Membrane Hydrocarbon Core Research Articles

Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes.

We present a comparative all-atom molecular dynamics simulation study of 18 biomembrane systems with lipid compositions corresponding to eukaryotic, bacterial, and archaebacterial membranes together with three single-component lipid bilayers. A total of 105 lipid types used in this study include diverse sterols and glycerol-based lipids with acyl chains of various lengths, unsaturation degrees, and branched or cyclic moieties. Our comparative analysis provides deeper insight into the influences of sterols and lipid unsaturation on the structural and mechanical properties of these biomembranes, including water permeation into the membrane hydrocarbon core. For sterol-containing membranes, sterol fraction is correlated with the membrane thickness, the area compressibility modulus, and lipid order but anticorrelated with the area per lipid and sterol tilt angles. Similarly, for all 18 biomembranes, lipid order is correlated with the membrane thickness and area compressibility modulus. Sterols and lipid unsaturation produce opposite effects on membrane thickness, but only sterols influence water permeation into the membrane. All membrane systems are accessible for public use in CHARMM-GUI Archive. They can be used as templates to expedite future modeling of realistic cell membranes with transmembrane and peripheral membrane proteins to study their structure, dynamics, molecular interactions, and function in a nativelike membrane environment.

Membrane Deformation Modulated by Hydration and Cholesterol Unveiled by Solid-State 2H NMR Spectroscopy

Phospholipid membranes are biological liquid crystals in which intermolecular interactions at mesoscopic length scales play key roles in the emergence of membrane physical properties like structure and rigidity. Such interactions modulated by membrane hydration [1] and cholesterol [2] have been investigated using solid-state 2H NMR spectroscopy. The average structure is manifested by the lineshapes through principal values of static or residual coupling tensors due to quadrupolar interactions. The residual quadrupolar couplings (RQCs) yield segmental order parameters for the individual acyl segments (i), providing average membrane properties such as bilayer thickness, area/lipid, and spontaneous curvature [3]. We show that membrane dehydration and increased cholesterol content result in greater RQCs, indicative of membrane thickening. Elastic membrane deformations are exhibited as collective order-director fluctuations (ODF) contributing to the nuclear magnetic relaxation. At mesoscopic length scales the thermal fluctuations connect to membrane mechanical properties via the fluctuation-dissipation theorem. Model-free interpretation of the functional dependence of spin-lattice relaxation rates, R1Z, on segmental order parameters (square-law) reveals emergent material properties in the liquid-crystalline state. The R1Z relaxation dispersion and temperature dependence of square-law plots indicate a nematic-like membrane hydrocarbon core. Solid-state 2H NMR relaxation studies demonstrate that both dehydration and increased cholesterol content in the membrane lead to decreased slopes of square-law plots, indicating an increase in membrane bending rigidity, consistent with neutron spin-echo (NSE) measurements. Analogous 2H NMR studies with various membrane lipid compositions and peptide-reconstituted membranes have addressed lipid-mediated cell signaling and lipid-protein interactions. Molecular dynamics simulations provide further insights on the correspondence of the solid-state NMR and NSE results. [1] K.J. Mallikarjunaiah et al. (2019) Phys. Chem. Chem. Phys. 21, 18422. [2] S. Chakraborty et al. (2020) Proc. Natl. Acad. Sci. 117, 21896. [3] Mallikarjunaiah et al. (2011) Biophys. J. 100, 98.

EPA and DHA containing phospholipids have contrasting effects on membrane structure

Omega-3 FAs EPA and DHA influence membrane fluidity, lipid rafts, and signal transduction. A clinical trial, Reduction of Cardiovascular Events with Icosapent Ethyl—Intervention Trial, demonstrated that high-dose EPA (4 g/d icosapent ethyl) reduced composite cardiovascular events in statin-treated high-risk patients. EPA benefits correlated with on-treatment levels, but similar trials using DHA-containing formulations did not show event reduction. We hypothesized that differences in clinical efficacy of various omega-3 FA preparations could result from differential effects on membrane structure. To test this, we used small-angle X-ray diffraction to compare 1-palmitoyl-2-eicosapentaenoyl-sn-glycero-3-phosphocholine (PL-EPA), 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PL-DHA), and 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PL-AA) in membranes with and without 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol. Electron density profiles (electrons/Å3 vs. Å) were used to determine membrane structure, including membrane width (d-space). PL-EPA and PL-DHA had similar membrane structures without POPC and/or cholesterol but had contrasting effects in the presence of POPC and cholesterol. PL-EPA increased membrane hydrocarbon core electron density over an area of ±0–10 Å from the center, indicating an extended orientation. PL-DHA increased electron density in the phospholipid head group region, concomitant with disordering in the hydrocarbon core and a similar d-space (58 Å). Adding equimolar amounts of PL-EPA and PL-DHA produced changes that were attenuated compared with their separate effects. PL-AA increased electron density centered ±12 Å from the membrane center. The contrasting effects of PL-EPA, PL-DHA, and PL-AA on membrane structure may contribute to differences observed in the biological activities and clinical actions of various omega-3 FAs.

Abstract 14758: Contrasting Effects of Phospholipid Linked Eicosapentaenoic Acid and Arachidonic Acid on Membrane Structure and Stability

Background: Treatment with prescription, high dose, stable icosapent ethyl (IPE), which is metabolized to eicosapentaenoic acid (EPA), significantly reduced clinical events in high-risk patients with either cardiovascular disease or diabetes plus other risk factors (REDUCE-IT). Previous studies suggest that the benefits of EPA, an omega-3 fatty acid (O3FA), correlate positively with its levels and ratio to arachidonic acid (AA) in circulation and cellular membranes. Unlike EPA, AA is an omega-6 fatty acid (O6FA) that, along with its metabolites, contributes to inflammation and diabetes. Objective: The purpose of this study was to compare the separate and combined effects of phospholipid-linked EPA and AA on membrane structure. Methods: Small angle x-ray diffraction approaches compared the effects of 1-palmitoyl-2-eicosapentaenoyl-sn-glycero-3-phosphocholine (PL-EPA) and 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PL-AA) at a 1:20 ratio in membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol (C) at a 0.3:1 C:PL ratio. As a control, we also evaluated membranes consisting of POPC and C only at the same C:PL ratio. Electron density profiles (electrons/Å 3 vs Å) generated from the diffraction data served to determine membrane structure, including its width or d -space, at 1 Å resolution. Results: Addition of PL-EPA increased membrane hydrocarbon core electron density over a broad area ± 0-10 Å from the membrane center, indicating a stabilizing effect on surrounding phospholipid acyl chains. By contrast, PL-AA caused a smaller, bimodal increase in electron density centered at ± 7 Å from the center of the membrane corresponding to its terminal double bonds. The membrane widths of the PL-EPA and PL-AA containing membranes were similar at 58 ± 0.7 Å and 57 ± 0.5 Å, respectively. The combination of PL-EPA with PL-AA highly attenuated the stabilizing effects of EPA on the membrane. Conclusion: PL-EPA causes membrane stability in a manner that is disrupted by the presence of PL-AA. The contrasting effects of PL-EPA and PL-AA on membrane structure may contribute to differences in biological activity.

Abstract 335: Distinct Effects of Eicosapentaenoic Acid and Docosahexaenoic Acid Linked Phospholipids on Membrane Structure

In REDUCE-IT, prescription eicosapentaenoic acid (EPA), an omega-3 fatty acid (O3FA), significantly reduced ischemic events in patients with diabetes or cardiovascular disease. Treatments containing docosahexaenoic acid (DHA) have not shown similar benefits in other trials. EPA and DHA differentially influence lipid oxidation, signal transduction, fluidity, and cholesterol domain formation, potentially due to distinct membrane interactions. Small angle x-ray diffraction approaches compared the separate and combined effects of 1-palmitoyl-2-eicosapentaenoyl-sn-glycero-3-phosphocholine (PL-EPA) and 1-palmitoyl-2-docosahexaenoic-sn-glycero-3-phosphocholine (PL-DHA) at a 1:20 ratio in membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PL-OA) and cholesterol (C) at a 0.3:1 C:PL ratio. As a control, we also evaluated membranes consisting of PL-OA and C only. Electron density profiles (electrons/Å 3 vs Å) generated from the diffraction data served to determine membrane structure, including its width or d -space, at 1 Å resolution (Fig. 1A). Addition of PL-EPA increased membrane hydrocarbon core electron density over a broad area ± 0-10 Å from the membrane center, indicating an energetically favorable extended membrane orientation for EPA, stabilized by van der Waals interactions (Fig. 1B). By contrast, PL-DHA increased electron density in the phospholipid head group region concomitant with disordering in the hydrocarbon core ± 0-9 Å (Fig. 1C). Addition of the PL-O3FAs did not alter the overall membrane width (57 ± 1 Å). The combination of PL-EPA with PL-DHA highly attenuated their separate effects on the hydrocarbon core and headgroup (Fig. 1D). The contrasting EPA and DHA effects on membrane structure signify distinct molecular orientations that may contribute to observed differences in biological activity.

The Penetration Depth for Hanatoxin Partitioning into the Membrane Hydrocarbon Core Measured with Neutron Reflectivity.

Hanatoxin (HaTx) from spider venom works as an inhibitor of Kv2.1 channels, most likely by interacting with the voltage sensor (VS). However, the way in which this water-soluble peptide modifies the gating remains poorly understood as the VS is deeply embedded within the bilayer, although it would change its position depending on the membrane potential. To determine whether HaTx can indeed bind to the VS, the depth at which HaTx penetrates into the POPC membranes was measured with neutron reflectivity. Our results successfully demonstrate that HaTx penetrates into the membrane hydrocarbon core (∼9 Å from the membrane surface), not lying on the membrane-water interface as reported for another voltage sensor toxin (VSTx). This difference in penetration depth suggests that the two toxins fix the voltage sensors at different positions with respect to the membrane normal, thereby explaining their different inhibitory effects on the channels. In particular, results from MD simulations constrained by our penetration data clearly demonstrate an appropriate orientation for HaTx to interact with the membranes, which is in line with the biochemical information derived from stopped-flow analysis through delineation of the toxin-VS binding interface.

Eicosapentaenoic acid and docosahexaenoic acid have distinct membrane locations and lipid interactions as determined by X-ray diffraction

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) differentially influence lipid oxidation, signal transduction, fluidity, and cholesterol domain formation, potentially due in part to distinct membrane interactions. We used small angle X-ray diffraction to evaluate the EPA and DHA effects on membrane structure. Membrane vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol (C) (0.3C:POPC mole ratio) were prepared and treated with vehicle, EPA, or DHA (1:10 mol ratio to POPC). Electron density profiles generated from the diffraction data showed that EPA increased membrane hydrocarbon core electron density over a broad area, up to ± 20 Å from the membrane center, indicating an energetically favorable extended orientation for EPA likely stabilized by van der Waals interactions. By contrast, DHA increased electron density in the phospholipid head group region starting at ± 12 Å from the membrane center, presumably due to DHA-surface interactions, with coincident reduction in electron density in the membrane hydrocarbon core centered ± 7–9 Å from the membrane center. The membrane width (d-space) decreased by 5 Å in the presence of vehicle as the temperature increased from 10 °C to 30 °C due to increased acyl chain trans-gauche isomerizations, which was unaffected by addition of EPA or DHA. The influence of DHA on membrane structure was modulated by temperature changes while the interactions of EPA were unaffected. The contrasting EPA and DHA effects on membrane structure indicate distinct molecular locations and orientations that may contribute to observed differences in biological activity.

Abstract 159: Eicosapentaenoic Acid and Docosahexaenoic Acid Have Distinct Membrane Locations and Lipid Interactions as Determined by X-ray Diffraction

Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) differentially influence lipid oxidation, signal transduction, fluidity, and cholesterol domain formation, potentially due to distinct membrane interactions. We used small angle x-ray diffraction to test EPA and DHA effects on model membrane structure. Vesicles were prepared to model human peripheral cell membranes using 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) and cholesterol (C) (0.3 C:POPC mole ratio), and treated with vehicle, EPA, or DHA (1:10 mole ratio to POPC). Membrane width ( d- space) was 59.5 Å at 10°C, decreasing to 54.7 Å at 30°C due to increased acyl chain dynamics. EPA or DHA had no effect on membrane d -space (<1 Å change). Electron density profiles from diffraction data were superimposed on corresponding vehicle profiles (Fig. 1). EPA increased membrane hydrocarbon core electron density over a broad area, up to ± 20 Å from the membrane center, indicating an energetically favorable extended membrane orientation for EPA, stabilized by van der Waals interactions. By contrast, DHA increased electron density in the phospholipid head group region starting at ± 12 Å from the membrane center, due to DHA-surface interactions, resulting in a pronounced electron density reduction and increased disorder in the membrane hydrocarbon core centered ± 7-9 Å from the membrane center. DHA disordering effects were less apparent at higher temperatures, likely due to greater rotational dynamics, while EPA effects were stable. The contrasting EPA and DHA effects on membrane structure signify distinct molecular locations/orientations and may contribute to observed differences in biological activity.

Hanatoxin inserts into phospholipid membranes without pore formation

Hanatoxin (HaTx), a 35-residue polypeptide from spider venom, functions as an inhibitor of Kv2.1 channels by interacting with phospholipids prior to affecting the voltage-sensor. However, how this water-soluble peptide modifies the gating remains poorly understood, as the voltage-sensor is deeply embedded within the bilayer. To determine how HaTx interacts with phospholipid bilayers, in this study, we examined the toxin-induced partitioning of liposomal membranes. HPLC-results from high-speed spin-down vesicles with HaTx demonstrated direct binding. Dynamic light scattering (DLS) and leakage assay results further indicated that neither membrane pores nor membrane fragmentations were observed in the presence of HaTx. To clarify the binding details, Langmuir trough experiments were performed with phospholipid monolayers by mimicking the external leaflet of membrane bilayers, indicating the involvement of acyl chains in such interactions between HaTx and phospholipids. Our current study thus describes the interaction pattern of HaTx with vesicle membranes, defining a membrane-partitioning mechanism for peptide insertion involving the membrane hydrocarbon core without pore formation.

REDOR solid-state NMR as a probe of the membrane locations of membrane-associated peptides and proteins

Rotational-echo double-resonance (REDOR) solid-state NMR is applied to probe the membrane locations of specific residues of membrane proteins. Couplings are measured between protein 13CO nuclei and membrane lipid or cholesterol 2H and 31P nuclei. Specific 13CO labeling is used to enable unambiguous assignment and 2H labeling covers a small region of the lipid or cholesterol molecule. The 13CO–31P and 13CO–2H REDOR respectively probe proximity to the membrane headgroup region and proximity to specific insertion depths within the membrane hydrocarbon core. One strength of the REDOR approach is use of chemically-native proteins and membrane components. The conventional REDOR pulse sequence with 100kHz 2H π pulses is robust with respect to the 2H quadrupolar anisotropy. The 2H T1’s are comparable to the longer dephasing times (τ’s) and this leads to exponential rather than sigmoidal REDOR buildups. The 13CO–2H buildups are well-fitted to A×(1−e−γτ) where A and γ are fitting parameters that are correlated as the fraction of molecules (A) with effective 13CO–2H coupling d=3γ/2. The REDOR approach is applied to probe the membrane locations of the “fusion peptide” regions of the HIV gp41 and influenza virus hemagglutinin proteins which both catalyze joining of the viral and host cell membranes during initial infection of the cell. The HIV fusion peptide forms an intermolecular antiparallel β sheet and the REDOR data support major deeply-inserted and minor shallowly-inserted molecular populations. A significant fraction of the influenza fusion peptide molecules form a tight hairpin with antiparallel N- and C-α helices and the REDOR data support a single peptide population with a deeply-inserted N-helix. The shared feature of deep insertion of the β and α fusion peptide structures may be relevant for fusion catalysis via the resultant local perturbation of the membrane bilayer. Future applications of the REDOR approach may include samples that contain cell membrane extracts and use of lower temperatures and dynamic nuclear polarization to reduce data acquisition times.

Multiple locations of peptides in the hydrocarbon core of gel-phase membranes revealed by peptide (13)C to lipid (2)H rotational-echo double-resonance solid-state nuclear magnetic resonance.

Membrane locations of peptides and proteins are often critical to their functions. Solid-state rotational-echo double-resonance (REDOR) nuclear magnetic resonance is applied to probe the locations of two peptides via peptide 13CO to lipid 2H distance measurements. The peptides are KALP, an α-helical membrane-spanning peptide, and HFP, the β-sheet N-terminal fusion peptide of the HIV gp41 fusion protein that plays an important role in HIV–host cell membrane fusion. Both peptides are shown to have at least two distinct locations within the hydrocarbon core of gel-phase membranes. The multiple locations are attributed to snorkeling of lysine side chains for KALP and to the distribution of antiparallel β-sheet registries for HFP. The relative population of each location is also quantitated. To the best of our knowledge, this is the first clear experimental support of multiple peptide locations within the membrane hydrocarbon core. These data are for gel-phase membranes, but the approach should work for liquid-ordered membranes containing cholesterol and may be applicable to liquid-disordered membranes with appropriate additional analysis to take into account protein and lipid motion. This paper also describes the methodological development of 13CO–2H REDOR using the lyophilized I4 peptide that is α-helical and 13CO-labeled at A9 and 2Hα-labeled at A8. The I4 spins are well-approximated as an ensemble of isolated 13CO–2H spin pairs each separated by 5.0 Å with a 37 Hz dipolar coupling. A pulse sequence with rectangular 100 kHz 2H π pulses results in rapid and extensive buildup of REDOR (ΔS/S0) with a dephasing time (τ). The buildup is well-fit by a simple exponential function with a rate of 24 Hz and an extent close to 1. These parameter values reflect nonradiative transitions between the 2H spin states during the dephasing period. Each spin pair spends approximately two-thirds of its time in the 13CO–2H (m = ±1) states and approximately one-third of its time in the 13CO–2H (m = 0) state and contributes to the ΔS/S0 buildup during the former but not the latter time segments.

Studies on Lactoferricin-derived Escherichia coli Membrane-active Peptides Reveal Differences in the Mechanism of N-Acylated Versus Nonacylated Peptides

To improve the low antimicrobial activity of LF11, an 11-mer peptide derived from human lactoferricin, mutant sequences were designed based on the defined structure of LF11 in the lipidic environment. Thus, deletion of noncharged polar residues and strengthening of the hydrophobic N-terminal part upon adding a bulky hydrophobic amino acid or N-acylation resulted in enhanced antimicrobial activity against Escherichia coli, which correlated with the peptides' degree of perturbation of bacterial membrane mimics. Nonacylated and N-acylated peptides exhibited different effects at a molecular level. Nonacylated peptides induced segregation of peptide-enriched and peptide-poor lipid domains in negatively charged bilayers, although N-acylated peptides formed small heterogeneous domains resulting in a higher degree of packing defects. Additionally, only N-acylated peptides perturbed the lateral packing of neutral lipids and exhibited increased permeability of E. coli lipid vesicles. The latter did not correlate with the extent of improvement of the antimicrobial activity, which could be explained by the fact that elevated binding of N-acylated peptides to lipopolysaccharides of the outer membrane of gram-negative bacteria seems to counteract the elevated membrane permeabilization, reflected in the respective minimal inhibitory concentration for E. coli. The antimicrobial activity of the peptides correlated with an increase of membrane curvature stress and hence bilayer instability. Transmission electron microscopy revealed that only the N-acylated peptides induced tubular protrusions from the outer membrane, whereas all peptides caused detachment of the outer and inner membrane of E. coli bacteria. Viability tests demonstrated that these bacteria were dead before onset of visible cell lysis.

Inhibition of phospholipase A2 in rat brain modifies different membrane fluidity parameters in opposite ways

Fluidity is an important neuronal membrane property and it is influenced by the concentration of polyunsaturated fatty acids (PUFAs) in membrane phospholipids. Phospholipase A(2) (PLA(2)) is a key enzyme in membrane phospholipid metabolism, generating free PUFAs. In Alzheimer disease (AD), reduced PLA(2) activity, specifically of calcium-dependent cytosolic PLA(2) (cPLA(2)) and calcium-independent intracellular PLA(2) (iPLA(2)), and phospholipid metabolism was reported in the frontal cortex and hippocampus. This study investigated the effects of in vivo infusion of the dual cPLA(2) and iPLA(2) inhibitor MAFP into rat brain on PLA(2) activity and membrane fluidity parameters in the postmortem frontal cortex and dorsal hippocampus. PLA(2) activity was measured by radioenzymatic assay and membrane fluidity was determined by fluorescence anisotropy technique using three different probes: DPH, TMA-DPH, and pyrene. MAFP significantly inhibited PLA(2) activity, reduced the flexibility of fatty acyl chains (indicated by increased DPH anisotropy), increased the fluidity in the lipid-water interface (indicated by decreased TMA-DPH anisotropy), and increased the lipid lateral diffusion in the hydrocarbon core (represented by pyrene excimer formation) of membranes in both brain areas. The findings suggest that reduced cPLA(2) and iPLA(2) activities in AD brain might contribute to the cognitive impairment, in part, through alterations in membrane fluidity parameters.

Polar Groups in Membrane Channels: Consequences of Replacing Alanines with Serines in Membrane-Spanning Gramicidin Channels

To explore the consequences of burying polar, hydrogen-bonding hydroxyl groups within the hydrocarbon core of lipid bilayer membranes, we examined the structural and functional effects of alanine-to-serine substitutions in bilayer-spanning gramicidin channels. A native Ala was replaced by Ser at position 3 or 5 in the gramicidin A (gA) sequence: formyl-VG(2)A(3)LA(5)VVVWLWLWLW-ethanolamide (d-residues underlined). In the head-to-head dimers that form the conducting, membrane-spanning gA channels, these sequence positions are located near the lipid bilayer center (and subunit interface). The sequence substitutions at positions 3 and 5 were tested within the context of having either Gly or d-Ala at position 2, because d-Ala(2) causes the channel lifetimes to increase 3-fold relative to Gly(2) [Mattice et al. (1995) Biochemistry 34, 6827]. Size-exclusion chromatograms and circular dichroism spectra show that the Ala --> Ser replacements are well tolerated and have little effect on channel structure. In planar bilayers, the Ser-substituted gramicidins form well-defined channels, with cation conductances that are approximately 60% of those of the reference channels. The Ser-substituted channels are structurally equivalent to native gramicidin channels, as demonstrated by the formation of heterodimeric channels between a Ser-containing subunit and a native gramicidin subunit. These hybrid channels exhibit rectification, attributable to asymmetric placement of the single Ser hydroxyl group with respect to the bilayer center. Compared to the corresponding Ala-containing reference channels, the polar Ser residues decrease the analogues' channel-forming potency by 3 orders of magnitude, indicating a substantial energetic penalty ( approximately 15 kJ/mol) for burying the polar Ser side chain in the bilayer hydrophobic core.

Effect of Dipole Modifying Agents on the Surfactin Induced Conductance of Planar Lipid Bilayers

We studied effects of compounds changing membrane dipole potential on membrane conductance induced by antimicrobial lipopeptide surfactin. Surfactin added on both sides of an artificial lipid bilayer from diphytanoyl phosphocholine in 1 M KCl (pH 6.5) produces an increase of the membrane conductance as a result of ion channel formation. Increasing a membrane dipole potential adding RH 421 to the bilayer bathing solution (10 µM , both sides) leads to ∼40 times increase of a steady-state conductance. At the same time, addition of phloretin (20 µM), known to decrease the dipole potential, results in decrease of the surfactin-induced conductance by ∼30 times. We note, that the effects of dipole modifiers on the surfactin-induced membrane conductance are clearly opposite to the effects observed with the same modifiers in case of syringomycin E-induced conductance of lipid bilayers [Ostroumova et al., Langmuir, 2008]. As we suggested earlier, the influence of dipole modifiers on syringomycin activity may be related to a promotion/retardation of a movement of positively charged syringomycin molecules in the direction of membrane hydrocarbon core. In contrast to syringomycin, surfactin is negatively charged. Hence, one can expect an inversion of the effect of dipole modifiers in case of surfactin. The obtained results are in agreement with the model proposed in [Ostroumova et al., Langmuir, 2008].The study was supported in part by the Russian Fund for Basic Research (09-04-48860), the State Program of Molecular and Cell Biology, the grant of St.-Petersburg Administration for young scientists, and the State contract (FAE Π-1372).

Positioning of proteins in membranes: A computational approach

A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene-like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water-soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were approximately 1 A and 2 degrees, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 A depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26 degrees in asymmetric structures. Calculated hydrophobic boundaries of proteins are located approximately 5 A lower than lipid phosphates and correspond to the zero membrane depth parameter of spin-labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/.

Active Metabolite of Atorvastatin Inhibits Membrane Cholesterol Domain Formation by an Antioxidant Mechanism

The advanced atherosclerotic lesion is characterized by the formation of microscopic cholesterol crystals that contribute to mechanisms of inflammation and apoptotic cell death. These crystals develop from membrane cholesterol domains, a process that is accelerated under conditions of hyperlipidemia and oxidative stress. In this study, the comparative effects of hydroxymethylglutaryl-CoA (HMG-CoA) reductase inhibitors (statins) on oxidative stress-induced cholesterol domain formation were tested in model membranes containing physiologic levels of cholesterol using small angle x-ray diffraction approaches. In the absence of HMG-CoA reductase, only the atorvastatin active o-hydroxy metabolite (ATM) blocked membrane cholesterol domain formation as a function of oxidative stress. This effect of ATM is attributed to electron donation and proton stabilization mechanisms associated with its phenoxy group located in the membrane hydrocarbon core. ATM inhibited lipid peroxidation in human low density lipoprotein and phospholipid vesicles in a dose-dependent manner, unlike its parent and other statins (pravastatin, rosuvastatin, simvastatin). These findings indicate an atheroprotective effect of ATM on membrane lipid organization through a potent antioxidant mechanism.

Scanning the Membrane-bound Conformation of Helix 1 in the Colicin E1 Channel Domain by Site-directed Fluorescence Labeling

Helix 1 of the membrane-associated closed state of the colicin E1 channel domain was studied by site-directed fluorescence labeling where bimane was covalently attached to a single cysteine residue in each mutant protein. A number of fluorescence properties of the tethered bimane fluorophore were measured in the membrane-bound state of the channel domain, including fluorescence emission maximum, fluorescence quantum yield, fluorescence anisotropy, membrane bilayer penetration depth, surface accessibility, and apparent polarity. The data show that helix 1 is an amphipathic alpha-helix that is situated parallel to the membrane surface. A least squares fit of the various data sets to a harmonic function indicated that the periodicity and angular frequency for helix 1 are typical for an amphipathic alpha-helix (3.7 +/- 0.1 residues per turn and 97 +/- 3.0 degrees, respectively) that is partially bathing into the membrane bilayer. Dual fluorescence quencher analysis also revealed that helix 1 is peripherally membrane-associated, with one face of the helix dipping into the lipid bilayer and the other face projecting toward the solvent. Finally, our data suggest that the helical boundaries of helix 1, at least at the C-terminal region, remain unaffected upon binding to the surface of the membrane in support of a toroidal pore model for this colicin.

Interface connections of a transmembrane voltage sensor

Voltage-sensitive ion channels open and close in response to changes in transmembrane (TM) potential caused by the motion of the S4 voltage sensors. These sensors are alpha-helices that include four or more positively charged amino acids, most commonly arginine. The so-called paddle model, based on the high-resolution structure of the KvAP K+ channel [Jiang, et al. (2003) Nature 423, 33-41], posits that the S4 sensors move within the membrane bilayer in response to TM voltage changes. Direct exposure of S4 sensors to lipid is contrary to the classical expectation that the dielectric contrast between the membrane hydrocarbon core and water presents an insurmountable energetic penalty to burial of electric charges. Nevertheless, recent experiments have shown that a helix with the sequence of KvAP S4 can be inserted across the endoplasmic reticulum membrane. To reconcile this result with the classical energetics argument, we have carried out a molecular dynamics simulation of an isolated TM S4 helix in a lipid bilayer. The simulation reveals a stabilizing hydrogen-bonded network of water and lipid phosphates around the arginines that reduces the effective thickness of the bilayer hydrocarbon core to approximately 10 A in the vicinity of the helix. It suggests that bilayer phospholipids can adapt locally to strongly perturbing protein elements, causing the phospholipids to become a structural extension of the protein.

Age- and sex-dependent effects of ethanol on hippocampal hemicholinium-3 sensitive choline carriers during postnatal development of rats.

Vulnerability of hippocampal hemicholinium-3 (HC-3)-sensitive carriers to ethanol was evaluated in vitro during rat postnatal development. The high-affinity uptake of [3H]choline (HACU) and the specific binding of [3H]HC-3 were measured on synaptosomes from 7-, 14-, and 60-day-and 3-month-old male and female Wistar rats. Marked increases of basal (between 7 and 60 days of age) and of stimulated HACU levels via K(+)-depolarization (between 14 days and 3 months) but only a mild elevation in [3H]HC-3 binding (between 7 days and 3 months) associated with alterations in the binding site number were found. On the mature tissue, ethanol at high concentrations (5%) moderately inhibited the choline transport under basal conditions but totally eliminated depolarization effects. However, both age- and sex-dependent alterations in basal HACU mediated by high or low pharmacologically relevant alcohol concentrations (50-100 mM) were observed in the immature tissue. Namely, the dose- and incubation time-dependent inhibition of HACU associated with changes in the transport velocity was found in postnatal male but not female tissue. [3H]HC-3 binding site was not markedly sensitive to ethanol actions. Anisotropy measurements in the region of the hydrophilic heads of phospholipid bilayers and in the membrane hydrocarbon core indicated penetration of 100 mM ethanol to immature female but not male tissue. Our results suggest the noncompetitive binding of alcohol to choline carriers from immature male tissue and correspond with data reporting significant sexual dimorphism of postnatal hippocampal neurons. The direct effects of ethanol on male choline carriers can contribute to the inhibition of acetylcholine synthesis and to sex-dependent neurotoxic effects of alcohol applied in vivo during early and late postnatal period.