[Show abstract][Hide abstract] ABSTRACT: The Na+, K+-ATPase is essential for ionic homeostasis in animal cells. The dephospho- enzyme contains Na+ selective inward facing sites whereas the phosphoenzyme contains K+ selective outward facing sites. Under normal physiological conditions, K+ inhibits cytoplasmic Na+ activation of the enzyme. Acetamidinium (Acet+) and formamidinium (Form+) have been shown to permeate the pump through the outward facing sites. Here, we show that these cations, unlike K+, are unable to enter the inward facing sites in the dephosphorylated enzyme. Consistently, the organic cations exhibited little to no antagonism to cytoplasmic Na+ activation. Na+,K+-ATPase structures revealed a previously undescribed rotamer transition of the hydroxymethyl side chain of the absolutely conserved Thr772 of the α-subunit. The side chain contributes its hydroxyl to Na+ in site I in the E1 form and rotates to contribute its methyl group toward K+ in the E2 form. Molecular dynamics simulations to the E1.AlF4-.ADP.3Na+ structure indicated
Journal of Biological Chemistry 12/2014; · 4.60 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Globotriaosylceramide (Gb3 ) is a glycosphingolipid present in the plasma membrane that is the natural receptor of the bacterial Shiga toxin. The unsaturation level of Gb3 acyl chains has a drastic impact on lipid bilayer properties and phase behaviour, and on many Gb3-related cellular processes. For example: the Shiga toxin B subunit forms tubular invaginations in the presence of Gb3 with an unsaturated acyl chain (U-Gb3 ) while in the presence of Gb3 with a saturated acyl chain (S-Gb3 ) such invagination does not occur. We have used all-atom molecular dynamics simulations to investigate the effects of the Gb3 concentration and its acyl chain saturation on the phase behaviour of a mixed bilayer of dioleoylphosphatidylcholine and Gb3 . The simulation results show that: 1) The Gb3 acyl chains (longer tails) from one leaflet interdigitate into the opposing leaflet and lead to significant bilayer rigidification and immobilisation of the lipid tails. S-Gb3 can form a highly ordered, relatively immobile phase which is resistant to bending while these changes for U-Gb3 are not significant. 2) At low concentrations of Gb3 , U-Gb3 and S-Gb3 have a similar impact on the bilayer reminiscent of the effect of sphingomyelin lipids and 3) At higher Gb3 concentrations, U-Gb3 mixes better with dioleoylphosphatidylcholine than S-Gb3 . Our simulations also provide the first molecular level structural model of Gb3 in membranes.
[Show abstract][Hide abstract] ABSTRACT: Cholesteryl esters (CEs) are a form of cholesterol (CHOL) storage in the living cells, as opposed to free CHOL. CEs are major constituents of low density lipoprotein particles. Therefore, CEs are implicated in provoking atherosclerosis. Arranged into cytoplasmic lipid droplets (LDs), CEs are stored intracellularly. They can also be transported extracellularly by means of lipoproteins. In this work, large-scale molecular dynamics (MD) simulations are used to characterize molecular structure of LDs containing various fractions (10-50 mol%) of cholesteryl oleate (CO) with respect to triolein (TO) fraction. The simulated LDs were covered by a phospholipid monolayer formed by a mixture of POPC (75 mol%) and POPE (25 mol%) molecules. We report that most CO molecules are located within the hydrophobic core of LDs, whereas a small fraction (0.3-1.9 mol%) penetrates the monolayer. The solubility of CO in the phospholipid monolayer is relatively small. Due to a good miscibility with TO molecules, CO forms a liquid phase inside LD at 333 K. There is long-range order in the liquid TO-CO droplet core up to 8 nm from the phospholipid interface, resulting from the structuring of hydrophilic groups. This structuring slowly decays in the direction towards the LD center-of-mass. No sorting of TO and CO is detected, irrespective of the molar fractions simulated. The distribution of CO within the LDs is significant in determining the rate of their hydrolysis by surface-bound enzyme lipases, and thus has a subsequent impact on the levels of CO in plasma and LDLs.
The Journal of Physical Chemistry B 09/2014; · 3.38 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Lipid droplets (LDs) are primary repositories of esterified fatty acids and sterols in animal cells. These organelles originate on the lumenal or cytoplasmic side of endoplasmic reticulum (ER) membrane and are released to the cytosol. In contrast to other intracellular organelles, LDs are composed of a mass of hydrophobic lipid esters coved by phospholipid monolayer. The small size and unique architecture of LDs makes it complicated to study LD structure by modern experimental methods. We discuss coarse-grained molecular dynamics (MD) simulations of LD formation in systems containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), triolein (TO), cholesterol (CHOL), and water. We find that (1) there is more cholesterol in the LD core, than at the interface. (2) No crystallization occurs inside the LD core. (3) According to coarse-grained simulations, the presence of PE lipids at the interface has a little impact on distribution of components and on the overall LD structure . (4) The thickness of the lipid monolayer at the surface of the droplet is similar to the thickness of one leaflet of a bilayer. Computer simulations are shown to be a mighty tool to provide molecular-level insights, which are not available to the experimental techniques.
The Journal of Physical Chemistry B 08/2014; · 3.38 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Ladderanes, which are multiple fused cyclobutane rings, are unique structures available only in nature. Anammox bacteria produce ladderane phospholipids during their life cycle, but the synthesis mechanism still remains a mystery. The function of ladderane lipids in the membrane is unclear as well. According to previous speculations, ladderane moieties of the bilayer might decrease permeability for certain molecules, which should not diffuse out of the compartment enclosed by the ladderane-containing membrane. We report the first atomistic-precision molecular dynamics simulations of bilayers containing ladderane lipids. The structural and thermodynamics differences among (1) pure ladderane containing bilayer, (2) POPC bilayer, and (3) their equimolar mixture are discussed. Potentials of mean force are reported for the translocation of a hydrazine molecule through all investigated bilayers. All bilayers offer a potential energy barrier to hydrazine. Contrary to expectations, the presence of the ladderane lipids somewhat lowers the barrier for translocation of hydrazine. We conclude that the presence of ladderane phospholipids in anammox bacteria does not serve as a barrier to hydrazine. It may serve as a barrier to larger and noxious intermediates in the anammox reaction, or, the true mission of ladderane lipids must be located in a different plane.
Chemistry and Physics of Lipids 04/2014; · 2.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Thioridazine is a well-known dopamine-antagonist drug with a wide range of pharmacological properties ranging from neuroleptic to antimicrobial and even anticancer activity. Thioridazine is a critical component of a promising multi-drug therapy against M. tuberculosis. Amongst the various proposed mechanisms of action, the cell membrane-mediated one is peculiarly tempting due to the distinctive feature of phenothiazine drug family to accumulate in selected body tissues. In this study, we employ long-scale molecular dynamics simulations to investigate the interactions of three different concentrations of thioridazine with zwitterionic and negatively charged model lipid membranes. Thioridazine partitions into the interfacial region of membranes and modifies their structural and dynamic properties, however dissimilarly so at the highest membrane-occurring concentration, that appears to be obtainable only for the negatively charged bilayer. We show that the origin of such changes is the drug induced decrease of the interfacial tension, which ultimately leads to the significant membrane expansion. Our findings support the hypothesis that the phenothiazines therapeutic activity may arise from the drug-membrane interactions, and reinforce the wider, emerging view of action of many small, bioactive compounds.
Journal of Computer-Aided Molecular Design 03/2014; · 3.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We claim that (1) cholesterol protects bilayers from disruption caused by lipid oxidation by sequestering conical shaped oxidized lipid species such as 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PZPC) away from phospholipid, because cholesterol and the oxidized lipid have complementary shapes and (2) mixtures of cholesterol and oxidized lipids can self-assemble into bilayers much like lysolipid–cholesterol mixtures. The evidence for bilayer protection comes from molecular dynamics (MD) simulations and dynamic light scattering (DLS) measurements. Unimodal size distributions of extruded vesicles (LUVETs) made up of a mixture of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and PZPC containing high amounts of PZPC are only obtained when cholesterol is present in high concentrations. In simulations, bilayers containing high amounts of PZPC become porous, unless cholesterol is also present. The protective effect of cholesterol on oxidized lipids has been observed previously using electron paramagnetic resonance (EPR) and electron microscopy imaging of vesicles. The evidence for the pairing of cholesterol and PZPC comes mainly from correlated 2-D density and thickness plots from simulations, which show that these two molecules co-localize in bilayers. Further evidence that the two molecules can cohabitate comes from self-assembly simulations, where we show that cholesterol-oxidized lipid mixtures can form lamellar phases at specific concentrations, reminiscent of lysolipid–cholesterol mixtures. The additivity of the packing parameters of cholesterol and PZPC explains their cohabitation in a planar bilayer. Oxidized lipids are ubiquitously present in significant amounts in high- and low-density lipoprotein (HDL and LDL) particles, diseased tissues, and in model phospholipid mixtures containing polyunsaturated lipids. Therefore, our hypothesis has important consequences for cellular cholesterol trafficking; diseases related to oxidized lipids, and to biophysical studies of phase behaviour of cholesterol-containing phospholipid mixtures.
[Show abstract][Hide abstract] ABSTRACT: Mutations within ion transporting proteins may severely affect their ability to properly traffic ions and thus perturb the delicate balance of ion gradients. Somatic gain-of-function mutations of the Na+, K+-ATPase α1-subunit have been found in aldosterone-producing adenomas that are amongst the causes of hypertension. We use Molecular Dynamics simulations to investigate structural consequences of these mutations, namely Leu97 substitution by Arg (L97R), Val325 substitution by Gly (V325G), deletion of 93-97 residues (Del93-97) and deletion-substitution of 953-956 residues by Ser (EETA956S) that show inward leak currents under physiological conditions. First three mutations affect the structural context of the key ion binding residue Glu327 at binding site II, which leads to the loss of the ability to correctly bind ions and to occlude the pump. The mutated residue in L97K is more hydrated, which ultimately leads to the observed proton leak. V325G mimics the structural behavior of Leu97, however it does not promote the hydration of surrounding residues. In Del93-97, a broader opening is observed due to the rearrangement of the kinked trans-membrane helix 1, M1, which may explain the sodium leak measured with the mutant. The last mutant, EETA956S, opens an additional water pathway near the C-terminus, affecting the III sodium-specific binding site. The results are in excellent agreement with recent electrophysiology measurements and suggest how three mutations prevent the occlusion of the Na+, K+-ATPase, with a possibility of transforming the pump into a passive ion channel, while the fourth mutation provides an insight into the sodium binding in the E1 state.
[Show abstract][Hide abstract] ABSTRACT: We investigate the effect of an applied electric potential on the mechanics of a coarse grained POPC bilayer under tension. The size and duration of our simulations allow for a detailed and accurate study of the fluctuations. Effects on the fluctuation spectrum, tension, bending rigidity, and bilayer thickness are investigated in detail. In particular, the least square fitting technique is used to calculate the fluctuation spectra. The simulations confirm a recently proposed theory that the effect of an applied electric potential on the membrane will be moderated by the elastic properties of the membrane. In agreement with the theory, we find that the larger the initial tension the larger the effect of the electric potential. Application of the electric potential increases the amplitude of the long wavelength part of the spectrum and the bending rigidity is deduced from the short wavelength fluctuations. The effect of the applied electric potential on the bending rigidity is non-existent within error bars. However, when the membrane is stretched there is a point where the bending rigidity is lowered due to a decrease of the thickness of the membrane. All these effects should prove important for mechanosensitive channels and biomembrane mechanics in general.
The Journal of Chemical Physics 10/2013; 139(16):164902. · 3.12 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The compound 2,6-diisopropylphenol (Propofol, PRF) is widely used for inducing general anesthesia, but the mechanism of PRF action remains relatively poorly understood at the molecular level. This work examines the possibility that a potential mode of action of PRF is to modulate the lipid order in target membranes. The effect on monolayers and bilayers of dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC) was probed using Langmuir monolayer isotherms, differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD). Increasing amounts of PRF in a DPPC monolayer causes a decrease in isothermal compressibility modulus at the phase transition. A partition constant for PRF in DPPC liposomes on the order of K≈1500M(-1) was found, and the partitioning was found to be enthalpy-driven above the melting temperature (Tm). A decrease in Tm with PRF content was found whereas the bilayer melting enthalpy ΔHm remains almost constant. The last finding indicates that PRF incorporates into the membrane at a depth near the phosphatidylcholine headgroup, in agreement with our MD-simulations. The simulations also reveal that PRF partitions into the membrane on a timescale of 0.5 microsecond and has a cholesterol-like ordering effect on DPPC in the fluid phase. The vertical location of the PRF binding site in a bacterial ligand-gated ion channel coincides with the location found in our MD-simulations. Our results suggest that multiple physicochemical mechanisms may determine anesthetic potency of PRF, including effects on proteins that are mediated through the bilayer.
Chemistry and Physics of Lipids 08/2013; · 2.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Several small drugs and medicinal plant extracts such as the Indian spice extract curcumin have a wide range of useful pharmacological properties, which cannot be ascribed to binding to a single protein target alone. The lipid bilayer membrane is thought to mediate the effects of many such molecules directly via the perturbation of the plasma membrane structure and dynamics, or indirectly by modulating trans-membrane protein conformational equilibria. Furthermore, for bioavailability, drugs need to interact with and eventually permeate the lipid bilayer barrier on the surface of cells. Biophysical studies of the interactions of drugs and plant extracts is therefore of interest. Molecular dynamics (MD) simulations, which can access time and length scales not simultaneously accessible by other experimental methods, are often applied to obtain quantitative molecular and thermodynamic descriptions of these interactions, also often with complementary biophysical measurements. In this review, we survey recent MD simulations of small drug-like molecules with membranes, and provide a biophysical description of possible routes of membrane-mediated pharmacological effects of drugs. The review is not exhaustive, and in particular, we use molecules containing aromatic ring-like structures to develop our hypotheses. We also show that some drugs and anesthetics may have an effect on lipid bilayer analogous to cholesterol. This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Products of phospholipid oxidation can produce lipids with a carbonyl moiety at the end of a shortened lipid acyl tail, such as 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine (POVPC). The carbonyl tail of POVPC can covalently bond to the free tertiary amine of a phosphatidylethanolamine lipid in a Schiff base reaction to form a conjugate lipid (SCH) with two head groups, and three acyl tails (Fig. 1). We investigate the conformations and properties of this unique class of adduct lipids using Molecular Dynamics Simulations, and show that their insertion into lipid bilayers of POPC increases the average cross-sectional area per lipid and decreases bilayer thickness. Significant increase in acyl tail fluidity is only observed at 25% SCH concentration. The SCH lipids occupy a larger area per lipid than expected for a lipid with three acyl tails, owing to the interfacial location of the long spacer between the two head groups of the SCH lipids. Schiff base formation of lipids can alter the concentration, homeostasis and localizations of phosphatidylserine and phosphatidylethanol lipids in membranes, and can therefore influence several membrane-associated processes including fusion and budding. The current work provides the first detailed structural model of this unique new class of lipids that may have important roles to play in modulating membrane properties and cell physiology.
Biochimica et Biophysica Acta 04/2013; · 4.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Until recently, construction of bilayers was an exclusive mission of nature. It requires careful choice of compounds, whose delicate interplay between head group attraction and chain repulsion engenders a truly unique balance over a narrow temperature range. We report the investigation of artificial bilayers composed of long-chained organic ions, such as dodecyltrimethylammonium (DMA+) and perfluorooctaonate (PFO–). Various ratios of DMA/PFO surfactants result in bilayers of different stability, thickness, area per molecule, and density profiles. In our quest for water filtration, we incorporated aquaporin protein into the DMA/PFO bilayer but did not observe sufficient stability of the system. We discuss further steps to utilize these surfactant bilayers as highly selective, salt-impermeable membranes.
[Show abstract][Hide abstract] ABSTRACT: The term ‘gastrophysics’ has been proposed to describe an emerging scientific discipline that employs an arsenal of the most powerful theoretical, simulational, and experimental techniques from the physical sciences to study the empirical world of cooking and gastronomy. In the same way that biology has inspired the field of biophysics, gastronomy is the source of inspiration for gastrophysics. In particular, gastrophysics aims at exploiting recent advances in the physical sciences to forward the scientific study of food, the raw materials used, the effects of processing food, and quantitative aspects of the physical basis for food quality, flavor, appreciation, and absorption in the human body. In this study, we focused on questions pertaining to the texture and flavor of a particular type of raw material, namely, the red seaweed, dulse (Palmaria palmata), and demonstrate how a combination of physical chemistry, biophotonics, and atomic-scale molecular simulation might shed some light on these questions, particularly in relation to the physical mechanism of the umami sensation.
[Show abstract][Hide abstract] ABSTRACT: Lipid peroxidation plays a key role in the alteration of cell membrane's properties. Here we used as model systems multilamellar vesicles (MLVs) made of the first two products in the oxidative cascade of linoleoyl lecithin, namely 1-palmitoyl-2-(13-hydroperoxy-9,11-octadecanedienoyl)-lecithin (HpPLPC) and 1-palmitoyl-2-(13-hydroxy-9,11-octadecanedienoyl)-lecithin (OHPLPC), exhibiting a hydroperoxide or a hydroxy group at position 13, respectively. The two oxidized lipids were used either pure or in a 1:1 molar ratio mixture with untreated 1-palmitoyl-2-linoleoyl-lecithin (PLPC). The model membranes were doped with spin-labeled lipids to study bilayer alterations by electron paramagnetic resonance (EPR) spectroscopy. Two different spin-labeled lipids were used, bearing the doxyl ring at position (n) 5 or 16: γ-palmitoyl-β-(n-doxylstearoyl)-lecithin (n-DSPPC) and n-doxylstearic acid (n-DSA). Small changes in the acyl chain order in the sub-polar region and at the methyl-terminal induced by lipid peroxidation were detected by X-band EPR. Concomitantly, the polarity and proticity of the membrane bilayer in those regions were investigated at W band in frozen samples. Analysis of the g(xx) and A(zz) parameters revealed that OHPLPC, but mostly HpPLPC, induced a measurable increase in polarity and H-bonding propensity in the central region of the bilayer. Molecular dynamics simulation performed on 16-DSA in the PLPC-HpPLPC bilayer revealed that water molecules are statistically favored with respect to the hydroperoxide groups to interact with the nitroxide at the methyl-terminal, confirming that the H-bonds experimentally observed are due to increased water penetration in the bilayer. The EPR and MD data on model membranes demonstrate that cell membrane damage by oxidative stress cause alteration of water penetration in the bilayer.
Biochimica et Biophysica Acta 10/2012; · 4.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The fifth taste quality, umami, arises from binding of glutamate to the umami receptor T1R1/T1R3. The umami taste is enhanced several-fold upon addition of free nucleotides such as guanosine-5'-monophosphate (GMP) to glutamate-containing food. GMP may operate via binding to the ligand-binding domain of the T1R1 part of the umami receptor at an allosteric site. Using molecular dynamics simulations, we show that GMP can stabilize the closed (active) state of T1R1 by binding to the outer vestibule of the so-called Venus flytrap domain of the receptor. The transition between the closed and open conformations was accessed in the simulations. Using principal component analysis, we show that the dynamics of the Venus flytrap domain along the hinge-bending motion that activates signaling is dampened significantly upon binding of glutamate, and further slows down upon binding of GMP at an allosteric site, thus suggesting a molecular mechanism of cooperativity between GMP and glutamate.
[Show abstract][Hide abstract] ABSTRACT: Phosphorylation is one of the major mechanisms for posttranscriptional modification of proteins. The addition of a compact, negatively charged moiety to a protein can significantly change its function and localization by affecting its structure and interaction network. We have used all-atom Molecular Dynamics simulations to investigate the structural consequences of phosphorylating the Na(+)/K(+)-ATPase (NKA) residue Ser(936), which is the best characterized phosphorylation site in NKA, targeted in vivo by protein kinase A (PKA). The Molecular Dynamics simulations suggest that Ser(936) phosphorylation opens a C-terminal hydrated pathway leading to Asp(926), a transmembrane residue proposed to form part of the third sodium ion-binding site. Simulations of a S936E mutant form, for which only subtle effects are observed when expressed in Xenopus oocytes and studied with electrophysiology, does not mimic the effects of Ser(936) phosphorylation. The results establish a structural association of Ser(936) with the C terminus of NKA and indicate that phosphorylation of Ser(936) can modulate pumping activity by changing the accessibility to the ion-binding site.
Journal of Biological Chemistry 03/2012; 287(19):15959-65. · 4.60 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacological properties of which arise from its interaction with the lipid bilayer component of the plasma membrane. Prior simulations show that salicylate orders zwitterionic lipid membranes. However, this is in conflict with Raman scattering and vesicle fluctuation analysis data, which suggest the opposite. We show using extensive molecular dynamics simulations, cumulatively >2.5 μs, that salicylic acid indeed disorders membranes with concomitant membrane thinning and that the conflict arose because prior simulations suffered from artifacts related to the sodium-ion induced condensation of zwitterionic lipids modeled by the Berger force field. Perillic acid is a terpenoid plant extract that has antiinfective and anticancer properties, and is extensively used in eastern medicine. We found that perillic acid causes large-scale membrane thinning and could therefore exert its antimicrobial properties via a membrane-lytic mechanism reminiscent of antimicrobial peptides. Being more amphipathic, perillic acid is more potent in disrupting lipid headgroup packing, and significantly modifies headgroup dipole orientation. Like salicylate, the membrane thinning effect of perillic acid is masked by the presence of sodium ions. As an alternative to sodium cations, we advocate the straightforward solution of using larger countercations like potassium or tetra-methyl-ammonium that will maintain electroneutrality but not interact strongly with, and thus not condense, the lipid bilayer.