Biochim. Biophys. Acta [JOURNAL]
Sun
200 papers
Solubility and diffusion of oxygen in phospholipid membranes.
Möller MN, Li Q, Chinnaraj M … +3 more , Cheung HC, Lancaster JR, Denicola A
Biochim Biophys Acta · 2016 Nov · PMID 27614191 · Publisher ↗
The transport of oxygen and other nonelectrolytes across lipid membranes is known to depend on both diffusion and solubility in the bilayer, and to be affected by changes in the physical state and by the lipid compositio...
The transport of oxygen and other nonelectrolytes across lipid membranes is known to depend on both diffusion and solubility in the bilayer, and to be affected by changes in the physical state and by the lipid composition, especially the content of cholesterol and unsaturated fatty acids. However, it is not known how these factors affect diffusion and solubility separately. Herein we measured the partition coefficient of oxygen in liposome membranes of dilauroyl-, dimiristoyl- and dipalmitoylphosphatidylcholine in buffer at different temperatures using the equilibrium-shift method with electrochemical detection. The apparent diffusion coefficient was measured following the fluorescence quenching of 1-pyrenedodecanoate inserted in the liposome bilayers under the same conditions. The partition coefficient varied with the temperature and the physical state of the membrane, from below 1 in the gel state to above 2.8 in the liquid-crystalline state in DMPC and DPPC membranes. The partition coefficient was directly proportional to the partial molar volume and was then associated to the increase in free-volume in the membrane as a function of temperature. The apparent diffusion coefficients were corrected by the partition coefficients and found to be nearly the same, with a null dependence on viscosity and physical state of the membrane, probably because the pyrene is disturbing the surrounding lipids and thus becoming insensitive to changes in membrane viscosity. Combining our results with those of others, it is apparent that both solubility and diffusion increase when increasing the temperature or when comparing a membrane in the gel to one in the fluid state.
Macrophage fatty acid oxidation and its roles in macrophage polarization and fatty acid-induced inflammation.
Namgaladze D, Brüne B
Biochim Biophys Acta · 2016 Nov · PMID 27614008 · Publisher ↗
Recent research considerably changed our knowledge how cellular metabolism affects the immune system. We appreciate that metabolism not only provides energy to immune cells, but also actively influences diverse immune ce...
Recent research considerably changed our knowledge how cellular metabolism affects the immune system. We appreciate that metabolism not only provides energy to immune cells, but also actively influences diverse immune cell phenotypes. Fatty acid metabolism, particularly mitochondrial fatty acid oxidation (FAO) emerges as an important regulator of innate and adaptive immunity. Catabolism of fatty acids also modulates the progression of disease, such as the development of obesity-driven insulin resistance and type II diabetes. Here, we summarize (i) recent developments in research how FAO modulates inflammatory signatures in macrophages in response to saturated fatty acids, and (ii) the role of FAO in regulating anti-inflammatory macrophage polarization. In addition, we define the contribution of AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptors (PPARs), in controlling macrophage biology towards fatty acid metabolism and inflammation.
d-3-Deoxy-dioctanoylphosphatidylinositol induces cytotoxicity in human MCF-7 breast cancer cells via a mechanism that involves downregulation of the D-type cyclin-retinoblastoma pathway.
Gradziel CS, Jordan PA, Jewel D … +4 more , Dufort FJ, Miller SJ, Chiles TC, Roberts MF
Biochim Biophys Acta · 2016 Nov · PMID 27600289 · Full text
Phosphatidylinositol analogs (PIAs) were originally designed to bind competitively to the Akt PH domain and prevent membrane translocation and activation. d-3-Deoxy-dioctanoylphosphatidylinositol (d-3-deoxy-diCPI), but n...
Phosphatidylinositol analogs (PIAs) were originally designed to bind competitively to the Akt PH domain and prevent membrane translocation and activation. d-3-Deoxy-dioctanoylphosphatidylinositol (d-3-deoxy-diCPI), but not compounds with altered inositol stereochemistry (e.g., l-3-deoxy-diCPI and l-3,5-dideoxy-diCPI), is cytotoxic. However, high resolution NMR field cycling relaxometry shows that both cytotoxic and non-toxic PIAs bind to the Akt1 PH domain at the site occupied by the cytotoxic alkylphospholipid perifosine. This suggests that another mechanism for cytotoxicity must account for the difference in efficacy of the synthetic short-chain PIAs. In MCF-7 breast cancer cells, with little constitutively active Akt, d-3-deoxy-diCPI (but not l-compounds) decreases viability concomitant with increased cleavage of PARP and caspase 9, indicative of apoptosis. d-3-Deoxy-diCPI also induces a decrease in endogenous levels of cyclins D1 and D3 and blocks downstream retinoblastoma protein phosphorylation. siRNA-mediated depletion of cyclin D1, but not cyclin D3, reduces MCF-7 cell proliferation. Thus, growth arrest and cytotoxicity induced by the soluble d-3-deoxy-diCPI occur by a mechanism that involves downregulation of the D-type cyclin-pRb pathway independent of its interaction with Akt. This ability to downregulate D-type cyclins contributes, at least in part, to the anti-proliferative activity of d-3-deoxy-diCPI and may be a common feature of other cytotoxic phospholipids.
Oligoubiquitination of tissue factor on Lys255 promotes Ser253-dephosphorylation and terminates TF release.
Ettelaie C, Collier ME, Featherby S … +2 more , Greenman J, Maraveyas A
Biochim Biophys Acta · 2016 Nov · PMID 27599717 · Publisher ↗
Restriction of tissue factor (TF) activity at the cell surface and TF release are critical for prevention of excessive coagulation. This study examined the regulation of TF dephosphorylation and its release through ubiqu...
Restriction of tissue factor (TF) activity at the cell surface and TF release are critical for prevention of excessive coagulation. This study examined the regulation of TF dephosphorylation and its release through ubiquitination. A plasmid containing the sequence to express the tandem protein TF-tGFP was mutated to include an arginine-substitution at Lys255 within TF. MDA-MB-231 cell line, and HCAEC endothelial cells were transfected and subsequently activated with PAR2-agonist peptide. The wild-type and mutant TF-tGFP were immunoprecipitated from the cell lysates and the ubiquitination and phosphorylation state of TF examined. Analysis of the proteins showed that arginine-substitution of Lys255 within TF prevented its ubiquitination while the wild-type TF-tGFP was oligoubiquitinated. The TF-associated oligoubiquitin chain was estimated to contain up to 4 ubiquitin units, with the linkage formed between Lys63 of one ubiquitin unit, and the C-terminus of the next unit. The Lys255→Arg substitution of TF-tGFP prolonged the phosphorylation of Ser253 within TF, compared to the wild-type TF-tGFP, lengthened the presence of TF-tGFP at the cell surface and extended the duration of TF-tGFP release from cells following PAR2 activation. A biotinylated 19-mer peptide corresponding to the C-terminus of TF (TFc) was used as substrate to show that the ubiquitination of TF was mediated by the Ube2D family of E2-enzymes and involved Mdm2. Moreover, double-phosphorylation of TFc was prerequisite for ubiquitination, with subsequent dephosphorylation of Ser253 by phosphatase PP2A. In conclusion, oligoubiquitination of Lys255 within TF permits PP2A to bind and dephosphorylate Ser253 and occurs to terminate TF release and contain its activity.
Aβ-Induced Drp1 phosphorylation through Akt activation promotes excessive mitochondrial fission leading to neuronal apoptosis.
Kim DI, Lee KH, Gabr AA … +4 more , Choi GE, Kim JS, Ko SH, Han HJ
Biochim Biophys Acta · 2016 Nov · PMID 27599716 · Publisher ↗
Mitochondrial dysfunction is known as one of causative factors in Alzheimer's disease (AD), inducing neuronal cell death. Mitochondria regulate their functions through changing their morphology. The present work was unde...
Mitochondrial dysfunction is known as one of causative factors in Alzheimer's disease (AD), inducing neuronal cell death. Mitochondria regulate their functions through changing their morphology. The present work was undertaken to investigate whether Amyloid β (Aβ) affects mitochondrial morphology in neuronal cells to induce apoptosis. Aβ treatment induced not only the fragmentation of mitochondria but also neuronal apoptosis in association with an increase in caspase-9 and -3 activity. Calcium influx induced by Aβ up-regulated the activation of Akt through CaMKII resulting in changes to the phosphorylation level of Drp1 in a time-dependent manner. Translocation of Drp1 from the cytosol to mitochondria was blocked by CB-124005 (an Akt inhibitor). Recruitment of Drp1 to mitochondria led to ROS generation and mitochondrial fission, accompanied by dysfunction of mitochondria such as loss of membrane potential and ATP production. ROS generation and mitochondrial dysfunction by Aβ were attenuated when treated with Mdivi-1, a selective Drp1 inhibitor. Furthermore, the sustained Akt activation induced not only the fragmentation of mitochondria but also the activation of mTOR, eventually suppressing autophagy. Inhibition of autophagic clearance of Aβ led to increased ROS levels and aggravating mitochondrial defects, which were blocked by Rapamycin (an mTOR inhibitor). In conclusion, sustained phosphorylation of Akt by Aβ directly activates Drp1 and inhibits autophagy through the mTOR pathway. Together, these changes elicit abundant mitochondrial fragmentation resulting in ROS-mediated neuronal apoptosis.
Stimulated release and functional activity of surface expressed metalloproteinase ADAM17 in exosomes.
Groth E, Pruessmeyer J, Babendreyer A … +8 more , Schumacher J, Pasqualon T, Dreymueller D, Higashiyama S, Lorenzen I, Grötzinger J, Cataldo D, Ludwig A
Biochim Biophys Acta · 2016 Nov · PMID 27599715 · Publisher ↗
By mediating proteolytic shedding on the cell surface the disintegrin and metalloproteinases ADAM10 and ADAM17 function as critical regulators of growth factors, cytokines and adhesion molecules. We here report that stim...
By mediating proteolytic shedding on the cell surface the disintegrin and metalloproteinases ADAM10 and ADAM17 function as critical regulators of growth factors, cytokines and adhesion molecules. We here report that stimulation of lung epithelial A549 tumor cells with phorbol-12-myristate-13-acetate (PMA) leads to the downregulation of the surface expressed mature form of ADAM17 without affecting ADAM10 expression. This reduction could not be sufficiently explained by metalloproteinase-mediated degradation, dynamin-mediated internalization or microdomain redistribution of ADAM17. Instead, surface downregulation of ADAM17 was correlated with the presence of its mature form in exosomes. Exosomal ADAM17 release was also observed in monocytic and primary endothelial cells where it could be induced by stimulation with lipopolysaccharide. Antibody-mediated surface labelling of ADAM17 revealed that at least part of exosomal ADAM17 was oriented with the metalloproteinase domain outside and had been expressed on the cell surface. Suppression of iRHOM2-mediated ADAM17 maturation prevented surface expression and exosomal release of ADAM17. Further, deletion of the protease's C-terminus or cell treatment with a calcium chelator diminished exosomal release as well as surface downregulation of ADAM17, underlining that both processes are closely associated. Co-incubation of ADAM17 containing exosomes with cells expressing the ADAM17 substrates TGFα or amphiregulin lead to increased shedding of both substrates. This was prevented when exosomes were prepared from cells with shRNA-mediated ADAM17 knockdown. These data indicate that cell stimulation can downregulate expression of mature ADAM17 from the cell surface and induce release of exosomal ADAM17, which can then distribute and contribute to substrate shedding on more distant cells.
Ouabain interactions with the α4 isoform of the sodium pump trigger non-classical steroid hormone signaling and integrin expression in spermatogenic cells.
Upmanyu N, Dietze R, Kirch U … +1 more , Scheiner-Bobis G
Biochim Biophys Acta · 2016 Nov · PMID 27599714 · Publisher ↗
In addition to the ubiquitous α1 isoform of the sodium pump, sperm cells also express a male-specific α4 isoform whose function has been associated with sperm motility, fertility, and capacitation. Here we investigate in...
In addition to the ubiquitous α1 isoform of the sodium pump, sperm cells also express a male-specific α4 isoform whose function has been associated with sperm motility, fertility, and capacitation. Here we investigate in the murine spermatogenic cell line GC-2 interactions of the α4 isoform with the cardiotonic steroid ouabain in signaling cascades involved in the non-classical action of steroid hormones. Exposure of GC-2 cells to low concentrations of ouabain stimulates the phosphorylation of Erk1/2 and of the transcription factors CREB and ATF-1. As a consequence of this signaling cascade, ouabain stimulates on the mRNA level the expression of integrins αv, β3 and α5, whose expression is also modulated by the cAMP response element. Increased expression of integrins αv and β3 is also seen in cultures of seminiferous tubules exposed to 10nM ouabain. At the protein level we observed a significant stimulation of β3 integrin expression by ouabain. Abrogation of α4 isoform expression by siRNA leads to the complete suppression of all ouabain-induced signaling mentioned above, including its stimulatory effect on the expression of β3 integrin. The results presented here demonstrate for the first time the induction of signaling cascades through the interaction of ouabain with the α4 isoform in a germ-cell derived cell line. The novel finding that these interactions lead to increased expression of integrins in GC-2 cells and the confirmation of these results in the ex vivo experiments indicate that hormone/receptor-like interactions of ouabain with the α4 isoform might be of significance for male physiology.
Nonsense mediated RNA decay and evolutionary capacitance.
Raxwal VK, Riha K
Biochim Biophys Acta · 2016 Dec · PMID 27599370 · Publisher ↗
Nonsense mediated RNA decay (NMD) is well-known as an RNA quality control mechanism that sequesters a substantial portion of RNA from expression by targeting it for degradation. However, a number of recent studies across...
Nonsense mediated RNA decay (NMD) is well-known as an RNA quality control mechanism that sequesters a substantial portion of RNA from expression by targeting it for degradation. However, a number of recent studies across a range of organisms indicate a broader role for NMD in gene regulation and transcriptome homeostasis. Here we propose a novel role for NMD as a buffering system with the capability of accumulating and subsequently releasing a wide spectrum of cryptic genetic variation in response to environmental stimuli, and hence facilitating adaptive evolution. We discuss this role for NMD in the context of evolution of plant pathogen defense, whereby NMD may promote rapid diversification of intracellular immune receptors by mitigating the potentially harmful impact of their newly formed variants on plant fitness.
Corrigendum to "Mechanism of voltage-gated channel formation in lipid membranes" [Biochim. Biophys. Acta 1858 (2016) 748-755].
Guidelli R, Becucci L
Biochim Biophys Acta · 2016 Nov · PMID 27598232 · Publisher ↗
Abstract loading — click title to view on PubMed.
Acylation of lysine residues in human plasma high density lipoprotein increases stability and plasma clearance in vivo.
Yang Y, Rosales C, Gillard BK … +2 more , Gotto AM, Pownall HJ
Biochim Biophys Acta · 2016 Nov · PMID 27594697 · Full text
Although human plasma high density lipoproteins (HDL) concentrations negatively correlate with atherosclerotic cardiovascular disease, underlying mechanisms are unknown. Thus, there is continued interest in HDL structure...
Although human plasma high density lipoproteins (HDL) concentrations negatively correlate with atherosclerotic cardiovascular disease, underlying mechanisms are unknown. Thus, there is continued interest in HDL structure and functionality. Numerous plasma factors disrupt HDL structure while inducing the release of lipid free apolipoprotein (apo) AI. Given that HDL is an unstable particle residing in a kinetic trap, we tested whether HDL could be stabilized by acylation with acetyl and hexanoyl anhydrides, giving AcHDL and HexHDL respectively. Lysine analysis with fluorescamine showed that AcHDL and HexHDL respectively contained 11 acetyl and 19 hexanoyl groups. Tests with biological and physicochemical perturbants showed that HexHDL was more stable than HDL to perturbant-induced lipid free apo AI formation. Like the reaction of streptococcal serum opacity factor against HDL, the interaction of HDL with its receptor, scavenger receptor class B member 1 (SR-B1), removes CE from HDL. Thus, we tested and validated the hypothesis that selective uptake of HexHDL-[H]CE by Chinese Hamster Ovary cells expressing SR-B1 is less than that of HDL-[H]CE; thus, selective SR-B1 uptake of HDL-CE depends on HDL instability. However, in mice, plasma clearance, hepatic uptake and sterol secretion into bile were faster from HexHDL-[H]CE than from HDL-[H]CE. Collectively, our data show that acylation increases HDL stability and that the reaction of plasma factors with HDL and SR-B1-mediated uptake are reduced by increased HDL stability. In vivo data suggest that HexHDL promotes charge-dependent reverse cholesterol transport, by a mechanism that increases hepatic sterol uptake via non SR-B1 receptors, thereby increasing bile acid output.
Analysis of amino acid residues in the predicted transmembrane pore influencing transport kinetics of the hepatic drug transporter organic anion transporting polypeptide 1B1 (OATP1B1).
Gruetz M, Sticht H, Glaeser H … +2 more , Fromm MF, König J
Biochim Biophys Acta · 2016 Nov · PMID 27594653 · Publisher ↗
The hepatic uptake transporters OATP1B1 (SLCO1B1) and OATP1B3 (SLCO1B3) mediate the uptake of endogenous metabolites and drugs from blood into hepatocytes. Alterations of transport function are accompanied with variation...
The hepatic uptake transporters OATP1B1 (SLCO1B1) and OATP1B3 (SLCO1B3) mediate the uptake of endogenous metabolites and drugs from blood into hepatocytes. Alterations of transport function are accompanied with variations in drug plasma concentrations and the risk of adverse drug effects. Thus, knowledge on amino acids determining substrate recognition or transport kinetics are important to predict alterations in transport kinetics. Therefore, we analyzed the charged amino acids His54 and Tyr169, both located at the extracellular entry of the predicted transmembrane pore of OATP1B1. Based on a computational analysis we established HEK293 cell lines overexpressing the mutant OATP1B1 proteins HEK-OATP1B1p.H54Q, -p.H54A, -p.Y169H and -p.Y169A and analyzed protein expression, localization and transport kinetics of the four OATP1B1 substrates bromosulfophthalein, estradiaol-17β-glucuronide, taurocholate and pravastatin. Consequences on transport were detected for all mutants and these were different for each amino acid exchange and for each substrate tested. For example, the exchange H54Q resulted in reduced transport for BSP (78% of wildtype OATP1B1 transport at 0.05μM, P<0.01) with reduced affinity to this substrate (K value increases from 0.76μM to 8.04μM) but in stimulated E17βG transport (138% compared to wildtype transport at 10μM, P<0.001). Investigating amino acid exchanges located at the extracellular entry of the transport pore of the OATP1B1 protein we demonstrated that these residues are involved in modulating transport kinetics and this participation strongly depends on the substrate and not on the physicochemical character of the investigated amino acid.
Sex-determining region Y-box 9 acts downstream of NADPH oxidase to influence the effect of leptin on PPARγ1 expression in hepatic stellate cells.
Qiao H, Cao Q, Fu Y … +6 more , Guan W, Cheng F, Wu J, Jia X, Chen H, Zhou Y
Biochim Biophys Acta · 2016 Nov · PMID 27593694 · Publisher ↗
Leptin, an adipocyte-derived hormone, promotes liver fibrogenesis and inhibits the expression of peroxisome-proliferator activated receptor γ (PPARγ), a key transcription factor in inhibition of hepatic stellate cell (HS...
Leptin, an adipocyte-derived hormone, promotes liver fibrogenesis and inhibits the expression of peroxisome-proliferator activated receptor γ (PPARγ), a key transcription factor in inhibition of hepatic stellate cell (HSC) activation, in HSCs. This research aimed to further investigate the mechanisms underlying leptin regulation of PPARγ1 in HSCs in vivo and in vitro. Results demonstrated that sex-determining region Y-box 9 (Sox9) could bind to a site around -2275 within leptin response region of PPARγ1 promoter and inhibited PPARγ1 expression. Sox9 upregulated the expressions of α1(I)collagen and alpha-smooth muscle actin in HSCs. Leptin stimulated Sox9 expression and Sox9 binding to PPARγ1 promoter. The signaling pathways of NADPH oxidase, β-catenin, and delta-like homolog1 (DLK1) mediated leptin upregulation of Sox9 expression. Moreover, there existed crosstalk between NADPH oxidase pathway and β-catenin or DLK1 signaling pathway. Human liver specimens of cirrhosis were shown to be of a large number of the positive HSCs for p47phox (playing a central role in NADPH oxidase activity), 4-hydroxynonenal (a lipid peroxidation product), Sox9, and α-smooth muscle actin whereas PPARγ-positive HSCs were rarely detected. These results might deepen understanding of the molecular mechanisms for leptin inhibition of PPARγ1 expression in HSCs and for the liver fibrosis associated with leptin.
Regulation of glucose homeostasis and insulin action by ceramide acyl-chain length: A beneficial role for very long-chain sphingolipid species.
Montgomery MK, Brown SH, Lim XY … +10 more , Fiveash CE, Osborne B, Bentley NL, Braude JP, Mitchell TW, Coster AC, Don AS, Cooney GJ, Schmitz-Peiffer C, Turner N
Biochim Biophys Acta · 2016 Nov · PMID 27591968 · Publisher ↗
In a recent study, we showed that in response to high fat feeding C57BL/6, 129X1, DBA/2 and FVB/N mice all developed glucose intolerance, while BALB/c mice displayed minimal deterioration in glucose tolerance and insulin...
In a recent study, we showed that in response to high fat feeding C57BL/6, 129X1, DBA/2 and FVB/N mice all developed glucose intolerance, while BALB/c mice displayed minimal deterioration in glucose tolerance and insulin action. Lipidomic analysis of livers across these five strains has revealed marked strain-specific differences in ceramide (Cer) and sphingomyelin (SM) species with high-fat feeding; with increases in C16-C22 (long-chain) and reductions in C>22 (very long-chain) Cer and SM species observed in the four strains that developed HFD-induced glucose intolerance. Intriguingly, the opposite pattern was observed in sphingolipid species in BALB/c mice. These strain-specific changes in sphingolipid acylation closely correlated with ceramide synthase 2 (CerS2) protein content and activity, with reduced CerS2 levels/activity observed in glucose intolerant strains and increased content in BALB/c mice. Overexpression of CerS2 in primary mouse hepatocytes induced a specific elevation in very long-chain Cer, but despite the overall increase in ceramide abundance, there was a substantial improvement in insulin signal transduction, as well as decreased ER stress and gluconeogenic markers. Overall our findings suggest that very long-chain sphingolipid species exhibit a protective role against the development of glucose intolerance and hepatic insulin resistance.
Characterisation of plasmalemmal shedding of vesicles induced by the cholesterol/sphingomyelin binding protein, ostreolysin A-mCherry.
Skočaj M, Yu Y, Grundner M … +10 more , Resnik N, Bedina Zavec A, Leonardi A, Križaj I, Guella G, Maček P, Kreft ME, Frangež R, Veranič P, Sepčić K
Biochim Biophys Acta · 2016 Nov · PMID 27591807 · Publisher ↗
Ostreolysin A (OlyA) is a 15-kDa protein that binds selectively to cholesterol/sphingomyelin membrane nanodomains. This binding induces the production of extracellular vesicles (EVs) that comprise both microvesicles with...
Ostreolysin A (OlyA) is a 15-kDa protein that binds selectively to cholesterol/sphingomyelin membrane nanodomains. This binding induces the production of extracellular vesicles (EVs) that comprise both microvesicles with diameters between 100nm and 1μm, and larger vesicles of around 10-μm diameter in Madin-Darby canine kidney cells. In this study, we show that vesiculation of these cells by the fluorescent fusion protein OlyA-mCherry is not affected by temperature, is not mediated via intracellular Ca signalling, and does not compromise cell viability and ultrastructure. Seventy-one proteins that are mostly of cytosolic and nuclear origin were detected in these shed EVs using mass spectroscopy. In the cells and EVs, 218 and 84 lipid species were identified, respectively, and the EVs were significantly enriched in lysophosphatidylcholines and cholesterol. Our collected data suggest that OlyA-mCherry binding to cholesterol/sphingomyelin membrane nanodomains induces specific lipid sorting into discrete patches, which promotes plasmalemmal blebbing and EV shedding from the cells. We hypothesize that these effects are accounted for by changes of local membrane curvature upon the OlyA-mCherry-plasmalemma interaction. We suggest that the shed EVs are a potentially interesting model for biophysical and biochemical studies of cell membranes, and larger vesicles could represent tools for non-invasive sampling of cytosolic proteins from cells and thus metabolic fingerprinting.
Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field.
Miguel V, Perillo MA, Villarreal MA
Biochim Biophys Acta · 2016 Nov · PMID 27591685 · Publisher ↗
Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water mode...
Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water model has been developed following the MARTINI parametrization strategy, the BMW-MARTINI [1]. We tested the BMW-MARTINI FF capability to describe some structural and thermodynamical properties of lipid monolayers and bilayers. We found that, since the surface tension values of oil/water interfaces calculated with the model are not correct, compression isotherms of lipid monolayers present artifacts. Also, this FF predicts DPPC and DAPC bilayers to remain in the L phase at temperatures as low as 283K, contrary to the expected from their experimental Tm values. Finally, simulations at constant temperature of bilayers of saturated lipids belonging to PC homologous, showed an increase in the mean molecular area (Mma) upon increasing the chain length, inversely to the experimental observation. We refined BMW-MARTINI FF by modifying as few parameters as possible in order to bring simulated and experimental measurements closer. We have also modified structural parameters of the lipid geometry that do not have direct influence in global properties of the bilayer membranes or monolayers, but serve to approach the obtained CG geometry to atomistic reference values. The refined FF is able to better reproduce phase transition temperatures and Mma for saturated PC bilayers than BMW-MARTINI and MARTINI FF. Finally, the simulated surface pressure-Mma isotherms of PC monolayers resemble the experimental ones and eliminate serious artifacts of previous models.
The developmental transcriptome sequencing of bovine skeletal muscle reveals a long noncoding RNA, lncMD, promotes muscle differentiation by sponging miR-125b.
Sun X, Li M, Sun Y … +6 more , Cai H, Lan X, Huang Y, Bai Y, Qi X, Chen H
Biochim Biophys Acta · 2016 Nov · PMID 27589905 · Publisher ↗
Pervasive transcription of the mammalian genome generates numerous long noncoding RNAs (lncRNAs), which are of crucial importance in diverse biological processes. Recent advances in high throughput sequencing technology...
Pervasive transcription of the mammalian genome generates numerous long noncoding RNAs (lncRNAs), which are of crucial importance in diverse biological processes. Recent advances in high throughput sequencing technology have helped to accelerate the pace of lncRNA discovery. However, no study on the overall expression patterns of lncRNAs during muscle development has been conducted. We reported here the first analysis of lncRNA landscape in bovine embryonic, neonatal and adult skeletal muscle using Ribo-Zero RNA-Seq, a technology which can capture both poly(A) and poly(A) transcripts. We finally defined 7692 high-confidence lncRNAs and uncovered 401 lncRNAs differentially expressed among three developmental stages, including lncMD, a novel muscle-specific lncRNA which is gradually up-regulated during myoblast differentiation. lncMD overexpression upregulated, whereas lncMD silencing decreased the expression of two well-established myogenic markers, myosin heavy chain (MHC) and myogenin (MyoG). In-depth analyses showed that lncMD acts as a molecular sponge for miR-125b and that insulin-like growth factor 2 (IGF2) is a direct target of miR-125b in cattle. Moreover, lncMD level was positively correlated with IGF2 mRNA level in bovine muscle tissues, a vital corollary to ceRNA function. Altogether, our research showed that lncMD acts as a ceRNA to sequester miR-125b, leading to heightened IGF2 expression and thus promotes muscle differentiation. Our findings also complement the reference genome annotation of cattle, which will likely be useful for further functional lncRNA cloning and more comprehensive studies on lncRNA regulation in muscle development.
The interaction of sorafenib and regorafenib with membranes is modulated by their lipid composition.
Haralampiev I, Scheidt HA, Abel T … +4 more , Luckner M, Herrmann A, Huster D, Müller P
Biochim Biophys Acta · 2016 Nov · PMID 27581086 · Publisher ↗
Sorafenib and regorafenib are small-molecule kinase inhibitors approved for the treatment of locally recurrent or metastatic, progressive, differentiated thyroid carcinoma, renal cell carcinoma, and hepatocellular carcin...
Sorafenib and regorafenib are small-molecule kinase inhibitors approved for the treatment of locally recurrent or metastatic, progressive, differentiated thyroid carcinoma, renal cell carcinoma, and hepatocellular carcinoma (sorafenib) and of colorectal cancer (regorafenib). As of now, the mechanisms, which are responsible for their antitumor activities, are not completely understood. Given the lipophilic nature of the molecules, it can be hypothesized that the pharmacological impact is mediated by the interaction with cellular membranes as it is true for many pharmacologically active molecules. However, an interaction of sorafenib or regorafenib with lipid membranes has not yet been investigated in detail. Here, we characterized the interaction of both drugs with lipid membranes by applying a variety of biophysical approaches including nuclear magnetic resonance, electron spin resonance, and fluorescence spectroscopy. We found that sorafenib and regorafenib bind to lipid membranes by inserting into the lipid-water interface of the bilayer. This membrane embedding causes a disturbance of bilayer structure leading to an increased permeability of the membrane for polar molecules. One approach shows that the extent of the effects depends on the membrane lipid composition underlining a particular role of phosphatidylcholine and cholesterol. Our data for the first time characterize the impact of sorafenib and regorafenib on the lipid membrane structure and dynamics, which may contribute to a better understanding of their effectiveness in the treatment of malignancies as well as of their side effects.
Connexin hemichannels explain the ionic imbalance and lead to atrophy in denervated skeletal muscles.
Cisterna BA, Vargas AA, Puebla C … +1 more , Sáez JC
Biochim Biophys Acta · 2016 Nov · PMID 27580092 · Publisher ↗
Denervated fast skeletal muscles undergo atrophy, which is associated with an increase in sarcolemma permeability and protein imbalance. However, the mechanisms responsible for these alterations remain largely unknown. R...
Denervated fast skeletal muscles undergo atrophy, which is associated with an increase in sarcolemma permeability and protein imbalance. However, the mechanisms responsible for these alterations remain largely unknown. Recently, a close association between de novo expression of hemichannels formed by connexins 43 and 45 and increase in sarcolemma permeability of denervated fast skeletal myofibers was demonstrated. However, it remains unknown whether these connexins cause the ionic imbalance of denervates fast myofibers. To elucidate the latter and the role of hemichannels formed by connexins (Cx HCs) in denervation-induced atrophy, skeletal myofibers deficient in Cx43 and Cx45 expression (Cx43Cx45:Myo-Cre mice) and control (Cx43Cx45 mice) were denervated and several muscle features were systematically analyzed at different post-denervation (PD) times (1, 3, 5, 7 and 14days). The following sequence of events was found in denervated myofibers of Cx43Cx45 mice: 1) from day 3 PD, increase in sarcolemmal permeability, 2) from day 5 PD, increases of intracellular Ca and Na signals as well as a significant increase in protein synthesis and degradation, yielding a negative protein balance and 3) from day 7 PD, a fall in myofibers cross-section area. All the above alterations were either absent or drastically reduced in denervated myofibers of Cx43Cx45:Myo-Cre mice. Thus, the denervation-induced Cx HCs expression is an early event that precedes the electrochemical gradient dysregulation across the sarcolemma and critically contributes to the progression of skeletal muscle atrophy. Consequently, Cx HCs could be a therapeutic target to drastically prevent the denervation-induced atrophy of fast skeletal muscles.
Diffusion of glycophorin A in human erythrocytes.
Giger K, Habib I, Ritchie K … +1 more , Low PS
Biochim Biophys Acta · 2016 Nov · PMID 27580023 · Full text
Several lines of evidence suggest that glycophorin A (GPA) interacts with band 3 in human erythrocyte membranes including: i) the existence of an epitope shared between band 3 and GPA in the Wright b blood group antigen,...
Several lines of evidence suggest that glycophorin A (GPA) interacts with band 3 in human erythrocyte membranes including: i) the existence of an epitope shared between band 3 and GPA in the Wright b blood group antigen, ii) the fact that antibodies to GPA inhibit the diffusion of band 3, iii) the observation that expression of GPA facilitates trafficking of band 3 from the endoplasmic reticulum to the plasma membrane, and iv) the observation that GPA is diminished in band 3 null erythrocytes. Surprisingly, there is also evidence that GPA does not interact with band 3, including data showing that: i) band 3 diffusion increases upon erythrocyte deoxygenation whereas GPA diffusion does not, ii) band 3 diffusion is greatly restricted in erythrocytes containing the Southeast Asian Ovalocytosis mutation whereas GPA diffusion is not, and iii) most anti-GPA or anti-band 3 antibodies do not co-immunoprecipitate both proteins. To try to resolve these apparently conflicting observations, we have selectively labeled band 3 and GPA with fluorescent quantum dots in intact erythrocytes and followed their diffusion by single particle tracking. We report here that band 3 and GPA display somewhat similar macroscopic and microscopic diffusion coefficients in unmodified cells, however perturbations of band 3 diffusion do not cause perturbations of GPA diffusion. Taken together the collective data to date suggest that while weak interactions between GPA and band 3 undoubtedly exist, GPA and band 3 must have separate interactions in the membrane that control their lateral mobility.
Neurological disease mutations of α3 Na,K-ATPase: Structural and functional perspectives and rescue of compromised function.
Holm R, Toustrup-Jensen MS, Einholm AP … +3 more , Schack VR, Andersen JP, Vilsen B
Biochim Biophys Acta · 2016 Nov · PMID 27577505 · Publisher ↗
Na,K-ATPase creates transmembrane ion gradients crucial to the function of the central nervous system. The α-subunit of Na,K-ATPase exists as four isoforms (α1-α4). Several neurological phenotypes derive from α3 mutation...
Na,K-ATPase creates transmembrane ion gradients crucial to the function of the central nervous system. The α-subunit of Na,K-ATPase exists as four isoforms (α1-α4). Several neurological phenotypes derive from α3 mutations. The effects of some of these mutations on Na,K-ATPase function have been studied in vitro. Here we discuss the α3 disease mutations as well as information derived from studies of corresponding mutations of α1 in the light of the high-resolution crystal structures of the Na,K-ATPase. A high proportion of the α3 disease mutations occur in the transmembrane sector and nearby regions essential to Na and K binding. In several cases the compromised function can be traced to disturbance of the Na specific binding site III. Recently, a secondary mutation was found to rescue the defective Na binding caused by a disease mutation. A perspective is that it may be possible to develop an efficient pharmaceutical mimicking the rescuing effect.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe