Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study

Computational study of DMPC liposomes loaded with the N-(2-Hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) and determination of its antiproliferative activity in vitro in NIH-3T3 cells

N-(2-Hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) is a valproic acid (VPA) derivative that has shown promising antiproliferative effects in different cancer cell lines, such as A204, HeLa, and MDA-MB-231. However, its low water solubility could reduce its therapeutic effectiveness. To solve this problem, in this work, we incorporated HO-AAVPA into dimyristoyl-phosphatidylcholine (DMPC) liposomes in the presence or absence of cholesterol (CHOL). Using differential scanning calorimetry (DSC), we found that the transition enthalpy (ΔH_tr) of DMPC liposomes is reduced in the presence of CHOL and/or HO-AAVPA, indicating the favorable interactions between CHOL and/or HO-AAVPA and DMPC. Further, by molecular dynamics simulations it was possible to observed that HO-AAVPA migrates from the center of the bilayer toward the water and lipid interface of the DPMC bilayer systems exposing the amine group to water and the aliphatic chain toward the interior of the bilayer. As a consequence, we observed an ordering of the lipid bilayer. Moreover, CHOL harbors into the inner bilayer membrane, increasing the order parameter of the system. The liposomal solutions loaded with HO-AAVPA were tested in the NIH3T3 cell line, showing a reduction in cell proliferation compared to those cells presented without liposomes.Communicated by Ramaswamy H. Sarma.

Possible Role of Bent Structure of Methylated Lithocholic Acid on Artificial and Plasma Membranes

Bile acids form micelles that are essential for the absorption of dietary lipids. However, excessive bile acid micelles can disrupt the plasma membrane by removing phospholipids, resulting in cell death. We hypothesized that the bent geometrical structure of the steroid scaffold of bile acids decreases the lipid order (similar to unsaturated phospholipids with cis double bonds), disrupting the plasma membrane. Here, lithocholic acid (LCA), a bile acid, was methylated to prevent micellization. Methylated lithocholic acid (Me-LCA) was mixed with a thin phase-separated lipid bilayer comprising 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and cholesterol (Chol). Me-LCA was not localized in the DPPC-rich rigid phase but localized in the DOPC-rich fluid phase, and excess Me-LCA did not affect the phase separation. Me-LCA is distributed in the plasma and organelle membranes. However, Me-LCA with bent structure did not affect the membrane properties, membrane fluidity, and hydrophobicity of liposomes composed of DOPC, DPPC, and Chol and also did not affect the proliferation of cells.

Molecular interactions of hesperidin with DMPC/cholesterol bilayers

Since cell membranes are complex systems, the use of model lipid bilayers is quite important for the study of their interactions with bioactive molecules. Mammalian cell membranes require cholesterol (CHOL) for their structure and function. For this reason, the mixtures of phospholipid and cholesterol are necessary to use in model membrane studies to better simulate the real systems. In the present study, we investigated the effect of the incorporation of hesperidin in model membranes consisting of dimyristoylphosphatidylcholine (DMPC) and CHOL by using differential scanning calorimetry (DSC), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, and atomic force microscopy (AFM). ATR-FTIR results demonstrated that hesperidin increases the fluidity of the DMPC/CHOL binary system. DSC findings indicated that the presence of 5 mol% hesperidin induces a broadening of the main phase transition consisting of three overlapping components. AFM experiments showed that hesperidin increases the thickness of DMPC/CHOL lipid bilayer model membranes. In addition to experimental results, molecular docking studies were conducted with hesperidin and human lanosterol synthase (LS), which is an enzyme found in the final step of cholesterol synthesis, to characterize hesperidin's interactions with its surrounding via its hydroxyl and oxygen groups. Then, hesperidin's ADME/Tox (absorption, distribution, metabolism, excretion and toxicity) profile was computed to see the potential impact on living system. In conclusion, considering the data obtained from experimental studies, this work ensures molecular insights in the interaction between a flavonoid, as an antioxidant drug model, and lipids mimicking those found in mammalian membranes. Moreover, computational studies demonstrated that hesperidin may be a great potential for use as a therapeutic agent for hypercholesterolemia due to its antioxidant property.

Effect of encapsulated protein on the dynamics of lipid sponge phase: a neutron spin echo and molecular dynamics simulation study

Lipid membranes are highly mobile systems with hierarchical, time and length scale dependent, collective motions including thickness fluctuations, undulations, and topological membrane changes, which play an important role in membrane interactions. In this work we have characterised the effect of encapsulating two industrially important enzymes, β-galactosidase and aspartic protease, in lipid sponge phase nanoparticles on the dynamics of the lipid membrane using neutron spin echo (NSE) spectroscopy and molecular dynamics (MD) simulations. From NSE, reduced membrane dynamics were observed upon enzyme encapsulation, which were dependent on the enzyme concentration and type. By fitting the intermediate scattering functions (ISFs) with a modified Zilman and Granek model including nanoparticle diffusion, an increase in membrane bending rigidity was observed, with a larger effect for β-galactosidase than aspartic protease at the same concentration. MD simulations for the system with and without aspartic protease showed that the lipids relax more slowly in the system with protein due to the replacement of the lipid carbonyl-water hydrogen bonds with lipid-protein hydrogen bonds. This indicates that the most likely cause of the increase in membrane rigidity observed in the NSE measurements was dehydration of the lipid head groups. The dynamics of the protein itself were also studied, which showed a stable secondary structure of protein over the simulation, indicating no unfolding events occurred.

Chain ordering of phospholipids in membranes containing cholesterol: what matters?

Cholesterol (CHOL) drives lipid segregation and is thus a key player for the formation of lipid rafts and followingly for the ability of a cell to, e.g., enable selective agglomeration of proteins. The lipid segregation is driven by cholesterol's affinity for saturated lipids, which stands directly in relation to the ability of cholesterol to order the individual phospholipid (PL) acyl chains. In this work, molecular dynamics simulations of DPPC (dipalmitoylphosphatidylcholine, saturated lipid) and DLiPC (dilineoylphosphatidylcholine, unsaturated lipid) mixtures with cholesterol are used to elucidate the underlying mechanisms of the cholesterol ordering effect. To this end, all enthalpic contributions, experienced by the PL molecules, are recorded as a function of the PL's acyl chain order. This involves the PL-PL, the PL-cholesterol interaction, the interaction of the PLs with water, and the interleaflet interaction. This systematic analysis allows one to unravel differences of saturated and unsaturated lipids in terms of the different interaction factors. It turns out that cholesterol's impact on chain ordering stems not only from direct interactions with the PLs but is also indirectly present in the other energy contributions. Furthermore, the analysis sheds light on the relevance of the entropic contributions, related to the degrees of freedom of the acyl chain.

17O NMR spectroscopy as a tool to study hydrogen bonding of cholesterol in lipid bilayers

Cholesterol is a crucial component of biological membranes and can interact with other membrane components through hydrogen bonding. NMR spectroscopy has been used previously to investigate this bonding, however this study represents the first 17O NMR spectroscopy study of isotopically enriched cholesterol. We demonstrate the 17O chemical shift is dependent on hydrogen bonding, providing a novel method for the study of cholesterol in bilayers.

Cholesterol and cholesterol bilayer domains inhibit binding of alpha-crystallin to the membranes made of the major phospholipids of eye lens fiber cell plasma membranes

The concentration of α-crystallin decreases in the eye lens cytoplasm, with a corresponding increase in membrane-bound α-crystallin during cataract formation. The eye lens's fiber cell plasma membrane consists of extremely high cholesterol (Chol) content, forming cholesterol bilayer domains (CBDs) within the membrane. The role of high Chol content in the lens membrane is unclear. Here, we applied the continuous-wave electron paramagnetic resonance spin-labeling method to probe the role of Chol and CBDs on α-crystallin binding to membranes made of four major phospholipids (PLs) of the eye lens, i.e., phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylserine (PS), and phosphatidylethanolamine (PE). Small unilamellar vesicles (SUVs) of PC, SM*, and PS with 0, 23, 33, 50, and 60 mol% Chol and PE* with 0, 9, and 33 mol% Chol were prepared using the rapid solvent exchange method followed by probe-tip sonication. The 1 mol% CSL spin-labels used during SUVs preparation distribute uniformly within the Chol/PL membrane, enabling the investigation of Chol and CBDs' role on α-crystallin binding to the membrane. For PC, SM*, and PS membranes, the binding affinity (Ka) and the maximum percentage of membrane surface occupied (MMSO) by α-crystallin decreased with an increase in Chol concentration. The Ka and MMSO became zero at 50 mol% Chol for PC and 60 mol% Chol for SM* membranes, representing that complete inhibition of α-crystallin binding was possible before the formation of CBDs within the PC membrane but only after the formation of CBDs within the SM* membrane. The Ka and MMSO did not reach zero even at 60 mol% Chol in the PS membrane, representing CBDs at this Chol concentration were not sufficient for complete inhibition of α-crystallin binding to the PS membrane. Both the Ka and MMSO were zero at 0, 9, and 33 mol% Chol in the PE* membrane, representing no binding of α-crystallin to the PE* membrane with and without Chol. The mobility parameter profiles decreased with an increase in α-crystallin binding to the membranes; however, the decrease was more pronounced for the membrane with lower Chol concentration. These results imply that the membranes become more immobilized near the headgroup regions with an increase in α-crystallin binding; however, the Chol antagonizes the capacity of α-crystallin to decrease the mobility near the headgroup regions of the membranes. The maximum splitting profiles remained the same with an increase in α-crystallin concentration, but there was an increase in the maximum splitting with an increase in the Chol concentration in the membranes. It implies that membrane order near the headgroup regions does not change with an increase in α-crystallin concentration but increases with an increase in Chol concentration in the membrane. Based on our data, we hypothesize that the Chol and CBDs decrease hydrophobicity (increase polarity) near the membrane surface, inhibiting the hydrophobic binding of α-crystallin to the membranes. Thus, our data suggest that Chol and CBDs play a positive physiological role by preventing α-crystallin binding to lens membranes and possibly protecting against cataract formation and progression.

Role of the cholesterol hydroxyl group in the chemical exchange saturation transfer signal at -1.6 ppm

Chemical exchange saturation transfer (CEST) can provide metabolite-weighted images in the clinical setting; therefore, understanding the origin of each CEST signal is essential to revealing the changes in diseases at the molecular level, which would provide further insight for diagnoses and treatments. The CEST signal at -1.6 ppm is attributed to the choline methyl group of phosphatidylcholines. The methyl groups have no exchangeable protons, so the corresponding CEST signals must result from the relayed nuclear Overhauser effect (rNOE); however, the detailed mechanism remains unclear. Cholesterol is a major component of biological membranes, and its content is closely related to the dynamics and phases of these lipids. However, cholesterol has a hydroxyl group, which could participate in proton exchange to complete the rNOE process. In this study, we used liposomes containing cholesterol and its analogs (5α-cholestane and progesterone), which presumably have similar capabilities of influencing lipid bilayers, and found that the steroid hydroxyl group is the key to inducing the rNOE at -1.6 ppm. Our results suggest that the origin of the rNOE at -1.6 ppm likely requires an intermolecular NOE between the proton of the choline methyl group and that of the cholesterol hydroxyl group, and a chemical exchange between the cholesterol hydroxyl group and bulk water. However, the phenomenon in which the rNOE at -1.6 ppm appears when the cholesterol concentration is high seems to contradict the in vivo results, suggesting a more complicated mechanism associated with the rNOE at -1.6 ppm in biological membranes.

Computer simulations of protein-membrane systems

The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.

Red blood cells membrane micropolarity as a novel diagnostic indicator of type 1 and type 2 diabetes

Classification of the category of diabetes is extremely important for clinicians to diagnose and select the correct treatment plan. Glycosylation, oxidation and other post-translational modifications of membrane and transmembrane proteins, as well as impairment in cholesterol homeostasis, can alter lipid density, packing, and interactions of Red blood cells (RBC) plasma membranes in type 1 and type 2 diabetes, thus varying their membrane micropolarity. This can be estimated, at a submicrometric scale, by determining the membrane relative permittivity, which is the factor by which the electric field between the charges is decreased relative to vacuum. Here, we employed a membrane micropolarity sensitive probe to monitor variations in red blood cells of healthy subjects (n=16) and patients affected by type 1 (T1DM, n=10) and type 2 diabetes mellitus (T2DM, n=24) to provide a cost-effective and supplementary indicator for diabetes classification. We find a less polar membrane microenvironment in T2DM patients, and a more polar membrane microenvironment in T1DM patients compared to control healthy patients. The differences in micropolarity are statistically significant among the three groups (p<0.01). The role of serum cholesterol pool in determining these differences was investigated, and other factors potentially altering the response of the probe were considered in view of developing a clinical assay based on RBC membrane micropolarity. These preliminary data pave the way for the development of an innovative assay which could become a tool for diagnosis and progression monitoring of type 1 and type 2 diabetes.

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Dynamic flux of cholesterol is differentially altered in T1DM and T2DM.

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Red blood cell senses the dynamic flux of lipids by changing its micropolarity.

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Laurdan can measure micropolarity in red blood cells membranes.

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Differences in micropolarity between the three groups are statistically significant.

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Red blood cell Micropolarity is an innovative assay for diabetes classification.

Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics

The transporter associated with antigen processing (TAP) directly participates in the immune response as a key component of the cytosolic peptide to major histocompatibility complex (MHC) class I protein loading machinery. This makes TAP an important target for viruses avoiding recognition by CD8+ T lymphocytes. Its activity can be suppressed by the UL49.5 protein produced by bovine herpesvirus 1, although the mechanism of this inhibition has not been understood so far.

Therefore, the main goal of our study was to investigate the 3D structure of bovine herpesvirus 1 - encoded UL49.5 protein. The final structure of the inhibitor was established using circular dichroism (CD), 2D nuclear magnetic resonance (NMR), and molecular dynamics (MD) in membrane mimetic environments. In NMR studies, UL49.5 was represented by two fragments: the extracellular region (residues 1–35) and the transmembrane-intracellular fragment (residues 36–75), displaying various functions during viral invasion. After the empirical structure determination, a molecular docking procedure was used to predict the complex of UL49.5 with the TAP heterodimer.

Our results revealed that UL49.5 adopted a highly flexible membrane-proximal helical structure in the extracellular part. In the transmembrane region, we observed two short α-helices. Furthermore, the cytoplasmic part had an unordered structure. Finally, we propose three different orientations of UL49.5 in the complex with TAP. Our studies provide, for the first time, the experimental structural information on UL49.5 and structure-based insight in its mechanism of action which might be helpful in designing new drugs against viral infections.

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The UL49.5 viral protein forms a helical structure in the biological membrane

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Our NMR-based 3D structure of UL49.5 differs from the theoretical predictions

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Apart from the protruding N-terminal helix the structure is buried in the membrane

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Attention should be paid to the turns in the external and transmembrane domains

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Molecular docking proposes three possible structures of the UL49.5/TAP complexes

Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees

Cholesterol is an essential component of all animal cell membranes and plays an important role in maintaining the membrane structure and physical-chemical properties necessary for correct cell functioning. The presence of cholesterol is believed to be responsible for domain formation (lipid rafts) due to different interactions of cholesterol with saturated and unsaturated lipids. In order to get detailed atomistic insight into the behaviour of cholesterol in bilayers composed of lipids with varying degrees of unsaturation, we have carried out a series of molecular dynamics simulations of saturated and polyunsaturated lipid bilayers with different contents of cholesterol, as well as well-tempered metadynamics simulations with a single cholesterol molecule in these bilayers. From these simulations we have determined distributions of cholesterol across the bilayer, its orientational properties, free energy profiles, and specific interactions of molecular groups able to form hydrogen bonds. Both molecular dynamics and metadynamics simulations showed that the most unsaturated bilayer with 22:6 fatty acid chains shows behaviour which is most different from other lipids. In this bilayer, cholesterol is relatively often found in a "flipped" configuration with the hydroxyl group oriented towards the membrane middle plane. This bilayer has also the highest (least negative) binding free energy among liquid phase bilayers, and the lowest reorientation barrier. Furthermore, cholesterol molecules in this bilayer are often found to form head-to-tail contacts which may lead to specific clustering behaviour. Overall, our simulations support ideas that there can be a subtle interconnection between the contents of highly unsaturated fatty acids and cholesterol, deficiency or excess of each of them is related to many human afflictions and diseases.

Effect of general anesthetics on the properties of lipid membranes of various compositions

Computer simulations of four lipid membranes of different compositions, namely neat DPPC and PSM, and equimolar DPPC-cholesterol and PSM-cholesterol mixtures, are performed in the presence and absence of the general anesthetics diethylether and sevoflurane both at 1 and 600 bar. The results are analyzed in order to identify membrane properties that are potentially related to the molecular mechanism of anesthesia, namely that change in the same way in any membrane with any anesthetics, and change oppositely with increasing pressure. We find that the lateral lipid density satisfies both criteria: it is decreased by anesthetics and increased by pressure. This anesthetic-induced swelling is attributed to only those anesthetic molecules that are located close to the boundary of the apolar phase. This lateral expansion is found to lead to increased lateral mobility of the lipids, an effect often thought to be related to general anesthesia; to an increased fraction of the free volume around the outer preferred position of anesthetics; and to the decrease of the lateral pressure in the nearby range of the ester and amide groups, a region into which anesthetic molecules already cannot penetrate. All these changes are reverted by the increase of pressure. Another important finding of this study is that cholesterol has an opposite effect on the membrane properties than anesthetics, and, correspondingly, these changes are less marked in the presence of cholesterol. Therefore, changes in the membrane that can lead to general anesthesia are expected to occur in the membrane domains of low cholesterol content.

Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations

Biological membranes are heterogeneous structures with complex electrostatic profiles arising from lipids, sterols, membrane proteins, and water molecules. We investigated the effect of cholesterol and its derivative 6-ketocholestanol (6-kc) on membrane electrostatics by directly measuring the dipole electric field (F⃗d) within lipid bilayers containing cholesterol or 6-kc at concentrations of 0-40 mol% through the vibrational Stark effect (VSE). We found that adding low concentrations of cholesterol, up to ∼10 mol %, increases F⃗d, while adding more cholesterol up to 40 mol% lowers F⃗d. In contrast, we measured a monotonic increase in F⃗d as 6-kc concentration increased. We propose that this membrane electric field is affected by multiple factors: the polarity of the sterol molecules, the reorientation of the phospholipid dipole due to sterol, and the impact of the sterol on hydrogen bonding with surface water. We used molecular dynamics simulations to examine the distribution of phospholipids, sterol, and helix in bilayers containing these sterols. At low concentrations, we observed clustering of sterols near the vibrational probe whereas at high concentrations, we observed spatial correlation between the positions of the sterol molecules. This work demonstrates how a one-atom difference in a sterol changes the physicochemical and electric field properties of the bilayer.

Lipid bilayer thickness determines cholesterol's location in model membranes

Cholesterol is an essential biomolecule of animal cell membranes, and an important precursor for the biosynthesis of certain hormones and vitamins. It is also thought to play a key role in cell signaling processes associated with functional plasma membrane microdomains (domains enriched in cholesterol), commonly referred to as rafts. In all of these diverse biological phenomena, the transverse location of cholesterol in the membrane is almost certainly an important structural feature. Using a combination of neutron scattering and solid-state ²H NMR, we have determined the location and orientation of cholesterol in phosphatidylcholine (PC) model membranes having fatty acids of different lengths and degrees of unsaturation. The data establish that cholesterol reorients rapidly about the bilayer normal in all the membranes studied, but is tilted and forced to span the bilayer midplane in the very thin bilayers. The possibility that cholesterol lies flat in the middle of bilayers, including those made from PC lipids containing polyunsaturated fatty acids (PUFAs), is ruled out. These results support the notion that hydrophobic thickness is the primary determinant of cholesterol's location in membranes.

Novel benzanthrone probes for membrane and protein studies

The applicability of a series of novel benzanthrone dyes to monitoring the changes in physicochemical properties of lipid bilayer and to differentiating between the native and aggregated protein states has been evaluated. Based on the quantitative parameters of the dye-membrane and dye-protein binding derived from the fluorimetric titration data, the most prospective membrane probes and amyloid tracers have been selected from the group of examined compounds. Analysis of the red edge excitation shifts of the membrane- and amyloid-bound dyes provided information on the properties of benzanthrone binding sites within the lipid and protein matrixes. To understand how amyloid specificity of benzanthrones correlates with their structure, quantitative structure activity relationship (QSAR) analysis was performed involving a range of quantum chemical molecular descriptors. A statistically significant model was obtained for predicting the sensitivity of novel benzanthrone dyes to amyloid fibrils.

Vesicle Origami and the Influence of Cholesterol on Lipid Packing

The artificial phospholipid Pad-PC-Pad was analyzed in 2D (monolayers at the air/water interface) and 3D (aqueous lipid dispersions) systems. In the gel phase, the two leaflets of a Pad-PC-Pad bilayer interdigitate completely, and the hydrophobic bilayer region has a thickness comparable to the length of a single phospholipid acyl chain. This leads to a stiff membrane with no spontaneous curvature. Forced into a vesicular structure, Pad-PC-Pad has faceted geometry, and in its extreme form, tetrahedral vesicles were found as predicted a decade ago. Above the main transition temperature, a noninterdigitated Lα phase with fluid chains has been observed. The addition of cholesterol leads to a slight decrease of the main transition temperature and a gradual decrease in the transition enthalpy until the transition vanishes at 40 mol % cholesterol in the mixture. Additionally, cholesterol pulls the chains apart, and a noninterdigitated gel phase is observed. In monolayers, cholesterol has an ordering effect on liquid-expanded phases and disorders condensed phases. The wavenumbers of the methylene stretching vibration indicate the formation of a liquid-ordered phase in mixtures with 40 mol % cholesterol.

Computer modelling studies of the bilayer/water interface

This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers

Coarse-grained (CG) models for mixed dimyristoylphosphatidylcholine (DMPC)/cholesterol lipid bilayers are constructed using the recently developed multiscale coarse-graining (MS-CG) method. The MS-CG method permits a systematic fit of the bonded and nonbonded interactions and system pressure to trajectory and force data derived from an underlying reference all-atom molecular dynamics (MD) simulation. The CG sites for lipid and cholesterol molecules are associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic MD data. Corresponding models with four-site and seven-site representations of the cholesterol molecule were also developed. The latter CG models differed by the bonding scheme of CG sites to represent intramolecular interactions. A one-site MS-CG model based on the TIP3P potential was used for water, with the interaction site placed at the molecular geometrical center, and the analytical fit of the model is presented. The MS-CG models were then used to conduct simulations in the constant NPT ensemble which reproduce accurately the structural properties as seen in the full all-atom MD simulation.

Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation

Coarse graining of membrane simulations by translating atomistic dynamics to densities and fields with Milestoning is discussed. The space of the membrane system is divided into cells and the different cells are characterized by order parameters presenting the number densities. The dynamics of the order parameters are probed with Milestoning. The methodology is illustrated here for a phospholipid membrane system (a hydrated bilayer of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) lipid molecules). Significant inhomogeneity in membrane internal number density leads to complex free energy landscape and local maps of transition times. Dynamics and distributions of cavities within the membrane assist the permeation of nonpolar solutes such as xenon atoms. It is illustrated that quantitative and detailed dynamics of water transport through DOPC membrane can be analyzed using Milestoning with fields. The reaction space for water transport includes at least two slow variables: the normal to the membrane plane, and the water density.

Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes?

Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham - Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this description, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.

Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration

We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

Cholesterol as a co-solvent and a ligand for membrane proteins

As of mid 2013 a Medline search on "cholesterol" yielded over 200,000 hits, reflecting the prominence of this lipid in numerous aspects of animal cell biology and physiology under conditions of health and disease. Aberrations in cholesterol homeostasis underlie both a number of rare genetic disorders and contribute to common sporadic and complex disorders including heart disease, stroke, type II diabetes, and Alzheimer's disease. The corresponding author of this review and his lab stumbled only recently into the sprawling area of cholesterol research when they discovered that the amyloid precursor protein (APP) binds cholesterol, a topic covered by the Hans Neurath Award lecture at the 2013 Protein Society Meeting. Here, we first provide a brief overview of cholesterol-protein interactions and then offer our perspective on how and why binding of cholesterol to APP and its C99 domain (β-CTF) promotes the amyloidogenic pathway, which is closely related to the etiology of Alzheimer's disease.

Comparative computer simulation study of cholesterol in hydrated unary and binary lipid bilayers and in an anhydrous crystal

Models created with molecular dynamics simulations are used to compare the organization and dynamics of cholesterol (Chol) molecules in three different environments: (1) a hydrated pure Chol bilayer that models the Chol bilayer domain, which is a pure Chol domain embedded in the bulk membrane; (2) a 2-palmitoyl-3-oleoyl-d-glycerol-1-phosphorylcholine bilayer saturated with cholesterol (POPC-Chol50) that models the bulk membrane; (3) a Chol crystal. The computer model of the hydrated pure Chol bilayer is stable on the microsecond time scale. Some structural characteristics of Chol molecules in the Chol bilayer are similar to those in the POPC-Chol50 bilayer (e.g., tilt of Chol rings and chains), while others are similar to those in Chol crystals (e.g., surface area per Chol, bilayer thickness). The key result of this study is that the Chol bilayer has, unexpectedly, a dynamic structure, with Chol mobility similar to that in the POPC-Chol50 bilayer though slower. This is the major difference compared to Chol crystals, where Chol molecules are immobile. Also, water accessibility to Chol-OH groups in the Chol bilayer is not limited. On average, each Chol molecule makes 2.3 hydrogen bonds with water in the Chol bilayer, compared with 1.7 hydrogen bonds in the POPC-Col50 bilayer.

Power-law trapping of water molecules on the lipid-membrane surface induces water retardation

Cell membranes provide unique local environments for biological reactions, where the diffusion of biomolecules as well as water molecules plays critical roles. Translational and rotational motions of water molecules near membranes are known to be slower than those in bulk. Using all-atom molecular dynamics simulations of a membrane, we show that the temperature dependence of the water molecular motions on the membrane surface is different from that in bulk. Decreasing temperature enhances the water retardation on the membrane surface, and the lateral motions of water molecules are correlated with the vertical motions. We find that trapping times of water molecules onto membrane surfaces are distributed according to a power-law distribution and that the power-law exponents depend linearly on temperature, suggesting a random energy landscape picture. Moreover, we find that water molecules on the membrane surfaces exhibit subdiffusions in translational motions.

Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol's molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup's phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

Differential dynamic and structural behavior of lipid-cholesterol domains in model membranes

Changes in the cholesterol (Chol) content of biological membranes are known to alter the physicochemical properties of the lipid lamella and consequently the function of membrane-associated enzymes. To characterize these changes, we used steady-state and time resolved fluorescence spectroscopy and two photon-excitation microscopy techniques. The membrane systems were chosen according to the techniques that were used: large unilamellar vesicles (LUVs) for cuvette and giant unilamellar vesicles (GUVs) for microscopy measurements; they were prepared from dipalmitoyl phosphatidylcholine (DPPC) and dioctadecyl phosphatidylcholine (DOPC) in mixtures that are well known to form lipid domains. Two fluorescent probes, which insert into different regions of the bilayer, were selected: 1,6-diphenyl-1,3,5-hexatriene (DPH) was located at the deep hydrophobic core of the acyl chain regions and 2-dimethylamino-6-lauroylnaphthalene (Laurdan) at the hydrophilic-hydrophobic membrane interface. Our spectroscopy results show that (i) the changes induced by cholesterol in the deep hydrophobic phospholipid acyl chain domain are different from the ones observed in the superficial region of the hydrophilic-hydrophobic interface, and these changes depend on the state of the lamella and (ii) the incorporation of cholesterol into the lamella induces an increase in the orientation dynamics in the deep region of the phospholipid acyl chains with a corresponding decrease in the orientation at the region close to the polar lipid headgroups. The microscopy data from DOPC/DPPC/Chol GUVs using Laurdan generalized polarization (Laurdan GP) suggest that a high cholesterol content in the bilayer weakens the stability of the water hydrogen bond network and hence the stability of the liquid-ordered phase (Lo).