattering that yield ensemble-averaged information, cryo-EM provides direct visualization of individual vesicles and can therefore reveal variability that would otherwise be obscured by averaging. Moreover, because the contrast mechanism involves inherent properties of the lipid phases themselves, no extrinsic probes are required. We explain and discuss various complementary analyses of spatially resolved thickness and intensity measurements that enable an assessment of the membrane's phase state. The method opens a window to nanodomain structure in synthetic and biological membranes that should lead to an improved understanding of lipid raft phenomena.

Lipids in Extracellular Vesicles: What Can Be Learned about Membrane Structure and Function?

Extracellular vesicles, such as exosomes, can be used as interesting models to study the structure and function of biological membranes as these vesicles contain only one membrane (i.e., one lipid bilayer). In addition to lipids, they contain proteins, nucleic acids, and various other molecules. The lipid composition of exosomes is here compared to HIV particles and detergent-resistant membranes, which also have a high content of sphingolipids, cholesterol, and phosphatidylserine (PS). We discuss interactions between the lipids in the two bilayers, and especially those between PS 18:0/18:1 in the inner leaflet and the very-long-chain sphingolipids in the outer leaflet, and the importance of cholesterol for these interactions. We also briefly discuss the involvement of ether-linked phospholipids (PLs) in such lipid raft-like structures, and the possible involvement of these and other lipid classes in the formation of exosomes. The urgent need to improve the quality of quantitative lipidomic studies is highlighted.

On the Mechanism of Membrane Permeabilization by Tamoxifen and 4-Hydroxytamoxifen.

Tamoxifen (TMX), commonly used in complementary therapy for breast cancer, also displays known effects on the structure and function of biological membranes. This work presents an experimental and simulation study on the permeabilization of model phospholipid membranes by TMX and its derivative 4-hydroxytamoxifen (HTMX). TMX induces rapid and extensive vesicle contents leakage in phosphatidylcholine (PC) liposomes, with the effect of HTMX being much weaker. Fitting of the leakage curves for TMX, yields two rate constants, corresponding to a fast and a slow process, whereas in the case of HTMX, only the slow process takes place. Interestingly, incorporation of phosphatidylglycerol (PG) or phosphatidylethanolamine (PE) protects PC membranes from TMXinduced permeabilization. Fourier-transform infrared spectroscopy (FTIR) shows that, in the presence of TMX there is a shift in the νCH2 band frequency, corresponding to an increase in gauche conformers, and a shift in the νC=O band frequency, indicating a dehydration of the polar region. A preferential association of TMX with PC, in mixed PC/PE systems, is observed by differential scanning calorimetry. Molecular dynamics (MD) simulations support the experimental results, and provide feasible explanations to the protecting effect of PG and PE. These findings add new information to explain the various mechanisms of the anticancer actions of TMX, not related to the estrogen receptor, and potential side effects of this drug.

Predicting hydration properties of proteins.

Membrane proteins are essential in biological cellular function and membrane structure. They can perform various functions depending on their amino acid peptide chain sequence, and their three-dimensional (3D) folded structure. This 3D structure is determined by the electrostatic interactions among the neighboring residues, the proteins’ specific placement of amino acid residues, and hydration properties under physiological conditions within the peptide chain, as well as their hydropathy and the electrostatic interactions between neighboring residues. Despite their importance to cellular function, there are gaps in the understanding of the protein properties in terms of their assembly and interactions with other biomolecules based on surface amino acids as well as how these properties change due to surrounding interactions of neighboring residues in the peptide chain. Several computational techniques have been used to obtain insights into the characterization of protein hydration behavior. Computational simulations have been used; however, these approaches are limited by increasing high computational costs. Here we present a novel computational approach method that uses molecular dynamics simulations to provide hydropathy of the characterization of amino acid residues at a fraction of the computational cost based on their interactions at the protein surface. Understanding the behavior of membrane protein surfaces can provide greater insight into their functions in a cellular membrane, such as structural support and ion transport. The versatility of this method is demonstrated by the modelling of a wide range of 14 various proteins, including globular and those characterized by both membrane proteins and non-membrane classifications. This approach comes at a lower computational cost of other methods by only taking a fraction of the time to implement and analyze. The computational method is very affordable and can be extended to various biomolecules.

Changes in Milk Fat Globules and Membrane Proteins Prepared from pH-Adjusted Bovine Raw Milk.

Milk fat globules (MFGs) have tri-layer biological membrane structures, and their compositions are gaining more interest for their physiological benefits. In this study, the changes in MFGs and milk fat globule membrane (MFGM) proteins after cream separation from different pH bovine raw milk were investigated. Raw milk samples were adjusted to pH 5.30 and 6.30 using citric acid at 25 °C. The effect of pH and centrifugation on the structure of MFGs was evaluated by means of particle size, zeta potential and confocal laser scanning microscopy (CLSM). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to analyze the proteins in the obtained fractions. It was found that both pH and centrifugation could affect the particle size of all samples. As the volume distribution (Dv; Dv (10), Dv(50)and Dv (90)) decreased, the corresponding specific surface area (SSA) increased, and span and uniformity values showed the same trend. The decrease in the zeta potential of MFG correlated with the Dv(50), which was further confirmed by CLSM observation. More butyrophilin (BTN) and periodic acid Schiff 6/7 (PAS 6/7) were lost in cream samples at pH 5.30. The findings could provide valuable knowledge for the application of MFGs ingredient in the food industry since their structures and compositions could affect their potential functional and physiological properties.

ВЛИЯНИЕ ЭКСТРАКТА RUMEX CONFERTUS НА МЕТАБОЛИЧЕСКИЕ ПРОЦЕССЫ В ОРГАНИЗМЕ

Vital physiological and metabolic processes occurring in the human body are associated with free radical oxidation, which affects the structure, permeability and physico-chemical properties of biological membranes. Horse sorrel is used for scurvy, gout, diabetes, jaundice, hypertension, rheumatism, skin diseases – scabies, lichen, eczema, burns, as well as diseases of the digestive and cardiovascular systems. The purpose of the research: to study the technology of obtaining liquid extract of horse sorrel roots and to study its antioxidant activity on the body. Liquid extract of horse sorrel roots and auxiliary substances were used as the object of the study: dimethyl sulfoxide DMSO, ethyl alcohol 96%, quercetin, lecithin. When performing the work, equipment was used: liquid chromatograph "Color Yauza-01-AA", SF-LEKISS 1207UV. The object of the study of the total antioxidant activity were extracts of horse sorrel roots obtained using ethyl alcohol in concentration: 30%, 40%, 50%, 60%, 70%, 80%. The total content of antioxidants in the studied liquid extracts of horse sorrel roots was determined by two methods: using a liquid chromatograph "Color Yauza-01-AA" with an amperometric detector. The quantitative content of antioxidants was determined according to the calibration schedule. The conversion was carried out for gallic acid and quercetin. Using a model of iron-induced lipid peroxidation in the system of lecithin (phosphotidylcholine) liposomes, the studied liquid extracts were evaluated by reducing the accumulation of peroxide compounds. The study was carried out at a concentration of 200 mcg/ml to 500 mcg/ml of horse sorrel extract and increasing the dose.

Cholesterol’s balancing act: Defying the status quo

The structure and organization of biological membranes have fascinated biophysicists and cell biologists for decades. Some key findings that have energized the field include the discovery of domains in lipid mixtures (1) and the subsequent raft hypothesis linking them to cellular phenomena (2), as well as the discovery of compositional asymmetry in cell bilayers (3), which put lipid membranes on the map of energetically regulated physiological players. Almost all current knowledge about lipid and bilayer biophysics is rooted in studies of symmetric model membranes in the form of closed lipid vesicles.

Exploiting neutron scattering contrast variation in biological membrane studies.

Biological membranes composed of lipids and proteins are central for the function of all cells and individual components, such as proteins, that are readily studied by a range of structural approaches, including x-ray crystallography and cryo-electron microscopy. However, the study of complex molecular mixtures within the biological membrane structure and dynamics requires techniques that can study nanometer thick molecular bilayers in an aqueous environment at ambient temperature and pressure. Neutron methods, including scattering and spectroscopic approaches, are useful since they can measure structure and dynamics while also being able to penetrate sample holders and cuvettes. The structural approaches, such as small angle neutron scattering and neutron reflectometry, detect scattering caused by the difference in neutron contrast (scattering length) between different molecular components such as lipids or proteins. Usually, the bigger the contrast, the clearer the structural data, and this review uses examples from our research to illustrate how contrast can be increased to allow the structures of individual membrane components to be resolved. Most often this relies upon the use of deuterium in place of hydrogen, but we also discuss the use of magnetic contrast and other elements with useful scattering length values.

Molecular‐scale structure of a high‐curvature membrane

Cells utilize molecular machines to form and remodel their membrane‐defined compartments’ compositions, shapes, and connections. The regulated activity of these membrane remodeling machines drives processes like vesicular traffic and organelle homeostasis. Although molecular patterning within membranes is essential to cellular life, characterizing the composition and structure of realistic biological membranes on the molecular length scale remains a challenge, particularly during membrane shape transformations. Here, we employed an ESCRT‐III protein coating model system to investigate how membrane‐binding proteins bind to and alter the structural patterns within lipid bilayers. We observe leaflet‐level and localized lipid structures within a constricted and thinned membrane nanotube. To map the fine structure of these membranes, we compared simulated bilayer nanotubes with experimental cryo‐EM reconstructions of native membranes and membranes containing halogenated lipid analogs. Halogenated lipids scatter electrons more strongly, and analysis of their surplus scattering enabled us to estimate the concentrations of lipids within each leaflet and to estimate lipid shape and sorting changes induced by high curvature and lipid‐protein interactions. Specifically, we found that cholesterol enriched within the inner leaflet due to its spontaneous curvature, while acidic lipids enriched in the outer leaflet due to electrostatic interactions with the protein coat. The docosahexaenoyl (DHA) polyunsaturated chain‐containing lipid SDPC enriched strongly at membrane‐protein contact sites. Simulations and imaging of brominated SDPC showed how a pair of phenylalanine residues opens a hydrophobic defect in the outer leaflet and how DHA tails stabilize the defect and “snorkel” up to the membrane surface to interact with these side chains. This highly curved nanotube differs markedly from protein‐free, flat bilayers in leaflet thickness, lipid diffusion, and other structural asymmetries with implications for our understanding of membrane mechanics.

NADPH-Cytochrome P450 Reductase Mediates the Fatty Acid Desaturation of ω3 and ω6 Desaturases from Mortierella alpina.

Fatty acid desaturases play an important role in maintaining the appropriate structure and function of biological membranes. The biochemical characterization of integral membrane desaturases, particularly ω3 and ω6 desaturases, has been limited by technical difficulties relating to the acquisition of large quantities of purified proteins, and by the fact that functional activities of these proteins were only tested in an NADH-initiated reaction system. The main aim of this study was to reconstitute an NADPH-dependent reaction system in vitro and investigate the kinetic properties of Mortierella alpina ω3 and ω6 desaturases in this system. After expression and purification of the soluble catalytic domain of NADPH–cytochrome P450 reductase, the NADPH-dependent fatty acid desaturation was reconstituted for the first time in a system containing NADPH, NADPH–cytochrome P450 reductase, cytochrome b5, M. alpina ω3 and ω6 desaturase and detergent. In this system, the maximum activity of ω3 and ω6 desaturase was 213.4 ± 9.0 nmol min−1 mg−1 and 10.0 ± 0.5 nmol min−1 mg−1, respectively. The highest kcat/Km value of ω3 and ω6 desaturase was 0.41 µM−1 min−1 and 0.09 µM−1 min−1 when using linoleoyl CoA (18:2 ω6) and oleoyl CoA (18:1 ω9) as substrates, respectively. M. alpina ω3 and ω6 desaturases were capable of using NADPH as reductant when mediated by NADPH–cytochrome P450 reductase; although, their efficiency is distinguishable from NADH-dependent desaturation. These results provide insights into the mechanisms underlying ω3 and ω6 fatty acid desaturation and may facilitate the production of important fatty acids in M. alpina.

Study of changes in proteolytic systems of rats under conditions of experimental chronic prostatitis

The aim of our research – to analyze the mechanisms of regulation of the body's proteolytic systems during inflammation, detection of inflammation markers in blood and prostate secretions in the simulation of chronic prostatitis (CP) in rats. 1. The leading link in the pathogenesis of many diseases is a change in the structure and functions of biological membranes – membranopathy, the consequence of which is a violation of histochemical barriers, which is manifested in an increase in the excretion of certain metabolites in the extracellular fluid. In the case of experimental CP in rats, the appearance in the secretion of the prostate gland of the components of KKS, which are determined in the secretion of the normal prostate in trace amounts, was noted. Inflammatory damage to the prostate was also evidenced by an increase in the proteolytic potential of prostate secretion due to an increase in kallikrein activity on the 21st day by 807.1% (р˂0.05), which leads to massive kininogenesis. Depletion of the adaptive and compensatory potential of the prostate gland was evidenced by a decrease in prekallikrein by 21.7% (р˂0.05) compared to the intact group of animals. A sharp increase in the activity of kallikrein in CP is probably compensated by an increase in the activity of its specific inhibitor – α2-macroglobulin, the level of which in the secretion of the CP increased on 225 % on the 21st day of the experiment compared to intact rats, and the increase in proteolytic potential – by an increase of 125 % in the inhibitory activity of α1-PI, a protein of the acute phase of inflammation. An increase in the content and activity of KKS components in the secretion of the prostate testifies to its inflammatory damage and violation of the permeability of the hematoprostatic barrier, which can be an important diagnostic criterion.

Atomic Force Microscopy combined with Fluorescence Lifetime Imaging Microscopy (AFM + FLIM): a powerful approach to explore the structure and dynamics of biological membranes

Atomic Force Microscopy combined with Fluorescence Lifetime Imaging Microscopy (AFM + FLIM): a powerful approach to explore the structure and dynamics of biological membranes

Design and simulation of the liposomal model by using a coarse-grained molecular dynamics approach towards drug delivery goals

The simulated liposome models provide events in molecular biological science and cellular biology. These models may help to understand the cell membrane mechanisms, biological cell interactions, and drug delivery systems. In addition, the liposomes model may resolve specific issues such as membrane transports, ion channels, drug penetration in the membrane, vesicle formation, membrane fusion, and membrane protein function mechanism. One of the approaches to investigate the lipid membranes and the mechanism of their formation is by molecular dynamics (MD) simulations. In this study, we used the coarse-grained MD simulation approach and designed a liposome model system. To simulate the liposome model, we used phospholipids that are present in the structure of natural cell membranes (1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)). Simulation conditions such as temperature, ions, water, lipid concentration were performed based on experimental conditions. Our results showed a liposome model (ellipse vesicle structure) during the 2100 ns was formed. Moreover, the analysis confirmed that the stretched and ellipse structure is the best structure that could be formed. The eukaryotic and even the bacterial cells have elliptical and flexible structures. Usually, an elliptical structure is more stable than other assembled structures. The results indicated the assembly of the lipids is directed through short-range interactions (electrostatic interactions and, van der Waals interactions). Total energy (Van der Waals and electrostatic interaction energy) confirmed the designed elliptical liposome structure has suitable stability at the end of the simulation process. Our findings confirmed that phospholipids DOPC and DOPE have a good tendency to form bilayer membranes (liposomal structure) based on their geometric shapes and chemical-physical properties. Finally, we expected the simulated liposomal structure as a simple model to be useful in understanding the function and structure of biological cell membranes. Furthermore, it is useful to design optimal, suitable, and biocompatible liposomes as potential drug carriers.

Fluidity is the way to life: lipid phase separation in bacterial membranes.

A hallmark of biological membranes is the dynamic localization of lipids and proteins. Lipids respond to temperature reduction below a critical point with phase separation, and poikilothermic animals and also bacteria adapt their lipid content to prevent gel phase formation in membranes. In a new study, Gohrbandt etal (2022) show that reduced membrane fluidity in bacterial cells causes reversible phase separation without membrane rupture invivo, highlighting the physical robustness of biological membranes.

Multifunctional Biomedical Materials Derived from Biological Membranes.

The delicate structure and fantastic functions of biological membranes are the successful evolutionary results of a long-term natural selection process. Their excellent biocompatibility and biofunctionality are widely utilized to construct multifunctional biomedical materials mainly by directly camouflaging materials with single or mixed biological membranes, decorating or incorporating materials with membrane-derived vesicles(e.g., exosomes), and designing multifunctional materials with the structure/functions of biological membranes. Here, the structure-function relationship of some important biological membranes and biomimetic membranes are discussed, such as various cell membranes, extracellular vesicles, and membranes from bacteria and organelles. Selected literature examples of multifunctional biomaterials derived from biological membranes for biomedical applications, such as drug- and gene-delivery systems, tissue-repair scaffolds, bioimaging, biosensors, and biological detection, are also highlighted. These designed materials show excellent properties, such as long circulation time, disease-targeted therapy, excellent biocompatibility, and selective recognition. Finally, perspectives and challenges associated with the clinical applications of biological-membrane-derived materials are discussed.

Recent progress of vibrational spectroscopic study on the interfacial structure of biomimetic membranes

Understanding the molecular structure of biological membranes and their dynamic hydration information at the molecular level will provide great insights into the interaction mechanisms and the function of biological membranes. However, it is still unattainable for many techniques because of the high complexity of the natural biological membranes caused by multi-components including phospholipid, protein, cholesterol, peptidoglycan and polysaccharide as well as the different location and distribution of each component. The development and application of biomimetic membranes largely overcome the complexity of the natural biological membranes and greatly stimulate the study of membrane interfaces. Vibrational spectroscopy, which relies on the interaction of light and matter, is a powerful technology for in-situ and real-time exploring the structure and hydration of biomimetic membranes interface. Based on the progress of the vibrational spectroscopy technology, the molecular structure and interface hydration information of biomimetic membranes have been continually revealed. In this study, we reviewed the research on the structural characteristics of different biomimetic membrane systems using vibrational spectroscopy in recent years, as well as a prospect for its development.