Browsing by Subject "MEMBRANES"

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  • Owen, Michael C.; Kulig, Waldemar; Rog, Tomasz; Vattulainen, Ilpo; Strodel, Birgit (2018)
    In an effort to delineate how cholesterol protects membrane structure under oxidative stress conditions, we monitored the changes to the structure of lipid bilayers comprising 30 mol% cholesterol and an increasing concentration of Class B oxidized 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) glycerophospholipids, namely, 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PoxnoPC), and 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), using atomistic molecular dynamics simulations. Increasing the content of oxidized phospholipids (oxPLs) from 0 to 60 mol% oxPL resulted in a characteristic reduction in bilayer thickness and increase in area per lipid, thereby increasing the exposure of the membrane hydrophobic region to water. However, cholesterol was observed to help reduce water injury by moving into the bilayer core and forming more hydrogen bonds with the oxPLs. Cholesterol also resists altering its tilt angle, helping to maintain membrane integrity. Water that enters the 1-nm-thick core region remains part of the bulk water on either side of the bilayer, with relatively few water molecules able to traverse through the bilayer. In cholesterol-rich membranes, the bilayer does not form pores at concentrations of 60 mol% oxPL as was shown in previous simulations in the absence of cholesterol.
  • Augustyn, Bozena; Stepien, Piotr; Poojari, Chetan; Mobarak, Edouard; Polit, Agnieszka; Wisniewska-Becker, Anna; Rog, Tomasz (2019)
    Nanodiscs are suitable tools for studies of membrane proteins (MPs) due to their ability to mimic native biological membranes, and several MP structures are solved in nanodiscs. Among the various cell membrane components, cholesterol (CHL) is known to regulate protein function and its concentration can reach up to 50 mol %. However, studies comprising cholesterol are challenging due to its hydrophobic nature, hence, nanodiscs with only a low cholesterol concentration have been studied. To overcome the problem, cholesterol analogs with high solubility in polar solutions are often used, and one of them is cholesteryl hemisuccinate (CHS). Nevertheless, in molecular dynamics (MD) simulation, this is not an obstacle. In this study, we performed MD simulations of nanodiscs containing neutral phosphatidylcholine (POPC) lipids, negatively charged phosphatidylglycerol (POPG) lipids, CHL, or negatively charged cholesterol analog, CHS. Our simulations show that CHS increases the order of lipids in nanodiscs; the effect is, however, weaker than CHL and even smaller in nanodiscs. Furthermore, CHS gathered around scaffold proteins while cholesterol was uniformly distributed in the nanodiscs. Thus, nanodiscs with CHS are heterogeneous and not equivalent to nanodiscs with CHL. Finally, we also observed the increased concentration of POPG near the scaffold proteins, driven by electrostatic interactions. The MD results are experimentally validated using electron paramagnetic resonance spectroscopy. These results show that nanodiscs are, in fact, complex structures not easily comparable with planar lipid bilayers.
  • Ruokonen, Suvi-Katriina; Sanwald, Corinna; Robciuc, Alexandra; Hietala, Sami; Rantamäki, Antti H.; Witos, Joanna; King, Alistair W. T.; Lämmerhofer, Michael; Wiedmer, Susanne K. (2018)
    This study aims at extending the understanding of the toxicity mechanism of ionic liquids (ILs) using various analytical methods and cytotoxicity assays. The cytotoxicity of eight ILs and one zwitterionic compound was determined using mammalian and bacterial cells. The time dependency of the IL toxicity was assessed using human corneal epithelial cells. Hemolysis was performed using human red blood cells and the results were compared with destabilization data of synthetic liposomes upon addition of ILs. The effect of the ILs on the size and zeta potential of liposomes revealed information on changes in the lipid bilayer. Differential scanning calorimetry was used to study the penetration of the ILs into the lipid bilayer. Pulsed field gradient nuclear magnetic resonance spectroscopy was used to determine whether the ILs occurred as unimers, micelles, or if they were bound to liposomes. The results show that the investigated ILs can be divided into three groups based on the cytotoxicity mechanism: cell wall disrupting ILs, ILs exerting toxicity through both cell wall penetration and metabolic alteration, and ILs affecting solely on cell metabolism.
  • Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Rog, Tomasz; Vattulainen, Ilpo (2017)
    Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cellcell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.
  • Persson, Martina; Opdahl, Signe; Risnes, Kari; Gross, Raz; Kajantie, Eero; Reichenberg, Abraham; Gissler, Mika; Sandin, Sven (2020)
    Introduction The complex etiology of autism spectrum disorder (ASD) is still unresolved. Preterm birth ( Author summaryWhy was this study done? Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by persistent impairments in social communication and restricted and repetitive behaviors. The etiology remains unresolved. Length of gestation, including preterm birth, has been linked to risk of ASD, but reliable estimates of risks for the whole range of gestational ages (GAs) are lacking. The primary objective of this study was to provide a detailed and robust description of ASD risk across the entire range of GA while taking fetal sex and size at birth into account. What did the researchers do and find? This study was based on population-based data from national medical registries in three Nordic countries-Sweden, Finland, and Norway-and included 3,526,174 singletons born 1995 to 2015. Relative risks (RRs) of ASD by GA at birth were estimated with log binominal regression. The RR of ASD increased by each week of GA, pre- as well as postterm, from 40 to 24 weeks of gestation and from 40 to 44 weeks of gestation, independently of sex and birth weight for GA. What do these findings mean? On a population level, the risks of ASD were increased in children born either pre- or postterm, including children born close to week 40. We found that the risk of ASD increased weekly, with each week further away from 40 weeks of gestation.
  • Polley, Anirban; Orlowski, Adam; Danne, Reinis; Gurtovenko, Andrey A.; de la Serna, Jorge Bernardino; Eggeling, Christian; Davis, Simon J.; Rog, Tomasz; Vattulainen, Ilpo (2017)
    Proteins embedded in the plasma membrane mediate interactions with the cell environment and play decisive roles in many signaling events. For cell-cell recognition molecules, it is highly likely that their structures and behavior have been optimized in ways that overcome the limitations of membrane tethering. In particular, the ligand binding regions of these proteins likely need to be maximally exposed. Here we show by means of atomistic simulations of membrane-bound CD2, a small cell adhesion receptor expressed by human T-cells and natural killer cells, that the presentation of its ectodomain is highly dependent on membrane lipids and receptor glycosylation acting in apparent unison. Detailed analysis shows that the underlying mechanism is based on electrostatic interactions complemented by steric interactions between glycans in the protein and the membrane surface. The findings are significant for understanding the factors that render membrane receptors accessible for binding and signaling.
  • Dusa, Filip; Chen, Wen; Witos, Joanna; Rantamäki, Antti; King, Alistair; Sklavounos, Evangelos; Roth, Michal; Wiedmer, Susanne (2020)
    The cell membrane is mainly composed of lipid bilayers with inserted proteins and carbohydrates. Lipid bilayers made of purified or synthetic lipids are widely used for estimating the effect of target compounds on cell membranes. However, the composition of such biomimetic membranes is much simpler than the composition of biological membranes. Interactions between compounds and simple composition biomimetic membranes might not demonstrate the effect of target compounds as precisely as membranes with compositions close to real organisms. Therefore, the aim of our study is to construct biomimetic membrane closely mimicking the state of natural membranes. Liposomes were prepared from lipids extracted from L-alpha-phosphatidylcholine, Escherichia coli, yeast (Saccharomyces cerevisiae) and bovine liver cells through agitation and sonication. They were immobilized onto silicon dioxide (SiO2) sensor surfaces using N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid buffer with calcium chloride. The biomimetic membranes were successfully immobilized onto the SiO2 sensor surface and detected by nanoplasmonic sensing. The immobilized membranes were exposed to choline carboxylates. The membrane disruption effect was, as expected, more pronounced with increasing carbohydrate chain length of the carboxylates. The results correlated with the toxicity values determined using Vibrio fischeri bacteria. The yeast extracted lipid membranes had the strongest response to introduction of choline laurate while the bovine liver lipid extracted liposomes were the most sensitive towards the shorter choline carboxylates. This implies that the composition of the cell membrane plays a crucial role upon interaction with choline carboxylates, and underlines the necessity of testing membrane systems of different origin to obtain an overall image of such interactions.
  • Wiikinkoski, Elmo W.; Xu, Junhua; Zhang, Wenzhong; Hietala, Sami; Koivula, Risto T. (2018)
    The aim of an ongoing study is to develop ion exchange materials to be used in low pH in mineral acids for the uptake and separation of trivalent lanthanides and actinides. We present material development of alpha-zirconium phosphate (ZrP), namely the effects of its crystallinity and acidity on other material properties and on Eu(III) and Am(III) trace ion exchange. One-pot synthesis for three ZrP products having a time for (re)crystallization of 1 hour, 5 hours and 25 hours, is reported. Characterization techniques include X-ray diffraction, solid-state nuclear magnetic resonance, infrared spectroscopy, thermal analysis, electron microscopy, pK(a1) determination, and Eu-152(III) and Am-241(III) ion exchange studies, i.e. distribution-, selectivity- and metal binding coefficient determinations. As crystallinity and crystallite size increase, so do Eu(III) and Am(III) metal binding coefficients. The acidity and Eu(III) and Am(III) distribution- and selectivity coefficients increase in the reverse order. Findings are discussed with separation in mind. Promising separation factors (Eu:Am) of up to 90 were achieved in pH less than 1 in nitric acid.
  • Baron, Ludivine; Paatero, Anja Onerva; Morel, Jean-David; Impens, Francis; Guenin-Mace, Laure; Saint-Auret, Sarah; Blanchard, Nicolas; Dillmann, Rabea; Niang, Fatoumata; Pellegrini, Sandra; Taunton, Jack; Paavilainen, Ville O.; Demangel, Caroline (2016)
    Mycolactone, an immunosuppressive macrolide released by the human pathogen Mycobacterium ulcerans, was previously shown to impair Sec61-dependent protein translocation, but the underlying molecular mechanism was not identified. In this study, we show that mycolactone directly targets the alpha subunit of the Sec61 translocon to block the production of secreted and integral membrane proteins with high potency. We identify a single-amino acid mutation conferring resistance to mycolactone, which localizes its interaction site near the lumenal plug of Sec61 alpha. Quantitative proteomics reveals that during T cell activation, mycolactone-mediated Sec61 blockade affects a selective subset of secretory proteins including key signal-transmitting receptors and adhesion molecules. Expression of mutant Sec61 alpha in mycolactone-treated T cells rescued their homing potential and effector functions. Furthermore, when expressed in macrophages, the mycolactone-resistant mutant restored IFN-gamma receptor-mediated antimicrobial responses. Thus, our data provide definitive genetic evidence that Sec61 is the host receptor mediating the diverse immunomodulatory effects of mycolactone and identify Sec61 as a novel regulator of immune cell functions.
  • Stefanovic, Vedran; Andersson, Sture; Vento, Maximo (2019)
    Spontaneous preterm birth (PTB) is one of the major complications of pregnancy and the main cause of neonatal mortality and morbidity. Despite the efforts devoted to the understanding of this obstetrical syndrome and improved medical care, there has been a tendency for the PTB rate to increase in the last decades globally. The costs of the screening for spontaneous PTB, its management, and treatment of the sequelae represent a major burden to the health service economy of high-income countries. In this scenario, it has been widely acknowledged that oxidative stress (OS) plays an important role in the pathogenicity of human disease in wide range of areas of medicine. There is an emerging evidence that an imbalance between pro-and-antioxidants may be associated with spontaneous PTB. However, there are still many controversies on the mechanisms by which OS are involved in the pathogenesis of prematurity. Moreover, the crucial question whether the OS is the cause or consequence of the disease is yet to be answered. The purpose of this article is to briefly summarize the current knowledge and controversies on oxidative stress-related spontaneous PTB and to give a critical approach on future perspectives on this topic as a classical example of translational medicine. Placenta-mediated pregnancy adverse outcome associated with OS leading to iatrogenic PTB (e.g. pre-eclampsia, intrauterine growth restriction, gestational diabetes) will not be discussed.
  • Sánchez, Julio; Espinosa, Carolina; Pooch, Fabian; Tenhu, Heikki; Pizarro, Guadalupe del C.; Oyarzún, Diego P. (2018)
    This work is focused on the removal of Cr(VI) ions from aqueous solution using polymer-enhanced ultrafiltration (PEUF) techniques with water-soluble poly(N,N-dimethylaminoethyl methacrylate), PDMAEMA, used as sorbent. The polymer was prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization at different reaction times, characterized by size exclusion chromatography (SEC) and proton nuclear magnetic resonance (1H NMR). The sorption of Cr(VI) was studied by PEUF as a function of pH, the polymer:Cr(VI) molar ratio, and the presence of interfering ions. The PEUF-enrichment mode was used to saturate the polymer and further determine the release of Cr(VI) and regeneration of the polymer using sorption-desorption process. The RAFT polymerization showed a yield in the range 46% to 79% (determined by 1H NMR) for polymers with molecular weight (Mn) between 28 and 195 kg mol−1. The polydispersity estimated by SEC was between 1.1 and 1.8. The capacity of PDMAEMA as sorbent of Cr(VI), by the PEUF technique showed an efficient removal of Cr(VI) (100%, 25 mg L−1 in the feed) at pH 4 using polymer:Cr molar ratio of 40:1. The presence of interfering ions does not significantly decrease the retention capacity of PDMAEMA. Finally the results indicated that PDMAEMA can release Cr(VI) and be regenerated.
  • Liekkinen, Juho; Enkavi, Giray; Javanainen, Matti; Olmeda, Barbara; Pérez-Gil, Jesús; Vattulainen, Ilpo (2020)
    Surfactant protein B (SP-B) is essential in transferring surface-active phospholipids from membrane-based surfactant complexes into the alveolar air-liquid interface. This allows maintaining the mechanical stability of the surfactant film under high pressure at the end of expiration; therefore, SP-B is crucial in lung function. Despite its necessity, the structure and the mechanism of lipid transfer by SP-B have remained poorly characterized. Earlier, we proposed higher-order oligomerization of SP-B into ring-like supramolecular assemblies. In the present work, we used coarse-grained molecular dynamics simulations to elucidate how the ring-like oligomeric structure of SP-B determines its membrane binding and lipid transfer. In particular, we explored how SP-B interacts with specific surfactant lipids, and how consequently SP-B reorganizes its lipid environment to modulate the pulmonary surfactant structure and function. Based on these studies, there are specific lipid-protein interactions leading to perturbation and reorganization of pulmonary surfactant layers. Especially, we found compelling evidence that anionic phospholipids and cholesterol are needed or even crucial in the membrane binding and lipid transfer function of SP-B. Also, on the basis of the simulations, larger oligomers of SP-B catalyze lipid transfer between adjacent surfactant layers. Better understanding of the molecular mechanism of SP-B will help in the design of therapeutic SP-B-based preparations and novel treatments for fatal respiratory complications, such as the acute respiratory distress syndrome. (C) 2020 The Author(s). Published by Elsevier Ltd.
  • Wester, Niklas; Mynttinen, Elsi; Etula, Jarkko; Lilius, Tuomas; Kalso, Eija; Kauppinen, Esko I.; Laurila, Tomi; Koskinen, Jari (2019)
    In clinical settings, the dosing and differential diagnosis of the poisoning of morphine (MO) and codeine (CO) is challenging due to interindividual variations in metabolism. However, direct electrochemical detection of these analytes from biological matrices is inherently challenging due to interference from large concentrations of anions, such as ascorbic acid (AA) and uric acid (UA), as well as fouling of the electrode by proteins. In this work, a disposable Nafion-coated single-walled carbon nanotube network (SWCNT) electrode was developed. We show facile electron transfer and efficient charge separation between the interfering anions and positively charged MO and CO, as well as significantly reduced matrix effect in human plasma. The Nafion coating alters the voltammetric response of MO and CO, enabling simultaneous detection. With this SWCNT/Nafion electrode, two linear ranges of 0.05-1 and 1-10 mu M were found for MO and one linear range of 0.1-50 mu M for CO. Moreover, the selective and simultaneous detection of MO and CO was achieved in large excess of AA and UA, as well as, for the first time, in unprocessed human plasma. The favorable properties of this electrode enabled measurements in plasma with only mild dilution and without the precipitation of proteins.
  • Tiainen, Tony; Lobanova, Marina; Karjalainen, Erno; Tenhu, Heikki; Hietala, Sami (2020)
    Nanodiamonds (NDs) can considerably improve the mechanical and thermal properties of polymeric composites. However, the tendency of NDs to aggregate limits the potential of these non-toxic, mechanically- and chemically-robust nanofillers. In this work, tough, flexible, and stimuli-responsive polyelectrolyte films composed of cross-linked poly(butyl acrylate-co-dimethylaminoethyl methacrylate) (P(BA-co-DMAEMA)) were prepared by photopolymerization. The effects of the added carboxylate-functionalized NDs on their mechanical and stimuli-responsive properties were studied. When the negatively charged NDs were added to the polymerization media directly, the mechanical properties of the films changed only slightly, because of the uneven distribution of the aggregated NDs in the films. In order to disperse and distribute the NDs more evenly, a prepolymerized polycation block copolymer complexing agent was used during the photopolymerization process. This approach improved the mechanical properties of the films and enhanced their thermally-induced, reversible phase-transition behavior.
  • Lolicato, Fabio; Joly, Loic; Martinez-Seara, Hector; Fragneto, Giovanna; Scoppola, Ernesto; Bombelli, Francesca Baldelli; Vattulainen, Ilpo; Akola, Jaakko; Maccarini, Marco (2019)
    Understanding the molecular mechanisms governing nanoparticle-membrane interactions is of prime importance for drug delivery and biomedical applications. Neutron reflectometry (NR) experiments are combined with atomistic and coarse-grained molecular dynamics (MD) simulations to study the interaction between cationic gold nanoparticles (AuNPs) and model lipid membranes composed of a mixture of zwitterionic di-stearoyl-phosphatidylcholine (DSPC) and anionic di-stearoyl-phosphatidylglycerol (DSPG). MD simulations show that the interaction between AuNPs and a pure DSPC lipid bilayer is modulated by a free energy barrier. This can be overcome by increasing temperature, which promotes an irreversible AuNP incorporation into the lipid bilayer. NR experiments confirm the encapsulation of the AuNPs within the lipid bilayer at temperatures around 55 degrees C. In contrast, the AuNP adsorption is weak and impaired by heating for a DSPC-DSPG (3:1) lipid bilayer. These results demonstrate that both the lipid charge and the temperature play pivotal roles in AuNP-membrane interactions. Furthermore, NR experiments indicate that the (negative) DSPG lipids are associated with lipid extraction upon AuNP adsorption, which is confirmed by coarse-grained MD simulations as a lipid-crawling effect driving further AuNP aggregation. Overall, the obtained detailed molecular view of the interaction mechanisms sheds light on AuNP incorporation and membrane destabilization.
  • Vidova, Veronika; Pol, Jaroslav; Volny, Michael; Novak, Petr; Havlicek, Vladimir; Wiedmer, Susanne K.; Holopainen, Juha M. (2010)