Folding speeds of helical membrane proteins

Membrane proteins play key roles in human health, contributing to cellular signaling, ATP synthesis, immunity, and metabolite transport. Protein folding is the pivotal early step for their proper functioning. Understanding how this class of proteins adopts their native folds could potentially aid in drug design and therapeutic interventions for misfolding diseases. It is an essential piece in the whole puzzle to untangle their kinetic complexities, such as how rapid membrane proteins fold, how their folding speeds are influenced by changing conditions, and what mechanisms are at play. This review explores the folding speed aspect of multipass α-helical membrane proteins, encompassing plausible folding scenarios based on the timing and stability of helix packing interactions, methods for characterizing the folding time scales, relevant folding steps and caveats for interpretation, and potential implications. The review also highlights the recent estimation of the so-called folding speed limit of helical membrane proteins and discusses its consequent impact on the current picture of folding energy landscapes.

Efficacy of acidified water-in-oil emulsions against desiccated Salmonella as a function of acid carbon chain-length and membrane viscosity

Sanitizing low-moisture food (LMF) processing equipment is challenging due to the increased heat resistance of Salmonella spp. in low-water activity (a_w) environments. Food-grade oils mixed with acetic acid have been shown effective against desiccated Salmonella. In this study, different hydrocarbon chain-length (C_n) organic acids were tested against desiccated Salmonella by using 1% v/v water-in-oil (W/O) emulsion as the delivery system for 200 mM acid. Fluorescence lifetime imaging microscopy (FLIM) was utilized with a BODIPY-based molecular rotor to evaluate membrane viscosity under environmental conditions such as desiccation and temperature elevation. Drying hydrated Salmonella cells to 75% equilibrium relative humidity (ERH) increased the membrane viscosity from 1,199 to 1,309 mPa·s (cP) at 22°C. Heating to 45°C decreased the membrane viscosity of hydrated cells from 1,199 to 1,082 mPa·s, and decreased that of the desiccated cells from 1,309 to 1,245 mPa·s. At both 22°C and 45°C, desiccated Salmonella was highly susceptible (>6.5 microbial log reduction (MLR) per stainless-steel coupon) to a 30-min treatment with the W/O emulsions formulated with short carbon chain acids (C_1-3). By comparison, the emulsion formulations with longer carbon chain acids (C_4-12) showed little to no MLR at 22°C, but achieved >6.5 MLR at 45°C. Based upon the decreased Salmonella membrane viscosity and the increased antimicrobial efficacy of C_4-12 W/O emulsions with increasing temperature, we propose that heating can make the membrane more fluid which may allow the longer carbon chain acids (C_4-12) to permeate or disrupt membrane structures.

The effect of cholesterol on highly curved membranes measured by nanosecond Fluorescence Correlation Spectroscopy

Small lipid vesicles (with diameter ≤ 100nm) with their highly curved membranes comprise a special class of biological lipid bilayers. The mechanical properties of such membranes are critical for their function, e.g. exocytosis. Cholesterol is a near-universal regulator of membrane properties in animal cells. Yet measurements of the effect of cholesterol on the mechanical properties of membranes have remained challenging, and the interpretation of such measurements has remained a matter of debate. Here we show that nanosecond fluorescence correlation spectroscopy (FCS) can directly measure the ns-microsecond rotational correlation time (τr) of a lipid probe in high curvature vesicles with extraordinary sensitivity. Using a home-built 4-Pi fluorescence cross-correlation spectrometer containing polarization-modulating elements, we measure the rotational correlation time (τr) of Nile Red in neurotransmitter vesicle mimics. As the cholesterol mole fraction increases from 0 to 50 %, τr increases from 17 ± 1 to 112 ± 12 ns, indicating a viscosity change of nearly a factor of 7. These measurements are corroborated by solid-state NMR results, which show that the order parameter of the lipid acyl chains increases by about 50% for the same change in cholesterol concentration. Additionally, we measured the spectral parameters of polarity-sensitive fluorescence dyes, which provide an indirect measure of viscosity. The green/red ratio of Nile Red and the generalized polarization of Laurdan show consistent increases of 1.3x and 2.6x, respectively. Our results demonstrate that rotational FCS can directly measure the viscosity of highly curved membranes with higher sensitivity and wider dynamic range compared to other conventional techniques. Significantly, we observe that the viscosity of neurotransmitter vesicle mimics is remarkably sensitive to their cholesterol content.

Age-Related Features of the Viscosity of Plasma and Mitochondrial Membranes of Hepatocytes in Liver Cirrhosis

The viscosity of plasma and mitochondrial membranes of hepatocytes was studied in young (3-month-old) and old (9-month-old) male Wistar rats. It was shown that viscosity of hepatocyte plasma and mitochondrial membranes in young rats under optimal vital functions in the area of protein-lipid membrane contacts was significantly lower than in old rats. No age-related differences in the viscosity of lipid-lipid membrane contacts and in the polarity of protein-lipid contacts and lipid layers were found. Liver cirrhosis induced by carbon tetrachloride and ethanol administration was associated with increased fluidity of the plasma and mitochondrial membranes of hepatocytes in rats of both age groups. The decrease in membrane viscosity in young rats occurred due to a decrease of the viscosity in the area of protein-lipid and lipid-lipid contacts, while in old rats in the area of protein-lipid contacts. Carbon tetrachloride and ethanol did not affect the polarity of lipid contacts and lipid layers.

Lattice Boltzmann simulations on the tumbling to tank-treading transition: effects of membrane viscosity

The tumbling to tank-treading (TB-TT) transition for red blood cells (RBCs) has been widely investigated, with a main focus on the effects of the viscosity ratio [Formula: see text] (i.e., the ratio between the viscosities of the fluids inside and outside the membrane) and the shear rate [Formula: see text] applied to the RBC. However, the membrane viscosity [Formula: see text] plays a major role in a realistic description of RBC dynamics, and only a few works have systematically focused on its effects on the TB-TT transition. In this work, we provide a parametric investigation on the effect of membrane viscosity [Formula: see text] on the TB-TT transition for a single RBC. It is found that, at fixed viscosity ratios [Formula: see text], larger values of [Formula: see text] lead to an increased range of values of capillary number at which the TB-TT transition occurs; moreover, we found that increasing [Formula: see text] or increasing [Formula: see text] results in a qualitatively but not quantitatively similar behaviour. All results are obtained by means of mesoscale numerical simulations based on the lattice Boltzmann models. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

Hydrodynamic shear dissipation and transmission in lipid bilayers

Vital biological processes, such as trafficking, sensing, and motility, are facilitated by cellular lipid membranes, which interact mechanically with surrounding fluids. Such lipid membranes are only a few nanometers thick and composed of a liquid crystalline structure known as the lipid bilayer. Here, we introduce an active, noncontact, two-point microrheology technique combining multiple optical tweezers probes with planar freestanding lipid bilayers accessible on both sides. We use the method to quantify both fluid slip close to the bilayer surface and transmission of fluid flow across the structure, and we use numerical simulations to determine the monolayer viscosity and the intermonolayer friction. We find that these physical properties are highly dependent on the molecular structure of the lipids in the bilayer. We compare ordered-phase with liquid disordered-phase lipid bilayers, and we find the ordered-phase bilayers to be 10 to 100 times more viscous but with 100 times less intermonolayer friction. When a local shear is applied by the optical tweezers, the ultralow intermonolayer friction results in full slip of the two leaflets relative to each other and as a consequence, no shear transmission across the membrane. Our study sheds light on the physical principles governing the transfer of shear forces by and through lipid membranes, which underpin cell behavior and homeostasis.

Cysteine, glutathione and a new genetic code: biochemical adaptations of the primordial cells that spread into open water and survived biospheric oxygenation

Life most likely developed under hyperthermic and anaerobic conditions in close vicinity to a stable geochemical source of energy. Epitomizing this conception, the first cells may have arisen in submarine hydrothermal vents in the middle of a gradient established by the hot and alkaline hydrothermal fluid and the cooler and more acidic water of the ocean. To enable their escape from this energy-providing gradient layer, the early cells must have overcome a whole series of obstacles. Beyond the loss of their energy source, the early cells had to adapt to a loss of external iron-sulfur catalysis as well as to a formidable temperature drop. The developed solutions to these two problems seem to have followed the principle of maximum parsimony: Cysteine was introduced into the genetic code to anchor iron-sulfur clusters, and fatty acid unsaturation was installed to maintain lipid bilayer viscosity. Unfortunately, both solutions turned out to be detrimental when the biosphere became more oxidizing after the evolution of oxygenic photosynthesis. To render cysteine thiol groups and fatty acid unsaturation compatible with life under oxygen, numerous counter-adaptations were required including the advent of glutathione and the addition of the four latest amino acids (methionine, tyrosine, tryptophan, selenocysteine) to the genetic code. In view of the continued diversification of derived antioxidant mechanisms, it appears that modern life still struggles with the initially developed strategies to escape from its hydrothermal birthplace. Only archaea may have found a more durable solution by entirely exchanging their lipid bilayer components and rigorously restricting cysteine usage.

How cholesterol stiffens unsaturated lipid membranes

Cholesterol is an integral component of eukaryotic cell membranes and a key molecule in controlling membrane fluidity, organization, and other physicochemical parameters. It also plays a regulatory function in antibiotic drug resistance and the immune response of cells against viruses, by stabilizing the membrane against structural damage. While it is well understood that, structurally, cholesterol exhibits a densification effect on fluid lipid membranes, its effects on membrane bending rigidity are assumed to be nonuniversal; i.e., cholesterol stiffens saturated lipid membranes, but has no stiffening effect on membranes populated by unsaturated lipids, such as 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). This observation presents a clear challenge to structure-property relationships and to our understanding of cholesterol-mediated biological functions. Here, using a comprehensive approach-combining neutron spin-echo (NSE) spectroscopy, solid-state deuterium NMR (²H NMR) spectroscopy, and molecular dynamics (MD) simulations-we report that cholesterol locally increases the bending rigidity of DOPC membranes, similar to saturated membranes, by increasing the bilayer's packing density. All three techniques, inherently sensitive to mesoscale bending fluctuations, show up to a threefold increase in effective bending rigidity with increasing cholesterol content approaching a mole fraction of 50%. Our observations are in good agreement with the known effects of cholesterol on the area-compressibility modulus and membrane structure, reaffirming membrane structure-property relationships. The current findings point to a scale-dependent manifestation of membrane properties, highlighting the need to reassess cholesterol's role in controlling membrane bending rigidity over mesoscopic length and time scales of important biological functions, such as viral budding and lipid-protein interactions.

A finite difference method with subsampling for immersed boundary simulations of the capsule dynamics with viscoelastic membranes

The membrane or interfacial viscosity is an important property in many multiphase and biofluidic situations, such as the red blood cell dynamics and emulsion stability. The immersed boundary method (IBM), which incorporates the dynamic flow-membrane interaction via force distribution and velocity interpolation, has been extensively employed in simulations of such systems. Unfortunately, direct implementation of membrane viscosity in IBM suffers severe numerical instability, which causes an IBM calculation to break down before generating any useful results. Few attempts have been recently reported; however, several concerns exist in these attempts, such as the inconsistency to the classical definition of membrane viscosity, the inability to model the shear and dilatational viscosities separately, the unjustified mathematical formulations, and the complicated algorithms and computation. To overcome these concerns, in this paper, we propose a finite difference approach for implementing membrane viscosity in immersed boundary simulations. The viscous stress is obtained via finite difference approximations to the differential strain-stress relationship, with the help of a subsampling scheme to reduce the numerical noise in the calculated strain rates. This simple method has also avoided the complicated matrix calculations in previous attempts, and hence, a better computational efficiency is expected. Detailed mathematical description of the method and key steps for its implementation in immersed boundary programs are provided. Validation and illustration calculations are performed, and our results are compared with analytical solutions and previous publications with satisfactory agreement. The influences of membrane mesh resolution and simulation time step are also examined; and the results show no indication that our finite difference method has downgraded the general IBM accuracy. Based on these simulations and analysis, we believe that our method would be a better choice for future IBM simulations of capsule dynamics with viscoelastic membranes.

Did you know that your animals have consciousness?

Consciousness is the greatest enigma in human history. For centuries scientists and researchers have tried to describe it without coming to conclusions. In the last years with the neurosciences development, consciousness has become the common goal of numerous studies. But consciousness has always been studied only in humans, but after "Cambridge Declaration on Consciousness" in 2012, even non-human animalsthey feel possessed of the consciousness. According to "theory Orch-OR" of Hameroff and Penrose we have conducted a study on Alaskan malamute and German shepherd to analysed a triplet of platelet fatty acids (linoleic acid; palmitic acid; arachidonic acid). Through these analysis and the relative mapping of subjects within a SOM it was possible to make an assessment of the possible onset of mood disorders in the dogs. A critical analysis of the results obtained shows that animals have molecular analogies with humans compared to mood disorders. The German shepherd and Alaskan malamute, indeed, have, in the case of major depression, a bio-chemical profile, the most similar to man.

17β-Estradiol Directly Lowers Mitochondrial Membrane Microviscosity and Improves Bioenergetic Function in Skeletal Muscle

Menopause results in a progressive decline in 17β-estradiol (E2) levels, increased adiposity, decreased insulin sensitivity, and a higher risk for type 2 diabetes. Estrogen therapies can help reverse these effects, but the mechanism(s) by which E2 modulates susceptibility to metabolic disease is not well understood. In young C57BL/6N mice, short-term ovariectomy decreased-whereas E2 therapy restored-mitochondrial respiratory function, cellular redox state (GSH/GSSG), and insulin sensitivity in skeletal muscle. E2 was detected by liquid chromatography-mass spectrometry in mitochondrial membranes and varied according to whole-body E2 status independently of ERα. Loss of E2 increased mitochondrial membrane microviscosity and H₂O₂ emitting potential, whereas E2 administration in vivo and in vitro restored membrane E2 content, microviscosity, complex I and I + III activities, H₂O₂ emitting potential, and submaximal OXPHOS responsiveness. These findings demonstrate that E2 directly modulates membrane biophysical properties and bioenergetic function in mitochondria, offering a direct mechanism by which E2 status broadly influences energy homeostasis.

Dynamic Cellular Interactions with Extracellular Matrix Triggered by Biomechanical Tuning of Low-Rigidity, Supported Lipid Membranes

The behavior of cells in a tissue is regulated by chemical as well as physical signals arising from their microenvironment. While gel-based substrates have been widely used for mimicking a range of substrate rigidities, there is a need for the development of low rigidity substrates for mimicking the physical properties of soft tissues. In this study, the authors report the development of a supported lipid bilayer (SLB)-based low rigidity substrate for cell adhesion studies. SLBs are functionalized with either collagen I or fibronectin via covalent, amine coupling to a carboxyl group-modified lipid molecule. While the lipid molecules in the bilayer show long-range lateral mobility, the covalently functionalized extracellular matrix (ECM) proteins are immobile on the bilayer surface. Specific adhesion of cells results in an enrichment of the protein on the bilayer and the appearance of a zone of depletion around the cells. Further, the lateral reorganization of the ECM proteins is controlled by altering the fluidity of lipid molecules in the substrate. Thus, the experimental platform developed in this study can be utilized for addressing basic questions related to cell adhesion on low rigidity substrates as well as biomedical applications requiring adhesion of cells to low rigidity substrates.

Probing Membrane Viscosity and Interleaflet Friction of Supported Lipid Bilayers by Tracking Electrostatically Adsorbed, Nano-Sized Vesicles

Particle tracking is used to measure the diffusional motion of nanosized (≈100 nm), lipid vesicles that are electrostatically adsorbed onto a solid supported lipid bilayer. It is found that the motion of membrane-adhering vesicles is Brownian and depends inversely on the vesicle size, but is insensitive to the vesicle surface charge. The measured diffusivity agrees well with the Evans-Sackmann model for the diffusion of inclusions in supported, fluidic membranes. The agreement implies that the vesicle motion is coupled to that of a nanoscopic lipid cluster in the upper leaflet, which slides over the lower leaflet. The diffusivity of membrane-adhering vesicles is therefore predominantly governed by the interleaflet friction coefficient, while the diffusivity of single lipids is mainly governed by the membrane viscosity. Combined with fluorescence recovery after photobleaching analysis, the interleaflet friction coefficient and the membrane viscosity are determined by applying the Evans-Sackmann model to the measured diffusivity of membrane adhering vesicles and that of supported membrane lipids. This approach provides an alternative to existing methods for measuring the interleaflet friction coefficient and the membrane viscosity.

Biophysical alterations in lipid rafts from human cerebral cortex associate with increased BACE1/AβPP interaction in early stages of Alzheimer's disease

In the present study, we have assessed the biophysical properties of lipid rafts from different brain areas in subjects exhibiting early neuropathological stages of Alzheimer's disease (AD). By means of steady-state fluorescence polarization analyses using two environment-sensitive fluorescent probes, we demonstrate that lipid rafts from cerebellum, and frontal and entorhinal cortices, exhibit different biophysical behaviors depending on the stage of the disease. Thus, while membrane anisotropies were similar in the cerebellum along stages, lipid rafts from frontal and entorhinal cortices at AD stages I/II and AD III were significantly more liquid-ordered than in control subjects, both at the aqueous interface and hydrophobic core of the raft membrane. Thermotropic analyses demonstrated the presence of Arrhenius breakpoints between 28.3-32.0 °C, which were not influenced by the disease stage. However, analyses of membrane microviscosity (ηapp) demonstrate that frontal and entorhinal lipid rafts are notably more viscous and liquid-ordered all across the membrane from early stages of the disease. These physicochemical alterations in lipid rafts do not correlate with changes in cholesterol or sphingomyelin levels, but to reduced unsaturation index and increased saturate/polyunsaturated ratios in phospholipid acyl chains. Moreover, we demonstrate that β-secretase/AβPP (amyloid-β protein precursor) interaction and lipid raft microviscosity are strongly, and positively, correlated in AD frontal and entorhinal cortices. These observations strengthens the hypothesis that physical properties of these microdomains modulate the convergence of amyloidogenic machinery toward lipid rafts, and also points to a critical role of polyunsaturated fatty acids in amyloidogenic processing of AβPP.

Genotype-induced changes in biophysical properties of frontal cortex lipid raft from APP/PS1 transgenic mice

Alterations in the lipid composition of lipid rafts have been demonstrated both in human brain and transgenic mouse models, and it has been postulated that aberrant lipid composition in lipid rafts is partly responsible for neuronal degeneration. In order to assess the impact of lipid changes on lipid raft functional properties, we have aimed at determining relevant physicochemical modifications in lipid rafts purified from frontal cortex of wild type (WT) and APP/PS1 double transgenic mice. By means of steady-state fluorescence anisotropy analyses using two lipid soluble fluorescent probes, TMA-DPH (1-[(4-trimethyl-amino)phenyl]-6-phenyl-1,3,5-hexatriene) and DPH (1,6-diphenyl-1,3,5-hexatriene), we demonstrate that cortical lipid rafts from WT and APP/PS1 animals exhibit different biophysical behaviors, depending on genotype but also on age. Thus, aged APP/PS1 animals exhibited slightly more liquid-ordered lipid rafts than WT counterparts. Membrane microviscosity η_app analyses demonstrate that WT lipid rafts are more fluid than APP/PS1 animals of similar age, both at the aqueous interface and hydrophobic core of the membrane. η_app in APP/PS1 animals was higher for DPH than for TMA-DPH under similar experimental conditions, indicating that the internal core of the membrane is more viscous than the raft membrane at the aqueous interface. The most dramatic changes in biophysical properties of lipid rafts were observed when membrane cholesterol was depleted with methyl-β-cyclodextrin. Overall, our results indicate that APP/PS1 genotype strongly affects physicochemical properties of lipid raft. Such alterations appear not to be homogeneous across the raft membrane axis, but rather are more prominent at the membrane plane. These changes correlate with aberrant proportions of sphingomyelin, cholesterol, and saturated fatty acids, as well as polyunsaturated fatty acids, measured in lipid rafts from frontal cortex in this familial model of Alzheimer's Disease.

Alterations of hepatic Na+,K+-atpase and bile flow by estrogen: effects on liver surface membrane lipid structure and function

Administration of the synthetic estrogen ethinyl estradiol (17alpha-ethinyl-1,3,5-estratriene-3,17beta-diol) decreases hepatic Na(+),K(+)-ATPase (ATP phosphohydrolase; EC 3.6.1.3) activity and bile flow to 50% and alters the composition and structure of surface membrane lipid in rats. Although the content of phospholipids was not changed by treatment, free cholesterol (130%) and cholesterol esters (400%) were increased in liver surface membrane fractions. These observations correlate with changes in membrane viscosity, as shown by electron spin resonance probes. Both rotational correlation time, using the isotropic probe methyl (12-nitroxyl)stearate, and the order parameter, determined by the anisotropic probe 5-nitroxylstearic acid, were significantly increased in liver surface membrane fractions from rats treated with ethinyl estradiol. Administration of Triton WR-1339, a nonionic detergent that corrects hepatic and serum lipid changes caused by ethinyl estradiol treatment, restored toward normal elevated membrane lipids and viscosity as well as Na(+),K(+)-ATPase activity and bile flow. Although restoration of normal liver surface membrane structure and function may be due to reversal of abnormal lipid composition, detergents also may directly alter membrane enzyme activity. Addition of Triton WR-1339 in vitro increased Na(+),K(+)-ATPase activity and reduced membrane viscosity of surface membranes from rats treated with ethinyl estradiol. Triton had no effect on either parameter in normal membrane preparations. Studies of membrane structure and function both in vivo and in vitro suggest that alterations in lipid composition may alter Na(+),K(+)-ATPase function and bile flow.