Influence of Cholesterol on the Oxygen Permeability of Membranes: Insight from Atomistic Simulations

Metabolic reprogramming of hypoxic tumor-associated macrophages through CSF-1R targeting favors treatment efficiency in colorectal cancers

BACKGROUND

Tumor-associated macrophages participate in the complex network of support that favors tumor growth. Among the various strategies that have been developed to target these cells, the blockade of the colony-stimulating factor 1 receptor (CSF-1R) receptor is one of the most promising ones. Here, we characterize the resulting state of human macrophages exposed to a CSF-1R kinase inhibitor.

METHODS

Using RNA sequencing and metabolomics approach, we characterize the reprogramming of human monocyte-derived macrophages under CSF-1R targeting.

RESULTS

We find that CSF-1R receptor inhibition in human macrophages is able to impair cholesterol synthesis, fatty acid metabolism and hypoxia-driven expression of dihydropyrimidine dehydrogenase, an enzyme responsible for the 5-fluorouracil macrophage-mediated chemoresistance. We show that this inhibition of the CSF-1R receptor leads to a downregulation of the expression of sterol regulatory element-binding protein 2, a transcription factor that controls cholesterol and fatty acid synthesis. We also show that the inhibition of extracellular signal-regulated kinase 1/2 phosphorylation resulting from targeting the CSF-1R receptor destabilizes the expression of hypoxic induced factor 2 alpha in hypoxia resulting in the downregulation of dihydropyrimidine dehydrogenase expression restoring the sensitivity to 5-fluorouracil in colorectal cancer.

CONCLUSIONS

These results reveal the unexpected metabolic rewiring resulting from the CSF-1R receptor targeting of human macrophages and its potential to reverse macrophage-mediated chemoresistance in colorectal tumors.

Cholesterol inhibits oxygen permeation through biological membranes: mechanism against double-bond peroxidation

The presence of oxygen molecules (O2) in biological membranes promotes lipid peroxidation of phospholipids with unsaturated acyl chains. On the other hand, cholesterol is considered to be an antioxidant molecule as it has a significant barrier effect on the permeation of O2 across membranes. However, a comprehensive explanation of how cholesterol affects the distribution and diffusion of O2 within lipid bilayers is yet to be established. In this study, we investigated the interaction of oxygen molecules with polyunsaturated lipid bilayers using molecular dynamics (MD) simulations. The degree of lipid unsaturation and the concentration of cholesterol were varied to study the permeation of O2. The free energy profile of O2 diffusing from the water phase to the lipid bilayer was calculated using biased umbrella MD simulations. The results show that O2 passively translocates into the membrane without changing the physical properties of the bilayer. Interestingly, in the unsaturated lipid bilayers the presence of cholesterol led to a significantly decreased permeation of O2 and an increase in the lipid chain order. Our results indicate that the hydroxyl groups of cholesterol strongly interact with the O2 molecules effectively inhibiting interactions between the oxygens and the double bonds in unsaturated lipid tails. In addition, a linear relationship between permeation and the ratio of membrane thickness and area per lipid was found. These insights can help our understanding of how the degree of unsaturation in a lipid tail and cholesterol affect lipid peroxidation at the molecular level.

The chemical biology of dinitrogen trioxide

Dinitrogen trioxide (N 2 O 3 ) mediates low-molecular weight and protein S- and N-nitrosation, with recent reports suggesting a role in the formation of nitrating intermediates as well as in nitrite-dependent hypoxic vasodilatation. However, the reactivity ofN 2 O 3 in biological systems results in an extremely short half-life that renders this molecule essentially undetectable by currently available technologies. As a result, evidence for in vivoN 2 O 3 formation derives from the detection of nitrosated products as well as from in vitro kinetic determinations, isotopic labeling studies, and spectroscopic analyses. This review will discuss mechanisms ofN 2 O 3 formation, reactivity and decomposition, as well as address the role of sub-cellular localization as a key determinant of its actions. Finally, evidence will be discussed supporting different roles forN 2 O 3 as a biologically relevant signaling molecule.

Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems

The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer systems, most permeability studies have been performed under equilibrium conditions, in large part due to the challenges associated with creating concentration gradients in simulations utilizing periodic boundary conditions. To enhance the scientific understanding of permeation and complement the existing computational means of characterizing membrane permeability, we developed a non-equilibrium method that enables the generation and maintenance of steady-state gradients in MD simulations. We utilize PBCs advantageously by imposing a directional bias to the motion of permeants so that their crossing of the boundary replenishes the gradient, like a previous study on ions. Under these conditions, a net flow of permeants across membranes may be observed to determine bulk permeability by a direct application of J=PΔc. In the present study, we explore the results of its application to an exemplary O2 and POPC bilayer system, demonstrating accurate and precise permeability measurements. In addition, we illustrate the impact of permeant concentration and the choice of thermostat on the permeability. Moreover, we demonstrate that energetics of permeation can be closely examined by the dissipation of the gradient across the membrane to gain nuanced insights into the thermodynamics of permeability.

Biophysical Modelling for Insight into Oxygen Diffusion, Distribution, and Measurement

Building on an extensive history of physiological and systems-oriented modelling, my group and others have recently used molecular simulation studies to understand oxygen (O2) transport and localisation. Molecular simulations enable biophysical insight into processes difficult to study with experiments alone and are sometimes described as a "computational microscope." Our work has emphasised lipid membrane contributions to oxygen diffusion and uptake, suggesting that lipid-based pathways along membranes and lipid deposits are likely to accelerate diffusive transport through cells and tissues. Moreover, the lipid and fluid fractions of the tissue are expected to be primary determinants of the local oxygen partial pressure (pO2) as well as the oxygen permeability. Measurements using molecular probes can be influenced by the local molecular environment, due to differential solubility of both the probe and the oxygen molecules in various components of the cell's complex solvent system. The biomolecular simulation work complements experimental studies, which enable evaluation of the models' accuracy and their applicability to real biological systems. Further work is needed to assess fully the possible influence of nanoscale crowders and obstacles (especially protein molecules) on tissue-level diffusive transport of oxygen. Likewise, water-rich carbohydrate layers, such as the glycocalyx, should be evaluated as potential barriers to oxygen transport. Insights gained through biophysical modelling studies could be broadly relevant to clinical phenomena affected by tissue oxygenation, such as tumour radiotherapy, ischaemia, neuropathy, and wound healing.

Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes

Liposomes are considered as advanced drug delivery systems for cancer treatment. A generation of pH-sensitive liposomes is being developed that use fatty acids (FAs) as a trigger for drug release in tumor tissues. However, FAs are also known to enhance permeability, and it is unclear whether FAs in liposomes may cause drug leakage or premature drug release. The passive permeability of the drug through the membrane of the liposome is thus a crucial factor for timely drug delivery. To investigate how the curvature and lipid composition of liposomes affect their passive permeability, coarse-grained molecular dynamics were performed. The permeability was determined with a counting method. Flat bilayers and three liposomes with varying diameters were studied, which had varying lipid compositions of dipalmitoylphosphatidylcholine, cholesterol, and deprotonated or neutral saturated FAs. The investigated permeants were water and two other small permeants, which have different free energy profiles (solubility) across the membrane. First, for the curvature effect, our results showed that curvature increases the water permeability by reducing the membrane thickness. The permeability increase for water is about a factor of 1.7 for the most curved membranes. However, a high curvature decreases permeability for permeants with free energy profiles that are a mix of wells and barriers in the headgroup region of the membrane. Importantly, the type of experimental setup is expected to play a dominant role in the permeability value, i.e., whether permeants are escaping or entering the liposomes. Second, for the composition effect, FAs decrease both the area per lipid (APL) and the membrane thickness, resulting in permeability increases of up to 55%. Cholesterol has a similar effect on the APL but has the opposite impact on membrane thickness and permeability. Therefore, FAs and cholesterol have opposing effects on permeability, with cholesterol's effect being slightly stronger in our simulated bilayers. As all permeability values were well within a factor of 2, and with liposomes usually being larger and less curved in experimental applications, it can be concluded that the passive drug release from a pH-sensitive liposome does not seem to be significantly affected by the presence of FAs.

Cholesterol, Eukaryotic Lipid Domains, and an Evolutionary Perspective of Transmembrane Signaling

Transmembrane signaling is essential for complex life forms. Communication across a bilayer lipid barrier is elaborately organized to convey precision and to fine-tune strength. Looking back, the steps that it has taken to enable this seemingly mundane errand are breathtaking, and with our survivorship bias, Darwinian. While this review is to discuss eukaryotic membranes in biological functions for coherence and theoretical footing, we are obliged to follow the evolution of the biological membrane through time. Such a visit is necessary for our hypothesis that constraints posited on cellular functions are mainly via the biomembrane, and relaxation thereof in favor of a coordinating membrane environment is the molecular basis for the development of highly specialized cellular activities, among them transmembrane signaling. We discuss the obligatory paths that have led to eukaryotic membrane formation, its intrinsic ability to signal, and how it set up the platform for later integration of protein-based receptor activation.

Integrated transcriptome and miRNA sequencing analyses reveal that hypoxia stress induces immune and metabolic disorders in gill of genetically improved farmed tilapia (GIFT, Oreochromis niloticus)

The survival and growth of fish are significantly impacted by a hypoxic environment (low dissolved oxygen). In this study, we compared tissue structure, physiological changes, and mRNA/miRNA transcriptome, in gills of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) between the hypoxic group (DO: 0.55 mg/L, HG) and the control group (DO: 5 mg/L, CG). The results showed that the gill filaments in the hypoxic group showed curling, engorgement, and apoptotic cells increased, and that exposure for 96 h resulted in a reduction in the antioxidant capacity. We constructed and sequenced miRNA and mRNA libraries from gill tissues of GIFT at 96 h of hypoxia stress. Between the HG and CG, a total of 14 differentially expressed (DE) miRNAs and 1557 DE genes were obtained. GO and KEGG enrichment showed that DE genes were mainly enriched in immune and metabolic pathways such as natural killer cell mediated cytotoxicity, steroid biosynthesis, primary immunodeficiency, and synthesis and degradation of ketone bodies. Based on the results of mRNA sequencing and screening for miRNA-mRNA pairs, we selected and verified six DE miRNAs and their probable target genes. The sequencing results were consistent with the qRT-PCR validation results. The result showed that under hypoxia stress, the innate immune response was up-regulated, and the adaptive immune response was down-regulated in the gill of GIFT. The synthesis of cholesterol in gill cells is reduced, which is conducive to the absorption of solvent oxygen. These findings offer fresh information about the processes of fish adaptation to hypoxic stress.

Interplay between Nrf2 and αB-crystallin in the lens and heart of zebrafish under proteostatic stress

A coordinated oxidative stress response, partly triggered by the transcription factor Nrf2, protects cells from the continual production of reactive oxygen species. Left unbuffered, reactive oxygen species can lead to protein aggregation that has been implicated in a spectrum of diseases such as cataract of the ocular lens and myopathy of the heart. While proteostasis is maintained by diverse families of heat shock proteins, the interplay between the oxidative and proteostatic stress responses in the lens and heart has not been investigated. Capitalizing on multiple zebrafish lines that have compromised function of Nrf2 and/or the two zebrafish small heat shock proteins αBa- and αBb-crystallin, we uncovered a transcriptional relationship that leads to a substantial increase in αBb-crystallin transcripts in the heart in response to compromised function of Nrf2. In the lens, the concomitant loss of function of Nrf2 and αBa-crystallin leads to upregulation of the cholesterol biosynthesis pathway, thus mitigating the phenotypic consequences of the αBa-crystallin knockout. By contrast, abrogation of Nrf2 function accentuates the penetrance of a heart edema phenotype characteristic of embryos of αB-crystallin knockout lines. Multiple molecular pathways, such as genes involved in extracellular interactions and implicated in cardiomyopathy, are revealed from transcriptome profiling, thus identifying novel targets for further investigation. Together, our transcriptome/phenotypic analysis establishes an intersection between oxidative stress and chaperone responses in the lens and heart.

Path sampling with memory reduction and replica exchange to reach long permeation timescales

Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. Next, recent and current developments in three RETIS aspects are discussed: several new Monte Carlo moves in the path-sampling algorithm, memory reduction by reducing pathlengths, and exploitation of parallel computing with CPU-imbalanced replicas. Finally, the memory reduction presenting a new replica exchange implementation, coined REPPTIS, is showcased with a permeant needing to pass a membrane with two permeation channels, either representing an entropic or energetic barrier. The REPPTIS results showed clearly that inclusion of some memory and enhancing ergodic sampling via replica exchange moves are both necessary to obtain correct permeability estimates. In an additional example, ibuprofen permeation through a dipalmitoylphosphatidylcholine membrane was modeled. REPPTIS succeeded in estimating the permeability of this amphiphilic drug molecule with metastable states along the permeation pathway. In conclusion, the presented methodological advances allow for deeper insight into membrane biophysics even if the pathways are slow, as RETIS and REPPTIS push the permeability calculations to longer timescales.

Lipid packing in biological membranes governs protein localization and membrane permeability

Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment are not well understood due to the inherent complexities associated with the relevant length and timescales that limit both direct experimental measurements and their interpretation. In this context, computer simulations hold immense potential to investigate molecular-level interactions and mechanisms that lead to PM heterogeneity and its functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the local topological changes in lipid environment using the nonaffine deformation framework. Furthermore, we probe the packing defects in these membranes, which can be considered as the conjugate of membrane order assessed in terms of the nonaffine parameter. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind their functions. Our observations suggest that heterogeneity in mixed phase membranes is a consequence of local lipid topology and its temporal evolution, which give rise to disparate lipid packing in ordered and disordered domains. This in turn governs the distinct nature of packing defects in these domains that can play a crucial role in preferential localization of proteins in mixed phase membranes. Furthermore, we observe that lipid packing also leads to contrasting distribution of free volume in the membrane core region in ordered and disordered membranes, which can lead to distinctive membrane permeability of small molecules. Our results, thus, indicate that heterogeneity in mixed phase membranes closely governs the membrane functions that may emerge from packing-related basic design principles.

Defining permeability of curved membranes in molecular dynamics simulations

Many phospholipid membranes in the cell have a high curvature; for instance, in caveolae, mitochondrial crystae, nanotubes, membrane pearls, small liposomes, or exosomes. Molecular dynamics (MD) simulations are a computational tool to gain insight in the transport behavior at the atomic scale. Membrane permeability is a key kinetic property that might be affected in these highly curved membranes. Unfortunately, the geometry of highly curved membranes creates ambiguity in the permeability value, even with an arbitrarily large factor purely based on geometry, caused by the radial flux not being a constant value in steady state. In this contribution, the ambiguity in permeability for liposomes is countered by providing a new permeability definition. First, the inhomogeneous solubility diffusion model based on the Smoluchowski equation is solved analytically under radial symmetry, from which the entrance and escape permeabilities are defined. Next, the liposome permeability is defined guided by the criterion that a flat and curved membrane should have equal permeability, in case these were to be carved out from an imaginary homogeneous medium. With this criterion, our new definition allows for a fair comparison of flat and curved membranes. The definition is then transferred to the counting method, which is a practical computational approach to derive permeability by counting complete membrane crossings. Finally, the usability of the approach is illustrated with MD simulations of diphosphatidylcholine (DPPC) bilayers, without or with some cholesterol content. Our new liposome permeability definition allows us to compare a spherically shaped membrane with its flat counterpart, thus showcasing how the curvature effect on membrane transport may be assessed.

Association of dyslipidemia and hypoxemia in patients with obstructive sleep apnea hypopnea syndrome: a cross-sectional study

OBJECTIVE

Studies have shown that dyslipidemia may contribute to chronic tissue hypoxia. However, it remains unclear whether dyslipidemia affects chronic hypoxia in patients with obstructive sleep apnea hypopnea syndrome (OSAHS). Therefore, from a clinical practice perspective, the purpose of this study was to investigate the effect of dyslipidemia on chronic hypoxia in OSAHS patients.

METHOD

In athis cross-sectional survey, 320 consecutive OSAHS patients were enrolled. By screening under different conditions, 211 patients were finally enrolled in the study. Patients were grouped according to apnea-hypopnea index (AHI), into a mild-to-moderate (AHI < 30) group and severe OSAHS group (AHI ≥ 30).

RESULTS

Comparative analysis shows that 45% of mild-to-moderate OSAHS patients had severe hypoxemia. Univariate and multivariate regression analyses showed that AHI, triglycerides (TG), and high-density lipoprotein cholesterol (HDL-C) had independent effects on lowest oxygen saturation (LSpO₂), and that AHI and TG levels had independent effects on mean oxygen saturation (MSpO₂). The patients were stratified by AHI and further grouped by TG and HDL-C abnormalities in each subgroup. A difference analysis showed that LSpO₂ and MSpO₂ were significantly decreased in OSAHS patients with dyslipidemia (high TG and low HDL-C levels) in the AHI ≥ 30 subgroup (P < 0.05). Finally, in order to further clarify the impact of the selected indicators of hypoxemia in OSAHS patients with different degrees of airway obstruction, subgroup analysis was conducted based on OSAHS severity. In the AHI < 30 subgroup, LSpO₂ was significantly decreased in patients with abnormal HDL-C.

CONCLUSION

The results of this study indicate that abnormalities in TG and HDL-C, in addition to upper airway obstruction, are among the factors that aggravate chronic hypoxia in tissues from OSAHS patients.

Detection of intralayer alignment in multicomponent lipids by dynamic speckle pattern analysis

Multicomponent mixtures of bilayer lipids, thanks to the coexistence of liquid-crystalline phases in their structures, may be used in the development of functional membranes. In such membranes interlayer ordering distributes across membrane lamellae, resulting in long-range alignment of phase-separated domains. In this paper, we explore the dynamics of this phenomenon by laser speckle pattern analysis. We show that cholesterol content decreases the activity, and the rate of the domains size development is related to the change of physical roughness of the multicomponent lipid mixture. Our results are in agreement with the previous experimental reports. However, our experimental procedure is an easy-to-implement and effective methodology.

Modulating Nucleus Oxygen Concentration by Altering Intramembrane Cholesterol Levels: Creating Hypoxic Nucleus in Oxic Conditions

We propose a novel mechanism by which cancer cells can modulate the oxygen concentration within the nucleus, potentially creating low nuclear oxygen conditions without the need of an hypoxic micro-environment and suited for allowing cancer cells to resist chemo- and radio-therapy. The cells ability to alter intra-cellular oxygen conditions depends on the amount of cholesterol present within the cellular membranes, where high levels of cholesterol can yield rigid membranes that slow oxygen diffusion. The proposed mechanism centers on the competition between (1) the diffusion of oxygen within the cell and across cellular membranes that replenishes any consumed oxygen and (2) the consumption of oxygen in the mitochondria, peroxisomes, endoplasmic reticulum (ER), etc. The novelty of our work centers around the assumption that the cholesterol content of a membrane can affect the oxygen diffusion across the membrane, reducing the cell ability to replenish the oxygen consumed within the cell. For these conditions, the effective diffusion rate of oxygen becomes of the same order as the oxygen consumption rate, allowing the cell to reduce the oxygen concentration of the nucleus, with implications to the Warburg Effect. The cellular and nucleus oxygen content is indirectly evaluated experimentally for bladder (T24) cancer cells and during the cell cycle, where the cells are initially synchronized using hydroxeaurea (HU) at the late G1-phase/early S-phase. The analysis of cellular and nucleus oxygen concentration during cell cycle is performed via (i) RT-qPCR gene analysis of hypoxia inducible transcription factors (HIF) and prolyl hydroxylases (PHD) and (ii) radiation clonogenic assay every 2 h, after release from synchronization. The HIF/PHD genes allowed us to correlate cellular oxygen with oxygen concentration in the nucleus that is obtained from the cells radiation response, where the amount DNA damage due to radiation is directly related to the amount of oxygen present in the nucleus. We demonstrate that during the S-phase cells can become hypoxic in the late S-phase/early G2-phase and therefore the radiation resistance increases 2- to 3-fold.

Atherogenesis, Transcytosis, and the Transmural Cholesterol Flux: A Critical Review

The recently described phenomenon of cholesterol-loaded low-density lipoproteins (LDL) entering the arterial wall from the lumen by transcytosis has been accepted as an alternative for the long-held concept that atherogenesis involves only passive LDL movement across an injured or dysfunctional endothelial barrier. This active transport of LDL can now adequately explain why plaques (atheromas) appear under an intact, uninjured endothelium. However, the LDL transcytosis hypothesis is still questionable, mainly because the process serves no clear physiological purpose. Moreover, central components of the putative LDL transcytosis apparatus are shared by the counter process of cholesterol efflux and reverse cholesterol transport (RCT) and therefore can essentially create an energy-wasting futile cycle and paradoxically be pro- and antiatherogenic simultaneously. Hence, by critically reviewing the literature, we wish to put forward an alternative interpretation that, in our opinion, better fits the experimental evidence. We assert that most of the accumulating cholesterol (mainly as LDL) reaches the intima not from the lumen by transcytosis, but from the artery's inner layers: the adventitia and media. We have named this directional cholesterol transport transmural cholesterol flux (TCF). We suggest that excess cholesterol, diffusing from the avascular (i.e., devoid of blood and lymph vessels) media's smooth muscle cells, is cleared by the endothelium through its apical membrane. A plaque is formed when this cholesterol clearance rate lags behind its rate of arrival by TCF.

The HVCN1 voltage-gated proton channel contributes to pH regulation in canine ventricular myocytes

KEY POINTS

Intracellular pH (pH_i ) regulation is crucial for cardiac function, as acidification depresses contractility and causes arrhythmias. H⁺ ions are generated in cardiomyocytes from metabolic processes and particularly from CO₂ hydration, which has been shown to facilitate CO₂ -venting from mitochondria. Currently, the NHE1 Na⁺ /H⁺ exchanger is viewed as the dominant H⁺ -extrusion mechanism in cardiac muscle. We show that the HVCN1 voltage-gated proton channel is present and functional in canine ventricular myocytes, and that HVCN1 and NHE1 both contribute to pH_i regulation. HVCN1 provides an energetically-efficient mechanism of H⁺ -extrusion that would not cause Na⁺ -loading, which can cause pathology, and that could contribute to transport-mediated CO₂ disposal. These results provide a major advance in our understanding of pH_i regulation in cardiac muscle.

ABSTRACT

Regulation of intracellular pH (pH_i ) in cardiomyocytes is crucial for cardiac function; however, currently known mechanisms for direct or indirect extrusion of acid from cardiomyocytes seem insufficient for energetically-efficient extrusion of the massive H⁺ loads generated under in vivo conditions. In cardiomyocytes, voltage-sensitive H⁺ channel activity mediated by the HVCN1 proton channel would be a highly efficient means of disposing of H⁺ , while avoiding Na⁺ -loading, as occurs during direct acid extrusion via Na⁺ /H⁺ exchange or indirect acid extrusion via Na⁺ -HCO₃ ^- cotransport. PCR and immunoblotting demonstrated expression of HVCN1 mRNA and protein in canine heart. Patch clamp analysis of canine ventricular myocytes revealed a voltage-gated H⁺ current that was highly H⁺ -selective. The current was blocked by external Zn²⁺ and the HVCN1 blocker 5-chloro-2-guanidinobenzimidazole (ClGBI). Both the gating and Zn²⁺ blockade of the current were strongly influenced by the pH gradient across the membrane. All characteristics of the observed current were consistent with the known hallmarks of HVCN1-mediated H⁺ current. Inhibition of HVCN1 and the NHE1 Na⁺ /H⁺ exchanger, singly and in combination, showed that either mechanism is largely sufficient to maintain pH_i in beating cardiomyocytes, but that inhibition of both activities causes rapid acidification. These results show that HVCN1 is expressed in canine ventricular myocytes and provides a major H⁺ -extrusion activity, with a capacity similar to that of NHE1. In the beating heart in vivo, this activity would allow Na⁺ -independent extrusion of H⁺ during each action potential and, when functionally coupled with anion transport mechanisms, could facilitate transport-mediated CO₂ disposal. Abstract figure legend The HVCN1 proton channel is expressed in canine ventricular myocytes and contributes to H⁺ extrusion. This article is protected by copyright. All rights reserved.

Shape transformations of red blood cells in the capillary and their possible connections to oxygen transportation

In this work, a series of numerical simulations have been performed to obtain the steady shapes of red blood cells under a shear force field in the capillary. Two possible classes of steady shapes, the axisymmetric parachute and the non-axisymmetric parachute, are found. If we assume that oxygen diffusion across the red cell membrane is mediated by membrane curvature, it is found that the non-axisymmetric parachute will be more favorable due to its special shape which enables it to have a larger portion of membrane patch capable of releasing oxygen to tissues.

Oxygen Storage in Stacked Phospholipid Membranes Under an Oxygen Gradient as a Model for Myelin Sheaths

Axons in the brain and peripheral nervous system are enveloped by myelin sheaths, which are composed of stacked membrane bilayers containing large fractions of cholesterol, phospholipids, and glycolipids. The oxygen availability to the nearby oxygen consuming cytochrome c oxidase in the mitochondria is essential for the well-functioning of a cell. By constructing a rate network model based on molecular dynamics simulations, and solving it for steady-state conditions, this work calculates the oxygen storage in stacked membranes under an oxygen gradient. It is found that stacking membranes increases the oxygen storage capacity, indicating that myelin can function as an oxygen reservoir. However, it is found that the storage enhancement levels out for stacks with a large number of bilayers, suggesting why myelin sheaths consist of only 10-300 membranes rather than thousands. The presence of additional water between the stacked bilayers, as seen in cancer cells, is shown to diminish myelin oxygen storage enhancement.

Blood bank storage of red blood cells increases RBC cytoplasmic membrane order and bending rigidity

Blood banks around the world store blood components for several weeks ensuring its availability for transfusion medicine. Red blood cells (RBCs) are known to undergo compositional changes during storage, which may impact the cells' function and eventually the recipients' health. We extracted the RBC's cytoplasmic membrane (RBCcm) to study the effect of storage on the membranes' molecular structure and bending rigidity by a combination of X-ray diffraction (XRD), X-ray diffuse scattering (XDS) and coarse grained Molecular Dynamics (MD) simulations. Blood was stored in commercial blood bags for 2 and 5 weeks, respectively and compared to freshly drawn blood. Using mass spectrometry, we measured an increase of fatty acids together with a slight shift towards shorter tail lengths. We observe an increased fraction (6%) of liquid ordered (lo) domains in the RBCcms with storage time, and an increased lipid packing in these domains, leading to an increased membrane thickness and membrane order. The size of both, lo and liquid disordered (ld) lipid domains was found to decrease with increased storage time by up to 25%. XDS experiments reveal a storage dependent increase in the RBCcm's bending modulus κ by a factor of 2.8, from 1.9 kBT to 5.3 kBT. MD simulations were conducted in the absence of proteins. The results show that the membrane composition has a small contribution to the increased bending rigidity and suggests additional protein-driven mechanisms.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Atomistic simulations modify interpretation of spin-label oximetry data. Part 1: intensified water-lipid interfacial resistances

The role of membrane cholesterol in cellular function and dysfunction has been the subject of much inquiry. A few studies have suggested that cholesterol may slow oxygen diffusive transport, altering membrane physical properties and reducing oxygen permeability. The primary experimental technique used in recent years to study membrane oxygen transport is saturation-recovery electron paramagnetic resonance (EPR) oximetry, using spin-label probes targeted to specific regions of a lipid bilayer. The technique has been used, in particular, to assess the influence of cholesterol on oxygen transport and membrane permeability. The reliability of such EPR recordings at the water-lipid interface near the phospholipid headgroups has been challenged by all-atom molecular dynamics (MD) simulation data that show substantive agreement with spin-label probe measurements throughout much of the bilayer. This work uses further MD simulations, with an updated oxygen model, to determine the location of the maximum resistance to permeation and the rate-limiting barrier to oxygen permeation in 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) and POPC/cholesterol bilayers at 25 and 35°C. The current simulations show a spike of resistance to permeation in the headgroup region that was not detected by EPR but was predicted in early theoretical work by Diamond and Katz. Published experimental nuclear magnetic resonance (NMR) oxygen measurements provide key validation of the MD models and indicate that the positions and relative magnitudes of the phosphatidylcholine resistance peaks are accurate. Consideration of the headgroup-region resistances predicts bilayer permeability coefficients lower than estimated in EPR studies, giving permeabilities lower than the permeability of unstirred water layers of the same thickness. Here, the permeability of POPC at 35°C is estimated to be 13 cm/s, compared with 10 cm/s for POPC/cholesterol and 118 cm/s for simulation water layers of similar thickness. The value for POPC is 12 times lower than estimated from EPR measurements, while the value for POPC/cholesterol is 5 times lower. These findings underscore the value of atomic resolution models for guiding the interpretation of experimental probe-based measurements.

Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility-diffusion model

Permeability is a key property in various fields such as membrane technology for chemical separation and transport of substances through cell membranes. At the molecular scale, the counting method uses the number of membrane crossings in a conventional unbiased molecular dynamics simulation to predict the permeability. This contribution investigates under which conditions the counting method has insufficient statistics. An equation is derived for a compartmental model based on the inhomogeneous solubility-diffusion (Smoluchowski) model, giving insight into how the flux correlates with the solubility of permeants. This equation shows that a membrane crossing is a rare event not only when the membrane forms a large free energy barrier but also when the membrane forms a deep free energy well that traps permeants. Such a permeant trap has a high permeability; yet, the counting method suffers from poor statistics. To illustrate this, coarse-grained MD was run for 16 systems of dipalmitoylphosphatidylcholine bilayer membranes with different permeant types. The composition rule for permeability is shown to also hold for fluxes, and it is highlighted that the considered thickness of the membrane causes uncertainty in the permeability calculation of highly permeable membranes. In conclusion, a high permeability in itself is not an effective indicator of the sampling efficiency of the counting method, and caution should be taken for permeants whose solubility varies greatly over the simulation box. A practical consequence relevant in, e.g., drug design is that a drug with high membrane permeability might get trapped by membranes thus reducing its efficacy.

Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers

Permeation of small molecules through membranes is a fundamental biological process, and molecular dynamics simulations have proven to be a promising tool for studying the permeability of membranes by providing a precise characterization of the free energy and diffusivity. In this study, permeation of ethanol through three different membranes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), PO-phosphatidylethanolamine (POPE), and PO-phosphatidylcholine (POPC) is studied. Permeabilities are calculated and compared with two different approaches based on Fick's first law and the inhomogeneous solubility-diffusion model. Microsecond simulation of double bilayers of these membranes provided a direct measurement of permeability by a flux-based counting method. These simulations show that a membrane of POPC has the highest permeability, followed by POPE and POPS. Due to the membrane-modulating properties of ethanol, the permeability increases as functions of concentration and saturation of the inner leaflet in a double bilayer setting, as opposed to the customary definition as a proportionality constant. This concentration dependence is confirmed by single bilayer simulations at different ethanol concentrations ranging from 1% to 18%, where permeability estimates are available from transition-based counting and the inhomogeneous solubility-diffusion model. We show that the free energy and diffusion profiles for ethanol lack accuracy at higher permeant concentrations due to non-Markovian kinetics caused by collective behavior. In contrast, the counting method provides unbiased estimates. Finally, the permeabilities obtained from single bilayer simulations are combined to represent natural gradients felt by a cellular membrane, which accurately models the non-equilibrium effects on ethanol permeability from single bilayer simulations in equilibrium.

Assessment of transient changes in oxygen diffusion of single red blood cells using a microfluidic analytical platform

Red blood cells (RBCs) capability to deliver oxygen (O₂) has been routinely measured by P50. Although this defines the ability of RBCs to carry O₂ under equilibrium states, it cannot determine the efficacy of O₂ delivery in dynamic blood flow. Here, we developed a microfluidic analytical platform (MAP) that isolates single RBCs for assessing transient changes in their O₂ release rate. We found that in vivo (biological) and in vitro (blood storage) aging of RBC could lead to an increase in the O₂ release rate, despite a decrease in P50. Rejuvenation of stored RBCs (Day 42), though increased the P50, failed to restore the O₂ release rate to basal level (Day 0). The temporal dimension provided at the single-cell level by MAP could shed new insights into the dynamics of O₂ delivery in both physiological and pathological conditions.

Tracing molecular properties throughout evolution: A chemoinformatic approach

Evolution of metabolism is a longstanding yet unresolved question, and several hypotheses were proposed to address this complex process from a Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative analysis of genomes are being used to detect signatures of natural selection at the gene and population level, as an attempt to understand the origin of primordial metabolism and its expansion. These studies, however, are still mainly centered on genes and the proteins they encode, somehow neglecting the small organic chemicals that support life processes. In this work, we selected steroids as an ancient family of metabolites widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has imprinted on molecular properties throughout the evolutionary process. Our results clearly show that sterols, the primal steroids that first appeared, have more conserved properties and that, from then on, more complex compounds with increasingly diverse properties have emerged, suggesting that chemical diversification parallels the expansion of biological complexity. In a wider context, these findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of metabolism.

Updated Evaluation of Cholesterol's Influence on Membrane Oxygen Permeability

There is a surprising gap in knowledge regarding the mechanism of oxygen (O2) diffusional delivery at the level of tissues and cells. Yet, the effectiveness of tumor radiotherapy, the success of tissue engineering, and healthy metabolism all require ample intracellular oxygen. Tissue-level diffusion takes place in a complex and crowded macromolecular environment. Cholesterol-rich cellular membranes have been thought to reduce oxygen flux. Here, we use atomistic molecular dynamics simulations to update prior estimates of bilayer permeability and related parameters for 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) and POPC/cholesterol bilayers, using a modified O2 model with improved membrane-water partitioning behavior. This work estimates an oxygen permeability coefficient of 15 ± 1 cm/s for POPC and 11.5 ± 0.4 cm/s for POPC/cholesterol (1:1 molecular ratio) at 37 °C. The permeability of POPC is found to be ~1/3 that of a water layer of similar thickness, and the permeability of POPC/cholesterol is estimated to be 20-30% below that of POPC. Void pathway visualization and free energy data support channeling of oxygen toward the center of cholesterol-incorporating membranes, while partition coefficient data suggest reduced membrane solubility of oxygen due to cholesterol. Further study is needed to understand whether diffusion pathway changes due to cholesterol and other molecular compositional factors influence oxygen availability within tissue.

O2 permeability of lipid bilayers is low, but increases with membrane cholesterol

Oxygen on its transport route from lung to tissue mitochondria has to cross several cell membranes. The permeability value of membranes for O₂ (P_O2), although of fundamental importance, is controversial. Previous studies by mostly indirect methods diverge between 0.6 and 125 cm/s. Here, we use a most direct approach by observing transmembrane O₂ fluxes out of 100 nm liposomes at defined transmembrane O₂ gradients in a stopped-flow system. Due to the small size of the liposomes intra- as well as extraliposomal diffusion processes do not affect the overall kinetics of the O₂ release process. We find, for cholesterol-free liposomes, the unexpectedly low P_O2 value of 0.03 cm/s at 35 °C. This P_O2 would present a serious obstacle to O₂ entering or leaving the erythrocyte. Cholesterol turns out to be a novel major modifier of P_O2, able to increase P_O2 by an order of magnitude. With a membrane cholesterol of 45 mol% as it occurs in erythrocytes, P_O2 rises to 0.2 cm/s at 35 °C. This P_O2 is just sufficient to ensure complete O₂ loading during passage of erythrocytes through the lung's capillary bed under the conditions of rest as well as maximal exercise.

Discerning Membrane Steady-State Oxygen Flux by Monte Carlo Markov Chain Modeling

Molecular oxygen (O2) permeability coefficients for lipid bilayers have previously been estimated using both electron paramagnetic resonance (EPR) oximetry and molecular dynamics simulation data. Yet, neither technique captures the fluxes that exist physiologically. Here, the dynamic steady state is modeled using a stochastic approach built on atomic resolution molecular dynamics simulation data. A Monte Carlo Markov chain technique is used to examine membrane-level fluxes of oxygen in lipid-water systems. At steady state, the concentration of oxygen is found to be higher inside the model membranes than in surrounding water, consistent with the known favorable partitioning of O2 toward the lipid phase. Pure phospholipid 1-palmitoyl,2-oleoyl-phosphatidylcholine (POPC) bilayers accrue ~40% more O2 molecules at steady state than POPC/cholesterol bilayers (1:1 molecular ratio) mimicking the red blood cell membrane. Steady-state levels of oxygen were reached inside both bilayer types within the same timeframe, but depletion of oxygen from the bilayer interior occurred 17% faster for POPC than for POPC/cholesterol. Likewise, first-order rate constants estimated for accrual to steady state were the same for POPC and POPC/cholesterol, at 190 μs-1, while first-order rate constants for depletion of the accrued O2 from the bilayers differed, at 95 μs-1 for POPC and 81 μs-1 for POPC/cholesterol (lower by 15%). These results are consistent with prior experiments in red blood cells (RBCs) with varying membrane cholesterol content, in which additional cholesterol slowed oxygen uptake and release. Further work is needed to understand whether differences in RBC membrane cholesterol content would affect the delivery of oxygen to tissues.

Simulation Study of Breast Cancer Lipid Changes Affecting Membrane Oxygen Permeability: Effects of Chain Length and Cholesterol

Tumor radiotherapy relies on intracellular oxygen (O2) to generate reactive species that trigger cell death, yet hypoxia is common in cancers of the breast. De novo lipid synthesis in tumors supports cell proliferation but also may lead to unusually high levels of the 16:1 palmitoleoyl (Y) phospholipid tail, which is two carbons shorter than the 18:1 oleoyl (O) tail abundant in normal breast tissue. Here, we use atomic resolution molecular dynamics simulations to test two hypotheses: (1) the shorter, 16:1 Y, tail of the de novo lipid biosynthesis product 1-palmitoyl,2-palmitoleoyl-phosphatidylcholine (PYPC) promotes lower membrane permeability relative to the more common lipid 1-palmitoyl,2-oleoylphosphatidylcholine (POPC), by reducing oxygen solubility in the interleaflet region, and (2) cholesterol further lessens the permeability of PYPC by reducing overall O2 solubility and promoting PYPC tail order adjacent to the rigid cholesterol ring system. The simulations conducted here indicate that PYPC has a permeability of 14 ± 1 cm/s at 37 °C, comparable to 15.4 ± 0.4 cm/s for POPC. Inclusion of cholesterol in a 1:1 ratio with phospholipid intensifies the effect of chain length, giving permeabilities of 10.2 ± 0.2 cm/s for PYPC/cholesterol and 11.0 ± 0.6 cm/s for POPC/cholesterol. These findings indicate that PYPC may not substantially influence membrane-level oxygen flux and is unlikely to hinder breast tissue oxygenation.

How does oxygen diffuse from capillaries to tissue mitochondria? Barriers and pathways

Timely delivery of oxygen (O₂ ) to tissue mitochondria is so essential that elaborate circulatory systems have evolved to minimize diffusion distances within tissue. Yet, knowledge is surprisingly limited regarding the diffusion pathway between blood capillaries and tissue mitochondria. An established and growing body of work examines the influence cellular and extracellular structures may have on subcellular oxygen availability. This brief review discusses the physiological and pathophysiological significance of oxygen availability, highlights recent computer modelling studies of transport at the cell-membrane level, and considers alternative diffusion pathways within tissue. Experimental and computer modelling studies suggest that oxygen diffusion may be accelerated by cellular lipids, relative to cytosolic and interstitial fluids. Such acceleration, or 'channelling', would occur due to greatly enhanced oxygen solubility in lipids, especially near the midplane of lipid bilayers. Rapid long-range movement would be promoted by anisotropically enhanced lateral diffusion of oxygen along the midplane and by junctions holding lipid structures in close proximity to one another throughout the tissue. Clarifying the biophysical mechanism of oxygen transport within tissue will shed light on limitations and opportunities in tumour radiotherapy and tissue engineering.

The influence of H/D kinetic isotope effect on radiation-induced transformations of hydroxyl-containing compounds in aqueous solutions

Vicinal diols and its derivatives can be exploited as model compounds for the investigation of radiation-induced free-radical transformations of hydroxyl-containing biomolecules such as carbohydrates, phospholipids, ribonucleotides, amino acids, and peptides. In this paper, for the first time, the prospects of isotope reinforcement approach in inhibiting free-radical transformations of hydroxyl-containing compounds in aqueous solutions are investigated on the example of radiolysis of 1,2-propanediol and 1,2-propanediol-2-d₁ aqueous solutions. At an absorbed dose rate of 0.110 ± 0.003 Gy·s^-1 a profound kinetic isotope effect (KIE) is observed for the non-branched chain formation of acetone, which is a final dehydration product of predominant carbon-centred radicals CH₃·C(OH)CH₂OH. In 0.1 and 1 M deaerated solutions at pH 7.00 ± 0.01, the values of KIE are 8.9 ± 1.7 and 15.3 ± 3.1, respectively. A rationale for the fact that a strong KIE takes place only in the case of chain processes, which may occur during free-radical transformations of vicinal diols, is also provided herein based on the results of 2-propanol and 2-propanol-2-d₁ indirect radiolysis. Lastly, the lack of KIE is shown in the case of 2-butanone formation from 2,3-butanediol or 2,3-butanediol-2,3-d₂. This indicates that the type (primary, secondary) of the β-carbonyl radicals formed as a result of CH₃·C(OH)CH(OH)R (R = H, CH₃) dehydration determines the manifestation of the effect.

Membrane permeability of small molecules from unbiased molecular dynamics simulations

Permeation of many small molecules through lipid bilayers can be directly observed in molecular dynamics simulations on the nano- and microsecond timescale. While unbiased simulations provide an unobstructed view of the permeation process, their feasibility for computing permeability coefficients depends on various factors that differ for each permeant. The present work studies three small molecules for which unbiased simulations of permeation are feasible within less than a microsecond, one hydrophobic (oxygen), one hydrophilic (water), and one amphiphilic (ethanol). Permeabilities are computed using two approaches: counting methods and a maximum-likelihood estimation for the inhomogeneous solubility diffusion (ISD) model. Counting methods yield nearly model-free estimates of the permeability for all three permeants. While the ISD-based approach is reasonable for oxygen, it lacks precision for water due to insufficient sampling and results in misleading estimates for ethanol due to invalid model assumptions. It is also demonstrated that simulations using a Langevin thermostat with collision frequencies of 1/ps and 5/ps yield oxygen permeabilities and diffusion constants that are lower than those using Nosé-Hoover by statistically significant margins. In contrast, permeabilities from trajectories generated with Nosé-Hoover and the microcanonical ensemble do not show statistically significant differences. As molecular simulations become more affordable and accurate, calculation of permeability for an expanding range of molecules will be feasible using unbiased simulations. The present work summarizes theoretical underpinnings, identifies pitfalls, and develops best practices for such simulations.

Cholesterol Reduces Partitioning of Antifungal Drug Itraconazole into Lipid Bilayers

Cholesterol plays a crucial role in modulating the physicochemical properties of biomembranes, both increasing mechanical strength and decreasing permeability. Cholesterol is also a common component of vesicle-based delivery systems, including liposome-based drug delivery systems (LDSs). However, its effect on the partitioning of drug molecules to lipid membranes is very poorly recognized. Herein, we performed a combined experimental/computational study of the potential for the use of the LDS formulation for the delivery of the antifungal drug itraconazole (ITZ). We consider the addition of cholesterol to the lipid membrane. Since ITZ is only weakly soluble in water, its bioavailability is limited. Use of an LDS has thus been proposed. We studied lipid membranes composed of cholesterol, 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), and ITZ using a combination of computational molecular dynamics (MD) simulations of lipid bilayers and Brewster angle microscopy (BAM) experiments of monolayers. Both experimental and computational results show separation of cholesterol and ITZ. Cholesterol has a strong preference to orient parallel to the bilayer normal. However, ITZ, a long and relatively rigid molecule with weakly hydrophilic groups along the backbone, predominantly locates below the interface between the hydrocarbon chain region and the polar region of the membrane, with its backbone oriented parallel to the membrane surface; the orthogonal orientation in the membrane could be the cause of the observed separation. In addition, fluorescence measurements demonstrated that the affinity of ITZ for the lipid membrane is decreased by the presence of cholesterol, which is thus probably not a suitable formulation component of an LDS designed for ITZ delivery.

Pathways of Oxygen Diffusion in Cells and Tissues : Hydrophobic Channeling via Networked Lipids

Oxygen delivery to tissue mitochondria relies on simple diffusion in the target cells and tissues. As such, intracellular availability of O2 in tissue depends on its solubility and diffusivity in complex and heterogeneous macromolecular environments. The path of oxygen diffusion is key to its rate of transfer, especially where pathways of differing favorability are present. Most commonly, aqueous media, such as interstitial fluid and cytoplasm, are assumed to provide the dominant diffusion path. Here, the 'hydrophobic channeling' hypothesis is revisited, and several lines of evidence pointing toward lipid-accelerated oxygen diffusion pathways are discussed. The implications of hydrophobic channeling are considered in light of extended membrane networks in cells and tissues.

Permeability of membranes in the liquid ordered and liquid disordered phases

The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits the correspondence of cellular rafts and liquid ordered (Lo) phases of three-component lipid bilayers to examine permeability. Molecular dynamics simulations of Lo phase dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol show that oxygen and water transit a leaflet through the DOPC and cholesterol rich boundaries of hexagonally packed DPPC microdomains, freely diffuse along the bilayer midplane, and escape the membrane along the boundary regions. Electron paramagnetic resonance experiments provide critical validation: the measured ratio of oxygen concentrations near the midplanes of liquid disordered (Ld) and Lo bilayers of DPPC/DOPC/cholesterol is 1.75 ± 0.35, in very good agreement with 1.3 ± 0.3 obtained from simulation. The results show how cellular rafts can be structurally rigid signaling platforms while remaining nearly as permeable to small molecules as the Ld phase.

The Evolution of Cholesterol-Rich Membrane in Oxygen Adaption: The Respiratory System as a Model

The increase in atmospheric oxygen levels imposed significant environmental pressure on primitive organisms concerning intracellular oxygen concentration management. Evidence suggests the rise of cholesterol, a key molecule for cellular membrane organization, as a cellular strategy to restrain free oxygen diffusion under the new environmental conditions. During evolution and the increase in organismal complexity, cholesterol played a pivotal role in the establishment of novel and more complex functions associated with lipid membranes. Of these, caveolae, cholesterol-rich membrane domains, are signaling hubs that regulate important in situ functions. Evolution resulted in complex respiratory systems and molecular response mechanisms that ensure responses to critical events such as hypoxia facilitated oxygen diffusion and transport in complex organisms. Caveolae have been structurally and functionally associated with respiratory systems and oxygen diffusion control through their relationship with molecular response systems like hypoxia-inducible factors (HIF), and particularly as a membrane-localized oxygen sensor, controlling oxygen diffusion balanced with cellular physiological requirements. This review will focus on membrane adaptations that contribute to regulating oxygen in living systems.

Hypoxia-induced remodelling of goldfish membranes

Hypoxia-tolerant animals use metabolic suppression as an essential strategy to survive low oxygen. Ectotherms can alter membrane lipid composition in response to changes in environmental temperature, but it is currently unknown whether chronic hypoxia can also elicit membrane restructuring. The goal of this study was to investigate a possible physiological link between membrane remodelling and metabolic suppression in goldfish exposed to prolonged hypoxia (4 weeks at 10% air saturation). We have tested the hypothesis that chronic hypoxia would modulate membrane lipid composition in ways that are consistent with known mechanisms of ion pump inhibition. Because homeoviscous membrane restructuring could interfere with the response to hypoxia, measurements were made at 2 temperatures. Results show that hypoxic goldfish suppress metabolic rate by 74% (at 13 °C) and 63% (at 20 °C). This study is the first to reveal that cold-acclimated animals undergo extensive, tissue-specific restructuring of membrane lipids as they reach minimal metabolic rates. However, hypoxia does not affect membrane composition in fish acclimated to 20 °C. The strong membrane response of cold-acclimated fish involves increases in cholesterol abundance (in white muscle and gills) and in fatty acid saturation, mainly caused by a reduction in %22:6 (docosahexaenoic acid in gills and liver). Major ion pumps like Na⁺/K⁺-ATPase are known to be inhibited by cholesterol and activated by 22:6. Because ion pumping by membrane-bound ATPases accounts for a large fraction of basal cellular energy use, we propose that the membrane responses reported here could be a novel mechanism to promote metabolic suppression in cold-acclimated animals.

Diffusion and Transport of Reactive Species Across Cell Membranes

This chapter includes an overview of the structure of cell membranes and a review of the permeability of membranes to biologically relevant oxygen and nitrogen reactive species, namely oxygen, singlet oxygen, superoxide, hydrogen peroxide, hydroxyl radical, nitric oxide, nitrogen dioxide, peroxynitrite and also hydrogen sulfide. Physical interactions of these species with cellular membranes are discussed extensively, but also their relevance to chemical reactions such as lipid peroxidation. Most of these species are involved in different cellular redox processes ranging from physiological pathways to damaging reactions against biomolecules. Cell membranes separate and compartmentalize different processes, inside or outside cells, and in different organelles within cells. The permeability of these membranes to reactive species varies according to the physicochemical properties of each molecule. Some of them, such as nitric oxide and oxygen, are small and hydrophobic and can traverse cellular membranes virtually unhindered. Nitrogen dioxide and hydrogen sulfide find a slightly higher barrier to permeation, but still their diffusion is largely unimpeded by cellular membranes. In contrast, the permeability of cellular membranes to the more polar hydrogen peroxide, is up to five orders of magnitude lower, allowing the formation of concentration gradients, directionality and effective compartmentalization of its actions which can be further regulated by specific aquaporins that facilitate its diffusion through membranes. The compartmentalizing effect on anionic species such as superoxide and peroxynitrite is even more accentuated because of the large energetic barrier that the hydrophobic interior of membranes presents to ions that may be overcome by protonation or the use of anion channels. The large difference in cell membrane permeability for different reactive species indicates that compartmentalization is possible for some but not all of them.

Molecular Dynamics Simulations of Membrane Permeability

This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

Diffusion of nitric oxide and oxygen in lipoproteins and membranes studied by pyrene fluorescence quenching

Oxygen and nitric oxide are small hydrophobic molecules that usually need to diffuse a considerable distance to accomplish their biological functions and necessarily need to traverse several lipid membranes. Different methods have been used to study the diffusion of these molecules in membranes and herein we focus in the quenching of fluorescence of pyrenes inserted in the membrane. The pyrene derivatives have long fluorescence lifetimes (around 200 ns) that make them very sensitive to fluorescence quenching by nitric oxide, oxygen and other paramagnetic species. Results show that the apparent diffusion coefficients in membranes are similar to those in water, indicating that diffusion of these molecules in membranes is not considerably limited by the lipids. This high apparent diffusion in membranes is a consequence of both a favorable partition of these molecules in the hydrophobic interior of membranes and a high diffusion coefficient. Altering the composition of the membrane results in slight changes in diffusion, indicating that in most cases the lipid membranes will not hinder the passage of oxygen or nitric oxide. The diffusion of nitric oxide in the lipid core of low density lipoprotein is also very high, supporting its role as an antioxidant. In contrast to the high permeability of membranes to nitric oxide and oxygen, the permeability to other reactive species such as hydrogen peroxide and peroxynitrous acid is nearly five orders of magnitude lower.

Microscopic view of lipids and their diverse biological functions

Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model

The balance of normal and radial (lateral) diffusion of oxygen in phospholipid membranes is critical for biological function. Based on the Smoluchowski equation for the inhomogeneous solubility-diffusion model, Bayesian analysis (BA) can be applied to molecular dynamics trajectories of oxygen to extract the free energy and the normal and radial diffusion profiles. This paper derives a theoretical formalism to convert these profiles into characteristic times and lengths associated with entering, escaping, or completely crossing the membrane. The formalism computes mean first passage times and holds for any process described by rate equations between discrete states. BA of simulations of eight model membranes with varying lipid composition and temperature indicate that oxygen travels 3 to 5 times further in the radial than in the normal direction when crossing the membrane in a time of 15 to 32 ns, thereby confirming the anisotropy of passive oxygen transport in membranes. Moreover, the preceding times and distances estimated from the BA are compared to the aggregate of 280 membrane exits explicitly observed in the trajectories. BA predictions for the distances of oxygen radial diffusion within the membrane are statistically indistinguishable from the corresponding simulation values, yet BA oxygen exit times from the membrane interior are approximately 20% shorter than the simulation values, averaged over seven systems. The comparison supports the BA approach and, therefore, the applicability of the Smoluchowski equation to membrane diffusion. Given the shorter trajectories required for the BA, these results validate the BA as a computationally attractive alternative to direct observation of exits when estimating characteristic times and radial distances. The effect of collective membrane undulations on the BA is also discussed.

Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes

Translocation of sterols between cellular membrane leaflets is of key importance in membrane organization, dynamics, and signaling. We present a novel translocation mechanism that differs in a unique manner from the established ones. The bobbing mechanism identified here is demonstrated for tail-oxidized sterols, but is expected to be viable for any molecule containing two polar centers at the opposite sides of the molecule. The mechanism renders translocation across a lipid membrane possible without a change in molecular orientation. For tail-oxidized sterols, the bobbing mechanism provides an exceptionally facile means to translocate these signaling molecules across membrane structures and may thus represent an important pathway in the course of their biological action.

Reduced Oxygen Permeability upon Protein Incorporation Within Phospholipid Bilayers

Intracellular oxygenation is key to energy metabolism as well as tumor radiation therapy. Although integral proteins are ubiquitous in membranes, few studies have considered their effects on molecular oxygen permeability. Published experimental work with rhodopsin and bacteriorhodopsin has led to the hypothesis that integral proteins lessen membrane oxygen permeability, as well as the permeability of the lipid region. The current work uses atomistic molecular dynamics simulations to test the influence of an ungated potassium channel protein on the oxygen permeability of palmitoyloleoylphosphatidylcholine (POPC) bilayers with and without cholesterol. Consistent with experiment, whole-membrane oxygen permeability is cut in half upon adding 30 wt% potassium channel protein to POPC, and the apparent permeability of the lipid portion of the membrane decreases by 40%. Unexpectedly, oxygen is found to interact directly with the protein surface, accompanied by a 40% reduction of the apparent whole-membrane diffusion coefficient. Similar effects are seen in systems combining the potassium channel with 1:1 POPC/cholesterol, but the magnitude of permeability reduction is smaller by ~30%. Overall, the simulations indicate that integral proteins can reduce oxygen permeability by altering the diffusional path and the local diffusivity. This effect may be especially important in the protein-dense membranes of mitochondria.