A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2

Phosphoinositides like phosphatidylinositol 4,5-bisphosphate (PIP₂) are negatively charged lipids that play a pivotal role in membrane trafficking, signal transduction, and protein anchoring. We have designed a force field for the PIP₂ headgroup using quantum mechanical methods and characterized its properties inside a lipid bilayer using molecular dynamics simulations. Macroscopic properties such as area/headgroup, density profiles, and lipid order parameters calculated from these simulations agree well with the experimental values. However, microscopically, the PIP₂ introduces a local perturbation of the lipid bilayer. The average PIP₂ headgroup orientation of 45° relative to the bilayer normal induces a unique, distance-dependent organization of the lipids that surround PIP₂. The headgroups of these lipids preferentially orient closer to the bilayer normal. This perturbation creates a PIP₂ lipid microdomain with the neighboring lipids. We propose that the PIP₂ lipid microdomain enables the PIP₂ to function as a membrane-bound anchoring molecule.     

Lipid Membrane Structure and Dynamics Studied by All-Atom Molecular Dynamics Simulations of Hydrated Phospholipid Bilayers

Abstract

The structure and dynamics of phosphatidylcholine bilayers are examined by reviewing the results of several nanoseconds of molecular dynamics simulations on a number of bilayer and monolayer models. The lengths of these simulations, the longest single one of which was 2 nanoseconds, were sufficiently long to effectively sample many of the longer-scale motions governing the behaviour of biomembranes. These simulations reproduce many experimental observables well and provide a degree of resolution currently unavailable experimentally.     

Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin

The Escherichia coli UraA H⁺-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a “proton trap” that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane.     

Analysis of Sub-τc and Supra-τc Motions in Protein Gβ1 Using Molecular Dynamics Simulations

The functions of proteins depend on the dynamical behavior of their native states on a wide range of timescales. To investigate these dynamics in the case of the small protein Gβ1, we analyzed molecular dynamics simulations with the model-free approach of nuclear magnetic relaxation. We found amplitudes of fast timescale motions (sub-τ_c, where τ_c is the rotational correlation time) consistent with S² obtained from spin relaxation measurements as well as amplitudes of slow timescale motions (supra-τ_c) in quantitative agreement with S² order parameters derived from residual dipolar coupling measurements. The slow timescale motions are associated with the large variations of the ³J couplings that follow transitions between different conformational substates. These results provide further characterization of the large structural fluctuations in the native states of proteins that occur on timescales longer than the rotational correlation time.     

Coupling exo- and endocytosis: An essential role for PIP2 at the synapse

Chemical synapses are specialist points of contact between two neurons, where information transfer takes place. Communication occurs through the release of neurotransmitter substances from small synaptic vesicles in the presynaptic terminal, which fuse with the presynaptic plasma membrane in response to neuronal stimulation. However, as neurons in the central nervous system typically only possess ~ 200 vesicles, high levels of release would quickly lead to a depletion in the number of vesicles, as well as leading to an increase in the area of the presynaptic plasma membrane (and possible misalignment with postsynaptic structures). Hence, synaptic vesicle fusion is tightly coupled to a local recycling of synaptic vesicles. For a long time, however, the exact molecular mechanisms coupling fusion and subsequent recycling remained unclear. Recent work now indicates a unique role for the plasma membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP₂), acting together with the vesicular protein synaptotagmin, in coupling these two processes. In this work, we review the evidence for such a mechanism and discuss both the possible advantages and disadvantages for vesicle recycling (and hence signal transduction) in the nervous system. This article is part of a Special Issue entitled Lipids and Vesicular Transport.     

Regulation of sperm motility by PIP2(4,5) and actin polymerization

Actin polymerization and development of hyperactivated (HA) motility are two processes that take place during sperm capacitation. In previous studies, we demonstrated that the increase in F-actin during capacitation depends upon inactivation of the actin severing protein, gelsolin, by its binding to phosphatydilinositol-4, 5-bisphosphate (PIP₂). Here, we showed for the first time the involvement of PIP₂/gelsolin in human sperm motility before and during capacitation. Activation of gelsolin by causing its release from PIP₂ inhibited sperm motility, which could be restored by adding PIP₂ to the cells. Reduction of PIP₂ synthesis inhibited actin polymerization and motility, and increasing PIP₂ synthesis enhanced these activities. Furthermore, sperm demonstrating low motility contained low levels of PIP₂ and F-actin. During capacitation there was an increase in PIP₂ and F-actin levels in the sperm head and a decrease in the tail. In sperm with high motility, gelsolin was mainly localized to the sperm head before capacitation, whereas in low motility sperm, most of the gelsolin was localized to the tail before capacitation and translocated to the head during capacitation. We also showed that phosphorylation of gelsolin on tyrosine-438 depends on its binding to PIP₂. Activation of phospholipase C by Ca²⁺-ionophore or by activating the epidermal-growth-factor-receptor inhibits tyrosine phosphorylation of gelsolin. In conclusion, the data indicate that the increase of PIP₂ and/or F-actin in the head during capacitation enhances gelsolin translocation to the head. As a result the decrease of gelsolin in the tail allows keeping high level of F-actin in the tail, which is essential for the development of HA motility.     

Determination of prostaglandin F2α, E2, D2 and 6-keto-F1α in human cerebrospinal fluid

Prostaglandin (PG)F_2α, E₂, D₂ and 6-keto-F_1α were determined in human cerebrospinal fluid by a mass spectrometric technique. The samples were obtained from 12 patients with suspected intracranial disease. A 64 fold variation in PG levels was observed. The major PG was 6-keto-F_1α (0.12–15 ng/ml). PGF_2α and PGE₂ were present in lower concentrations PGD₂ was below the level of detection (0.05 ng/ml) except in one patient with extremely high total levels of PGs.     

大气CO2与O3浓度升高对毛竹叶片膜脂过氧化和抗氧化系统的影响

以盆栽一年生毛竹为材料,利用开顶式气室模拟大气O3和CO2浓度升高情景,分析毛竹叶片细胞膜脂过氧化、抗氧化酶(SOD、CAT、POD和APX)活性和渗透调节物质(可溶性糖和可溶性蛋白)含量的响应规律,为气候变化背景下的竹林适应性管理提供理论支撑.结果表明:(1)短期(30 d)高浓度O3(92～106 nL-L-1)胁迫能刺激毛竹叶片抗氧化酶活性和渗透调节物质含量显著提高,清除活性氧能力增强,并未出现细胞膜脂过氧化现象,即毛竹对短期高浓度O3具有较强的适应性;但长期(90 d)O3胁迫条件下,毛竹叶片抗氧化酶活性显著降低,叶片细胞膜脂过氧化程度加剧,膜结构破坏,发生严重的氧化伤害.(2)短期高浓度CO2(685～730 μmol·mol-1)处理总体上对毛竹叶片细胞膜脂过氧化和抗氧化酶系统活性影响并不明显;而长期高浓度CO2处理能一定程度上增强毛竹的抗氧化能力和渗透调节功能,减轻氧化损伤,体现了对毛竹的保护效应.(3)高浓度O3和CO2复合作用下,相对于单一高浓度O3胁迫,毛竹叶片能够维持较高的抗氧化酶活性和渗透调节物质含量,有效地调节活性氧产生与清除间的平衡,细胞膜脂过氧化程度变化不明显,说明高浓度CO2可在一定程度上缓解高浓度O3对毛竹所造成的生理伤害.     

Molecular Dynamics Simulations of the Rotary Motor F0 under External Electric Fields across the Membrane

The membrane-bound component F₀, which is a major component of the F₀F₁-ATP synthase, works as a rotary motor and plays a central role in driving the F₁ component to transform chemiosmotic energy into ATP synthesis. We conducted molecular dynamics simulations of b₂-free F₀ in a 1-palmitoyl-2-oleoyl-phosphatidylcholine lipid bilayer for tens of nanoseconds with two different protonation states of the cAsp-61 residue at the interface of the a-c complex in the absence of electric fields and under electric fields of ±0.03 V/nm across the membrane. To our surprise, we observed that the upper half of the N-terminal helix of the c₁ subunit rotated about its axis clockwise by 30°. An energetic analysis revealed that the electrostatic repulsion between this N-terminal helix and subunit c₁₂ was a major contributor to the observed rotation. A correlation map analysis indicated that the correlated motions of residues in the interface of the a-c complex were significantly reduced by external electric fields. The deuterium order parameter (S_CD) profile calculated by averaging all the lipids in the F₀-bound bilayer was not very different from that of the pure bilayer system, in agreement with recent ²H solid-state NMR experiments. However, by delineating the lipid properties according to their vicinity to F₀, we found that the S_CD profiles of different lipid shells were prominently different. Lipids close to F₀ formed a more ordered structure. Similarly, the lateral diffusion of lipids on the membrane surface also followed a shell-dependent behavior. The lipids in the proximity of F₀ exhibited very significantly reduced diffusional motion. The numerical value of S_CD was anticorrelated with that of the diffusion coefficient, i.e., the more ordered lipid structures led to slower lipid diffusion. Our findings will help elucidate the dynamics of F₀ depending on the protonation state and electric field, and may also shed some light on the interactions between the motor F₀ and its surrounding lipids under physiological conditions, which could help to rationalize its extraordinary energy conversion efficiency.     

Syntheses and characterization of the W(II) and W(III) N2 complexes, [WCl2(PMe3)3]2N2 and [WCl3(PMe3)2]2N2

Refluxing WCl₄(PMe₃)₃ under a nitrogen atmosphere in the presence of two equivalents of sodium amalgam leads to a reduction to the W(II) complex [cis,mer-WCl₂(PMe₃)₃]₂N₂ (1), which can be converted to [mer,trans-WCl₃(PMe₃)₂]₂N₂ (2) via appropriate oxidation/chlorination. Structural data have been obtained for both complexes, and demonstrate significantly increased steric crowding in 1 due to PMe₃/PMe₃ interactions. The N-N bond distances in the two compounds are similar, at 1.279(4) and 1.243(18) Å, respectively.     

Multiple Molecular Dynamics Simulations of TEM β-Lactamase: Dynamics and Water Binding of the Ω-Loop

The Ω-loop of TEM β-lactamase is involved in substrate recognition and catalysis. Its dynamical properties and interaction with water molecules were investigated by performing multiple molecular dynamics simulations of up to 50 ns. Protein flexibility was assessed by calculating the root mean-square fluctuations and the generalized order parameter, S². The residues in secondary structure elements are highly ordered, whereas loop regions are more flexible, which is in agreement with previous experimental observations. Interestingly, the Ω-loop (residues 161-179) is rigid with order parameters similar to secondary structure elements, with the exception of the tip of the loop (residues 173-177) that has a considerably higher flexibility and performs an opening and closing motion on the 50-ns timescale. The rigidity of the main part of the Ω-loop is mediated by stabilizing and highly conserved water bridges inside a cavity lined by the Ω-loop and residues 65-69 of the protein core. In contrast, the flexible tip of the Ω-loop lacks these interactions. Hydration of the cavity and exchange of the water molecules with the bulk solvent occurs via two pathways: the flexible tip that serves as a door to the cavity, and a temporary water channel involving the side chain of Arg¹⁶⁴.     

Effect of prostaglandins A1, A2, B1, B2, E2 and F2α on human umbilical cord vessels

The effect of six naturally occurring prostaglandins on isolated umbilical arteries and veins has been studied. All six prostaglandins had a constricting effect on the umbilical vessels. On the umbilical artery preparations the potencies in decreasing order were A₂>B₂>F_2α>B₁>E₂>A₁. Prostaglandin B₂ was more potent than PGA₂ on the umbilical vein. Polyphloretin phosphate (PPP) antagonised the constricting effect of all six prostaglandins without altering responses to 5-hydroxytryptamine.     

Crystal structures of MoCl2(O)(O2)(OPMePh2)2 and mixtures of MoCl2(O2)(OPPh3)2 and MoCl2(O)(O2)(OPPh3)2: allylic alcohol isomerization studies using MoCl2(O)(O2)(OPMePh2)2

Adding one equivalent of H₂O₂ to compounds of stoichiometry MoCl₂(O)₂(OPR₃)₂, OPR₃ = OPMePh₂ or OPPh₃, leads to the formation of oxo-peroxo compounds MoCl₂(O)(O₂)(OPR₃)₂. The compound MoCl₂(O)(O₂)(OPMePh₂)₂ crystallized with an unequal disorder, 63%:37%, between the oxo and peroxo ligands, as verified by single-crystal X-ray diffractometry, and can be isolated in reasonable yields. MoCl₂(O)(O₂)(OPPh₃)₂, was not isolated in pure form, co-crystallized with MoCl₂(O)₂(OPPh₃)₂ in two ratios, 18%:82% and 12%:88%, respectively, and did not contain any disorder in the arrangement of the oxo and peroxo groups. These complexes accomplish the isomerization of various allylic alcohols. A mechanism of this reaction has been constructed based on ¹⁸O isotopic studies and involves exchange between the alcohol and metal bonded O atoms.     

Synthesis, structure and properties of TTF-carboxylate bridged paddlewheel dirhodium complexes, Rh2(BuCO2)3(TTFCO2) and Rh2(BuCO2)2(TTFCO2)2

Reaction of tetrathiafulvalene carboxylic acid (TTFCO₂H) with paddlewheel dirhodium complex Rh₂(Bu^tCO₂)₄ yielded TTFCO₂-bridged complexes Rh₂(Bu^tCO₂)₃(TTFCO₂) (1) and cis- and trans-Rh₂(Bu^tCO₂)₂(TTFCO₂)₂ (cis- and trans-2). Their triethylamine adducts [1(NEt₃)₂] and cis-[2(NEt₃)₂] were purified and isolated with chromatographic separation, and characterized with single crystal X-ray analysis. Trans-[2(NEt₃)₂] is not completely separated from a mixture of cis- and trans-[2(NEt₃)₂], but its single crystals were obtained from a solution of the mixture. A three-step quasi-reversible oxidation process was observed for 1 in MeCN. The first two steps correspond to the oxidation of the TTFCO₂ moiety and the last one is the oxidation of the Rh₂ core. The oxidation of cis-2 is observed as a two-step process with very similar E_1/2 values to those of the first two processes for 1. Both 1⁺ and cis-2²⁺ in MeCN at room temperature show isotropic ESR spectra with a g value of 2.008 and a_H = 0.135 mT for two equivalent H atoms and a_H = 0.068 mT for one H atom. The redox and ESR data of cis-2 suggest that the intramolecular interaction between the TTF moieties is very small.     

Effects of intracerebroventricular administration of prostaglandins I2, E2, F2α and indomethacin on blood pressure in the rat

The effects of intraventricularly administered prostaglandins I₂ (PGI2), E₂ (PGE2), F_2α (PGF2α) and indomethacin on systemic blood pressure were investigated in conscious rats. PGI2 (1.25 – 10 g/kg) decreased blood pressure in a dose-related manner, whereas PGE2 (100 – 1000 ng/kg) dose-dependently increased blood pressure. Both PGF2α (0.31 – 20 μg/kg) and indomethacin (0.625 – 40 μg/kg) had no effects on blood pressure. These results indicate that intraventricular injection of PGI2 or PGE2 can induce significant changes in blood pressure, while endogenous prostaglandins synthesized in the brain seem to play a minor role in direct regulation of systemic blood pressure in the rat.     

Prostaglandins and renin release: III. Effects of PGE1, E2 F2α and D2 on renin release from rabbit renal cortical slices

We have investigated the direct effects of prostaglandins E₁, E₂, F_2α and D₂ on renin release from rabbit renal cortical slices. Prostaglandin E₁ (PGE₁) was the most potent stimulant of renin release, while PGE₂ was 20–30 fold less active. PGF_2α was found not to be an inhibitor of renin release as reported by others, but rather a weak agonist. PGD₂ up to a concentration of 10 μg/ml had no activity in this system. That the stimulation of renin release by PGE₁ is a direct effect is supported by the finding that PGE₁-induced release is not blocked by L-propranolol or by Δ^5,8,11,14-eicosatetraynoic acid (ETYA), a prostaglandin synthesis is inhibitor. The fatty acid precursor of PGE₁, Δ^8,11,14-eicosatrienoic acid, also stimulated renin release, an effect which was blocked by ETYA. In addition to the above findings, ethanol, a compound frequently used to dissolve prostaglandins, was shown to inhibit renin release.     

Determination of 6-keto-PGF1α, 2,3-dinor-6-keto-PGF1α, thromboxane B2, 2,3-dinor-thromboxane B2, PGE2, PGD2 and PGF2α in human urine by gas chromatography—negative ion chemical ionization mass spectrometry

A method for quantification of 6-keto-PGF_1α, 2,3-dinor-6-keto-PGF_1α, TXB₂, 2,3-dinor TXB₂, PGE₂, PGD₂ and PGF_2α in human urine samples, using gas chromatography—negative ion chemical ionization mass spectrometry, is described. Deuterated analogues were used as internal standards. Methoximation was carried out in urine samples which were subsequently applied to phenylboronic acid cartridges, reversed-phase cartridges and thin-layer chromatography. The eluents were further derivatized to pentafluorobenzyl ester trimethylsilyl ethers for final quantification by gas chromatography—mass spectrometry. The overall recovery was 77% for tritiated 6-keto-PGF_1α and 55% for tritiated TXB₂. Urinary levels of prostanoids were determined in a group of six volunteers before and after intake of the thromboxane synthase inhibitor Ridogrel, and related to creatinine clearance.     

Solution-mediated syntheses and characterizations of two new zincophosphites [C6H14N2]0.5[Zn(H2PO3)2] and [C4H12N2]0.5[(CH3)2NH2][Zn2(HPO3)3]

Two new zincophosphites [C₆H₁₄N₂]_0.5[Zn(H₂PO₃)₂] 1 and [C₄H₁₂N₂]_0.5[(CH₃)₂NH₂][Zn₂(HPO₃)₃] 2 have been solvothermally synthesized in mixed solvents of N,N-dimethylformamide (DMF) and 1,4-dioxane (DOA), respectively. Single-crystal X-ray diffraction analysis reveals that compound 1 exhibits a neutral inorganic chain formed by ZnO₄ and HPO₂(OH) units. Interestingly, the left- and right-handed hydrogen-bonded helical chains are alternately formed via the hydrogen-bonds between two adjacent chains. Compound 2 exhibits a layer structure with 4- and 12-MRs formed by ZnO₄ and HPO₃ units, in which two kinds of organic amine molecules both act as countercations to compensate the overall negative electrostatic charge of the anionic network.     

Surface lipid composition of C3 and C4 plants

The characteristic surface lipid compositions of several C₃ and C₄ plants are discussed. C₄ plants produce surface lipids (epicuticular waxes) made up of the ubiquitous classes of aliphatic compounds: free fatty acids, aldehydes, primary alcohols, alkanes and aliphatic linear esters. C₃ plants synthesize surface lipids comprising the ubiquitous classes and either of the two following groups of compound: (i) lβ-diketones, hydroxy lβ-diketones, alkan-2-ol esters; (il) ketones and secondary alcohols with the functional group in the middle of the hydrocarbon chain. These features are suggested to represent physioIogical characteristics of the plant and to be related to ecological adaptations. Wax class compositions might also be an ancillary method for defining the C₃ or C₄ mechanism of CO₂ assimilation in cases where uncertainty exists.     

Synthesis and characterization of SrCu2(O2CR)3(bdmap)3 and Bi2(O2CCH3)4(bdmap)2(H2O) (R = CH3, CF3; bdmap = 1,3-bis(dimethylamino)-2-propanolato)

New mixed metal complexes SrCu₂(O₂CR)₃(bdmap)₃ (R = CF₃ (1a), CH₃ (1b)) and a new dinuclear bismuth complex Bi₂(O₂CCH₃)₄(bdmap)₂(H₂O) (2) have been synthesized. Their crystal structures have been determined by single-crystal X-ray diffraction analyses. Thermal decomposition behaviors of these complexes have been examined by TGA and X-ray powder diffraction analyses. While compound 1a decomposes to SrF₂ and CuO at about 380°C, compound 1b decomposes to the corresponding oxides above 800°C. Compound 2 decomposes cleanly to Bi₂O₃ at 330°C. The magnetism of 1a was examined by the measurement of susceptibility from 5–300 K. Theoretical fitting for the susceptibility data revealed that 1a is an antiferromagnetically coupled system with g = 2.012(7), −2J = 34.0(8) cm⁻¹. Crystal data for 1a: C₂₇H₅₁N₆O₉F₉Cu₂Sr/THF, monoclinic space group P2₁/m, A = 10.708(6), B = 15.20(1), C = 15.404(7) Å, β = 107.94(4)°, V = 2386(2) ų, Z = 2; for 1b: C₂₇H₆₀N₆O₉Cu₂Sr/THF, orthorhombic space group Pbcn, A = 19.164(9), B = 26.829(8), C = 17.240(9) Å, V = 8864(5) ų, Z = 8; for 2: C₂₂H₄₈O₁₁N₄Bi₂, monoclinic space group P2₁/c, A = 17.614(9), B = 10.741(3), C = 18.910(7) Å, β = 109.99(3)°, V = 3362(2) ų, Z = 4.