WorldWideScience

Sample records for biological membrane structure

  1. Structure Biology of Membrane Bound Enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Dax [Johns Hopkins Univ., Baltimore, MD (United States). School of Medicine. Dept. of Physiology

    2016-11-30

    The overall goal of the proposed research is to understand the membrane-associated active processes catalyzed by an alkane $\\square$-hydroxylase (AlkB) from eubacterium Pseudomonase oleovorans. AlkB performs oxygenation of unactivated hydrocarbons found in crude oils. The enzymatic reaction involves energy-demanding steps in the membrane with the uses of structurally unknown metal active sites featuring a diiron [FeFe] center. At present, a critical barrier to understanding the membrane-associated reaction mechanism is the lack of structural information. The structural biology efforts have been challenged by technical difficulties commonly encountered in crystallization and structural determination of membrane proteins. The specific aims of the current budget cycle are to crystalize AlkB and initiate X-ray analysis to set the stage for structural determination. The long-term goals of our structural biology efforts are to provide an atomic description of AlkB structure, and to uncover the mechanisms of selective modification of hydrocarbons. The structural information will help elucidating how the unactivated C-H bonds of saturated hydrocarbons are oxidized to initiate biodegradation and biotransformation processes. The knowledge gained will be fundamental to biotechnological applications to biofuel transformation of non-edible oil feedstock. Renewable biodiesel is a promising energy carry that can be used to reduce fossil fuel dependency. The proposed research capitalizes on prior BES-supported efforts on over-expression and purification of AlkB to explore the inner workings of a bioenergy-relevant membrane-bound enzyme.

  2. Biological Membrane Ion Channels Dynamics, Structure, and Applications

    CERN Document Server

    Chung, Shin-Ho; Krishnamurthy, Vikram

    2007-01-01

    Ion channels are biological nanotubes that are formed by membrane proteins. Because ion channels regulate all electrical activities in living cells, understanding their mechanisms at a molecular level is a fundamental problem in biology. This book deals with recent breakthroughs in ion-channel research that have been brought about by the combined effort of experimental biophysicists and computational physicists, who together are beginning to unravel the story of these exquisitely designed biomolecules. With chapters by leading experts, the book is aimed at researchers in nanodevices and biosensors, as well as advanced undergraduate and graduate students in biology and the physical sciences. Key Features Presents the latest information on the molecular mechanisms of ion permeation through membrane ion channels Uses schematic diagrams to illustrate important concepts in biophysics Written by leading researchers in the area of ion channel investigations

  3. Structural adaptations of proteins to different biological membranes

    Science.gov (United States)

    Pogozheva, Irina D.; Tristram-Nagle, Stephanie; Mosberg, Henry I.; Lomize, Andrei L.

    2013-01-01

    To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31 Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5 Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22 Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4 Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8 Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds. PMID:23811361

  4. Translocation across biological membranes: activity, structure and regulation of transporters

    NARCIS (Netherlands)

    Ruiz, Stephanie

    2017-01-01

    Alle cellen zijn omsloten door biologische membranen met selectief doorlatende membrane, die het mogelijk maken om omstandigheden "binnen" en "buiten" de cel te handhaven. De gereguleerde beweging van moleculen door deze membranen is nodig voor talrijke essentiële processen, waaronder het verkrijgen

  5. Physics of biological membranes

    Science.gov (United States)

    Mouritsen, Ole G.

    The biological membrane is a complex system consisting of an aqueous biomolecular planar aggregate of predominantly lipid and protein molecules. At physiological temperatures, the membrane may be considered a thin (˜50Å) slab of anisotropic fluid characterized by a high lateral mobility of the various molecular components. A substantial fraction of biological activity takes place in association with membranes. As a very lively piece of condensed matter, the biological membrane is a challenging research topic for both the experimental and theoretical physicists who are facing a number of fundamental physical problems including molecular self-organization, macromolecular structure and dynamics, inter-macromolecular interactions, structure-function relationships, transport of energy and matter, and interfacial forces. This paper will present a brief review of recent theoretical and experimental progress on such problems, with special emphasis on lipid bilayer structure and dynamics, lipid phase transitions, lipid-protein and lipid-cholesterol interactions, intermembrane forces, and the physical constraints imposed on biomembrane function and evolution. The paper advocates the dual point of view that there are a number of interesting physics problems in membranology and, at the same time, that the physical properties of biomembranes are important regulators of membrane function.

  6. Current strategies for protein production and purification enabling membrane protein structural biology.

    Science.gov (United States)

    Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E; Liu, Xiang-Qin; Rainey, Jan K

    2016-12-01

    Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

  7. Synthetic Biological Membrane (SBM)

    Data.gov (United States)

    National Aeronautics and Space Administration — The ultimate goal of the Synthetic Biological Membrane project is to develop a new type of membrane that will enable the wastewater treatment system required on...

  8. Shell and membrane theories in mechanics and biology from macro- to nanoscale structures

    CERN Document Server

    Mikhasev, Gennadi

    2015-01-01

    This book presents the latest results related to shells  characterize and design shells, plates, membranes and other thin-walled structures, a multidisciplinary approach from macro- to nanoscale is required which involves the classical disciplines of mechanical/civil/materials engineering (design, analysis, and properties) and physics/biology/medicine among others. The book contains contributions of a meeting of specialists (mechanical engineers, mathematicians, physicists and others) in such areas as classical and non-classical shell theories. New trends with respect to applications in mechanical, civil and aero-space engineering, as well as in new branches like medicine and biology are presented which demand improvements of the theoretical foundations of these theories and a deeper understanding of the material behavior used in such structures.

  9. Ninth International Workshop on Plant Membrane Biology

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    This report is a compilation of abstracts from papers which were discussed at a workshop on plant membrane biology. Topics include: plasma membrane ATP-ases; plant-environment interactions, membrane receptors; signal transduction; ion channel physiology; biophysics and molecular biology; vaculor H+ pumps; sugar carriers; membrane transport; and cellular structure and function.

  10. A Glimpse of Membrane Transport through Structures-Advances in the Structural Biology of the GLUT Glucose Transporters.

    Science.gov (United States)

    Yan, Nieng

    2017-08-18

    The cellular uptake of glucose is an essential physiological process, and movement of glucose across biological membranes requires specialized transporters. The major facilitator superfamily glucose transporters GLUTs, encoded by the SLC2A genes, have been a paradigm for functional, mechanistic, and structural understanding of solute transport in the past century. This review starts with a glimpse into the structural biology of membrane proteins and particularly membrane transport proteins, enumerating the landmark structures in the past 25years. The recent breakthrough in the structural elucidation of GLUTs is then elaborated following a brief overview of the research history of these archetypal transporters, their functional specificity, and physiological and pathophysiological significances. Structures of GLUT1, GLUT3, and GLUT5 in distinct transport and/or ligand-binding states reveal detailed mechanisms of the alternating access transport cycle and substrate recognition, and thus illuminate a path by which structure-based drug design may be applied to help discover novel therapeutics against several debilitating human diseases associated with GLUT malfunction and/or misregulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Mesoscopic models of biological membranes

    DEFF Research Database (Denmark)

    Venturoli, M.; Sperotto, Maria Maddalena; Kranenburg, M.

    2006-01-01

    Phospholipids are the main components of biological membranes and dissolved in water these molecules self-assemble into closed structures, of which bilayers are the most relevant from a biological point of view. Lipid bilayers are often used, both in experimental and by theoretical investigations...... to coarse grain a biological membrane. The conclusion of this comparison is that there can be many valid different strategies, but that the results obtained by the various mesoscopic models are surprisingly consistent. A second objective of this review is to illustrate how mesoscopic models can be used...

  12. Fusion of biological membranes

    Indian Academy of Sciences (India)

    small hemifusion diaphragm. To obtain a direct view of the fusion process, we have carried out extensive simulations of two bilayers, composed of block copolymers, which are immersed in a solvent which favors one of the blocks. As in the biological case, the membranes are placed under tension. This is essential as fusion ...

  13. Fusion of biological membranes

    Indian Academy of Sciences (India)

    Logo of the Indian Academy of Sciences. Indian Academy of ... Home; Journals; Pramana – Journal of Physics; Volume 64; Issue 6. Fusion of biological ... The process of membrane fusion has been examined by Monte Carlo simulation, and is found to be very different than the conventional picture. The differences in ...

  14. From biological membranes to biomimetic model membranes

    Directory of Open Access Journals (Sweden)

    Eeman, M.

    2010-01-01

    Full Text Available Biological membranes play an essential role in the cellular protection as well as in the control and the transport of nutrients. Many mechanisms such as molecular recognition, enzymatic catalysis, cellular adhesion and membrane fusion take place into the biological membranes. In 1972, Singer et al. provided a membrane model, called fluid mosaic model, in which each leaflet of the bilayer is formed by a homogeneous environment of lipids in a fluid state including globular assembling of proteins and glycoproteins. Since its conception in 1972, many developments were brought to this model in terms of composition and molecular organization. The main development of the fluid mosaic model was made by Simons et al. (1997 and Brown et al. (1997 who suggested that membrane lipids are organized into lateral microdomains (or lipid rafts with a specific composition and a molecular dynamic that are different to the composition and the dynamic of the surrounding liquid crystalline phase. The discovery of a phase separation in the plane of the membrane has induced an explosion in the research efforts related to the biology of cell membranes but also in the development of new technologies for the study of these biological systems. Due to the high complexity of biological membranes and in order to investigate the biological processes that occur on the membrane surface or within the membrane lipid bilayer, a large number of studies are performed using biomimicking model membranes. This paper aims at revisiting the fundamental properties of biological membranes in terms of membrane composition, membrane dynamic and molecular organization, as well as at describing the most common biomimicking models that are frequently used for investigating biological processes such as membrane fusion, membrane trafficking, pore formation as well as membrane interactions at a molecular level.

  15. Mesoscopic models of biological membranes

    DEFF Research Database (Denmark)

    Venturoli, M.; Sperotto, Maria Maddalena; Kranenburg, M.

    2006-01-01

    Phospholipids are the main components of biological membranes and dissolved in water these molecules self-assemble into closed structures, of which bilayers are the most relevant from a biological point of view. Lipid bilayers are often used, both in experimental and by theoretical investigations......, as model systems to understand the fundamental properties of biomembranes. The properties of lipid bilayers can be studied at different time and length scales. For some properties it is sufficient to envision a membrane as an elastic sheet, while for others it is important to take into account the details...... to coarse grain a biological membrane. The conclusion of this comparison is that there can be many valid different strategies, but that the results obtained by the various mesoscopic models are surprisingly consistent. A second objective of this review is to illustrate how mesoscopic models can be used...

  16. Fusion of biological membranes

    Indian Academy of Sciences (India)

    Abstract. The process of membrane fusion has been examined by Monte Carlo simu- lation, and is found to be very different than the conventional picture. The differences in mechanism lead to several predictions, in particular that fusion is accompanied by tran- sient leakage. This prediction has recently been verified.

  17. Fusion of biological membranes

    Indian Academy of Sciences (India)

    The process of membrane fusion has been examined by Monte Carlo simulation, and is found to be very different than the conventional picture. The differences in mechanism lead to several predictions, in particular that fusion is accompanied by transient leakage. This prediction has recently been verified. Self-consistent ...

  18. Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion.

    Science.gov (United States)

    Nguyen, Trung Hai; Zhang, Chao; Weichselbaum, Ewald; Knyazev, Denis G; Pohl, Peter; Carloni, Paolo

    2018-01-01

    Proton transport at water/membrane interfaces plays a fundamental role for a myriad of bioenergetic processes. Here we have performed ab initio molecular dynamics simulations of proton transfer along two phosphatidylcholine bilayers. As found in previous theoretical studies, the excess proton is preferably located at the water/membrane interface. Further, our simulations indicate that it interacts not only with phosphate head groups, but also with water molecules at the interfaces. Interfacial water molecules turn out to be oriented relative to the lipid bilayers, consistently with experimental evidence. Hence, the specific water-proton interaction may help explain the proton mobility experimentally observed at the membrane interface.

  19. The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions.

    Science.gov (United States)

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

    2011-03-04

    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion.

  20. Investigation of interactions in a biological membrane using structure factor/pair correlation function approach: a first communication on nerve myelin

    International Nuclear Information System (INIS)

    Gbordzoe, M.K.

    1984-09-01

    Interactions in biological and artificial membranes have been studied by applying mostly the methods of biochemical analysis and determination of thermodynamic parameters related to phase transition phenomena. Structure factor, obtained by measuring scattered intensity from small-angle X-ray or neutron scattering experiments, has been used mainly for determining electron density distribution. Drawing upon the experience of the theory of liquids, where Johnson and March (1963) and Johnson, Hutchinson and March (1964) first established the possibility of deriving interparticle potential from experimental measurement of structure factor, it is suggested that structure factor/distance correlation function approach, can be a useful method for studying interactions between various membrane components. Preliminary experimental data presented for nerve myelin are to demonstrate the possibility of studying interactions from the distance correlation function of a membrane pair. (author)

  1. On the mechanics of growing thin biological membranes

    Science.gov (United States)

    Rausch, Manuel K.; Kuhl, Ellen

    2014-02-01

    Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression.

  2. On the mechanics of growing thin biological membranes.

    Science.gov (United States)

    Rausch, Manuel K; Kuhl, Ellen

    2014-02-01

    Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression.

  3. Taming Membranes : Functional Immobilization of Biological Membranes in Hydrogels

    NARCIS (Netherlands)

    Kusters, Ilja; Mukherjee, Nobina; de Jong, Menno R.; Tans, Sander; Kocer, Armagan; Driessen, Arnold J. M.

    2011-01-01

    Single molecule studies on membrane proteins embedded in their native environment are hampered by the intrinsic difficulty of immobilizing elastic and sensitive biological membranes without interfering with protein activity. Here, we present hydrogels composed of nano-scaled fibers as a generally

  4. Cell membrane structures during exocytosis.

    Science.gov (United States)

    Savigny, Pascale; Evans, John; McGrath, Kathryn M

    2007-08-01

    Exocytosis is a key biological process that controls the neurotransmission and release of hormones from cells. In endocrine cells, hormones are packed into secretory vesicles and released into the extracellular environment via openings in the plasma membrane, a few hundred nanometers wide, which form as a result of fusion of the membranes of the granule and cell. The complex processes and dynamics that result in the formation of the fusion pore, as well as its structure, remain scantly understood. A number of different exocytosis mechanisms have been postulated. Furthermore, the possibility exists that several mechanisms occur simultaneously. We present here an investigation of the cell membrane dynamics during exocytosis in anterior pituitary cells, especially gonadotropes, which secrete LH, a hormone central to ovulation. Gonadotrope enrichment was achieved using immunolabeled magnetic nanobeads. Three complementary imaging techniques were used to realize a fine structure study of the dynamics of the exocytosis-like sites occurring during secretion. Living pituitary and gonadotrope-enriched cells were imaged with atomic force microscopy, as well as cells that had been fixed to obtain better resolution. Atomic force microscopy, along with scanning and transmission electron microscopy, studies of these cells revealed that there are at least two different site configurations: simple single fusion pores and a complex association of pores consisting of a simple primary site combined with secondary attachments.

  5. Testing of Synthetic Biological Membranes for Forward Osmosis Applications

    Science.gov (United States)

    Parodi, Jurek; Mangado, Jaione Romero; Stefanson, Ofir; Flynn, Michael; Mancinelli, Rocco; Kawashima, Brian; Trieu, Serena; Brozell, Adrian; Rosenberg, Kevan

    2016-01-01

    Commercially available forward osmosis membranes have been extensively tested for human space flight wastewater treatment. Despite the improvements achieved in the last decades, there is still a challenge to produce reliable membranes with anti-fouling properties, chemical resistance, and high flux and selectivity. Synthetic biological membranes that mimic the ones present in nature, which underwent millions of years of evolution, represent a potential solution for further development and progress in membrane technology. Biomimetic forward osmosis membranes based on a polymeric support filter and coated with surfactant multilayers have been engineered to investigate how different manufacturing processes impact the performance and structure of the membrane. However, initial results of the first generation prototype membranes tests reveal a high scatter in the data, due to the current testing apparatus set up. The testing apparatus has been upgraded to improve data collection, reduce errors, and to allow higher control of the testing process.

  6. Importance of the hexagonal lipid phase in biological membrane organisation

    Directory of Open Access Journals (Sweden)

    Juliette eJouhet

    2013-12-01

    Full Text Available Abstract:Domains are present in every natural membrane. They are characterised by a distinctive protein and/or lipid composition. Their size is highly variable from the nano- to the micrometer scale. The domains confer specific properties to the membrane leading to original structure and function. The determinants leading to domain organisation are therefore important but remain obscure. This review presents how the ability of lipids to organize into hexagonal II or lamellar phases can promote particular local structures within membranes. Since biological membranes are composed of a mixture of lipids, each with distinctive biophysical properties, lateral and transversal sorting of lipids can promote creation of domains inside the membrane through local modulation of the lipid phase. Lipid biophysical properties have been characterized for long based on in vitro analyses using non-natural lipid molecules; their re-examinations using natural lipids might open interesting perspectives on membrane architecture occurring in vivo in various cellular and physiological contexts.

  7. Structure and properties of cell membranes. Volume 3: Methodology and properties of membranes

    International Nuclear Information System (INIS)

    Benga, G.

    1985-01-01

    This book covers the topics: Quantum chemical approach to study the mechanisms of proton translocation across membranes through protein molecules; monomolecular films as biomembrane models; planar lipid bilayers in relation to biomembranes; relation of liposomes to cell membranes; reconstitution of membrane transport systems; structure-function relationships in cell membranes as revealed by X-ray techniques; structure-function relationships in cell membranes as revealed by spin labeling ESR; structure and dynamics of cell membranes as revealed by NMR techniques; the effect of dietary lipids on the composition and properties of biological membranes and index

  8. Disturb or stabilise? Effects of different molecules on biological membranes

    NARCIS (Netherlands)

    Siwko, Magdalena Elzbieta

    2008-01-01

    The properties of biological membranes are often regulated by special molecules produced by organisms. Knowledge about the mechanisms by which these molecules affect biological membranes is a key issue in understanding living organisms. The interactions between phospholipid membranes and different

  9. Study of structural model of biological membranes by synchrotron radiation; Estudo estrutural de membranas modelo utilizando radiacao sincrotron

    Energy Technology Data Exchange (ETDEWEB)

    Cavalcanti, Leide Passos

    2001-07-01

    The objective of this work has been to study, from the structural point of view, the process of incorporation of various types of hydrophobic compounds into the lamellar phase of liposomes and multilayers of the zwitterionic phospholipid DPPC. X-ray diffraction and scattering techniques using synchrotron radiation, have been used to monitor changes of several bilayer systems. Thermotropic phase transitions as well as the order of the lamellar packing were studied in situ experiments. The behavior of the L{beta}' and L{alpha} phases was followed as a function of the water content in dispersions of DPPC multi lamellar vesicles with the addition of the alkaloid Ellipticine in several concentrations. The results showed a decrease in the temperature of the pre-transition as well as that of the main transition (P{beta}' ->L{alpha}). The decrease of the lamellar spacing as a function of temperature in the liquid crystalline phase leads to the description of the thermal compression coefficient in the L{alpha} phase. It was also proved that addition of the anionic lipid Cardiolipin to the DPPC/water system it is possible to promote the incorporation of Ellipticine. The aforementioned methods were used in another set of experiments to study the lamellar phases of DPPC with the addition of Polycyclic Aromatic Hydrocarbons known to have various degrees of carcinogenic activity. It was verified that the main transition temperature as well as the spacing of the multilammelar vesicles in the L{alpha} phase have a change with the incorporation of these compounds. It was possible to show that the hydrophobic PAHs favor the formation of the liquid crystalline phase, causing a broadening of the P{beta}' -> L {alpha} phase transition.The results obtained in this work are basically important in the development of thermo sensitive liposomes, which can act as drug carriers. They also contribute to the understanding of the perturbations caused by the interaction of highly

  10. Dyneins: structure, biology and disease

    National Research Council Canada - National Science Library

    King, Stephen M

    2012-01-01

    .... From bench to bedside, Dynein: Structure, Biology and Disease offers research on fundamental cellular processes to researchers and clinicians across developmental biology, cell biology, molecular biology, biophysics, biomedicine...

  11. Osmoelastic coupling in biological structures: decrease in membrane fluidity and osmophobic association of phospholipid vesicles in response to osmotic stress.

    Science.gov (United States)

    Yamazaki, M; Ohnishi, S; Ito, T

    1989-05-02

    Poly(ethylene glycol)- (PEG-) induced change in membrane fluidity and aggregation of phospholipid vesicles were studied. A threshold concentration of PEG was required to induce the aggregation. This concentration increased with a decrease in the molecular weight of PEG, e.g., from 5% (w/w) with PEG 6000 (PEG with an average molecular weight of 7500) to more than 30% (w/w) with PEG 200. The aggregation was reversible upon dilution of PEG if the initial PEG concentration was smaller than a certain value, e.g., 22% (w/w) for PEG 6000. Addition of PEG caused a decrease in membrane fluidity of the vesicles detected by fluorescence anisotropy of diphenylhexatriene and by electron spin resonance of a spin-labeled fatty acid. The anisotropy change of diphenylhexatriene fluidity change had an inflection point at approximately 5% (w/w) of PEG 6000, which might suggest that the aggregation would make the decrease of membrane fluidity smaller. Transfer of lipid molecules between phospholipid vesicles was enhanced by the PEG-induced aggregation. The enhancement occurred not only upon direct addition of PEG to the suspending medium, but also upon dialysis of the vesicle suspension against a high concentration of PEG. All these features are consistent with osmoelastic coupling in the phospholipid membranes and the subsequent osmophobic association of the vesicles. The imbalance of osmolarity between the region adjacent to the vesicle surface (exclusion layer) and the bulk aqueous phase, which results from the preferential exclusion of PEG from the exclusion layer in the case of direct addition of PEG, exerts an osmotic stress on the vesicles.(ABSTRACT TRUNCATED AT 250 WORDS)

  12. Phase-field theories for mathematical modeling of biological membranes.

    Science.gov (United States)

    Lázaro, Guillermo R; Pagonabarraga, Ignacio; Hernández-Machado, Aurora

    2015-01-01

    Biological membranes are complex structures whose mechanics are usually described at a mesoscopic level, such as the Helfrich bending theory. In this article, we present the phase-field methods, a useful tool for studying complex membrane problems which can be applied to very different phenomena. We start with an overview of the general theory of elasticity, paying special attention to its derivation from a molecular scale. We then study the particular case of membrane elasticity, explicitly obtaining the Helfrich bending energy. Within the framework of this theory, we derive a phase-field model for biological membranes and explore its physical basis and interpretation in terms of membrane elasticity. We finally explain three examples of applications of these methods to membrane related problems. First, the case of vesicle pearling and tubulation, when lipidic vesicles are exposed to the presence of hydrophobic polymers that anchor to the membrane, inducing a shape instability. Finally, we study the behavior of red blood cells while flowing in narrow microchannels, focusing on the importance of membrane elasticity to the cell flow capabilities. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  13. Static and Dynamic Membrane Structures

    Directory of Open Access Journals (Sweden)

    Sergiu Ivanov

    2012-10-01

    Full Text Available While originally P systems were defined to contain multiset rewriting rules, it turned out that considering different types of rules may produce important results, such as increasing the computational power of the rules. This paper focuses on factoring out the concept of a membrane structure out of various P system models with the goal of providing useful formalisations. Both static and dynamic membrane structures are considered.

  14. Robust mixed conducting membrane structure

    DEFF Research Database (Denmark)

    2010-01-01

    The present invention provides a membrane structure, comprising in said order a first electronically conducting layer, an ionically conducting layer, and a second electronically conducting layer, characterized in that the first and second electronically conducting layers are internally short...... circuited. The present invention further provides a method of producing the above membrane structure, comprising the steps of : providing a ionically conducting layer; applying at least one layer of electronically conducting material on each side of said ionically conducting layer; sintering the multilayer...... structure; and impregnating the electronically conducting layers with a catalyst material or catalyst precursor material....

  15. A Mechanistic Study to Determine the Structural Similarities Between Artificial Membrane Strat-M™ and Biological Membranes and Its Application to Carry Out Skin Permeation Study of Amphotericin B Nanoformulations.

    Science.gov (United States)

    Kaur, Lakhvir; Singh, Kanwaldeep; Paul, Surinder; Singh, Sukhprit; Singh, Shashank; Jain, Subheet Kumar

    2018-02-27

    Type of biological membrane used in skin permeation experiment significantly affects skin permeation and deposition potential of tested formulations. In this study, a comparative study has been carried out to evaluate the potential of a synthetic membrane (Strat-M™) with rat, human, and porcine ear skin to carry out skin permeation study of nanoformulations of a high molecular weight drug, amphotericin B. Results demonstrated that the permeation of this high molecular weight drug through Strat-M™ showed close similitude to human skin. Value of correlation coefficient (R 2 ) of log diffusion between Strat-M™ and human skin was found to be 0.99 which demonstrated the similarities of Strat-M™ membrane to the human skin. In similarity factor analysis, the value of f 2 was also found to be 85, which further demonstrated the similarities of Strat-M™ membrane to human skin. Moreover, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Brunauer-Emmett-Teller (BET) analysis of synthetic and biological membranes depicted almost similar morphological features (thickness, pore size, surface morphology, and diameter) of synthetic membrane with human skin. The results of the study demonstrated Strat-M™ as a better alternative to carry out skin permeation experiment due to the consistent results, reproducibility, easy availability, and minimum variability with human skin.

  16. Flexoelectricity in soft materials and biological membranes

    Science.gov (United States)

    Deng, Qian; Liu, Liping; Sharma, Pradeep

    2014-01-01

    Flexoelectricity and the concomitant emergence of electromechanical size-effects at the nanoscale have been recently exploited to propose tantalizing concepts such as the creation of "apparently piezoelectric" materials without piezoelectric materials, e.g. graphene, emergence of "giant" piezoelectricity at the nanoscale, enhanced energy harvesting, among others. The aforementioned developments pertain primarily to hard ceramic crystals. In this work, we develop a nonlinear theoretical framework for flexoelectricity in soft materials. Using the concept of soft electret materials, we illustrate an interesting nonlinear interplay between the so-called Maxwell stress effect and flexoelectricity, and propose the design of a novel class of apparently piezoelectric materials whose constituents are intrinsically non-piezoelectric. In particular, we show that the electret-Maxwell stress based mechanism can be combined with flexoelectricity to achieve unprecedentedly high values of electromechanical coupling. Flexoelectricity is also important for a special class of soft materials: biological membranes. In this context, flexoelectricity manifests itself as the development of polarization upon changes in curvature. Flexoelectricity is found to be important in a number of biological functions including hearing, ion transport and in some situations where mechanotransduction is necessary. In this work, we present a simple linearized theory of flexoelectricity in biological membranes and some illustrative examples.

  17. Neutron structural biology

    International Nuclear Information System (INIS)

    Niimura, Nobuo

    1999-01-01

    Neutron structural biology will be one of the most important fields in the life sciences which will interest human beings in the 21st century because neutrons can provide not only the position of hydrogen atoms in biological macromolecules but also the dynamic molecular motion of hydrogen atoms and water molecules. However, there are only a few examples experimentally determined at present because of the lack of neutron source intensity. Next generation neutron source scheduled in JAERI (Performance of which is 100 times better than that of JRR-3M) opens the life science of the 21st century. (author)

  18. Corrugated Membrane Fuel Cell Structures

    Energy Technology Data Exchange (ETDEWEB)

    Grot, Stephen [President, Ion Power Inc.

    2013-09-30

    One of the most challenging aspects of traditional PEM fuel cell stacks is the difficulty achieving the platinum catalyst utilization target of 0.2 gPt/kWe set forth by the DOE. Good catalyst utilization can be achieved with state-of-the-art catalyst coated membranes (CCM) when low catalyst loadings (<0.3 mg/cm2) are used at a low current. However, when low platinum loadings are used, the peak power density is lower than conventional loadings, requiring a larger total active area and a larger bipolar plate. This results in a lower overall stack power density not meeting the DOE target. By corrugating the fuel cell membrane electrode structure, Ion Power?s goal is to realize both the Pt utilization targets as well as the power density targets of the DOE. This will be achieved by demonstrating a fuel cell single cell (50 cm2) with a twofold increase in the membrane active area over the geometric area of the cell by corrugating the MEA structure. The corrugating structure must be able to demonstrate the target properties of < 10 mOhm-cm2 electrical resistance at > 20 psi compressive strength over the active area, in combination with offering at least 80% of power density that can be achieved by using the same MEA in a flat plate structure. Corrugated membrane fuel cell structures also have the potential to meet DOE power density targets by essentially packaging more membrane area into the same fuel cell volume as compared to conventional stack constructions.

  19. Editorial: Molecular Organization of Membranes: Where Biology Meets Biophysics

    Czech Academy of Sciences Publication Activity Database

    Cebecauer, Marek; Holowka, D.

    2017-01-01

    Roč. 5, č. 113 (2017), s. 1-3 ISSN 2296-634X Institutional support: RVO:61388955 Keywords : nanodomains * membrane properties * cell membrane Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology

  20. NMR spectroscopic studies of membrane-bound biological systems

    International Nuclear Information System (INIS)

    Hohlweg, W.

    2013-01-01

    In the course of this thesis, biological NMR spectroscopy was employed in studying membrane-bound peptides and proteins, for which structural information is still comparatively hard to obtain. Initial work focused on various model peptides bound to membrane-mimicking micelles, studying the protonation state of arginine in a membrane environment. Strong evidence for a cation-π complex was found in TM7, a peptide which forms the seventh transmembrane helix of subunit a of the vacuolar-type H+-ATPase (V-ATPase). V-ATPase is a physiologically highly relevant proton pump, which is present in intracellular membranes of all eukaryotic organisms, as well as the plasma membrane of several specialized cells. Loss of functional V-ATPase is associated with human diseases such as osteopetrosis, distal renal tubular acidosis or the spreading of cancer. V-ATPase is considered a potential drug target in the treatment of osteoporosis and cancer, or in the development of novel contraceptives. Results from NMR solution structure determination, NMR titration experiments, paramagnetic relaxation enhancement experiments and tryptophan fluorescence spectroscopy confirm the existence of a buried cation-? complex formed between arginine residue R735, which is essential for proton transport, and neighbouring tryptophan and tyrosine residues. In vivo experiments in the yeast Saccharomyces cerevisiae using selective growth tests and fluorescence microscopy showed that formation of the cation-π complex is essential for V-ATPase function. Deletion of both aromatic residues, as well as only the one tryptophan residue leads to growth defects and inability to maintain vacuolar pH homeostasis. These findings shine new light on the still elusive mechanism of proton transport in V-ATPase, and show that arginine R735 may be directly involved in proton transfer across the membrane. (author) [de

  1. Dynamic membrane structure induces temporal pattern formation.

    Science.gov (United States)

    Lippoldt, J; Händel, C; Dietrich, U; Käs, J A

    2014-10-01

    The understanding of temporal pattern formation in biological systems is essential for insights into regulatory processes of cells. Concerning this problem, the present work introduces a model to explain the attachment/detachment cycle of MARCKS and PKC at the cell membrane, which is crucial for signal transduction processes. Our model is novel with regard to its driving mechanism: Structural changes within the membrane fuel an activator-inhibitor based global density oscillation of membrane related proteins. Based on simulated results of our model, phase diagrams were generated to illustrate the interplay of MARCKS and PKC. They predict the oscillatory behavior in the form of the number of peaks, the periodic time, and the damping constant depending on the amounts of MARCKS and PKC, respectively. The investigation of the phase space also revealed an unexpected intermediate state prior to the oscillations for high amounts of MARCKS in the system. The validation of the obtained results was carried out by stability analysis, which also accounts for further enhanced understanding of the studied system. It was shown, that the occurrence of the oscillating behavior is independent of the diffusion and the consumption of the reactants. The diffusion terms in the used reaction-diffusion equations only act as modulating terms and are not required for the oscillation. The hypothesis of our work suggests a new mechanism of temporal pattern formation in biological systems. This mechanism includes a classical activator-inhibitor system, but is based on the modifications of the membrane structure, rather than a reaction-diffusion system. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Biological black water treatment combined with membrane separation

    NARCIS (Netherlands)

    van Voorthuizen, E.M.; Zwijnenburg, A.; van der Meer, Walterus Gijsbertus Joseph; Temmink, Hardy

    2008-01-01

    Separate treatment of black (toilet) water offers the possibility to recover energy and nutrients. In this study three combinations of biological treatment and membrane filtration were compared for their biological and membrane performance and nutrient conservation: a UASB followed by effluent

  3. Systems biology of cellular membranes: a convergence with biophysics.

    Science.gov (United States)

    Chabanon, Morgan; Stachowiak, Jeanne C; Rangamani, Padmini

    2017-09-01

    Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  4. Increasing Diversity of Biological Membrane Fission Mechanisms.

    Science.gov (United States)

    Renard, Henri-François; Johannes, Ludger; Morsomme, Pierre

    2018-01-04

    Membrane fission is essential to life. It is required for many fundamental cellular processes, as diverse as cyto- and karyokinesis, organelle division, membrane repair, and membrane trafficking and endocytosis. While membrane fission was originally seen as resulting from the action of mechanoenzymes such as dynamin, it is clear that the reality is more complex. In this review, we propose an updated overview of fission mechanisms, and try to extract essential requirements for each. We also present examples of cellular processes that involve these fission mechanisms. Finally, we list pending questions, whether they are specific to a peculiar fission mechanism or more general to the field. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Membrane Domains and Their Relevance to the Organization of Biological Membranes

    DEFF Research Database (Denmark)

    Bagatolli, Luis

    2012-01-01

    approaches. Thus, a section containing a historical perspective of lipid domains has been added as an introduction, recapitulating how lipid domains came into view and discussing how this phenomenon influenced different models of biological membranes. General but important aspects of the physical basis...... approaches. This includes a section on experimental results showing correlations between simple lipid mixtures and some specialized natural membranous systems. The chapter ends by discussing the pros and cons of current biological membrane models considering membrane domains, and tackles new challenges...... and future perspectives on membrane-related studies. This last section includes a critical discussion about the appropriateness of connecting phenomena observed in model membrane systems with their natural counterpart – that is, biological membranes....

  6. Electrochemically etched nanoporous silicon membrane for separation of biological molecules in mixture

    International Nuclear Information System (INIS)

    Burham, Norhafizah; Hamzah, Azrul Azlan; Yunas, Jumril; Majlis, Burhanuddin Yeop

    2017-01-01

    This paper presents a technique for separating biological molecules in mixture using nanoporous silicon membrane. Nanopores were formed using electrochemical etching process (ECE) by etching a prefabricated silicon membrane in hydrofluoric acid (HF) and ethanol, and then directly bonding it with PDMS to form a complete filtration system for separating biological molecules. Tygon S3"™ tubings were used as fluid interconnection between PDMS molds and silicon membrane during testing. Electrochemical etching parameters were manipulated to control pore structure and size. In this work, nanopores with sizes of less than 50 nm, embedded on top of columnar structures have been fabricated using high current densities and variable HF concentrations. Zinc oxide was diluted with deionized (DI) water and mixed with biological molecules and non-biological particles, namely protein standard, serum albumin and sodium chloride. Zinc oxide particles were trapped on the nanoporous silicon surface, while biological molecules of sizes up to 12 nm penetrated the nanoporous silicon membrane. The filtered particles were inspected using a Zetasizer Nano SP for particle size measurement and count. The Zetasizer Nano SP results revealed that more than 95% of the biological molecules in the mixture were filtered out by the nanoporous silicon membrane. The nanoporous silicon membrane fabricated in this work is integratable into bio-MEMS and Lab-on-Chip components to separate two or more types of biomolecules at once. The membrane is especially useful for the development of artificial kidney. (paper)

  7. Electrochemically etched nanoporous silicon membrane for separation of biological molecules in mixture

    Science.gov (United States)

    Burham, Norhafizah; Azlan Hamzah, Azrul; Yunas, Jumril; Yeop Majlis, Burhanuddin

    2017-07-01

    This paper presents a technique for separating biological molecules in mixture using nanoporous silicon membrane. Nanopores were formed using electrochemical etching process (ECE) by etching a prefabricated silicon membrane in hydrofluoric acid (HF) and ethanol, and then directly bonding it with PDMS to form a complete filtration system for separating biological molecules. Tygon S3™ tubings were used as fluid interconnection between PDMS molds and silicon membrane during testing. Electrochemical etching parameters were manipulated to control pore structure and size. In this work, nanopores with sizes of less than 50 nm, embedded on top of columnar structures have been fabricated using high current densities and variable HF concentrations. Zinc oxide was diluted with deionized (DI) water and mixed with biological molecules and non-biological particles, namely protein standard, serum albumin and sodium chloride. Zinc oxide particles were trapped on the nanoporous silicon surface, while biological molecules of sizes up to 12 nm penetrated the nanoporous silicon membrane. The filtered particles were inspected using a Zetasizer Nano SP for particle size measurement and count. The Zetasizer Nano SP results revealed that more than 95% of the biological molecules in the mixture were filtered out by the nanoporous silicon membrane. The nanoporous silicon membrane fabricated in this work is integratable into bio-MEMS and Lab-on-Chip components to separate two or more types of biomolecules at once. The membrane is especially useful for the development of artificial kidney.

  8. Structural Studies of Biological Solids Using NMR

    Science.gov (United States)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  9. Membrane Binding of Recoverin: From Mechanistic Understanding to Biological Functionality

    Czech Academy of Sciences Publication Activity Database

    Timr, S.; Pleskot, Roman; Kadlec, J.; Kohagen, M.; Magarkar, A.; Jungwirth, P.

    2017-01-01

    Roč. 3, č. 8 (2017), s. 868-874 ISSN 2374-7943 Institutional support: RVO:61389030 Keywords : recoverin * membrane * myristoyl Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Cell biology Impact factor: 7.481, year: 2016

  10. Artificial membranes for membrane protein purification, functionality and structure studies.

    Science.gov (United States)

    Parmar, Mayuriben J; Lousa, Carine De Marcos; Muench, Stephen P; Goldman, Adrian; Postis, Vincent L G

    2016-06-15

    Membrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarizes some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  11. The role of antioxidant-protein interactions in biological membrane

    International Nuclear Information System (INIS)

    McGillivray, Duncan J; Singh, Rachna; Melton, Laurence D.; Worcester, David L.; Gilbert, Elliot P.

    2009-01-01

    Full text: Oxidative damage of cellular membranes has been linked to a variety of disease pathologies, including cardiac disease, Alzheimer's and complications due to diabetes. The oxidation of unsaturated and polyunsaturated fatty acid chains found in cellular membranes leads to significant alteration in membrane physical properties, including lipid orientation and membrane permeability, which ultimately affect biological function. Polyphenols are naturally occurring phytochemicals present in a number of fruit and vegetables that are of interest for their anti-oxidative powers. These polyphenols inhibit lipid oxidation in cellular membrane surfaces, although the mechanism of this inhibition is not entirely clear. Moreover, the polyphenols have significant binding affinity for proteins, which can lead to the formation of soluble and insoluble protein-polyphenol complexes Significantly, in the presence of casein proteins the oxidation inhibition the polyphenols in the membrane is significantly enhanced (as assessed by Lipid Peroxidation Inhibition Capacity assays). Thus the antioxidant pathway appears to involve these protein/polyphenol complexes, as well as direct antioxidant action by the polyphenol. Here we discuss neutron and x-ray scattering results from phospholipid membranes, looking at the positioning of two examples of polyphenolic antioxidants in phospholipid membranes, quercetin and phloretin, the antioxidants' impact on the membrane organisation, and the interaction between antioxidant and extra-membranous protein. This information sheds light on the mechanism of antioxidant protection in these systems, which may be used to understand biological responses to oxidative stress.

  12. Structural Biology Fact Sheet

    Science.gov (United States)

    ... beta sheets (blue; thinner, tangled strands). Credit: RCSB Protein Data Bank. Even though proteins are strings of amino acids, ... structure of more than 122,000 proteins. The Protein Data Bank stores these structures and gives scientists access to ...

  13. DNA-Tile Structures Induce Ionic Currents through Lipid Membranes.

    Science.gov (United States)

    Göpfrich, Kerstin; Zettl, Thomas; Meijering, Anna E C; Hernández-Ainsa, Silvia; Kocabey, Samet; Liedl, Tim; Keyser, Ulrich F

    2015-05-13

    Self-assembled DNA nanostructures have been used to create man-made transmembrane channels in lipid bilayers. Here, we present a DNA-tile structure with a nominal subnanometer channel and cholesterol-tags for membrane anchoring. With an outer diameter of 5 nm and a molecular weight of 45 kDa, the dimensions of our synthetic nanostructure are comparable to biological ion channels. Because of its simple design, the structure self-assembles within a minute, making its creation scalable for applications in biology. Ionic current recordings demonstrate that the tile structures enable ion conduction through lipid bilayers and show gating and voltage-switching behavior. By demonstrating the design of DNA-based membrane channels with openings much smaller than that of the archetypical six-helix bundle, our work showcases their versatility inspired by the rich diversity of natural membrane components.

  14. Interactions of Cyclic Hydrocarbons with Biological Membranes

    NARCIS (Netherlands)

    SIKKEMA, J; DEBONT, JAM; POOLMAN, B

    1994-01-01

    Many cyclic hydrocarbons, e.g. aromatics, cycloalkanes, and terpenes, are toxic to microorganisms. The primary site of the toxic action is probably the cytoplasmic membrane, but the mechanism of the toxicity is still poorly understood. The effects of cyclic hydrocarbons were studied in liposomes

  15. Electrospun superhydrophobic membranes with unique structures for membrane distillation.

    Science.gov (United States)

    Liao, Yuan; Loh, Chun-Heng; Wang, Rong; Fane, Anthony G

    2014-09-24

    With modest temperature demand, low operating pressure, and high solute rejection, membrane distillation (MD) is an attractive option for desalination, waste treatment, and food and pharmaceutical processing. However, large-scale practical applications of MD are still hindered by the absence of effective membranes with high hydrophobicity, high porosity, and adequate mechanical strength, which are important properties for MD permeation fluxes, stable long-term performance, and effective packing in modules without damage. This study describes novel design strategies for highly robust superhydrophobic dual-layer membranes for MD via electrospinning. One of the newly developed membranes comprises a durable and ultrathin 3-dimensional (3D) superhydrophobic skin and porous nanofibrous support whereas another was fabricated by electrospinning 3D superhydrophobic layers on a nonwoven support. These membranes exhibit superhydrophobicity toward distilled water, salty water, oil-in-water emulsion, and beverages, which enables them to be used not only for desalination but also for other processes. The superhydrophobic dual-layer membrane #3S-N with nanofibrous support has a competitive permeation flux of 24.6 ± 1.2 kg m(-2) h(-1) in MD (feed and permeate temperate were set as 333 and 293 K, respectively) due to the higher porosity of the nanofibrous scaffold. Meanwhile, the membranes with the nonwoven support exhibit greater mechanical strength due to this support combined with better long-term performance because of the thicker 3D superhydrophobic layers. The morphology, pore size, porosity, mechanical properties, and liquid enter pressure of water of these superhydrophobic composite membranes with two different structures are reported and compared with commercial polyvinylidene fluoride membranes.

  16. Lipophilic drug transfer between liposomal and biological membranes

    DEFF Research Database (Denmark)

    Fahr, Alfred; van Hoogevest, Peter; Kuntsche, Judith

    2006-01-01

    This review presents the current knowledge on the interaction of lipophilic, poorly water soluble drugs with liposomal and biological membranes. The center of attention will be on drugs having the potential to dissolve in a lipid membrane without perturbing them too much. The degree of interaction...... is described as solubility of a drug in phospholipid membranes and the kinetics of transfer of a lipophilic drug between membranes. Finally, the consequences of these two factors on the design of lipid-based carriers for oral, as well as parenteral use, for lipophilic drugs and lead selection of oral...... lipophilic drugs is described. Since liposomes serve as model-membranes for natural membranes, the assessment of lipid solubility and transfer kinetics of lipophilic drug using liposome formulations may additionally have predictive value for bioavailability and biodistribution and the pharmacokinetics...

  17. Modeling branching pore structures in membrane filters

    Science.gov (United States)

    Sanaei, Pejman; Cummings, Linda J.

    2016-11-01

    Membrane filters are in widespread industrial use, and mathematical models to predict their efficacy are potentially very useful, as such models can suggest design modifications to improve filter performance and lifetime. Many models have been proposed to describe particle capture by membrane filters and the associated fluid dynamics, but most such models are based on a very simple structure in which the pores of the membrane are assumed to be simple circularly-cylindrical tubes spanning the depth of the membrane. Real membranes used in applications usually have much more complex geometry, with interconnected pores which may branch and bifurcate. Pores are also typically larger on the upstream side of the membrane than on the downstream side. We present an idealized mathematical model, in which a membrane consists of a series of bifurcating pores, which decrease in size as the membrane is traversed. Feed solution is forced through the membrane by applied pressure, and particles are removed from the feed either by sieving, or by particle adsorption within pores (which shrinks them). Thus the membrane's permeability decreases as the filtration progresses, ultimately falling to zero. We discuss how filtration efficiency depends on the characteristics of the branching structure. Partial support from NSF DMS 1261596 is gratefully acknowledged.

  18. Neutron structural biology

    International Nuclear Information System (INIS)

    Niimura, Nobuo

    2008-01-01

    Hydrogen atoms and water molecules around proteins and nucleic acids play a crucial role in many physiological functions. Neutron diffraction provides an experimental method of directly locating hydrogen atoms. (a) Since almost all the H atom positions can be identified experimentally, the geometrical details of certain types of H-bonds can be visualized and (b) as far as mechanistic implications are concerned, the identification of protonation and deprotonation states of certain important amino acid residues can be carried out. (c) The hydration structure around proteins and the hydration networks around DNA oligomers have been successfully characterized in several outstanding cases. These will open the new field beyond the folding structure of bio-macromolecules such as: 1) Recognition of proteins and nucleic acids through the network structure of water molecules surrounding bio-macromolecules, and 2) The nature of chemical bond in proteins and nucleic acids elucidated by the accumulation of accurate structural information of hydrogen atoms. (author)

  19. Investigating Membranes: Using Artificial Membranes to Convey Chemistry and Biology Concepts

    Science.gov (United States)

    Zrelak, Yoshi; McCallister, Gary

    2009-01-01

    While not organic in nature, quick-"growing" artificial membranes can be a profound visual aid when teaching students about cellular processes and the chemical nature of membranes. Students are often intrigued when they see biological and chemical concepts come to life before their eyes. In this article, the authors share their approach to growing…

  20. Structural Biology Guides Antibiotic Discovery

    Science.gov (United States)

    Polyak, Steven

    2014-01-01

    Modern drug discovery programs require the contribution of researchers in a number of specialist areas. One of these areas is structural biology. Using X-ray crystallography, the molecular basis of how a drug binds to its biological target and exerts its mode of action can be defined. For example, a drug that binds into the active site of an…

  1. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

    The structure and dynamics of biological molecules are essential for their function. Consequently, a wealth of experimental techniques have been developed to study these features. However, while experiments yield detailed information about geometrical features of molecules, this information...

  2. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

    The structure and dynamics of biological molecules are essential for their function. Consequently, a wealth of experimental techniques have been developed to study these features. However, while experiments yield detailed information about geometrical features of molecules, this information is of...

  3. Neutron structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-03-01

    Neutron diffraction provides an experimental method of directly locating hydrogen atoms in protein which play important roles in physiological functions. However, there are relatively few examples of neutron crystallography in biology since it takes a lot of time to collect a sufficient number of Bragg reflections due to the low flux of neutrons illuminating the sample. In order to overcome the flux problem, we have successfully developed the neutron IP, where the neutron converter, {sup 6}Li or Gd, was mixed with a photostimulated luminescence material on flexible plastic support. Neutron Laue diffraction 2A data from tetragonal lysozyme were collected for 10 days with neutron imaging plates, and 960 hydrogen atoms in the molecule and 157 bound water molecules were identified. These results explain the proposed hydrolysis mechanism of the sugar by the lysozyme molecule and that lysozyme is less active at pH7.0. (author)

  4. Hierarchically structured, nitrogen-doped carbon membranes

    KAUST Repository

    Wang, Hong

    2017-08-03

    The present invention is a structure, method of making and method of use for a novel macroscopic hierarchically structured, nitrogen-doped, nano-porous carbon membrane (HNDCMs) with asymmetric and hierarchical pore architecture that can be produced on a large-scale approach. The unique HNDCM holds great promise as components in separation and advanced carbon devices because they could offer unconventional fluidic transport phenomena on the nanoscale. Overall, the invention set forth herein covers a hierarchically structured, nitrogen-doped carbon membranes and methods of making and using such a membranes.

  5. Fabrication of Ceramic Membrane Chromatography for Biologics Purification

    Directory of Open Access Journals (Sweden)

    Maizirwan Mel

    2011-12-01

    Full Text Available Chromatography is one of the most important separation processes of choice for the recovery/purification of proteins and complex bio-structures. Fabrication of chromatographic membranes and their efficiency in the chromatography process has been the subject of many recent researches. In this study, a coin-like, 13 mm diameter and 3 mm thick, ceramic membrane was fabricated to be used as a chromatographic medium. The membrane is used to replace the conventional resin-based chromatography columns. Hydroxyapatite (HA powder was used as a material for the membrane fabrication. In this project, a HA powder was produced using starch as pore creating agents. Characterization processes were done for the ceramic membrane using the suitable apparatuses. Three parameters of the fabrication process (starch wt %, compaction pressure and sintering temperature were manipulated to optimize the performance of the membrane. The fabricated membrane was placed in a (FPLC system to be tested for its performance as an adsorptive membrane. (IMAC process was run by immobilizing Ni2+ ions at the membrane particles surfaces. NP protein of the (NDV was used to test the membrane's ability to bind Histidine-tagged proteins. The optimum set of process parameters that yielded in the highest porosity and good chromatogram was determined to be 5 wt % starch, 3000 psi compaction pressure and 1100°C sintering temperature.ABSTRAK: Kromatografi merupakan satu daripada proses pengasingan yang penting yang dipilih untuk perolehan/penapisan protein dan biostruktur yang kompleks. Pemfabrikatan membran kromatografi dan kecekapannya dalam proses kromatografi merupakan fokus beberapa kajian terkini. Dalam kajian ini, membran seramik berbentuk duit syiling, berdiameter 13 mm dengan ketebalan 3 mm, direka untuk digunakan sebagai perantara kromatografi. Membran ini digunakan untuk menggantikan turus kromatografi berasaskan resin yang lazim. Serbuk hidroksiapatit (HA digunakan sebagai bahan

  6. Entropy and biological systems: experimentally-investigated entropy-driven stacking of plant photosynthetic membranes.

    Science.gov (United States)

    Jia, Husen; Liggins, John R; Chow, Wah Soon

    2014-02-24

    According to the Second Law of Thermodynamics, an overall increase of entropy contributes to the driving force for any physicochemical process, but entropy has seldom been investigated in biological systems. Here, for the first time, we apply Isothermal Titration Calorimetry (ITC) to investigate the Mg(2+)-induced spontaneous stacking of photosynthetic membranes isolated from spinach leaves. After subtracting a large endothermic interaction of MgCl₂ with membranes, unrelated to stacking, we demonstrate that the enthalpy change (heat change at constant pressure) is zero or marginally positive or negative. This first direct experimental evidence strongly suggests that an entropy increase significantly drives membrane stacking in this ordered biological structure. Possible mechanisms for the entropy increase include: (i) the attraction between discrete oppositely-charged areas, releasing counterions; (ii) the release of loosely-bound water molecules from the inter-membrane gap; (iii) the increased orientational freedom of previously-aligned water dipoles; and (iv) the lateral rearrangement of membrane components.

  7. Ice formation in model biological membranes in the presence of cryoprotectors

    Energy Technology Data Exchange (ETDEWEB)

    Kiselev, M.A. E-mail: kiselev@nf.jinr.ru; Lesieur, P.; Kisselev, A.M.; Ollivon, M

    2000-06-21

    Ice formation in model biological membranes is studied by SAXS and WAXS in the presence of cryoprotectors: dimethyl sulfoxide and glycerol. Three types of phospholipid membranes: DPPC, DMPC, DSPC are chosen for the investigation as well-studied model biological membranes. A special cryostat is used for sample cooling from 14.1 deg. C to -55.4 deg. C. The ice formation is detected only by WAXS in binary phospholipid/water and ternary phospholipid/cryoprotector/water systems in the condition of excess solvent. Ice formation in a binary phospholipid/water system creates an abrupt decrease of the membrane repeat distance by {delta}d, the so-called ice-induced dehydration of intermembrane space. The value of {delta}d decreases as the cryoprotector concentration increases. The formation of ice does not influence the membrane structure ({delta}d=0) for cryoprotector mole fractions higher than 0.05.

  8. Applications of membrane computing in systems and synthetic biology

    CERN Document Server

    Gheorghe, Marian; Pérez-Jiménez, Mario

    2014-01-01

    Membrane Computing was introduced as a computational paradigm in Natural Computing. The models introduced, called Membrane (or P) Systems, provide a coherent platform to describe and study living cells as computational systems. Membrane Systems have been investigated for their computational aspects and employed to model problems in other fields, like: Computer Science, Linguistics, Biology, Economy, Computer Graphics, Robotics, etc. Their inherent parallelism, heterogeneity and intrinsic versatility allow them to model a broad range of processes and phenomena, being also an efficient means to solve and analyze problems in a novel way. Membrane Computing has been used to model biological systems, becoming with time a thorough modeling paradigm comparable, in its modeling and predicting capabilities, to more established models in this area. This book is the result of the need to collect, in an organic way, different facets of this paradigm. The chapters of this book, together with the web pages accompanying th...

  9. Chemo-mechanical model of biological membranes for actuation mechanisms

    Science.gov (United States)

    Sundaresan, Vishnu-Baba; Leo, Donald J.

    2005-05-01

    Plants have the ability to develop large mechanical force from chemical energy available with bio-fuels. The energy released by ATP hydrolysis assists the transport of ions and fluids to achieve volumetric expansion and homeostasis. Materials that develop pressure and hence strain similar to bio-materials are classified as nastic materials. Recent calculations for controlled actuation of an active material inspired by biological transport mechanism demonstrated the feasibility of developing such a material with actuation energy densities on the order of 100 kJ/m3. Our initial investigation was based on capsules that generate pressure thus causing strain in the surrounding matrix material. Our present work focuses on our efforts to fabricate a representative actuation structure and describes the chemo-mechanical constitutive equation for such a material. The actuator considered in this work is a laminated arrangement of a hydraulic actuator plate with microscopic barrels and a fluid reservoir kept separated by a semi-permeable membrane dispersed with biological transporters. We present here our initial design and a mathematical model to predict the fluid flux and strain developed in such an actuator.

  10. Structural biology of Molecular machines

    Indian Academy of Sciences (India)

    Administrator

    a structural biology perspective. TANWEER HUSSAIN. Molecular Reproduction, Development and Genetics (MRDG). Indian Institute of Science (IISc). Bangalore. Symposium on “Molecular Machines: a multidiscipline enterprise” 1st July 2017. 28th mid-year meeting of Indian Academy of Sciences at IISc, Bangalore ...

  11. Emergent mechanics of biological structures

    Science.gov (United States)

    Dumont, Sophie; Prakash, Manu

    2014-01-01

    Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead. PMID:25368421

  12. Plant membranes a biophysical approach to structure, development and senescence

    CERN Document Server

    Leshem, Ya’Acov Y

    1992-01-01

    The plasma membrane is at once the window through which the cell senses the environment and the portal through which the environment influences the structure and activities of the cell. Its importance in cellular physiology can thus hardly be overestimated, since constant flow of materials between cell and environment is essential to the well-being of any biological system. The nature of the materials mov­ ing into the cell is also critical, since some substances are required for maintenance and growth, while others, because of their toxicity, must either be rigorously excluded or permitted to enter only after chemical alteration. Such alteration frequently permits the compounds to be sequestered in special cellular compartments having different types of membranes. This type of homogeneity, plus the fact that the wear and tear of transmembrane molecular traffic compels the system to be constantly monitored and repaired, means that the membrane system of any organism must be both structurally complex and dy­...

  13. Discovery of novel membrane binding structures and functions

    Science.gov (United States)

    Kufareva, Irina; Lenoir, Marc; Dancea, Felician; Sridhar, Pooja; Raush, Eugene; Bissig, Christin; Gruenberg, Jean; Abagyan, Ruben; Overduin, Michael

    2014-01-01

    The function of a protein is determined by its intrinsic activity in the context of its subcellular distribution. Membranes localize proteins within cellular compartments and govern their specific activities. Discovering such membrane-protein interactions is important for understanding biological mechanisms, and could uncover novel sites for therapeutic intervention. Here we present a method for detecting membrane interactive proteins and their exposed residues that insert into lipid bilayers. Although the development process involved analysis of how C1b, C2, ENTH, FYVE, Gla, pleckstrin homology (PH) and PX domains bind membranes, the resulting Membrane Optimal Docking Area (MODA) method yields predictions for a given protein of known three dimensional structures without referring to canonical membrane-targeting modules. This approach was tested on the Arf1 GTPase, ATF2 acetyltransferase, von Willebrand factor A3 domain and Neisseria gonorrhoeae MsrB protein, and further refined with membrane interactive and non-interactive FAPP1 and PKD1 pleckstrin homology domains, respectively. Furthermore we demonstrate how this tool can be used to discover unprecedented membrane binding functions as illustrated by the Bro1 domain of Alix, which was revealed to recognize lysobisphosphatidic acid (LBPA). Validation of novel membrane-protein interactions relies on other techniques such as nuclear magnetic resonance spectroscopy (NMR) which was used here to map the sites of micelle interaction. Together this indicates that genome-wide identification of known and novel membrane interactive proteins and sites is now feasible, and provides a new tool for functional annotation of the proteome. PMID:25394204

  14. Continuous Modeling of Calcium Transport Through Biological Membranes

    Science.gov (United States)

    Jasielec, J. J.; Filipek, R.; Szyszkiewicz, K.; Sokalski, T.; Lewenstam, A.

    2016-08-01

    In this work an approach to the modeling of the biological membranes where a membrane is treated as a continuous medium is presented. The Nernst-Planck-Poisson model including Poisson equation for electric potential is used to describe transport of ions in the mitochondrial membrane—the interface which joins mitochondrial matrix with cellular cytosis. The transport of calcium ions is considered. Concentration of calcium inside the mitochondrion is not known accurately because different analytical methods give dramatically different results. We explain mathematically these differences assuming the complexing reaction inside mitochondrion and the existence of the calcium set-point (concentration of calcium in cytosis below which calcium stops entering the mitochondrion).

  15. Structure and function in biology

    International Nuclear Information System (INIS)

    Hirs, C.H.W.

    1976-01-01

    A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

  16. Peroxynitrous acid induces structural and functional modifications to basement membranes and its key component, laminin

    DEFF Research Database (Denmark)

    Degendorfer, Georg; Chuang, Christine Y.; Hammer, Astrid

    2015-01-01

    Basement membranes (BM) are specialized extracellular matrices underlying endothelial cells in the artery wall. Laminin, the most abundant BM glycoprotein, is a structural and biologically active component. Peroxynitrous acid (ONOOH), a potent oxidizing and nitrating agent, is formed in vivo...

  17. Overcoming barriers to membrane protein structure determination

    NARCIS (Netherlands)

    Bill, Roslyn M.; Henderson, Peter J. F.; Iwata, So; Kunji, Edmund R. S.; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G.; Vogel, Horst

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new

  18. Ion transport through biological membranes an integrated theoretical approach

    CERN Document Server

    Mackey, Michael C

    1975-01-01

    This book illustrates some of the ways physics and mathematics have been, and are being, used to elucidate the underlying mechan­ isms of passive ion movement through biological membranes in general, and the membranes of excltable cells in particular. I have made no effort to be comprehensive in my introduction of biological material and the reader interested in a brief account of single cell electro­ physlology from a physically-oriented biologists viewpoint will find the chapters by Woodbury (1965) an excellent introduction. Part I is introductory in nature, exploring the basic electrical properties of inexcitable and excitable cell plasma membranes. Cable theory is utilized to illustrate the function of the non-decrementing action potential as a signaling mechanism for the long range trans­ mission of information in the nervous system, and to gain some in­ sight into the gross behaviour of neurons. The detailed analysis of Hodgkin and Huxley on the squid giant axon membrane ionic conductance properties...

  19. Dissipative structures and biological rhythms

    Science.gov (United States)

    Goldbeter, Albert

    2017-10-01

    Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms. Two tables present the main examples of cellular and supracellular rhythms ordered according to their period, and their role in physiology and pathophysiology. Among the rhythms discussed are neural and cardiac rhythms, metabolic oscillations such as those occurring in glycolysis in yeast, intracellular Ca++ oscillations, cyclic AMP oscillations in Dictyostelium amoebae, the segmentation clock that controls somitogenesis, pulsatile hormone secretion, circadian rhythms which occur in all eukaryotes and some bacteria with a period close to 24 h, the oscillatory dynamics of the enzymatic network driving the cell cycle, and oscillations in transcription factors such as NF-ΚB and tumor suppressors such as p53. Ilya Prigogine's concept of dissipative structures applies to temporal oscillations and allows us to unify within a common framework the various rhythms observed at different levels of biological organization, regardless of their period and underlying mechanism.

  20. Primate cathelicidin orthologues display different structures and membrane interactions.

    Science.gov (United States)

    Morgera, Francesca; Vaccari, Lisa; Antcheva, Nikolinka; Scaini, Denis; Pacor, Sabrina; Tossi, Alessandro

    2009-02-01

    The human cathelicidin LL-37 displays both direct antibacterial activities and the capacity to modulate host-cell activities. These depend on structural characteristics that are subject to positive selection for variation, as observed in a previous analysis of the CAMP gene (encoding LL-37) in primates. The altered balance between cationic and anionic residues in different primate orthologues affects intramolecular salt-bridging and influences the stability of the helical conformation and tendency to aggregate in solution of the peptide. In the present study, we have analysed the effects of these structural variations on membrane interactions for human LL-37, rhesus RL-37 and orang-utan LL-37, using several complementary biophysical and biochemical methods. CD and ATR (attenuated total reflection)-FTIR (Fourier-transform IR) spectroscopy on model membranes indicate that RL-37, which is monomeric and unstructured in bulk solution [F-form (free form)], and human LL-37, which is partly structured and probably aggregated [A-form (aggregated form)], bind biological membranes in different manners. RL-37 may insert more deeply into the lipid bilayer than LL-37, which remains aggregated. AFM (atomic force microscopy) performed on the same supported bilayer as used for ATR-FTIR measurements suggests a carpet-like mode of permeabilization for RL37 and formation of more defined worm-holes for LL-37. Comparison of data from the biological activity on bacterial cells with permeabilization of model membranes indicates that the structure/aggregation state also affects the trajectory of the peptides from bulk solution through the outer cell-wall layers to the membrane. The results of the present study suggest that F-form cathelicidin orthologues may have evolved to have primarily a direct antimicrobial defensive capacity, whereas the A-forms have somewhat sacrificed this to gain host-cell modulating functions.

  1. Structural Biology: Practical NMR Applications

    CERN Document Server

    Teng, Quincy

    2005-01-01

    This textbook begins with an overview of NMR development and applications in biological systems. It describes recent developments in instrument hardware and methodology. Chapters highlight the scope and limitation of NMR methods. While detailed math and quantum mechanics dealing with NMR theory have been addressed in several well-known NMR volumes, chapter two of this volume illustrates the fundamental principles and concepts of NMR spectroscopy in a more descriptive manner. Topics such as instrument setup, data acquisition, and data processing using a variety of offline software are discussed. Chapters further discuss several routine stategies for preparing samples, especially for macromolecules and complexes. The target market for such a volume includes researchers in the field of biochemistry, chemistry, structural biology and biophysics.

  2. Plasma membrane--cortical cytoskeleton interactions: a cell biology approach with biophysical considerations.

    Science.gov (United States)

    Kapus, András; Janmey, Paul

    2013-07-01

    From a biophysical standpoint, the interface between the cell membrane and the cytoskeleton is an intriguing site where a "two-dimensional fluid" interacts with an exceedingly complex three-dimensional protein meshwork. The membrane is a key regulator of the cytoskeleton, which not only provides docking sites for cytoskeletal elements through transmembrane proteins, lipid binding-based, and electrostatic interactions, but also serves as the source of the signaling events and molecules that control cytoskeletal organization and remolding. Conversely, the cytoskeleton is a key determinant of the biophysical and biochemical properties of the membrane, including its shape, tension, movement, composition, as well as the mobility, partitioning, and recycling of its constituents. From a cell biological standpoint, the membrane-cytoskeleton interplay underlies--as a central executor and/or regulator--a multitude of complex processes including chemical and mechanical signal transduction, motility/migration, endo-/exo-/phagocytosis, and other forms of membrane traffic, cell-cell, and cell-matrix adhesion. The aim of this article is to provide an overview of the tight structural and functional coupling between the membrane and the cytoskeleton. As biophysical approaches, both theoretical and experimental, proved to be instrumental for our understanding of the membrane/cytoskeleton interplay, this review will "oscillate" between the cell biological phenomena and the corresponding biophysical principles and considerations. After describing the types of connections between the membrane and the cytoskeleton, we will focus on a few key physical parameters and processes (force generation, curvature, tension, and surface charge) and will discuss how these contribute to a variety of fundamental cell biological functions. © 2013 American Physiological Society.

  3. Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes.

    Science.gov (United States)

    Kulig, Waldemar; Mikkolainen, Heikki; Olżyńska, Agnieszka; Jurkiewicz, Piotr; Cwiklik, Lukasz; Hof, Martin; Vattulainen, Ilpo; Jungwirth, Pavel; Rog, Tomasz

    2018-03-01

    Translocation of sterols between cellular membrane leaflets is of key importance in membrane organization, dynamics, and signaling. We present a novel translocation mechanism that differs in a unique manner from the established ones. The bobbing mechanism identified here is demonstrated for tail-oxidized sterols, but is expected to be viable for any molecule containing two polar centers at the opposite sides of the molecule. The mechanism renders translocation across a lipid membrane possible without a change in molecular orientation. For tail-oxidized sterols, the bobbing mechanism provides an exceptionally facile means to translocate these signaling molecules across membrane structures and may thus represent an important pathway in the course of their biological action.

  4. Review of Large Spacecraft Deployable Membrane Antenna Structures

    Science.gov (United States)

    Liu, Zhi-Quan; Qiu, Hui; Li, Xiao; Yang, Shu-Li

    2017-11-01

    The demand for large antennas in future space missions has increasingly stimulated the development of deployable membrane antenna structures owing to their light weight and small stowage volume. However, there is little literature providing a comprehensive review and comparison of different membrane antenna structures. Space-borne membrane antenna structures are mainly classified as either parabolic or planar membrane antenna structures. For parabolic membrane antenna structures, there are five deploying and forming methods, including inflation, inflation-rigidization, elastic ribs driven, Shape Memory Polymer (SMP)-inflation, and electrostatic forming. The development and detailed comparison of these five methods are presented. Then, properties of membrane materials (including polyester film and polyimide film) for parabolic membrane antennas are compared. Additionally, for planar membrane antenna structures, frame shapes have changed from circular to rectangular, and different tensioning systems have emerged successively, including single Miura-Natori, double, and multi-layer tensioning systems. Recent advances in structural configurations, tensioning system design, and dynamic analysis for planar membrane antenna structures are investigated. Finally, future trends for large space membrane antenna structures are pointed out and technical problems are proposed, including design and analysis of membrane structures, materials and processes, membrane packing, surface accuracy stability, and test and verification technology. Through a review of large deployable membrane antenna structures, guidance for space membrane-antenna research and applications is provided.

  5. High Cholesterol/Low Cholesterol: Effects in Biological Membranes: A Review.

    Science.gov (United States)

    Subczynski, Witold K; Pasenkiewicz-Gierula, Marta; Widomska, Justyna; Mainali, Laxman; Raguz, Marija

    2017-12-01

    Lipid composition determines membrane properties, and cholesterol plays a major role in this determination as it regulates membrane fluidity and permeability, as well as induces the formation of coexisting phases and domains in the membrane. Biological membranes display a very diverse lipid composition, the lateral organization of which plays a crucial role in regulating a variety of membrane functions. We hypothesize that, during biological evolution, membranes with a particular cholesterol content were selected to perform certain functions in the cells of eukaryotic organisms. In this review, we discuss the major membrane properties induced by cholesterol, and their relationship to certain membrane functions.

  6. Diffraction structural biology – a new horizon

    Energy Technology Data Exchange (ETDEWEB)

    Yamane, Takashi [Nagoya Industrial Science Research Institute, 1-13 Yotsuya-dori, Chikusa-ku, Nagoya 464-0819 (Japan); Helliwell, John R. [University of Manchester, Manchester M13 9PL (United Kingdom); Johnson, John E. [Scripps Research Institute, San Diego, CA (United States); Yasuoka, Noritake, E-mail: nori-yasuoka@nifty.com [AIST Kansai Center, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan); Sakabe, Noriyoshi [Photon Factory, KEK, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan)

    2013-11-01

    An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal. An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal.

  7. Probing Induced Structural Changes in Biomimetic Bacterial Cell Membrane Interactions with Divalent Cations

    Energy Technology Data Exchange (ETDEWEB)

    Holt, Allison M [ORNL; Standaert, Robert F [ORNL; Jubb, Aaron M [ORNL; Katsaras, John [ORNL; Johs, Alexander [ORNL

    2017-01-01

    Biological membranes, formed primarily by the self-assembly of complex mixtures of phospholipids, provide a structured scaffold for compartmentalization and structural processes in living cells. The specific physical properties of phospholipid species present in a given membrane play a key role in mediating these processes. Phosphatidylethanolamine (PE), a zwitterionic lipid present in bacterial, yeast, and mammalian cell membranes, is exceptional. In addition to undergoing the standard lipid polymorphic transition between the gel and liquid-crystalline phase, it can also assume an unusual polymorphic state, the inverse hexagonal phase (HII). Divalent cations are among the factors that drive the formation of the HII phase, wherein the lipid molecules form stacked tubular structures by burying the hydrophilic head groups and exposing the hydrophobic tails to the bulk solvent. Most biological membranes contain a lipid species capable of forming the HII state suggesting that such lipid polymorphic structural states play an important role in structural biological processes such as membrane fusion. In this study, the interactions between Mg2+ and biomimetic bacterial cell membranes composed of PE and phosphatidylglycerol (PG) were probed using differential scanning calorimetry (DSC), small-angle x-ray scattering (SAXS), and fluorescence spectroscopy. The lipid phase transitions were examined at varying ratios of PE to PG and upon exposure to physiologically relevant concentrations of Mg2+. An understanding of these basic interactions enhances our understanding of membrane dynamics and how membrane-mediated structural changes may occur in vivo.

  8. Environmental behaviour of tensile membrane structures

    OpenAIRE

    Elnokaly, Amira; Chilton, John; Wilson, Robin

    2002-01-01

    This paper considers the environmental properties of spaces enclosed by tensile membrane structures (TMS). Limitations in the understanding of the environmental and thermal performance of TMS have to some extent hindered their acceptance by building clients and the building industry. A review of the early attempts to model the thermal environment of spaces enclosed by TMS is given and their environmental and thermal properties are discussed. The lack of appropriate tools for the investigation...

  9. A glimpse of structural biology through X-ray crystallography.

    Science.gov (United States)

    Shi, Yigong

    2014-11-20

    Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

  10. Track structure in biological models.

    Science.gov (United States)

    Curtis, S B

    1986-01-01

    High-energy heavy ions in the galactic cosmic radiation (HZE particles) may pose a special risk during long term manned space flights outside the sheltering confines of the earth's geomagnetic field. These particles are highly ionizing, and they and their nuclear secondaries can penetrate many centimeters of body tissue. The three dimensional patterns of ionizations they create as they lose energy are referred to as their track structure. Several models of biological action on mammalian cells attempt to treat track structure or related quantities in their formulation. The methods by which they do this are reviewed. The proximity function is introduced in connection with the theory of Dual Radiation Action (DRA). The ion-gamma kill (IGK) model introduces the radial energy-density distribution, which is a smooth function characterizing both the magnitude and extension of a charged particle track. The lethal, potentially lethal (LPL) model introduces lambda, the mean distance between relevant ion clusters or biochemical species along the track. Since very localized energy depositions (within approximately 10 nm) are emphasized, the proximity function as defined in the DRA model is not of utility in characterizing track structure in the LPL formulation.

  11. Bicelles: A natural 'molecular goniometer' for structural, dynamical and topological studies of molecules in membranes.

    Science.gov (United States)

    Diller, Anna; Loudet, Cécile; Aussenac, Fabien; Raffard, Gérard; Fournier, Sylvie; Laguerre, Michel; Grélard, Axelle; Opella, Stanley J; Marassi, Francesca M; Dufourc, Erick J

    2009-06-01

    Major biological processes occur at the biological membrane. One of the great challenges is to understand the function of chemical or biological molecules inside the membrane; as well of those involved in membrane trafficking. This requires obtaining a complete picture of the in situ structure and dynamics as well as the topology and orientation of these molecules in the membrane lipid bilayer. These led to the creation of several innovative models of biological membranes in order to investigate the structure and dynamics of amphiphilic molecules, as well as integral membrane proteins having single or multiple transmembrane segments. Because the determination of the structure, dynamics and topology of molecules in membranes requires a macroscopic alignment of the system, a new membrane model called 'bicelles' that represents a crossover between lipid vesicles and classical micelles has become very popular due to its property of spontaneous self-orientation in magnetic fields. In addition, crucial factors involved in mimicking natural membranes, such as sample hydration, pH and salinity limits, are easy to control in bicelle systems. Bicelles are composed of mixtures of long chain (14-18 carbons) and short chain phospholipids (6-8 carbons) hydrated up to 98% with buffers and may adopt various morphologies depending on lipid composition, temperature and hydration. We have been developing bicelle systems under the form of nano-discs made of lipids with saturated or biphenyl-containing fatty acyl chains. Depending on the lipid nature, these membranous nano-discs may be macroscopically oriented with their normal perpendicular or parallel to the magnetic field, providing a natural 'molecular goniometer' for structural and topological studies, especially in the field of NMR. Bicelles can also be spun at the magic angle and lead to the 3D structural determination of molecules in membranes.

  12. A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes.

    Science.gov (United States)

    Tanizaki, Seiichiro; Feig, Michael

    2005-03-22

    Reliable computer simulations of complex biological environments such as integral membrane proteins with explicit water and lipid molecules remain a challenging task. We propose a modification of the standard generalized Born theory of homogeneous solvent for modeling the heterogeneous dielectric environments such as lipid/water interfaces. Our model allows the representation of biological membranes in the form of multiple layered dielectric regions with dielectric constants that are different from the solute cavity. The proposed new formalism is shown to predict the electrostatic component of solvation free energy with a relative error of 0.17% compared to exact finite-difference solutions of the Poisson equation for a transmembrane helix test system. Molecular dynamics simulations of melittin and bacteriorhodopsin are carried out and performed over 10 ns and 7 ns of simulation time, respectively. The center of melittin along the membrane normal in these stable simulations is in excellent agreement with the relevant experimental data. Simulations of bacteriorhodopsin started from the experimental structure remained stable and in close agreement with experiment. We also examined the free energy profiles of water and amino acid side chain analogs upon membrane insertion. The results with our implicit membrane model agree well with the experimental transfer free energy data from cyclohexane to water as well as explicit solvent simulations of water and selected side chain analogs.

  13. Lipid polymorphism and the functional roles of lipids in biological membranes

    NARCIS (Netherlands)

    Cullis, P.R.; Kruijff, B. de

    1979-01-01

    The reasons for the great variety of lipids found in biological membranes, and the relations between lipid composition and membrane function pose major unsolved problems in membrane biology. Perhaps the only major functional role of lipids which may be regarded as firmly established involves the

  14. Flexoelectricity in two-dimensional crystalline and biological membranes

    Science.gov (United States)

    Ahmadpoor, Fatemeh; Sharma, Pradeep

    2015-10-01

    The ability of a material to convert electrical stimuli into mechanical deformation, i.e. piezoelectricity, is a remarkable property of a rather small subset of insulating materials. The phenomenon of flexoelectricity, on the other hand, is universal. All dielectrics exhibit the flexoelectric effect whereby non-uniform strain (or strain gradients) can polarize the material and conversely non-uniform electric fields may cause mechanical deformation. The flexoelectric effect is strongly enhanced at the nanoscale and accordingly, all two-dimensional membranes of atomistic scale thickness exhibit a strong two-way coupling between the curvature and electric field. In this review, we highlight the recent advances made in our understanding of flexoelectricity in two-dimensional (2D) membranes--whether the crystalline ones such as dielectric graphene nanoribbons or the soft lipid bilayer membranes that are ubiquitous in biology. Aside from the fundamental mechanisms, phenomenology, and recent findings, we focus on rapidly emerging directions in this field and discuss applications such as energy harvesting, understanding of the mammalian hearing mechanism and ion transport among others.

  15. Factors Determining the Oxygen Permeability of Biological Membranes: Oxygen Transport Across Eye Lens Fiber-Cell Plasma Membranes.

    Science.gov (United States)

    Subczynski, Witold Karol; Widomska, Justyna; Mainali, Laxman

    2017-01-01

    Electron paramagnetic resonance (EPR) spin-label oximetry allows the oxygen permeability coefficient to be evaluated across homogeneous lipid bilayer membranes and, in some cases, across coexisting membrane domains without their physical separation. The most pronounced effect on oxygen permeability is observed for cholesterol, which additionally induces the formation of membrane domains. In intact biological membranes, integral proteins induce the formation of boundary and trapped lipid domains with a low oxygen permeability. The effective oxygen permeability coefficient across the intact biological membrane is affected not only by the oxygen permeability coefficients evaluated for each lipid domain but also by the surface area occupied by these domains in the membrane. All these factors observed in fiber cell plasma membranes of clear human eye lenses are reviewed here.

  16. Class I Cytokine Receptors: Structure and function in the Membrane

    DEFF Research Database (Denmark)

    Bugge, Katrine Østergaard

    Class I cytokine receptors are involved in important biological functions of both physiological and pathological nature in mammals. However, the molecular details of the cross-membrane signal transduction through these receptors remain obscure. One of the major reasons for this is the lack...... ample material of high quality for structural studies with NMR spectroscopy of several class I cytokine receptor TMDs. Furthermore, the structure of a class I cytokine receptor TMD in DHPC micelles was solved with solution-state NMR spectroscopy. Additionally, since structural studies of intact proteins...... receptor. This integrative structure opens up for interpreting these receptors in their intact form and offers unique insights on the topology of single-pass transmembrane receptors with intrinsically disordered domains. Dimerization of the TMDs of class I cytokine receptors has been shown to be important...

  17. Extracellular membrane vesicles in blood products-biology and clinical relevance

    Directory of Open Access Journals (Sweden)

    Emilija Krstova Krajnc

    2016-01-01

    Full Text Available Extracellular membrane vesicles are fragments shed from plasma membranes off all cell types that are undergoing apoptosis or are being subjected to various types of stimulation or stress.  Even in the process of programmed cell death (apoptosis, cell fall apart of varying size vesicles. They expose phosphatidylserine (PS on the outer leaflet of their membrane, and bear surface membrane antigens reflecting their cellular origin. Extracellular membrane vesicles have been isolated from many types of biological fluids, including serum, cerebrospinal fluid, urine, saliva, tears and conditioned culture medium. Flow cytometry is one of the many different methodological approaches that have been used to analyze EMVs. The method attempts to characterize the EMVs cellular origin, size, population, number, and structure. EMVs are present and accumulate in blood products (erythrocytes, platelets as well as in fresh frozen plasma during storage. The aim of this review is to highlight the importance of extracellular vesicles as a cell-to-cell communication system and the role in the pathogenesis of different diseases. Special emphasis will be given to the implication of extracellular membrane vesicles in blood products and their clinical relevance. Although our understanding of the role of  EMVs in disease is far from comprehensive, they display promise as biomarkers for different diseases in the future and also as a marker of quality and safety in the quality control of blood products.

  18. Ion transport across the biological membrane by computational protein design

    Science.gov (United States)

    Grigoryan, Gevorg

    The cellular membrane is impermeable to most of the chemicals the cell needs to take in or discard to survive. Therefore, transporters-a class of transmembrane proteins tasked with shuttling cargo chemicals in and out of the cell-are essential to all cellular life. From existing crystal structures, we know transporters to be complex machines, exquisitely tuned for specificity and controllability. But how could membrane-bound life have evolved if it needed such complex machines to exist first? To shed light onto this question, we considered the task of designing a transporter de novo. As our guiding principle, we took the ``alternating-access model''-a conceptual mechanism stating that transporters work by rocking between two conformations, each exposing the cargo-binding site to either the intra- or the extra-cellular environment. A computational design framework was developed to encode an anti-parallel four-helix bundle that rocked between two alternative states to orchestrate the movement of Zn(II) ions across the membrane. The ensemble nature of both states was accounted for using a free energy-based approach, and sequences were chosen based on predicted formation of the targeted topology in the membrane and bi-stability. A single sequence was prepared experimentally and shown to function as a Zn(II) transporter in lipid vesicles. Further, transport was specific to Zn(II) ions and several control peptides supported the underlying design principles. This included a mutant designed to retain all properties but with reduced rocking, which showed greatly depressed transport ability. These results suggest that early transporters could have evolved in the context of simple topologies, to be later tuned by evolution for improved properties and controllability. Our study also serves as an important advance in computational protein design, showing the feasibility of designing functional membrane proteins and of tuning conformational landscapes for desired function

  19. Biological evaluation of silver nanoparticles incorporated into chitosan-based membranes

    NARCIS (Netherlands)

    Shao, J.; Yu, N.; Kolwijck, E.; Wang, B.; Tan, K.W.; Jansen, J.A.; Walboomers, X.F.; Yang, F.

    2017-01-01

    AIM: To evaluate the antibacterial potential and biological performance of silver nanoparticles in chitosan-based membranes. MATERIALS & METHODS: Electrospun chitosan/poly(ethylene oxide) membranes with different amounts of silver nanoparticles were evaluated for antibacterial properties and

  20. Structural Biology of Proline Catabolic Enzymes.

    Science.gov (United States)

    Tanner, John J

    2017-11-13

    Proline catabolism refers to the 4-electron oxidation of proline to glutamate catalyzed by the enzymes proline dehydrogenase (PRODH) and l-glutamate γ-semialdehyde dehydrogenase (GSALDH, aka ALDH4A1). These enzymes and the intermediate metabolites of the pathway have been implicated in tumor growth and suppression, metastasis, hyperprolinemia metabolic disorders, schizophrenia susceptibility, life span extension, and pathogen virulence and survival. In some bacteria, PRODH and GSALDH are combined into a bifunctional enzyme known as proline utilization A (PutA). PutAs are not only virulence factors in some pathogenic bacteria but also fascinating systems for studying the coordination of metabolic enzymes via substrate channeling. Recent Advances: The past decade has seen an explosion of structural data for proline catabolic enzymes. This review surveys these structures, emphasizing protein folds, substrate recognition, oligomerization, kinetic mechanisms, and substrate channeling in PutA. Major unsolved structural targets include eukaryotic PRODH, the complex between monofunctional PRODH and monofunctional GSALDH, and the largest of all PutAs, trifunctional PutA. The structural basis of PutA-membrane association is poorly understood. Fundamental aspects of substrate channeling in PutA remain unknown, such as the identity of the channeled intermediate, how the tunnel system is activated, and the roles of ancillary tunnels. New approaches are needed to study the molecular and in vivo mechanisms of substrate channeling. With the discovery of the proline cycle driving tumor growth and metastasis, the development of inhibitors of proline metabolic enzymes has emerged as an exciting new direction. Structural biology will be important in these endeavors. Antioxid. Redox Signal. 00, 000-000.

  1. Membrane structure in disease and drug therapy

    National Research Council Canada - National Science Library

    Zimmer, G

    2000-01-01

    ...) interaction with membranous transport systems (opening or closing of ion or substrate channels); (2) reaction with receptors; (3) activation or inhibition of membrane enzymes; or (4) cytosolic membranous signaling and exchange. These consequences within the membrane influence intracellular wellbeing: life is possible only if a bala...

  2. Computational structural biology: methods and applications

    National Research Council Canada - National Science Library

    Schwede, Torsten; Peitsch, Manuel Claude

    2008-01-01

    ... sequencing reinforced the observation that structural information is needed to understand the detailed function and mechanism of biological molecules such as enzyme reactions and molecular recognition events. Furthermore, structures are obviously key to the design of molecules with new or improved functions. In this context, computational structural biology...

  3. The structure and function of cell membranes studied by atomic force microscopy.

    Science.gov (United States)

    Shi, Yan; Cai, Mingjun; Zhou, Lulu; Wang, Hongda

    2018-01-01

    The cell membrane, involved in almost all communications of cells and surrounding matrix, is one of the most complicated components of cells. Lack of suitable methods for the detection of cell membranes in vivo has sparked debates on the biochemical composition and structure of cell membranes over half a century. The development of single molecule techniques, such as AFM, SMFS, and TREC, provides a versatile platform for imaging and manipulating cell membranes in biological relevant environments. Here, we discuss the latest developments in AFM and the progress made in cell membrane research. In particular, we highlight novel structure models and dynamic processes, including the mechanical properties of the cell membranes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Effects of magnetic cobalt ferrite nanoparticles on biological and artificial lipid membranes

    Science.gov (United States)

    Drašler, Barbara; Drobne, Damjana; Novak, Sara; Valant, Janez; Boljte, Sabina; Otrin, Lado; Rappolt, Michael; Sartori, Barbara; Iglič, Aleš; Kralj-Iglič, Veronika; Šuštar, Vid; Makovec, Darko; Gyergyek, Sašo; Hočevar, Matej; Godec, Matjaž; Zupanc, Jernej

    2014-01-01

    Background The purpose of this work is to provide experimental evidence on the interactions of suspended nanoparticles with artificial or biological membranes and to assess the possibility of suspended nanoparticles interacting with the lipid component of biological membranes. Methods 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid vesicles and human red blood cells were incubated in suspensions of magnetic bare cobalt ferrite (CoFe2O4) or citric acid (CA)-adsorbed CoFe2O4 nanoparticles dispersed in phosphate-buffered saline and glucose solution. The stability of POPC giant unilamellar vesicles after incubation in the tested nanoparticle suspensions was assessed by phase-contrast light microscopy and analyzed with computer-aided imaging. Structural changes in the POPC multilamellar vesicles were assessed by small angle X-ray scattering, and the shape transformation of red blood cells after incubation in tested suspensions of nanoparticles was observed using scanning electron microscopy and sedimentation, agglutination, and hemolysis assays. Results Artificial lipid membranes were disturbed more by CA-adsorbed CoFe2O4 nanoparticle suspensions than by bare CoFe2O4 nanoparticle suspensions. CA-adsorbed CoFe2O4-CA nanoparticles caused more significant shape transformation in red blood cells than bare CoFe2O4 nanoparticles. Conclusion Consistent with their smaller sized agglomerates, CA-adsorbed CoFe2O4 nanoparticles demonstrate more pronounced effects on artificial and biological membranes. Larger agglomerates of nanoparticles were confirmed to be reactive against lipid membranes and thus not acceptable for use with red blood cells. This finding is significant with respect to the efficient and safe application of nanoparticles as medicinal agents. PMID:24741305

  5. Effects of magnetic cobalt ferrite nanoparticles on biological and artificial lipid membranes.

    Science.gov (United States)

    Drašler, Barbara; Drobne, Damjana; Novak, Sara; Valant, Janez; Boljte, Sabina; Otrin, Lado; Rappolt, Michael; Sartori, Barbara; Iglič, Aleš; Kralj-Iglič, Veronika; Šuštar, Vid; Makovec, Darko; Gyergyek, Sašo; Hočevar, Matej; Godec, Matjaž; Zupanc, Jernej

    2014-01-01

    The purpose of this work is to provide experimental evidence on the interactions of suspended nanoparticles with artificial or biological membranes and to assess the possibility of suspended nanoparticles interacting with the lipid component of biological membranes. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid vesicles and human red blood cells were incubated in suspensions of magnetic bare cobalt ferrite (CoFe2O4) or citric acid (CA)-adsorbed CoFe2O4 nanoparticles dispersed in phosphate-buffered saline and glucose solution. The stability of POPC giant unilamellar vesicles after incubation in the tested nanoparticle suspensions was assessed by phase-contrast light microscopy and analyzed with computer-aided imaging. Structural changes in the POPC multilamellar vesicles were assessed by small angle X-ray scattering, and the shape transformation of red blood cells after incubation in tested suspensions of nanoparticles was observed using scanning electron microscopy and sedimentation, agglutination, and hemolysis assays. Artificial lipid membranes were disturbed more by CA-adsorbed CoFe2O4 nanoparticle suspensions than by bare CoFe2O4 nanoparticle suspensions. CA-adsorbed CoFe2O4-CA nanoparticles caused more significant shape transformation in red blood cells than bare CoFe2O4 nanoparticles. Consistent with their smaller sized agglomerates, CA-adsorbed CoFe2O4 nanoparticles demonstrate more pronounced effects on artificial and biological membranes. Larger agglomerates of nanoparticles were confirmed to be reactive against lipid membranes and thus not acceptable for use with red blood cells. This finding is significant with respect to the efficient and safe application of nanoparticles as medicinal agents.

  6. The Rh protein family: gene evolution, membrane biology, and disease association.

    Science.gov (United States)

    Huang, Cheng-Han; Ye, Mao

    2010-04-01

    The Rh (Rhesus) genes encode a family of conserved proteins that share a structural fold of 12 transmembrane helices with members of the major facilitator superfamily. Interest in this family has arisen from the discovery of Rh factor's involvement in hemolytic disease in the fetus and newborn, and of its homologs widely expressed in epithelial tissues. The Rh factor and Rh-associated glycoprotein (RhAG), with epithelial cousins RhBG and RhCG, form four subgroups conferring upon vertebrates a genealogical commonality. The past decade has heralded significant advances in understanding the phylogenetics, allelic diversity, crystal structure, and biological function of Rh proteins. This review describes recent progress on this family and the molecular insights gleaned from its gene evolution, membrane biology, and disease association. The focus is on its long evolutionary history and surprising structural conservation from prokaryotes to humans, pointing to the importance of its functional role, related to but distinct from ammonium transport proteins.

  7. High Energy Density Nastic Structures Using Biological Transport Mechanisms

    Science.gov (United States)

    2007-02-28

    DATES COVERED Final Progress Report; 9/27/04 to 11/30/06 4. TITLE AND SUBTITLE High Energy Density Nastic Structures Using Biological Transport...permeable membranes. This concept is based on the pressurization of cells similar to the process that plants use to maintain homeostasis and regulate...cell function. In all plant systems, the transport of ions and fluid produce localized pressure changes (called turgor pressure) that perform many

  8. Structural biology at York Structural Biology Laboratory; laboratory information management systems for structural genomics

    Czech Academy of Sciences Publication Activity Database

    Dohnálek, Jan

    2005-01-01

    Roč. 12, č. 1 (2005), s. 3 ISSN 1211-5894. [Meeting of Structural Biologists /4./. 10.03.2005-12.03.2005, Nové Hrady] R&D Projects: GA MŠk(CZ) 1K05008 Keywords : structural biology * LIMS * structural genomics Subject RIV: CD - Macromolecular Chemistry

  9. Fuel-Cell Structure Prevents Membrane Drying

    Science.gov (United States)

    Mcelroy, J.

    1986-01-01

    Embossed plates direct flows of reactants and coolant. Membrane-type fuel-cell battery has improved reactant flow and heat removal. Compact, lightweight battery produces high current and power without drying of membranes.

  10. Atomic-level Analysis of Membrane Protein Structure

    OpenAIRE

    Hendrickson, Wayne A.

    2016-01-01

    Membrane proteins are substantially more challenging than natively soluble proteins as subjects for structural analysis. Thus, membrane proteins are greatly under-represented in structural databases. Recently, as a consequence of focused attention by consortium efforts and advances in methodology, the pace has accelerated for atomic-level structure determination of membrane proteins. Enabling advances have come in methods for protein production, for crystallographic analysis, and for cryo-EM ...

  11. Membrane Structure Studies by Means of Small-Angle Neutron Scattering (SANS)

    International Nuclear Information System (INIS)

    Knott, R. B.

    2008-01-01

    The basic model for membrane structure--a lipid bilayer with imbedded proteins--was formulated 35 years ago, however the detailed structure is still under active investigation using a variety of physical, chemical and computational techniques. Every biologically active cell is encapsulated by a plasma membrane with most cells also equipped with an extensive intracellular membrane system. The plasma membrane is an important boundary between the cytoplasm of the cell and the external environment, and selectively isolates the cell from that environment. Passive diffusion and/or active transport mechanisms are provided for water, ions, substrates etc. which are vital for cell metabolism and viability. Membranes also facilitate excretion of substances either as useful cellular products or as waste. Despite their complexity and diverse function, plasma membranes from quite different cells have surprisingly similar compositions. A typical membrane structure consists of a phospholipid bilayer with a number of proteins scattered throughout, along with carbohydrates (glycoproteins), glycolipids and sterols. The plasma membranes of most eukaryotic cells contain approximately equal weights of lipid and protein, which corresponds to about 100 lipid molecules per protein molecule. Clearly, lipids are a major constituent and the study of their structure and function in isolation provides valuable insight into the more complex intact multicomponent membrane. The membrane bound protein is the other major constituent and is a very active area of research for a number of reasons including the fact that over 60% of modern drugs act on their receptor sites. The interaction between the protein and the supporting lipid bilayer is clearly of major importance. Neutron scattering is a powerful technique for exploring the structure of membranes, either as reconstituted membranes formed from well characterised lipids, or as intact membranes isolated from selected biological systems. A brief

  12. Chlorosulfolipids: Structure, synthesis, and biological relevance

    OpenAIRE

    Bedke, D. Karl; Vanderwal, Christopher D.

    2010-01-01

    Chlorosulfolipids have been isolated from freshwater algae and from toxic mussels. They appear to have a structural role in algal membranes and have been implicated in Diarrhetic Shellfish Poisoning. Further fascinating aspects of these compounds include their stereochemically complex polychlorinated structures and the resulting strong conformational biases, and their poorly understood (yet surely compelling) biosynthesis. Discussions of each of these topics and of efforts in structural and s...

  13. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine

    Science.gov (United States)

    Pi, Jiang; Jin, Hua; Yang, Fen; Chen, Zheng W.; Cai, Jiye

    2014-10-01

    The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In

  14. West-Life, Tools for Integrative Structural Biology

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Structural biology is part of molecular biology focusing on determining structure of macromolecules inside living cells and cell membranes. As macromolecules determines most of the functions of cells the structural knowledge is very useful for further research in metabolism, physiology to application in pharmacology etc. As macromolecules are too small to be observed directly by light microscope, there are other methods used to determine the structure including nuclear magnetic resonance (NMR), X-Ray crystalography, cryo electron microscopy and others. Each method has it's advantages and disadvantages in the terms of availability, sample preparation, resolution. West-Life project has ambition to facilitate integrative approach using multiple techniques mentioned above. As there are already lot of software tools to process data produced by the techniques above, the challenge is to integrate them together in a way they can be used by experts in one technique but not experts in other techniques. One product ...

  15. A Dry Membrane Protection Technique to Allow Surface Acoustic Wave Biosensor Measurements of Biological Model Membrane Approaches

    Directory of Open Access Journals (Sweden)

    Marius Enachescu

    2013-09-01

    Full Text Available Model membrane approaches have attracted much attention in biomedical sciences to investigate and simulate biological processes. The application of model membrane systems for biosensor measurements is partly restricted by the fact that the integrity of membranes critically depends on the maintenance of an aqueous surrounding, while various biosensors require a preconditioning of dry sensors. This is for example true for the well-established surface acoustic wave (SAW biosensor SAM®5 blue. Here, a simple drying procedure of sensor-supported model membranes is introduced using the protective disaccharide trehalose. Highly reproducible model membranes were prepared by the Langmuir-Blodgett technique, transferred to SAW sensors and supplemented with a trehalose solution. Membrane rehydration after dry incorporation into the SAW device becomes immediately evident by phase changes. Reconstituted model membranes maintain their full functionality, as indicated by biotin/avidin binding experiments. Atomic force microscopy confirmed the morphological invariability of dried and rehydrated membranes. Approximating to more physiological recognition phenomena, the site-directed immobilization of the integrin VLA-4 into the reconstituted model membrane and subsequent VCAM-1 ligand binding with nanomolar affinity were illustrated. This simple drying procedure is a novel way to combine the model membrane generation by Langmuir-Blodgett technique with SAW biosensor measurements, which extends the applicability of SAM®5 blue in biomedical sciences.

  16. Physical origin of selectivity in ionic channels of biological membranes.

    Science.gov (United States)

    Laio, A; Torre, V

    1999-01-01

    This paper shows that the selectivity properties of monovalent cation channels found in biological membranes can originate simply from geometrical properties of the inner core of the channel without any critical contribution from electrostatic interactions between the permeating ions and charged or polar groups. By using well-known techniques of statistical mechanics, such as the Langevin equations and Kramer theory of reaction rates, a theoretical equation is provided relating the permeability ratio PB/PA between ions A and B to simple physical properties, such as channel geometry, thermodynamics of ion hydration, and electrostatic interactions between the ion and charged (or polar) groups. Diffusive corrections and recrossing rates are also considered and evaluated. It is shown that the selectivity found in usual K+, gramicidin, Na+, cyclic nucleotide gated, and end plate channels can be explained also in the absence of any charged or polar group. If these groups are present, they significantly change the permeability ratio only if the ion at the selectivity filter is in van der Waals contact with them, otherwise these groups simply affect the channel conductance, lowering the free energy barrier of the same amount for the two ions, thus explaining why single channel conductance, as it is experimentally observed, can be very different in channels sharing the same selectivity sequence. The proposed theory also provides an estimate of channel minimum radius for K+, gramicidin, Na+, and cyclic nucleotide gated channels.

  17. Tandem malonate-based glucosides (TMGs) for membrane protein structural studies

    DEFF Research Database (Denmark)

    Hussain, Hazrat; Mortensen, Jonas S.; Du, Yang

    2017-01-01

    High-resolution membrane protein structures are essential for understanding the molecular basis of diverse biological events and important in drug development. Detergents are usually used to extract these bio-macromolecules from the membranes and maintain them in a soluble and stable state...... in aqueous solutions for downstream characterization. However, many eukaryotic membrane proteins solubilized in conventional detergents tend to undergo structural degradation, necessitating the development of new amphiphilic agents with enhanced properties. In this study, we designed and synthesized a novel...... class of glucoside amphiphiles, designated tandem malonate-based glucosides (TMGs). A few TMG agents proved effective at both stabilizing a range of membrane proteins and extracting proteins from the membrane environment. These favourable characteristics, along with synthetic convenience, indicate...

  18. New membrane structures with proton conducting properties

    DEFF Research Database (Denmark)

    Nørgaard, Casper Frydendal

    Perfluorosulfonic acid membranes (e.g. Nafion®) are the most widely applied electrolytes in Polymer Electrolyte Membrane Fuel Cells (PEMFCs) because of their good chemical stability, mechanical properties and high proton conductivity, when well hydrated. The upper limit of operating temperature...... for these membranes is restricted by the loss of conductivity and dimensional stability as the temperature reaches the boiling point of water and the glass transition temperature of the polymer. At low relative humidity the membranes dehydrate, resulting in loss of conductivity and reduced dimensions. High...... [1, 2, 3]. Improved fuel cell performance from incorporation of hygroscopic oxides or solid proton conductors (e.g. zirconium phosphates) has been reported. The poster exhibits upcoming work in the field of composite electrolyte membranes at the University of Southern Denmark, combining radiation...

  19. Neutron structural biology. Beyond the folding structure

    International Nuclear Information System (INIS)

    Niimura, Nobuo

    2009-01-01

    Hydrogen atoms and water molecules around proteins and nucleic acids play a crucial role in many physiological functions. Neutron diffraction provides an experimental method of directly locating hydrogen atoms. (a) Since almost all the H atom positions can be identified experimentally, the geometrical details of certain types of H-bonds can be visualized and (b) as far as mechanistic implications are concerned, the identification of protonation and deprotonation states of certain important amino acid residues can be carried out. (c) The hydration structure around proteins and the hydration networks around DNA oligomers have been successfully characterized in several outstanding cases. These will open the new field beyond the folding structure of bio-macromolecules such as: 1) Recognition of proteins and nucleic acids through the network structure of water molecules surrounding bio-macromolecules, and 2) The nature of chemical bond in proteins and nucleic acids elucidated by the accumulation of accurate structural information of hydrogen atoms. (author)

  20. Effect of dope solution temperature on the membrane structure and membrane distillation performance

    Science.gov (United States)

    Nawi, N. I. M.; Bilad, M. R.; Nordin, N. A. H. M.

    2018-04-01

    Membrane distillation (MD) is a non-isothermal process applicable to purify water using hydrophobic membrane. Membrane in MD is hydrophobic, permeable to water vapor but repels liquid water. MD membrane is expected to pose high flux, high fouling and scaling resistances and most importantly high wetting resistance. This study develops flat-sheet polyvinylidene fluoride (PVDF) membrane by exploring both liquid-liquid and liquid-solid phase inversion technique largely to improve its wetting resistance and flux performance. We hypothesize that temperature of dope solution play roles in solid-liquid separation during membrane formation and an optimum balance between liquid-liquid and liquid-solid (crystallization) separation leads to highly performance PVDF membrane. Findings obtained from differential scanning calorimeter test show that increasing dope solution temperature reduces degree of PVDF crystallinity and suppresses formation of crystalline structure. The morphological images of the resulting membranes show that at elevated dope solution temperature (40, 60, 80 and 100°C), the spherulite-like structures are formed across the thickness of membranes ascribed from due to different type of crystals. The performance of direct-contact MD shows that the obtained flux of the optimum dope temperature (60°C) of 10.8 L/m2h is comparable to commercial PTFE-based MD membrane.

  1. Electron crystallography--the waking beauty of structural biology.

    Science.gov (United States)

    Pope, Christopher R; Unger, Vinzenz M

    2012-08-01

    Since its debut in the mid 1970s, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single-layered or double-layered two-dimensionally ordered arrays and the ability to obtain structural information from small and disordered crystals make this approach particularly useful for the study of membrane proteins in a lipid bilayer environment. Despite its unique advantages, technological hurdles have kept electron crystallography from reaching its full potential. Addressing the issues, recent initiatives developed high-throughput pipelines for crystallization and screening. Adding progress in automating data collection, image analysis and phase extension methods, electron crystallography is poised to raise its profile and may lead the way in exploring the structural biology of macromolecular complexes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Exosomes as therapeutic drug carriers and delivery vehicles across biological membranes: current perspectives and future challenges.

    Science.gov (United States)

    Ha, Dinh; Yang, Ningning; Nadithe, Venkatareddy

    2016-07-01

    Exosomes are small intracellular membrane-based vesicles with different compositions that are involved in several biological and pathological processes. The exploitation of exosomes as drug delivery vehicles offers important advantages compared to other nanoparticulate drug delivery systems such as liposomes and polymeric nanoparticles; exosomes are non-immunogenic in nature due to similar composition as body׳s own cells. In this article, the origin and structure of exosomes as well as their biological functions are outlined. We will then focus on specific applications of exosomes as drug delivery systems in pharmaceutical drug development. An overview of the advantages and challenges faced when using exosomes as a pharmaceutical drug delivery vehicles will also be discussed.

  3. Membrane tension: A challenging but universal physical parameter in cell biology.

    Science.gov (United States)

    Pontes, Bruno; Monzo, Pascale; Gauthier, Nils C

    2017-11-01

    The plasma membrane separates the interior of cells from the outside environment. The membrane tension, defined as the force per unit length acting on a cross-section of membrane, regulates many vital biological processes. In this review, we summarize the first historical findings and the latest advances, showing membrane tension as an important physical parameter in cell biology. We also discuss how this parameter must be better integrated and we propose experimental approaches for key unanswered questions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Antireflective "moth-eye" structures on tunable optical silicone membranes.

    Science.gov (United States)

    Brunner, Robert; Keil, Bettina; Morhard, Christoph; Lehr, Dennis; Draheim, Jan; Wallrabe, Ulrike; Spatz, Joachim

    2012-07-01

    Flexible silicone membranes are key components for tunable optical lenses. The elastic operation of the membranes impedes the use of classical layer systems for an antireflective (AR) effect. To overcome this limitation, we equipped optical elastomer membranes with "moth-eye" structures directly in the flexible silicone substrate. The manufacturing of the AR structures in the flexible membrane includes a mastering process based on block copolymer micelle nanolithography followed by a replication method. We investigate the performance of the resulting AR structures under strain of up to 20% membrane expansion. A significant transmittance enhancement of up to 2.5% is achieved over the entire visible spectrum, which means that more than half of the surface reflection losses are compensated by the AR structures.

  5. Depression, osteoporosis, serotonin and cell membrane viscosity between biology and philosophical anthropology

    Directory of Open Access Journals (Sweden)

    Gabrielli Fabio

    2011-03-01

    Full Text Available Abstract Due to the relationship between biology and culture, we believe that depression, understood as a cultural and existential phenomenon, has clear markers in molecular biology. We begin from an existential analysis of depression constituting the human condition and then shift to analysis of biological data confirming, according to our judgment, its original (ontological structure. In this way philosophy is involved at the anthropological level, in as much as it detects the underlying meanings of depression in the original biological-cultural horizon of human life. Considering the integration of knowledge it is the task of molecular biology to identify the aforementioned markers, to which the existential aspects of depression are linked to. In particular, recent works show the existence of a link between serotonin and osteoporosis as a result of a modified expression of the low-density lipoprotein receptor-related protein 5 gene. Moreover, it is believed that the hereditary or acquired involvement of tryptophan hydroxylase 2 (Tph2 or 5-hydroxytryptamine transporter (5-HTT is responsible for the reduced concentration of serotonin in the central nervous system, causing depression and affective disorders. This work studies the depression-osteoporosis relationship, with the aim of focusing on depressive disorders that concern the quantitative dynamic of platelet membrane viscosity and interactome cytoskeleton modifications (in particular Tubulin and Gsα protein as a possible condition of the involvement of the serotonin axis (gut, brain and platelet, not only in depression but also in connection with osteoporosis.

  6. Fouling of enhanced biological phosphorus removal-membrane bioreactors by humic-like substances.

    Science.gov (United States)

    Poorasgari, Eskandar; König, Katja; Fojan, Peter; Keiding, Kristian; Christensen, Morten Lykkegaard

    2014-12-01

    Fouling by free extracellular polymeric substances was studied in an enhanced biological phosphorus removal-membrane bioreactor. It was demonstrated that the free extracellular polymeric substances, primarily consisting of humic-like substances, were adsorbed to the membrane used in the enhanced biological phosphorus removal-membrane bioreactor plant. Infrared analyses indicated the presence of the humic-like substances on the membrane's active surface after filtration of the free extracellular polymeric substances suspension. Scanning electron microscopy showed the presence of a gel layer on the membrane surface after filtration of the free extracellular polymeric substances suspension. The gel layer caused a significant decline in water flux. This layer was not entirely removed by a backwashing, and the membrane's water flux could not be re-established. The membrane used in the enhanced biological phosphorus removal-membrane bioreactor plant showed infrared spectra similar to that fouled by the free extracellular polymeric substances suspension in the laboratory. Thus, the results of this study show the importance of humic-like substances in irreversible fouling of enhanced biological phosphorus removal-membrane bioreactor systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. a structural biology perspective TANWEER HUSSAIN

    Indian Academy of Sciences (India)

    Administrator

    2017-07-01

    Jul 1, 2017 ... Structural biology of Molecular machines. Determine the three-dimensional structure of the macromolecular complexes. X-ray crystallography. Crystals. X-ray diffraction. Electron density. Model. Cryo-electron microscopy (cryo-EM). Image. Particle picking. 2D class averages. 3D classification. 3D autorefine ...

  8. Structural Biology for A-Level Students

    Science.gov (United States)

    Philip, Judith

    2013-01-01

    The relationship between the structure and function of proteins is an important area in biochemistry. Pupils studying A-level Biology are introduced to the four levels of protein structure (primary, secondary, tertiary and quaternary) and how these can be used to describe the progressive folding of a chain of amino acid residues to a final,…

  9. Studying Membrane Protein Structure and Function Using Nanodiscs

    DEFF Research Database (Denmark)

    Huda, Pie

    The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

  10. Structural Aspects of Bacterial Outer Membrane Protein Assembly.

    Science.gov (United States)

    Calmettes, Charles; Judd, Andrew; Moraes, Trevor F

    2015-01-01

    The outer membrane of Gram-negative bacteria is predominantly populated by β-Barrel proteins and lipid anchored proteins that serve a variety of biological functions. The proper folding and assembly of these proteins is essential for bacterial viability and often plays a critical role in virulence and pathogenesis. The β-barrel assembly machinery (Bam) complex is responsible for the proper assembly of β-barrels into the outer membrane of Gram-negative bacteria, whereas the localization of lipoproteins (Lol) system is required for proper targeting of lipoproteins to the outer membrane.

  11. Membrane association of the PTEN tumor suppressor: neutron scattering and MD simulations reveal the structure of protein-membrane complexes.

    Science.gov (United States)

    Nanda, Hirsh; Heinrich, Frank; Lösche, Mathias

    2015-05-01

    Neutron reflection (NR) from planar interfaces is an emerging technology that provides unique and otherwise inaccessible structural information on disordered molecular systems such as membrane proteins associated with fluid bilayers, thus addressing one of the remaining challenges of structural biology. Although intrinsically a low-resolution technique, using structural information from crystallography or NMR allows the construction of NR models that describe the architecture of protein-membrane complexes at high resolution. In addition, a combination of these methods with molecular dynamics (MD) simulations has the potential to reveal the dynamics of protein interactions with the bilayer in atomistic detail. We review recent advances in this area by discussing the application of these techniques to the complex formed by the PTEN phosphatase with the plasma membrane. These studies provide insights in the cellular regulation of PTEN, its interaction with PI(4,5)P2 in the inner plasma membrane and the pathway by which its substrate, PI(3,4,5)P3, accesses the PTEN catalytic site. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Structure and Water Transport in Nafion Nanocomposite Membranes

    Science.gov (United States)

    Davis, Eric; Page, Kirt

    2014-03-01

    Perfluorinated ionomers, specifically Nafion, are the most widely used ion exchange membranes for vanadium redox flow battery applications, where an understanding of the relationship between membrane structure and transport of water/ions is critical to battery performance. In this study, the structure of Nafion/SiO2 nanocomposite membranes, synthesized using sol-gel chemistry, as well as cast directly from Nafion/SiO2 nanoparticle dispersions, was measured using both small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS). Through contrast match studies of the SiO2 nanoparticles, direct information on the change in the structure of the Nafion membranes and the ion-transport channels within was obtained, where differences in membrane structure was observed between the solution-cast membranes and the membranes synthesized using sol-gel chemistry. Additionally, water sorption and diffusion in these Nafion/SiO2 nanocomposite membranes were measured using in situ time-resolved Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy and dynamic vapor sorption (DVS).

  13. Nidovirus replication structures : hijacking membranes to support viral RNA synthesis

    NARCIS (Netherlands)

    Knoops, Kèvin

    2011-01-01

    Positive-stranded RNA viruses replicate in the cytoplasm of host cells and their replication complexes are associated with modified cell membranes. We investigated the structure of the nidovirus-induced membrane modifications and found that nidoviruses transform the endoplasmic reticulum into a

  14. Terahertz dielectric relaxation of biological water confined in model membranes made of lyotropic phospholipids

    NARCIS (Netherlands)

    Paparo, D.; Tielrooij, K.J.; Bakker, H.J.; Bonn, M.

    2009-01-01

    Understanding water-membrane interactions is a fundamental issue in biophysics since these interactions are at the basis of many key molecular processes occurring in membranes. The hydrogen-bond network of water molecules is highly dynamic and its dynamical structure influences membrane fluidity and

  15. The nonsteroidal anti-inflammatory drug indomethacin induces heterogeneity in lipid membranes: potential implication for its diverse biological action.

    Directory of Open Access Journals (Sweden)

    Yong Zhou

    2010-01-01

    Full Text Available The nonsteroidal anti-inflammatory drug (NSAID, indomethacin (Indo, has a large number of divergent biological effects, the molecular mechanism(s for which have yet to be fully elucidated. Interestingly, Indo is highly amphiphilic and associates strongly with lipid membranes, which influence localization, structure and function of membrane-associating proteins and actively regulate cell signaling events. Thus, it is possible that Indo regulates diverse cell functions by altering micro-environments within the membrane. Here we explored the effect of Indo on the nature of the segregated domains in a mixed model membrane composed of dipalmitoyl phosphatidyl-choline (di16:0 PC, or DPPC and dioleoyl phosphatidyl-choline (di18:1 PC or DOPC and cholesterol that mimics biomembranes.Using a series of fluorescent probes in a fluorescence resonance energy transfer (FRET study, we found that Indo induced separation between gel domains and fluid domains in the mixed model membrane, possibly by enhancing the formation of gel-phase domains. This effect originated from the ability of Indo to specifically target the ordered domains in the mixed membrane. These findings were further confirmed by measuring the ability of Indo to affect the fluidity-dependent fluorescence quenching and the level of detergent resistance of membranes.Because the tested lipids are the main lipid constituents in cell membranes, the observed formation of gel phase domains induced by Indo potentially occurs in biomembranes. This marked Indo-induced change in phase behavior potentially alters membrane protein functions, which contribute to the wide variety of biological activities of Indo and other NSAIDs.

  16. Extremophile bacteria glycolipids: structure and biological activity

    OpenAIRE

    Carillo, Sara

    2013-01-01

    Extremophile bacteria are able to survive in harsh life conditions, such as high or low temperatures (thermophiles and psychrophiles, respectively), high pressure (barophiles), high or low pH values (acidophiles or alkalophiles), environments characterized by high salt concentrations (halophiles). Structural features of the macromolecules belonging to the external layer are fundamental in adaptation mechanisms, e.g. it is well known that halophiles membrane phospholipids showed an increase...

  17. Molecular Interactions at Membranes

    DEFF Research Database (Denmark)

    Jagalski, Vivien

    Biological membranes are essential and complex structures in every living cell consisting of a fluid lipid bilayer sheet and membrane proteins. Its significance makes biological membranes not only interesting for medical research, but also has made it a target for toxins in the course of evolution....... Today, we know more than ever before about the properties of biological membranes. Advanced biophysical techniques and sophisticated membrane models allow us to answer specific questions about the structure of the components within membranes and their interactions. However, many detailed structural...... mechanisms of membrane compounds, including compounds associated with membranes, are still unknown due to the challenges that arise when probing the hydrophobic nature of the membrane's interior. For integral membrane proteins that span through the entire membrane, the amphiphilic environment is essential...

  18. Bobbing of Oxysterols: Molecular Mechanism for Translocation of Tail-Oxidized Sterols through Biological Membranes

    Czech Academy of Sciences Publication Activity Database

    Kulig, W.; Mikkolainen, H.; Olžyńska, Agnieszka; Jurkiewicz, Piotr; Cwiklik, Lukasz; Hof, Martin; Vattulainen, I.; Jungwirth, Pavel; Rog, T.

    2018-01-01

    Roč. 9, č. 5 (2018), s. 1118-1123 ISSN 1948-7185 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388955 ; RVO:61388963 Keywords : biological membranes * alcohols * cell membranes Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 9.353, year: 2016

  19. Structured population models in biology and epidemiology

    CERN Document Server

    Ruan, Shigui

    2008-01-01

    This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

  20. Sandwich-structured hollow fiber membranes for osmotic power generation

    KAUST Repository

    Fu, Feng Jiang

    2015-11-01

    In this work, a novel sandwich-structured hollow fiber membrane has been developed via a specially designed spinneret and optimized spinning conditions. With this specially designed spinneret, the outer layer, which is the most crucial part of the sandwich-structured membrane, is maintained the same as the traditional dual-layer membrane. The inner substrate layer is separated into two layers: (1) an ultra-thin middle layer comprising a high molecular weight polyvinylpyrrolidone (PVP) additive to enhance integration with the outer polybenzimidazole (PBI) selective layer, and (2) an inner-layer to provide strong mechanical strength for the membrane. Experimental results show that a high water permeability and good mechanical strength could be achieved without the expensive post treatment process to remove PVP which was necessary for the dual-layer pressure retarded osmosis (PRO) membranes. By optimizing the composition, the membrane shows a maximum power density of 6.23W/m2 at a hydraulic pressure of 22.0bar when 1M NaCl and 10mM NaCl are used as the draw and feed solutions, respectively. To our best knowledge, this is the best phase inversion hollow fiber membrane with an outer selective PBI layer for osmotic power generation. In addition, this is the first work that shows how to fabricate sandwich-structured hollow fiber membranes for various applications. © 2015 Elsevier B.V.

  1. Effect of Spinneret Dimension on Structure and Performance of Polyetherimide Hollow Fiber Membrane in Membrane Contactor

    Directory of Open Access Journals (Sweden)

    Gholamreza Bakeri

    2017-09-01

    Full Text Available In hollow fiber membrane fabrication process, a number of parameters such as dope compositions and flow rate, bore fluid type and flow rate, air gap etc. affect on the structure and characteristics of membrane. One of effective parameters is the dimension of spinneret and in this study; the effects of this parameter on the properties of polyetherimide (PEI hollow fiber membrane and its performance in membrane contactor were studied. A polymer solution was used for fabrication of two PEI membranes at the same fabrication conditions while the dimension of spinneret was different. Through the addition of water as the nonsolvent additive to the polymer solution, the thermodynamic stability of the solution decreased and upon the enhancement in the phase inversion process, the effects of chain reorientation or chain relaxation on the structure of hollow fiber membrane were minimized. The fabricated membranes were characterized by different tests and their performance in membrane contractor and in CO2 absorption test was evaluated in two cases: 1- distilled water in lumen side and pure CO2 in shell side, 2- distilled water in shell side and pure CO2 in lumen side. The results show that smaller dimension of spinneret enhances the properties of membrane such as 250% increase in mean pore size and 300% increase in gas permeation rate. In addition, the smaller dimension of the spinneret makes more pores in the structure of membrane that can be related to the shorter diffusion length of the coagulant. Furthermore, the CO2 absorption flux improves by 150%.

  2. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  3. Graphene-based structure, method of suspending graphene membrane, and method of depositing material onto graphene membrane

    Science.gov (United States)

    Zettl, Alexander K.; Meyer, Jannik Christian

    2013-04-02

    An embodiment of a method of suspending a graphene membrane across a gap in a support structure includes attaching graphene to a substrate. A pre-fabricated support structure having the gap is attached to the graphene. The graphene and the pre-fabricated support structure are then separated from the substrate which leaves the graphene membrane suspended across the gap in the pre-fabricated support structure. An embodiment of a method of depositing material includes placing a support structure having a graphene membrane suspended across a gap under vacuum. A precursor is adsorbed to a surface of the graphene membrane. A portion of the graphene membrane is exposed to a focused electron beam which deposits a material from the precursor onto the graphene membrane. An embodiment of a graphene-based structure includes a support structure having a gap, a graphene membrane suspended across the gap, and a material deposited in a pattern on the graphene membrane.

  4. Constitutive analysis of thin biological membranes with application to radial stretching of a hollow circular membrane

    Science.gov (United States)

    Lubarda, V. A.

    2010-06-01

    The constitutive analysis of the mechanical response of thin elastic membranes under inplane deformation is presented by using the multiplicative decomposition of the deformation gradient into its areal and distortional parts. Specific results are obtained for the Evans-Skalak form of the strain energy function. The solution to the problem of radial stretching of a hollow circular membrane obeying this constitutive model is then derived. The stress concentration factor is determined as a function of the relative hole size and the magnitude of the applied tension. The tension boundary is identified above which no compressive stress appears in the membrane. The limit boundary is introduced below which the membrane cannot support the applied loading without unstable wrinkling. For the loading between the tension and the limit boundary, nonuniformly distributed infinitesimal wrinkles appear within the inner portion of the membrane, carrying radial tension but no circumferential stress (tension field). The specific form of the strain energy function is used to describe this behavior, and to calculate the amount of the membrane area absorbed by infinitesimal wrinkles. The wrinkled portion is surrounded by the outer portion of the membrane carrying both radial and circumferential stresses. The limit boundary is reached when wrinkles spread throughout the membrane. It is shown that for a sufficiently large tension at the outer boundary, the wrinkling does not spread throughout the membrane no matter how large the applied tension at the inner boundary of the membrane is, provided that no rupture takes place. The limiting extent of the tension field in such cases is calculated. The linearized version of the analysis is characterized by a closed form solution.

  5. Structural investigation of membrane proteins by electron microscopy

    NARCIS (Netherlands)

    Moscicka, Katarzyna Beata

    2009-01-01

    Biological membranes are vital components of all living systems, forming the boundaries of cells and their organelles. They consist of a lipid bilayer and embedded proteins, which are nanomachines that fulfill key functions such as energy conversion, solute transport, secretion, and signal

  6. [THE ROLE OF BIOLOGICAL MEMBRANES IN DIFFERENTIAL DIAGNOSTICS OF SALMONELLA AND ACUTE ALCOHOL GASTROENTERITIS].

    Science.gov (United States)

    Makarov, V K; Makarov, P V

    2015-01-01

    We evaluated the influence of Salmonella infection and alcohol on biological membranes from the content of serum phospholipid fraction known to be a component ofenterocyte membranes. Any change of membrane phospholipid content leads to a change of their blood level. The study included 50 patients with acute alcohol gastroenteritis, 50 ones with salmonella gastroenteritis, and 50 healthy subjects. Both salmonellosis and alcohol caused differently directed changes in biological membranes. The mechanism of diarrhea in patients with salmonella and acute alcohol gastroenteritis is different. Diarrhea associated with alcohol gastroenteritis is due to enhanced viscosity of biomembranes that decreases in salmonella gastroenteritis. It suggests different approaches to the treatment of these conditions. The membrane destruction coefficient below 2 is an additional proof of alcoholic etiology of gastroenteritis whereas its value above 3 confirms the involvement of salmonellosis in pathogenesis of gastroenteritis.

  7. Ice breaking in GPCR structural biology

    Science.gov (United States)

    Zhao, Qiang; Wu, Bei-li

    2012-01-01

    G-protein-coupled receptors (GPCRs) are one of the most challenging targets in structural biology. To successfully solve a high-resolution GPCR structure, several experimental obstacles must be overcome, including expression, extraction, purification, and crystallization. As a result, there are only a handful of unique structures reported from this protein superfamily, which consists of over 800 members. In the past few years, however, there has been an increase in the amount of solved GPCR structures, and a few high-impact structures have been determined: the peptide receptor CXCR4, the agonist bound receptors, and the GPCR-G protein complex. The dramatic progress in GPCR structural studies is not due to the development of any single technique, but a combination of new techniques, new tools and new concepts. Here, we summarize the progress made for GPCR expression, purification, and crystallization, and we highlight the technical advances that will facilitate the future determination of GPCR structures. PMID:22286917

  8. Study of structural stability and damaging effect on membrane for four Aβ42 dimers.

    Directory of Open Access Journals (Sweden)

    Wei Feng

    Full Text Available Increasing evidence shows that Aβ oligomers are key pathogenic molecules in Alzheimer's disease. Among Aβ oligomers, dimer is the smallest aggregate and toxic unit. Therefore, understanding its structural and dynamic properties is quite useful to prevent the formation and toxicity of the Aβ oligomers. In this study, we performed molecular dynamic simulations on four Aβ42 dimers, 2NCb, CNNC, NCNC and NCCN, within the hydrated DPPC membrane. Four Aβ42 dimers differ in the arrangements of two Aβ42 peptides. This study aims to investigate the impact of aggregation pattern of two Aβ peptides on the structural stability of the Aβ42 dimer and its disruption to the biological membrane. The MD results demonstrate that the NCCN, CNNC and NCNC have the larger structural fluctuation at the N-terminus of Aβ42 peptide, where the β-strand structure converts into the coil structure. The loss of the N-terminal β-strand further impairs the aggregate ability of Aβ42 dimer. In addition, inserting Aβ42 dimer into the membrane can considerably decrease the average APL of DPPC membrane. Moreover this decrease effect is largely dependent on the distance to the location of Aβ42 dimer and its secondary structure forms. Based on the results, the 2NCb is considered as a stable dimeric unit for aggregating the larger Aβ42 oligomer, and has a potent ability to disrupt the membrane.

  9. Cell biology symposium: Membrane trafficking and signal transduction

    Science.gov (United States)

    In general, membrane trafficking is a broad group of processes where proteins and other large molecules are distributed throughout the cell as well as adjacent extracellular spaces. Whereas signal transduction is a process where signals are transmitted through a series of chemical or molecular event...

  10. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    As there is an interplay between network architecture and dynamics, structure plays an important role in communication and spreading of information in a network. ... Department of Mathematics and Statistics, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India; Department of Biological ...

  11. Mechanism of biological denitrification inhibition: procyanidins induce an allosteric transition of the membrane-bound nitrate reductase through membrane alteration.

    Science.gov (United States)

    Bardon, Clément; Poly, Franck; Piola, Florence; Pancton, Muriel; Comte, Gilles; Meiffren, Guillaume; Haichar, Feth el Zahar

    2016-05-01

    Recently, it has been shown that procyanidins from Fallopia spp. inhibit bacterial denitrification, a phenomenon called biological denitrification inhibition (BDI). However, the mechanisms involved in such a process remain unknown. Here, we investigate the mechanisms of BDI involving procyanidins, using the model strain Pseudomonas brassicacearum NFM 421. The aerobic and anaerobic (denitrification) respiration, cell permeability and cell viability of P. brassicacearum were determined as a function of procyanidin concentration. The effect of procyanidins on the bacterial membrane was observed using transmission electronic microscopy. Bacterial growth, denitrification, NO3- and NO2-reductase activity, and the expression of subunits of NO3- (encoded by the gene narG) and NO2-reductase (encoded by the gene nirS) under NO3 or NO2 were measured with and without procyanidins. Procyanidins inhibited the denitrification process without affecting aerobic respiration at low concentrations. Procyanidins also disturbed cell membranes without affecting cell viability. They specifically inhibited NO3- but not NO2-reductase.Pseudomonas brassicacearum responded to procyanidins by over-expression of the membrane-bound NO3-reductase subunit (encoded by the gene narG). Our results suggest that procyanidins can specifically inhibit membrane-bound NO3-reductase inducing enzymatic conformational changes through membrane disturbance and that P. brassicacearum responds by over-expressing membrane-bound NO3-reductase. Our results lead the way to a better understanding of BDI. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Carbon nanotube embedded PVDF membranes: Effect of solvent composition on the structural morphology for membrane distillation

    Science.gov (United States)

    Mapunda, Edgar C.; Mamba, Bhekie B.; Msagati, Titus A. M.

    2017-08-01

    Rapid population increase, growth in industrial and agricultural sectors and global climate change have added significant pressure on conventional freshwater resources. Tapping freshwater from non-conventional water sources such as desalination and wastewater recycling is considered as sustainable alternative to the fundamental challenges of water scarcity. However, affordable and sustainable technologies need to be applied for the communities to benefit from the treatment of non-conventional water source. Membrane distillation is a potential desalination technology which can be used sustainably for this purpose. In this work multi-walled carbon nanotube embedded polyvinylidene fluoride membranes for application in membrane distillation desalination were prepared via non-solvent induced phase separation method. The casting solution was prepared using mixed solvents (N, N-dimethylacetamide and triethyl phosphate) at varying ratios to study the effect of solvent composition on membrane morphological structures. Membrane morphological features were studied using a number of techniques including scanning electron microscope, atomic force microscope, SAXSpace tensile strength analysis, membrane thickness, porosity and contact angle measurements. It was revealed that membrane hydrophobicity, thickness, tensile strength and surface roughness were increasing as the composition of N, N-dimethylacetamide in the solvent was increasing with maximum values obtained between 40 and 60% N, N-dimethylacetamide. Internal morphological structures were changing from cellular structures to short finger-like and sponge-like pores and finally to large macro void type of pores when the amount of N, N-dimethylacetamide in the solvent was changed from low to high respectively. Multi-walled carbon nanotube embedded polyvinylidene fluoride membranes of desired morphological structures and physical properties can be synthesized by regulating the composition of solvents used to prepare the

  13. Magnetic apatite for structural insights on the plasma membrane.

    Science.gov (United States)

    Stanca, Sarmiza E; Müller, Robert; Dellith, Jan; Nietzsche, Sandor; Stöckel, Stephan; Biskup, Christoph; Deckert, Volker; Krafft, Christoph; Popp, Jürgen; Fritzsche, Wolfgang

    2015-01-21

    The iron oxide-hydroxyapatite (FeOxHA) nanoparticles reported here differ from those reported before by their advantage of homogeneity and simple preparation; moreover, the presence of carboxymethyldextran (CMD), together with hydroxyapatite (HA), allows access to the cellular membrane, which makes our magnetic apatite unique. These nanoparticles combine magnetic behavior, Raman label ability and the property of interaction with the cellular membrane; they therefore represent an interesting material for structural differentiation of the cell membrane. It was observed by Raman spectroscopy, scanning electron microscopy (SEM) and fluorescence microscopy that FeOxHA adheres to the plasma membrane and does not penetrate the membrane. These insights make the nanoparticles a promising material for magnetic cell sorting, e.g. in microfluidic device applications.

  14. Modulation of the molecular arrangement in artificial and biological membranes by phospholipid-shelled microbubbles.

    Science.gov (United States)

    Carugo, Dario; Aron, Miles; Sezgin, Erdinc; Bernardino de la Serna, Jorge; Kuimova, Marina K; Eggeling, Christian; Stride, Eleanor

    2017-01-01

    The transfer of material from phospholipid-coated microbubbles to cell membranes has been hypothesized to play a role in ultrasound-mediated drug delivery. In this study, we employed quantitative fluorescence microscopy techniques to investigate this phenomenon in both artificial and biological membrane bilayers in an acoustofluidic system. The results of the present study provide strong evidence for the transfer of material from microbubble coatings into cell membranes. Our results indicate that transfer of phospholipids alters the organization of molecules in cell membranes, specifically the lipid ordering or packing, which is known to be a key determinant of membrane mechanical properties, protein dynamics, and permeability. We further show that polyethylene-glycol, used in many clinical microbubble formulations, also has a major impact on both membrane lipid ordering and the extent of lipid transfer, and that this occurs even in the absence of ultrasound exposure. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Development and applications of infrared structural biology

    Science.gov (United States)

    Kang, Zhouyang

    Aspartic acid (Asp), Glutamic acid (Glu) and Tyrosine (Tyr) often play critical roles at the active sites of proteins. Probing the structural dynamics of functionally important Asp/Glu and Tyr provides crucial information for protein functionality. Time-resolved infrared structural biology offers strong advantages for its high structural sensitivity and broad dynamic range (picosecond to kilosecond). In order to connect the vibrational frequencies to specific structures of COO- groups and phenolic --OH groups, such as the number, type, and geometry of hydrogen bond interactions, we develop two sets of vibrational structural markers (VSM), built on the symmetric and asymmetric stretching frequencies for COO- and C-O stretching and C-O-H bending frequencies for phenolic --OH. Extensive quantum physics (density functional theory) based computational studies, combined with site-specific isotope labeling as well as site-directed mutagenesis, and experimental FTIR data on Asp/Glu in proteins, are used to establish a unique correlation between the vibrations and multiple types of hydrogen bonding interactions. Development of those vibrational structural markers significantly enhances the power of time-resolved infrared structural biology for the study of functionally important structural dynamics of COO- from Asp/Glu and phenolic --OH from Tyr residues in proteins, including rhodopsin for biological signaling, bacteriorhodopsin and PYP for proton transfer, photosystem II for energy transformation, and HIV protease for enzymatic catalysis. Furthermore, this approach can be adopted in the future development of vibrational structural markers for other functionally important amino acid residues in proteins, such as arginine (Arg), histidine (His), and serine (Ser).

  16. Lipid nanotechnologies for structural studies of membrane-associated proteins.

    Science.gov (United States)

    Stoilova-McPhie, Svetla; Grushin, Kirill; Dalm, Daniela; Miller, Jaimy

    2014-11-01

    We present a methodology of lipid nanotubes (LNT) and nanodisks technologies optimized in our laboratory for structural studies of membrane-associated proteins at close to physiological conditions. The application of these lipid nanotechnologies for structure determination by cryo-electron microscopy (cryo-EM) is fundamental for understanding and modulating their function. The LNTs in our studies are single bilayer galactosylceramide based nanotubes of ∼20 nm inner diameter and a few microns in length, that self-assemble in aqueous solutions. The lipid nanodisks (NDs) are self-assembled discoid lipid bilayers of ∼10 nm diameter, which are stabilized in aqueous solutions by a belt of amphipathic helical scaffold proteins. By combining LNT and ND technologies, we can examine structurally how the membrane curvature and lipid composition modulates the function of the membrane-associated proteins. As proof of principle, we have engineered these lipid nanotechnologies to mimic the activated platelet's phosphtaidylserine rich membrane and have successfully assembled functional membrane-bound coagulation factor VIII in vitro for structure determination by cryo-EM. The macromolecular organization of the proteins bound to ND and LNT are further defined by fitting the known atomic structures within the calculated three-dimensional maps. The combination of LNT and ND technologies offers a means to control the design and assembly of a wide range of functional membrane-associated proteins and complexes for structural studies by cryo-EM. The presented results confirm the suitability of the developed methodology for studying the functional structure of membrane-associated proteins, such as the coagulation factors, at a close to physiological environment. © 2014 Wiley Periodicals, Inc.

  17. Influence of the lipid membrane environment on structure and activity of the outer membrane protein Ail from Yersinia pestis.

    Science.gov (United States)

    Ding, Yi; Fujimoto, L Miya; Yao, Yong; Plano, Gregory V; Marassi, Francesca M

    2015-02-01

    The surrounding environment has significant consequences for the structural and functional properties of membrane proteins. While native structure and function can be reconstituted in lipid bilayer membranes, the detergents used for protein solubilization are not always compatible with biological activity and, hence, not always appropriate for direct detection of ligand binding by NMR spectroscopy. Here we describe how the sample environment affects the activity of the outer membrane protein Ail (attachment invasion locus) from Yersinia pestis. Although Ail adopts the correct β-barrel fold in micelles, the high detergent concentrations required for NMR structural studies are not compatible with the ligand binding functionality of the protein. We also describe preparations of Ail embedded in phospholipid bilayer nanodiscs, optimized for NMR studies and ligand binding activity assays. Ail in nanodiscs is capable of binding its human ligand fibronectin and also yields high quality NMR spectra that reflect the proper fold. Binding activity assays, developed to be performed directly with the NMR samples, show that ligand binding involves the extracellular loops of Ail. The data show that even when detergent micelles support the protein fold, detergents can interfere with activity in subtle ways. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Biologically Complex Planar Cell Plasma Membranes Supported on Polyelectrolyte Cushions Enhance Transmembrane Protein Mobility and Retain Native Orientation.

    Science.gov (United States)

    Liu, Han-Yuan; Chen, Wei-Liang; Ober, Christopher K; Daniel, Susan

    2018-01-23

    Reconstituted supported lipid bilayers (SLB) are widely used as in vitro cell-surface models because they are compatible with a variety of surface-based analytical techniques. However, one of the challenges of using SLBs as a model of the cell surface is the limited complexity in membrane composition, including the incorporation of transmembrane proteins and lipid diversity that may impact the activity of those proteins. Additionally, it is challenging to preserve the transmembrane protein native orientation, function, and mobility in SLBs. Here, we leverage the interaction between cell plasma membrane vesicles and polyelectrolyte brushes to create planar bilayers from cell plasma membrane vesicles that have budded from the cell surface. This approach promotes the direct incorporation of membrane proteins and other species into the planar bilayer without using detergent or reconstitution and preserves membrane constituents. Furthermore, the structure of the polyelectrolyte brush serves as a cushion between the planar bilayer and rigid supporting surface, limiting the interaction of the cytosolic domains of membrane proteins with this surface. Single particle tracking was used to analyze the motion of GPI-linked yellow fluorescent proteins (GPI-YFP) and neon-green fused transmembrane P2X2 receptors (P2X2-neon) and shows that this platform retains over 75% mobility of multipass transmembrane proteins in its native membrane environment. An enzyme accessibility assay confirmed that the protein orientation is preserved and results in the extracellular domain facing toward the bulk phase and the cytosolic side facing the support. Because the platform presented here retains the complexity of the cell plasma membrane and preserves protein orientation and mobility, it is a better representative mimic of native cell surfaces, which may find many applications in biological assays aimed at understanding cell membrane phenomena.

  19. Membrane Binding of Recoverin: From Mechanistic Understanding to Biological Functionality

    Czech Academy of Sciences Publication Activity Database

    Timr, Štěpán; Pleskot, Roman; Kadlec, Jan; Kohagen, Miriam; Magarkar, Aniket; Jungwirth, Pavel

    2017-01-01

    Roč. 3, č. 8 (2017), s. 868-874 ISSN 2374-7943 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : recoverin * membrane * myristoyl * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 7.481, year: 2016 http://pubs.acs.org/doi/full/10.1021/acscentsci.7b00210

  20. Membrane transport mechanism 3D structure and beyond

    CERN Document Server

    Ziegler, Christine

    2014-01-01

    This book provides a molecular view of membrane transport by means of numerous biochemical and biophysical techniques. The rapidly growing number of atomic structures of transporters in different conformations and the constant progress in bioinformatics have recently added deeper insights.   The unifying mechanism of energized solute transport across membranes is assumed to consist of the conformational cycling of a carrier protein to provide access to substrate binding sites from either side of a cellular membrane. Due to the central role of active membrane transport there is considerable interest in deciphering the principles of one of the most fundamental processes in nature: the alternating access mechanism.   This book brings together particularly significant structure-function studies on a variety of carrier systems from different transporter families: Glutamate symporters, LeuT-like fold transporters, MFS transporters and SMR (RND) exporters, as well as ABC-type importers.   The selected examples im...

  1. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Correct use of Membrane Elements in Structural Analysis

    Directory of Open Access Journals (Sweden)

    Rothman Timothy

    2016-01-01

    Full Text Available Structural analysis of consumer electronic devices such as phones and tablets involves Finite Element Analysis (FEA. Dynamic loading conditions such as device dropping and bending dictate accurate FEA models to reduce design risk in many areas. The solid elements typically used in structural analysis do not have integration points on the surface. The outer surface is of most interest because that is where the cracks start. Analysts employ a post processing trick through using membranes to bring accurate stress/strain results to the surface. This paper explains numerical issues with implementation of membranes and recommends a methodology for accurate structural analysis.

  3. Infrared spectroscopic study of photoreceptor membrane and purple membrane. Protein secondary structure and hydrogen deuterium exchange

    International Nuclear Information System (INIS)

    Downer, N.W.; Bruchman, T.J.; Hazzard, J.H.

    1986-01-01

    Infrared spectroscopy in the interval from 1800 to 1300 cm-1 has been used to investigate the secondary structure and the hydrogen/deuterium exchange behavior of bacteriorhodopsin and bovine rhodopsin in their respective native membranes. The amide I' and amide II' regions from spectra of membrane suspensions in D2O were decomposed into constituent bands by use of a curve-fitting procedure. The amide I' bands could be fit with a minimum of three theoretical components having peak positions at 1664, 1638, and 1625 cm-1 for bacteriorhodopsin and 1657, 1639, and 1625 cm-1 for rhodopsin. For both of these membrane proteins, the amide I' spectrum suggests that alpha-helix is the predominant form of peptide chain secondary structure, but that a substantial amount of beta-sheet conformation is present as well. The shape of the amide I' band was pH-sensitive for photoreceptor membranes, but not for purple membrane, indicating that membrane-bound rhodopsin undergoes a conformation change at acidic pH. Peptide hydrogen exchange of bacteriorhodopsin and rhodopsin was monitored by observing the change in the ratio of integrated absorbance (Aamide II'/Aamide I') during the interval from 1.5 to 25 h after membranes were introduced into buffered D2O. The fraction of peptide groups in a very slowly exchanging secondary structure was estimated to be 0.71 for bacteriorhodopsin at pD 7. The corresponding fraction in vertebrate rhodopsin was estimated to be less than or equal to 0.60. These findings are discussed in relationship to previous studies of hydrogen exchange behavior and to structural models for both proteins

  4. Increasing the Performance of Vacuum Membrane Distillation Using Micro-Structured Hydrophobic Aluminum Hollow Fiber Membranes

    Directory of Open Access Journals (Sweden)

    Chia-Chieh Ko

    2017-04-01

    Full Text Available This study develops a micro-structured hydrophobic alumina hollow fiber with a high permeate flux of 60 Lm−2h−1 and salt rejection over 99.9% in a vacuum membrane distillation process. The fiber is fabricated by phase inversion and sintering, and then modified with fluoroalkylsilanes to render it hydrophobic. The influence of the sintering temperature and feeding temperature in membrane distillation (MD on the characteristics of the fiber and MD performance are investigated. The vacuum membrane distillation uses 3.5 wt % NaCl aqueous solution at 70 °C at 0.03 bar. The permeate flux of 60 Lm−2h−1 is the highest, compared with reported data and is higher than that for polymeric hollow fiber membranes.

  5. Determination of the Fatty Acid Content of Biological Membranes: A Highly Versatile GC-MS Experiment

    Science.gov (United States)

    Schultz, Emeric; Pugh, Michael Eugene

    2001-07-01

    The experiment involves the GC-MS of fatty acid methyl esters (FAMEs) obtained from bacterial membranes. It takes about 2 h, from cell harvest to injection. This experiment is done in a lab course for non-science majors and in biochemistry. For non-science majors the focus is on GC-MS as a technique for fingerprinting and on the underlying basis of that fingerprinting. In biochemistry the focus is on the composition of membranes and how this changes with temperature--specifically how the ratio of saturated to unsaturated fatty acids changes to maintain constant cell fluidity. Combined with a parallel DNA experiment, the two major types of intermolecular forces important for the structure and function of biomolecules are compared. How this versatile experiment could be adapted in other chemistry courses is presented. The experiment has obvious appeal to biology majors, can be used to develop several important chemistry concepts, involves teamwork, and employs an important instrument. It could be used in the laboratory portion of a course other than biochemistry to fulfill the new ACS biochemistry requirement.

  6. Influence of attapulgite addition on the biological performance and microbial communities of submerged dynamic membrane bioreactor

    Directory of Open Access Journals (Sweden)

    Wensong Duan

    2017-12-01

    Full Text Available A submerged dynamic membrane bioreactor (sDMBR was developed to test the influence of attapulgite (AT addition on the treatment performances and the microbial community structure and function. The batch experimental results displayed the highest UV254 and dissolved organic carbon (DOC removal efficiencies with 5% AT/mixed liquid suspended solids addition dosage. The continuous sDMBR results showed that the removal efficiencies of chemical oxygen demand, NH4+-N, total nitrogen and total phosphorus significantly increased in the AT added sDMBR. Excitation emission matrix analysis demonstrated that the protein-like peaks and fulvic acid-like peaks were significantly decreased in both in the mixed liquid and the effluent of the AT added reactor. The obligate anaerobes were observed in the sDMBR with AT addition, such as Bacteroidetes and Gamma proteobacterium in the dynamic membrane, which played an important role in the process of sludge granulation. Bacterial community richness significantly increased after AT addition with predominated phyla of Proteobacteria and Bacteroidetes. Similarly, species abundance significantly increased in the AT added sDMBR. Further investigations with cluster proved that AT was a favorite biological carrier for the microbial ecology, which enriched microbial abundance and community diversity of the sDMBR.

  7. Develop Infrared Structural Biology for Probing Structural Dynamics of Protein Functions

    Science.gov (United States)

    Xie, Aihua; Kang, Zhouyang; Causey, Oliver; Liu, Charle

    2015-03-01

    Protein functions are carried out through a series of structural transitions. Lack of knowledge on functionally important structural motions of proteins impedes our understanding of protein functions. Infrared structural biology is an emerging technology with powerful applications for protein structural dynamics. One key element of infrared structural biology is the development of vibrational structural marker (VSM) database library that translates infrared spectroscopic signals into specific structural information. We report the development of VSM for probing the type, geometry and strength of hydrogen bonding interactions of buried COO- side chains of Asp and Glu in proteins. Quantum theory based first principle computational studies combined with bioinformatic hydrogen bond analysis are employed in this study. We will discuss the applications of VSM in mechanistic studies of protein functions. Infrared structural biology is expected to emerge as a powerful technique for elucidating the functional mechanism of a broad range of proteins, including water soluble and membrane proteins. This work is supported by OCAST HR10-078 and NSF DBI1338097.

  8. Atomic force microscopy on domains in biological model membranes

    NARCIS (Netherlands)

    Rinia, H.A.

    2001-01-01

    This thesis describes the preparation and imaging of supported lipid bilayers, which can be regarded as biological modelmembranes, in the light of the formation of domains. The bilayers were prepared with either the Langmuir-Blodgett method, or with vesicle fusion. They were imaged with Atomic Force

  9. Contribution of assimilable organic carbon to biological fouling in seawater reverse osmosis membrane treatment.

    Science.gov (United States)

    Weinrich, Lauren; LeChevallier, Mark; Haas, Charles N

    2016-09-15

    Biological fouling occurs on RO membranes when bacteria and nutrients are present in conditions that are conducive to growth and proliferation of the bacteria. Controlling microbial growth on the membranes is typically limited to biocide application (i.e., disinfectants) in seawater RO plants. However, biological growth and subsequent fouling has not been well-managed. Pretreatment has not been focused on nutrient limitation. This project used a biological assay, the assimilable organic carbon (AOC) test to evaluate pretreatment effects on the nutrient supply. The AOC test provided a useful surrogate measurement for the biodegradability or biofouling potential of RO feed water. Biofouling observed in controlled conditions at the bench- and pilot-scale resulted in statistically significant correlations between AOC and the operational effects caused by biofouling. Membrane fouling rates are observed through operational changes over time such as increased differential pressure between the membrane feed and concentrate locations and decreased permeate flux through the membrane. In full scale plants there were strong correlations when AOC was used as a predictor variable for increased differential pressure (0.28-0.55 bar from September-December 2012) and decreased specific flux (1.40 L per hour/(m(2) · bar)). Increased differential pressure was associated with RO membrane biological fouling when the median AOC was 50 μg/L during pilot testing. Conditions were also evaluated at the bench-scale using a flat sheet RO membrane. In a comparison test using 30 and 1000 μg/L AOC, fouling was detected on more portions of the membrane when AOC was higher. Biofilm and bacterial deposits were apparent from scanning electron microscope imaging and biomass measurements using ATP. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. An approach to membrane protein structure without crystals

    Science.gov (United States)

    Sorgen, Paul L.; Hu, Yonglin; Guan, Lan; Kaback, H. Ronald; Girvin, Mark E.

    2002-01-01

    The lactose permease of Escherichia coli catalyzes coupled translocation of galactosides and H+ across the cell membrane. It is the best-characterized member of the Major Facilitator Superfamily, a related group of membrane proteins with 12 transmembrane domains that mediate transport of various substrates across cell membranes. Despite decades of effort and their functional importance in all kingdoms of life, no high-resolution structures have been solved for any member of this family. However, extensive biochemical, genetic, and biophysical studies on lactose permease have established its transmembrane topology, secondary structure, and numerous interhelical contacts. Here we demonstrate that this information is sufficient to calculate a structural model at the level of helix packing or better. PMID:12391320

  11. The trans-membrane potential of biological membranes in computer simulation

    Czech Academy of Sciences Publication Activity Database

    Melcr, Josef; Timr, Štěpán; Jungwirth, Pavel

    2015-01-01

    Roč. 44, Suppl 1 (2015), S170 ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * trans-membrane potential Subject RIV: CF - Physical ; Theoretical Chemistry

  12. Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

    Science.gov (United States)

    Kalinin, Vladimir I.; Ivanchina, Natalia V.; Krasokhin, Vladimir B.; Makarieva, Tatyana N.; Stonik, Valentin A.

    2012-01-01

    Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

  13. The Tobacco mosaic virus Movement Protein Associates with but Does Not Integrate into Biological Membranes

    Science.gov (United States)

    Peiró, Ana; Martínez-Gil, Luis; Tamborero, Silvia; Pallás, Vicente

    2014-01-01

    ABSTRACT Plant positive-strand RNA viruses require association with plant cell endomembranes for viral translation and replication, as well as for intra- and intercellular movement of the viral progeny. The membrane association and RNA binding of the Tobacco mosaic virus (TMV) movement protein (MP) are vital for orchestrating the macromolecular network required for virus movement. A previously proposed topological model suggests that TMV MP is an integral membrane protein with two putative α-helical transmembrane (TM) segments. Here we tested this model using an experimental system that measured the efficiency with which natural polypeptide segments were inserted into the ER membrane under conditions approximating the in vivo situation, as well as in planta. Our results demonstrated that the two hydrophobic regions (HRs) of TMV MP do not span biological membranes. We further found that mutations to alter the hydrophobicity of the first HR modified membrane association and precluded virus movement. We propose a topological model in which the TMV MP HRs intimately associate with the cellular membranes, allowing maximum exposure of the hydrophilic domains of the MP to the cytoplasmic cellular components. IMPORTANCE To facilitate plant viral infection and spread, viruses encode one or more movement proteins (MPs) that interact with ER membranes. The present work investigated the membrane association of the 30K MP of Tobacco mosaic virus (TMV), and the results challenge the previous topological model, which predicted that the TMV MP behaves as an integral membrane protein. The current data provide greatly needed clarification of the topological model and provide substantial evidence that TMV MP is membrane associated only at the cytoplasmic face of the membrane and that neither of its domains is integrated into the membrane or translocated into the lumen. Understanding the topology of MPs in the ER is vital for understanding the role of the ER in plant virus transport

  14. The biological waste product formation in the light of the membrane hypothesis of aging.

    Science.gov (United States)

    Zs-Nagy, Imre

    2002-01-01

    The membrane hypothesis of aging (MHA) explains the biological waste product (lipofuscin) formation as a disbalance between the rates of protein synthesis and damage, as well as of elimination of the damaged components. Although, this concept has not been refuted on the basis of any experimental evidence, it has neither been widely accepted. During the last decade the general interest has turned toward the molecular genetics so intensely, that research aimed at clarifying cell biological mechanisms became so to say hibernated. Nowadays it is being recognized more and more that after the complete description of the human genetic code, attention has to be dedicated again to the cellular mechanisms explaining the function of the gene products (proteins). In this context, our experimental findings described during the recent years may become again the subject of interest. We have shown that the in vivo inhibition of the lysosomal thiol-proteinase functions by sublethal doses of leupeptin in young, adult and old mice results in a considerable increase (about 30%) of the immobile fraction of membrane proteins in hepatocyte plasma membrane, meanwhile the lateral diffusion constant of the still mobile membrane proteins increased. These observations were interpreted as signs of a general slowing down of protein turnover in the plasma membrane, just by inhibiting the elimination mechanisms in the lysosomes. This paper will discuss the theoretical conclusions and significance of these findings for the biological waste product formation, as a basic cell biological function.

  15. The radioinduced membranes injuries as biological dose indicators: mechanisms of studies and practical applications

    International Nuclear Information System (INIS)

    Vincent-Genod, Lucie

    2001-10-01

    After an accidental overexposure, the assessment of the received dose in biological dosimetry is performed by a method based on the effects of irradiation on the DNA molecule. But this technique shows some limitations; therefore we tried to find new bio-sensors of radiation exposure. We have pointed out that membrane is a critical target of ionising radiation after an in vitro and in vivo overexposure. In vitro, these modifications were involved in the radio-induced apoptotic pathway. The measure of membrane fluidity allowed us to obtain an overall view of cellular membrane. Moreover, in vivo, by changing the lipid nutritional status of animals, our results displayed the important role played by membrane lipid composition in radio-induced membrane alterations. Besides, membrane effects were adjusted by the extracellular physiological control, and in particular by the damages on membrane fatty acid pattern. Finally, we have tested the use of membrane fluidity index as a bio-sensor of radiation exposure on in vivo models and blood samples from medical total body irradiated patients. The results achieved on animal models suggested that the membrane fluidity index was a bio-sensor of radiation exposure. Nevertheless, the observations realised on patients highlight that the effect of the first dose fraction of the radiotherapy treatment had some difficulties to be noticed. Indeed, the combined treatment: chemotherapy and radiotherapy disturbed the membrane fluidity index measures. To conclude, whereas this parameter was not a bio-sensor of irradiation exposure usable in biological dosimetry, it may allow us to assess the radio-induced damages and their cellular but also tissue impacts. (author)

  16. Capacitive Structures for Gas and Biological Sensing

    KAUST Repository

    Sapsanis, Christos

    2015-04-01

    The semiconductor industry was benefited by the advances in technology in the last decades. This fact has an impact on the sensors field, where the simple transducer was evolved into smart miniaturized multi-functional microsystems. However, commercially available gas and biological sensors are mostly bulky, expensive, and power-hungry, which act as obstacles to mass use. The aim of this work is gas and biological sensing using capacitive structures. Capacitive sensors were selected due to its design simplicity, low fabrication cost, and no DC power consumption. In the first part, the dominant structure among interdigitated electrodes (IDEs), fractal curves (Peano and Hilbert) and Archimedean spiral was investigated from capacitance density perspective. The investigation consists of geometrical formula calculations, COMSOL Multiphysics simulations and cleanroom fabrication of the capacitors on a silicon substrate. Moreover, low-cost fabrication on flexible plastic PET substrate was conducted outside cleanroom with rapid prototyping using a maskless laser etching. The second part contains the humidity, Volatile Organic compounds (VOCs) and Ammonia sensing of polymers, Polyimide and Nafion, and metal-organic framework (MOF), Cu(bdc)2.xH2O using IDEs and tested in an automated gas setup for experiment control and data extraction. The last part includes the biological sensing of C - reactive protein (CRP) quantification, which is considered as a biomarker of being prone to cardiac diseases and Bovine serum albumin (BSA) protein quantification, which is used as a reference for quantifying unknown proteins.

  17. Structuring detergents for extracting and stabilizing functional membrane proteins.

    Directory of Open Access Journals (Sweden)

    Rima Matar-Merheb

    Full Text Available BACKGROUND: Membrane proteins are privileged pharmaceutical targets for which the development of structure-based drug design is challenging. One underlying reason is the fact that detergents do not stabilize membrane domains as efficiently as natural lipids in membranes, often leading to a partial to complete loss of activity/stability during protein extraction and purification and preventing crystallization in an active conformation. METHODOLOGY/PRINCIPAL FINDINGS: Anionic calix[4]arene based detergents (C4Cn, n=1-12 were designed to structure the membrane domains through hydrophobic interactions and a network of salt bridges with the basic residues found at the cytosol-membrane interface of membrane proteins. These compounds behave as surfactants, forming micelles of 5-24 nm, with the critical micellar concentration (CMC being as expected sensitive to pH ranging from 0.05 to 1.5 mM. Both by 1H NMR titration and Surface Tension titration experiments, the interaction of these molecules with the basic amino acids was confirmed. They extract membrane proteins from different origins behaving as mild detergents, leading to partial extraction in some cases. They also retain protein functionality, as shown for BmrA (Bacillus multidrug resistance ATP protein, a membrane multidrug-transporting ATPase, which is particularly sensitive to detergent extraction. These new detergents allow BmrA to bind daunorubicin with a Kd of 12 µM, a value similar to that observed after purification using dodecyl maltoside (DDM. They preserve the ATPase activity of BmrA (which resets the protein to its initial state after drug efflux much more efficiently than SDS (sodium dodecyl sulphate, FC12 (Foscholine 12 or DDM. They also maintain in a functional state the C4Cn-extracted protein upon detergent exchange with FC12. Finally, they promote 3D-crystallization of the membrane protein. CONCLUSION/SIGNIFICANCE: These compounds seem promising to extract in a functional state

  18. Structural Interfaces and Attachments in Biology

    CERN Document Server

    Birman, Victor; Genin, Guy

    2013-01-01

    Attachment of dissimilar materials in engineering and surgical practice is a perennial challenge. Bimaterial attachment sites are common locations for injury, repeated injury, and mechanical failure. Nature presents several highly effective solutions to the challenge of bimaterial attachment that differ from those found in engineering practice. Structural Interfaces and Attachments in Biology describes the attachment of dissimilar materials from multiple perspectives. The text will simultaneously elucidate natural bimaterial attachments and outline engineering principles underlying successful attachments to the communities of tissue engineers and surgeons. Included an in-depth analysis of the biology of attachments in the body and mechanisms by which robust attachments are formed, a review of current concepts of attaching dissimilar materials in surgical practice and a discussion of bioengineering approaches that are currently being developed. This book also: Provides the first comprehensive treatment of phys...

  19. Accuracy of determination of position and width of molecular groups in biological and lipid membranes via neutron diffraction.

    Science.gov (United States)

    Gordeliy, V I; Chernov, N I

    1997-07-01

    Neutron diffraction combined with the deuterium-labelled molecular groups of biological and model membrane components allows one to detect with high accuracy the structure of these objects. Experiments of this kind are only possible at unique high-flux neutron sources, and the planning of neutron-diffraction experiments must take into account some special requirements primarily related to the duration of the experiment and the accuracy of estimation of membrane structure parameters as a result of finite time of the measurements. This paper deals with the question of statistical accuracy of the position x(0) and width v of the distribution of deuterium labels in membranes along the normal of their plane, which are determined in a neutron diffraction experiment. It is shown that the accuracy of x(0) and v estimation does not depend on membrane constitution. It is dependent only on the scattering amplitude of the deuterium label, the label position x(0) and the distribution width v. Analytic calculations show that the statistical errors Deltax(0) and Deltav are inversely proportional to the scattering amplitude of the label and, as usual, to the square root of measurement time. The question of Deltax0 and Deltav dependence on the number of structure factors used in the calculations of x(0) and v is also studied. It is shown that, the accuracy of x(0) estimation is approximately constant with down to four structure factors used, and, with the number of the factors below four, it deteriorates drastically. Analogous is the behaviour of Deltav(h(max)) relation with one exception: abrupt deterioration of the accuracy occurs beginning with five structure factors used. One does not have to measure the highest diffraction reflections which takes a much longer time compared with the first ones. It is an important result. All the problems mentioned above have also been considered for the case of two different deuterium labels in membranes.

  20. FATE OF REVERSE OSMOSIS (RO) MEMBRANES DURING OXIDATION BY DISINFECTANTS USED IN WATER TREATMENT: IMPACT ON MEMBRANE STRUCTURE AND PERFORMANCES

    KAUST Repository

    Maugin, Thomas

    2013-12-01

    Providing pretreatment prior RO filtration is essential to avoid biofouling and subsequent loss of membrane performances. Chlorine is known to degrade polymeric membrane, improving or reducing membrane efficiency depending on oxidation conditions. This study aimed to assess the impact of alternative disinfectant, NH2Cl, as well as secondary oxidants formed during chloramination of seawater, e.g. HOBr, HOI, or used in water treatment e.g. ClO2, O3, on membrane structure and performances. Permeability, total and specific rejection (Cl-, SO4 2-, Br-, Boron), FTIR profile, elemental composition were analyzed. Results showed that each oxidant seems to react differently with the membrane. HOCl, HOBr, ClO2 and O3 improved membrane permeability but decreased rejection in different extent. In comparison, chloramines resulted in identical trends but oxidized membrane very slowly. On the contrary, iodine improved membrane rejection e.g. boron, but decreased permeability. Reaction conducted with chlorine, bromine, iodine and chloramines resulted in the incorporation of halogen in the membrane structure. All oxidant except iodine were able to break amide bonds of the membrane structure in our condition. In addition, chloramine seemed to react with membrane differently, involving a potential addition of nitrogen. Chloramination of seawater amplified membrane performances evolutions due to generation of bromochloramine. Moreover, chloramines reacted both with NOM and membrane during oxidation in natural seawater, leading to additional rejection drop.

  1. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

    Directory of Open Access Journals (Sweden)

    Katja Venko

    2017-01-01

    Full Text Available The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix–helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.

  2. A Trade Study of Two Membrane-Aerated Biological Water Processors

    Science.gov (United States)

    Allada, Ram; Lange, Kevin; Vega. Leticia; Roberts, Michael S.; Jackson, Andrew; Anderson, Molly; Pickering, Karen

    2011-01-01

    Biologically based systems are under evaluation as primary water processors for next generation life support systems due to their low power requirements and their inherent regenerative nature. This paper will summarize the results of two recent studies involving membrane aerated biological water processors and present results of a trade study comparing the two systems with regards to waste stream composition, nutrient loading and system design. Results of optimal configurations will be presented.

  3. Structure and membrane organization of photosystem II in green plants

    NARCIS (Netherlands)

    Hankamer, B; Barber, J; Boekema, EJ

    1997-01-01

    Photosystem II (PSII) is the pigment protein complex embedded in the thylakoid membrane of higher plants, algae, and cyanobacteria that uses solar energy to drive the photosynthetic water-splitting reaction. This chapter reviews the primary, secondary, tertiary, and quaternary structures of PSII as

  4. Designing CNC Knit for Hybrid Membrane And Bending Active Structures

    DEFF Research Database (Denmark)

    Tamke, Martin; Holden Deleuran, Anders; Gengnagel, Christoph

    2015-01-01

    specific properties and detailing. CNC knitting with high tenacity yarn enables this practice and offers an alternative to current woven membranes. The design and fabrication of an 8m high fabric tower through an interdisciplinary team of architects, structural and textile engineers, allowed to investigate...

  5. Membranolytic Activity of Bile Salts: Influence of Biological Membrane Properties and Composition

    Directory of Open Access Journals (Sweden)

    Alfred Blume

    2007-10-01

    Full Text Available The two main steps of the membranolytic activity of detergents: 1 the partitioning of detergent molecules in the membrane and 2 the solubilisation of the membrane are systematically investigated. The interactions of two bile salt molecules, sodium cholate (NaC and sodium deoxycholate (NaDC with biological phospholipid model membranes are considered. The membranolytic activity is analysed as a function of the hydrophobicity of the bile salt, ionic strength, temperature, membrane phase properties, membrane surface charge and composition of the acyl chains of the lipids. The results are derived from calorimetric measurements (ITC, isothermal titration calorimetry. A thermodynamic model is described, taking into consideration electrostatic interactions, which is used for the calculation of the partition coefficient as well as to derive the complete thermodynamic parameters describing the interaction of detergents with biological membranes (change in enthalpy, change in free energy, change in entropy etc. The solubilisation properties are described in a so-called vesicle-to-micelle phase transition diagram. The obtained results are supplemented and confirmed by data obtained from other biophysical techniques (DSC differential scanning calorimetry, DLS dynamic light scattering, SANS small angle neutron scattering.

  6. Different Structures of PVA Nanofibrous Membrane for Sound Absorption Application

    Directory of Open Access Journals (Sweden)

    Jana Mohrova

    2012-01-01

    Full Text Available The thin nanofibrous layer has different properties in the field of sound absorption in comparison with porous fibrous material which works on a principle of friction of air particles in contact with walls of pores. In case of the thin nanofibrous layer, which represents a sound absorber here, the energy of sonic waves is absorbed by the principle of membrane resonance. The structure of the membrane can play an important role in the process of converting the sonic energy to a different energy type. The vibration system acts differently depending on the presence of smooth fibers in the structure, amount of partly merged fibers, or structure of polymer foil as extreme. Polyvinyl alcohol (PVA was used as a polymer because of its good water solubility. It is possible to influence the structure of nanofibrous layer during the production process thanks to this property of polyvinyl alcohol.

  7. The amphiphilic nature of saponins and their effects on artificial and biological membranes and potential consequences for red blood and cancer cells.

    Science.gov (United States)

    Lorent, Joseph H; Quetin-Leclercq, Joëlle; Mingeot-Leclercq, Marie-Paule

    2014-11-28

    Saponins, amphiphiles of natural origin with numerous biological activities, are widely used in the cosmetic and pharmaceutical industry. Some saponins exhibit relatively selective cytotoxic effects on cancer cells but the tendency of saponins to induce hemolysis limits their anticancer potential. This review focused on the effects of saponin activity on membranes and consequent implications for red blood and cancer cells. This activity seems to be strongly related to the amphiphilic character of saponins that gives them the ability to self-aggregate and interact with membrane components such as cholesterol and phospholipids. Membrane interactions of saponins with artificial membrane models, red blood and cancer cells are reviewed with respect to their molecular structures. The review considered the mechanisms of these membrane interactions and their consequences including the modulation of membrane dynamics, interaction with membrane rafts, and membrane lysis. We summarized current knowledge concerning the mechanisms involved in the interactions of saponins with membrane lipids and examined the structure activity relationship of saponins regarding hemolysis and cancer cell death. A critical analysis of these findings speculates on their potential to further develop new anticancer compounds.

  8. Optical Antenna-Based Fluorescence Correlation Spectroscopy to Probe the Nanoscale Dynamics of Biological Membranes.

    Science.gov (United States)

    Winkler, Pamina M; Regmi, Raju; Flauraud, Valentin; Brugger, Jürgen; Rigneault, Hervé; Wenger, Jérôme; García-Parajo, María F

    2018-01-04

    The plasma membrane of living cells is compartmentalized at multiple spatial scales ranging from the nano- to the mesoscale. This nonrandom organization is crucial for a large number of cellular functions. At the nanoscale, cell membranes organize into dynamic nanoassemblies enriched by cholesterol, sphingolipids, and certain types of proteins. Investigating these nanoassemblies known as lipid rafts is of paramount interest in fundamental cell biology. However, this goal requires simultaneous nanometer spatial precision and microsecond temporal resolution, which is beyond the reach of common microscopes. Optical antennas based on metallic nanostructures efficiently enhance and confine light into nanometer dimensions, breaching the diffraction limit of light. In this Perspective, we discuss recent progress combining optical antennas with fluorescence correlation spectroscopy (FCS) to monitor microsecond dynamics at nanoscale spatial dimensions. These new developments offer numerous opportunities to investigate lipid and protein dynamics in both mimetic and native biological membranes.

  9. Micro-electromembrane extraction across free liquid membranes. Extractions of basic drugs from undiluted biological samples

    Czech Academy of Sciences Publication Activity Database

    Kubáň, Pavel; Boček, Petr

    2014-01-01

    Roč. 1337, Apr (2014), s. 32-39 ISSN 0021-9673 R&D Projects: GA ČR(CZ) GA13-05762S Institutional support: RVO:68081715 Keywords : micro-electromembrane extraction * free liquid membranes * biological samples Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.169, year: 2014

  10. Micro-electromembrane extraction across free liquid membranes. Extractions of basic drugs from undiluted biological samples

    Czech Academy of Sciences Publication Activity Database

    Kubáň, Pavel; Boček, Petr

    2014-01-01

    Roč. 1337, Apr (2014), s. 32-39 ISSN 0021-9673 R&D Projects: GA ČR(CZ) GA13-05762S Institutional support: RVO:68081715 Keywords : micro-electromembrane extraction * free liquid membranes * biological samples Subject RIV: CB - Analytical Chemistry , Separation Impact factor: 4.169, year: 2014

  11. Probing membrane protein structure using water polarization transfer solid-state NMR.

    Science.gov (United States)

    Williams, Jonathan K; Hong, Mei

    2014-10-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected (1)H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins. Copyright © 2014 Elsevier Inc. All

  12. 2010 Diffraction Methods in Structural Biology

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Ana Gonzalez

    2011-03-10

    Advances in basic methodologies have played a major role in the dramatic progress in macromolecular crystallography over the past decade, both in terms of overall productivity and in the increasing complexity of the systems being successfully tackled. The 2010 Gordon Research Conference on Diffraction Methods in Structural Biology will, as in the past, focus on the most recent developments in methodology, covering all aspects of the process from crystallization to model building and refinement, complemented by examples of structural highlights and complementary methods. Extensive discussion will be encouraged and it is hoped that all attendees will participate by giving oral or poster presentations, the latter using the excellent poster display area available at Bates College. The relatively small size and informal atmosphere of the meeting provides an excellent opportunity for all participants, especially younger scientists, to meet and exchange ideas with leading methods developers.

  13. Cytosol-dependent membrane fusion in ER, nuclear envelope and nuclear pore assembly: biological implications.

    Science.gov (United States)

    Rafikova, Elvira R; Melikov, Kamran; Chernomordik, Leonid V

    2010-01-01

    Endoplasmic reticulum and nuclear envelope rearrangements after mitosis are often studied in the reconstitution system based on Xenopus egg extract. In our recent work we partially replaced the membrane vesicles in the reconstitution mix with protein-free liposomes to explore the relative contributions of cytosolic and transmembrane proteins. Here we discuss our finding that cytosolic proteins mediate fusion between membranes lacking functional transmembrane proteins and the role of membrane fusion in endoplasmic reticulum and nuclear envelope reorganization. Cytosol-dependent liposome fusion has allowed us to restore, without adding transmembrane nucleoporins, functionality of nuclear pores, their spatial distribution and chromatin decondensation in nuclei formed at insufficient amounts of membrane material and characterized by only partial decondensation of chromatin and lack of nuclear transport. Both the mechanisms and the biological implications of the discovered coupling between spatial distribution of nuclear pores, chromatin decondensation and nuclear transport are discussed.

  14. Synergy and interactions among biological pathways leading to preterm premature rupture of membranes.

    Science.gov (United States)

    Lannon, Sophia M R; Vanderhoeven, Jeroen P; Eschenbach, David A; Gravett, Michael G; Adams Waldorf, Kristina M

    2014-10-01

    Preterm premature rupture of membranes (PPROM) occurs in 1% to 2% of births. Impact of PPROM is greatest in low- and middle-income countries where prematurity-related deaths are most common. Recent investigations identify cytokine and matrix metalloproteinase activation, oxidative stress, and apoptosis as primary pathways to PPROM. These biological processes are initiated by heterogeneous etiologies including infection/inflammation, placental bleeding, uterine overdistention, and genetic polymorphisms. We hypothesize that pathways to PPROM overlap and act synergistically to weaken membranes. We focus our discussion on membrane composition and strength, pathways linking risk factors to membrane weakening, and future research directions to reduce the global burden of PPROM. © The Author(s) 2014.

  15. Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions

    Science.gov (United States)

    Heim, Andrew J.; Li, Zhijun

    2012-03-01

    Membrane proteins are of particular biological and pharmaceutical importance, and computational modeling and structure prediction approaches play an important role in studies of membrane proteins. Developing an accurate model quality assessment program is of significance to the structure prediction of membrane proteins. Few such programs are proposed that can be applied to a broad range of membrane protein classes and perform with high accuracy. We developed a new model scoring function Interaction-based Quality assessment (IQ), based on the analysis of four types of inter-residue interactions within the transmembrane domains of helical membrane proteins. This function was tested using three high-quality model sets: all 206 models of GPCR Dock 2008, all 284 models of GPCR Dock 2010, and all 92 helical membrane protein models of the HOMEP set. For all three sets, the scoring function can select the native structures among all of the models with the success rates of 93, 85, and 100% respectively. For comparison, these three model sets were also adopted for a recently published model assessment program for membrane protein structures, ProQM, which gave the success rates of 85, 79, and 92% separately. These results suggested that IQ outperforms ProQM when only the transmembrane regions of the models are considered. This scoring function should be useful for the computational modeling of membrane proteins.

  16. Structural sensitivity of biological models revisited.

    Science.gov (United States)

    Cordoleani, Flora; Flora, Cordoleani; Nerini, David; David, Nerini; Gauduchon, Mathias; Mathias, Gauduchon; Morozov, Andrew; Andrew, Morozov; Poggiale, Jean-Christophe; Jean-Christophe, Poggiale

    2011-08-21

    Enhancing the predictive power of models in biology is a challenging issue. Among the major difficulties impeding model development and implementation are the sensitivity of outcomes to variations in model parameters, the problem of choosing of particular expressions for the parametrization of functional relations, and difficulties in validating models using laboratory data and/or field observations. In this paper, we revisit the phenomenon which is referred to as structural sensitivity of a model. Structural sensitivity arises as a result of the interplay between sensitivity of model outcomes to variations in parameters and sensitivity to the choice of model functions, and this can be somewhat of a bottleneck in improving the models predictive power. We provide a rigorous definition of structural sensitivity and we show how we can quantify the degree of sensitivity of a model based on the Hausdorff distance concept. We propose a simple semi-analytical test of structural sensitivity in an ODE modeling framework. Furthermore, we emphasize the importance of directly linking the variability of field/experimental data and model predictions, and we demonstrate a way of assessing the robustness of modeling predictions with respect to data sampling variability. As an insightful illustrative example, we test our sensitivity analysis methods on a chemostat predator-prey model, where we use laboratory data on the feeding of protozoa to parameterize the predator functional response. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Structural basis for catalysis at the membrane-water interface.

    Science.gov (United States)

    Dufrisne, Meagan Belcher; Petrou, Vasileios I; Clarke, Oliver B; Mancia, Filippo

    2017-11-01

    The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Ion induced changes in the structure of bordered pit membranes

    Directory of Open Access Journals (Sweden)

    Jinkee eLee

    2012-03-01

    Full Text Available Xylem hydraulic resistance varies with ion concentration in sap solution. It is assumed that this variation in resistance results from hydrogel like properties of pectins located in bordered pit membranes separating adjacent vessels. Although kinetics of the resistance change suggests swelling/deswelling behavior of the pectins, there is no direct evidence of this activity. In this report we provide evidence of structural changes in bordered pit membranes responding to variation in ionic concentration of solute around it using atomic force microscopy (AFM. AFM revealed bordered pit membranes as relatively smooth, soft and lacking any sharp edges surface when submerged in de-ionized water, in contrast to pictures from scanning electron microscope (SEM or AFM performed on air dry material. Exposure of the bordered pit membranes to 50 mM KCl solution resulted in significant changes in both surface physical properties with and elevation features as bordered pit membrane became harder, with visible edges of fibers and collapsed, while no change in porosity was observed. Analysis suggests a need for a major shift in our understanding to the physical bases of variable xylem resistance from change in porosity to change in pathway length. Findings support the role of actuating properties of hybrid hydrogel-cellulose materials in water redistribution and embolism resistance.

  19. Sine wave electropermeabilization reveals the frequency-dependent response of the biological membranes.

    Science.gov (United States)

    García-Sánchez, Tomás; Merla, Caterina; Fontaine, Jessica; Muscat, Adeline; Mir, Lluis M

    2018-02-02

    The permeabilization of biological membranes by electric fields, known as electroporation, has been traditionally performed with square electric pulses. These signals distribute the energy applied to cells in a wide frequency band. This paper investigates the use of sine waves, which are narrow band signals, to provoke electropermeabilization and the frequency dependence of this phenomenon. Single bursts of sine waves at different frequencies in the range from 8 kHz-130 kHz were applied to cells in vitro. Electroporation was studied in the plasma membrane and the internal organelles membrane using calcium as a permeabilization marker. Additionally, a double-shell electrical model was simulated to give a theoretical framework to our results. The electroporation efficiency shows a low pass filter frequency dependence for both the plasma membrane and the internal organelles membrane. The mismatch between the theoretical response and the observed behavior for the internal organelles membrane is explained by a two-step permeabilization process: first the permeabilization of the external membrane and afterwards that of the internal membranes. The simulations in the model confirm this two-step hypothesis when a variable plasma membrane conductivity is considered in the analysis. This study demonstrates how the use of narrow-band signals as sine waves is a suitable method to perform electroporation in a controlled manner. We suggest that the use of this type of signals could bring a simplification in the investigations of the very complex phenomenon of electroporation, thus representing an interesting option in future fundamental studies. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Structure and Function of the Membrane Deformation AAA ATPase Vps4

    Science.gov (United States)

    Hill, Christopher P.; Babst, Markus

    2011-01-01

    The ATPase Vps4 belongs to the type-I AAA family of proteins. Vps4 functions together with a group of proteins referred to as ESCRTs in membrane deformation and fission events. These cellular functions include vesicle formation at the endosome, cytokinesis and viral budding. The highly dynamic quaternary structure of Vps4 and its interactions with a network of regulators and co-factors have made the analysis of this ATPase challenging. Nevertheless, recent advances in the understanding of the cell biology of Vps4 together with structural information and in vitro studies are guiding mechanistic models of this ATPase. PMID:21925211

  1. Structure and interactions in biomaterials based on membrane-biopolymer self-assembly

    Science.gov (United States)

    Koltover, Ilya

    Physical and chemical properties of artificial pure lipid membranes have been extensively studied during the last two decades and are relatively well understood. However, most real membrane systems of biological and biotechnological importance incorporate macromolecules either embedded into the membranes or absorbed onto their surfaces. We have investigated three classes of self-assembled membrane-biopolymer biomaterials: (i) Structure, interactions and stability of the two-dimensional crystals of the integral membrane protein bacteriorhodopsin (bR). We have conducted a synchrotron x-ray diffraction study of oriented bR multilayers. The important findings were as follows: (1) the protein 2D lattice exhibited diffraction patterns characteristic of a 2D solid with power-law decay of in-plane positional correlations, which allowed to measure the elastic constants of protein crystal; (2) The crystal melting temperature was a function of the multilayer hydration, reflecting the effect of inter-membrane repulsion on the stability of protein lattice; (3) Preparation of nearly perfect (mosaicity video-enhanced light microscopy we have observed a membrane-distortion induced attraction between the particles with the interaction range of the order of particle diameter. Fluid membranes decorated with many particles exhibited: (i) a finite-sized two-dimensional closed packed aggregates and (ii) a one-dimensional ring-like aggregates. (iii) Structure, stability and interactions in the cationic lipid-DNA complexes. Cationic liposomes complexed with DNA are among the most promising synthetic non-viral carriers of DNA vectors currently used in gene therapy applications. We have established that DNA complexes with cationic lipid (DOTAP) and a neutral lipid (DOPC) have a compact multilayer liquid crystalline structure ( L ca ) with DNA intercalated between the lipid bilayers in a periodic 2D smectic phase. Furthermore, a different 2D columnar phase of complexes was found in mixtures

  2. Lipid membrane partitioning of lysolipids and fatty acids: Effects of membrane phase structure and detergent chain length

    DEFF Research Database (Denmark)

    Høyrup, Lise Pernille Kristine; Davidsen, Jesper; Jørgensen, Kent

    2001-01-01

    ) of the detergents. The calorimetric results reveal that the membrane partitioning of lysolipids depends strongly on the phase structure of the lipid membrane. This is manifested as a lysolipid partition coefficient, K, that is much larger for fluid-phase lipid membranes as compared to gel-phase lipid membranes...... of magnitude higher when the saturated acyl chain of the detergents increases by two carbon atoms. The obtained partition coefficients are of importance in relation to a deeper understanding of the interplay between global aqueous and local membrane concentrations of the detergents and the functional influence...

  3. A novel membrane distillation-thermophilic bioreactor system: biological stability and trace organic compound removal.

    Science.gov (United States)

    Wijekoon, Kaushalya C; Hai, Faisal I; Kang, Jinguo; Price, William E; Guo, Wenshan; Ngo, Hao H; Cath, Tzahi Y; Nghiem, Long D

    2014-05-01

    The removal of trace organic compounds (TrOCs) by a novel membrane distillation-thermophilic bioreactor (MDBR) system was examined. Salinity build-up and the thermophilic conditions to some extent adversely impacted the performance of the bioreactor, particularly the removal of total nitrogen and recalcitrant TrOCs. While most TrOCs were well removed by the thermophilic bioreactor, compounds containing electron withdrawing functional groups in their molecular structure were recalcitrant to biological treatment and their removal efficiency by the thermophilic bioreactor was low (0-53%). However, the overall performance of the novel MDBR system with respect to the removal of total organic carbon, total nitrogen, and TrOCs was high and was not significantly affected by the conditions of the bioreactor. All TrOCs investigated here were highly removed (>95%) by the MDBR system. Biodegradation, sludge adsorption, and rejection by MD contribute to the removal of TrOCs by MDBR treatment. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

  4. [Biomechanic and biological activity assessment of concavity-convex amniotic membrane].

    Science.gov (United States)

    Shao, Yi; Yu, Yao; Tan, Gang; Peng, Juan; Zhou, Qiong; Pei, Chonggang; Dong, Wenjia; Gao, Guiping

    2012-12-01

    This paper conducted research on biomechanical characteristics and biological activity of concavity-convex amniotic membrane (CCAM) and discussed its superiority as ocular surface repair material. Folding and compression with vacuum of fresh amniotic membrane were used to prepare CCAM. After cutting the striga of CCAM, sixteen CCAM tissue section were chosen at random to test their tensile strength using electronic universal testing machine. The bilayer amniotic membrane (BAM), the double-deck amniotic membrane (DAM) and the monolayer amniotic membrane (MAM) were as controls. The test parameters included yield strength, tensile strength, elongation at break, elastic modulus and so on. The cytokines of fresh amniotic membrane (FAM), MAM and CCAM were analyzed by radioimmunoassay method. The CCAM was obviously thicker than MAM and DAM. After 15 min in PBS, the CCAM tissue can recover the normal shape. The tensile strength and the elongation at break of CCAM were higher than those of the MAM and the DAM (P biomechanical properties than the MAM and the DAM, showing the superiority as ocular surface repair material.

  5. Biological nitrogen and phosphorus removal in membrane bioreactors: model development and parameter estimation.

    Science.gov (United States)

    Cosenza, Alida; Mannina, Giorgio; Neumann, Marc B; Viviani, Gaspare; Vanrolleghem, Peter A

    2013-04-01

    Membrane bioreactors (MBR) are being increasingly used for wastewater treatment. Mathematical modeling of MBR systems plays a key role in order to better explain their characteristics. Several MBR models have been presented in the literature focusing on different aspects: biological models, models which include soluble microbial products (SMP), physical models able to describe the membrane fouling and integrated models which couple the SMP models with the physical models. However, only a few integrated models have been developed which take into account the relationships between membrane fouling and biological processes. With respect to biological phosphorus removal in MBR systems, due to the complexity of the process, practical use of the models is still limited. There is a vast knowledge (and consequently vast amount of data) on nutrient removal for conventional-activated sludge systems but only limited information on phosphorus removal for MBRs. Calibration of these complex integrated models still remains the main bottleneck to their employment. The paper presents an integrated mathematical model able to simultaneously describe biological phosphorus removal, SMP formation/degradation and physical processes which also include the removal of organic matter. The model has been calibrated with data collected in a UCT-MBR pilot plant, located at the Palermo wastewater treatment plant, applying a modified version of a recently developed calibration protocol. The calibrated model provides acceptable correspondence with experimental data and can be considered a useful tool for MBR design and operation.

  6. Membrane-associated insulin-like growth factor (IGF binding structures in placental cells

    Directory of Open Access Journals (Sweden)

    ROMANA MASNIKOSA

    2003-11-01

    Full Text Available The biological activities of IGF-I and –II are mediated mainly by the type 1 IGF receptor (IGF 1R and controlled by their interaction with soluble proteins, the IGF binding proteins (IGFBPs. Although there is a growing body of evidence that some IGFBPs may be cell surface-bound, published data concerning cell association of IGFBP-1 are scarce and none of them concern placental cells. The cell membranes used in this study were isolated from term human placentae. Detergent-solubilized membranes were shown to contain two types of IGF binding structures that were separated by gel filtration on a Sephadex G-100 column. Proteins in the first peak were eluted at V0 (Mr > 100 kD and they bound IGF-I with greater specificity and affinity than IGF-II and insulin. Most likely, they represented the IGF 1R. Small proteins (Mr ~ 45 kD were eluted with the membrane proteins in the second maximum. They were able to bind IGF-I and IGF-II, but not insulin. The identity of these proteins was shown to be IGFBP-1 on the basis of their reaction with specific anti-IGFBP-1 antibodies. To the best of our knowledge, the existence of IGFBP-1 associated with human placental cell membranes has not been reported in the literature before. Colocalisation of IGFBP-1 with IGF 1R in cell membranes could provide efficient modulation of IGF 1R receptor-ligand interactions.

  7. Crystal structure of the plasma membrane proton pump

    DEFF Research Database (Denmark)

    Pedersen, Bjørn P.; Buch-Pedersen, Morten Jeppe; Morth, J. Preben

    2007-01-01

    -3, and Na1,K1-ATPase (the sodium-potassium pump) in animals4. The name P-type derives from the fact that these proteins exploit a phosphorylated reaction cycle intermediate of ATP hydrolysis5.The plasma membrane proton pumps belong to the type III P-type ATPase subfamily, whereas Na1,K1-ATPase and Ca21......- ATPase are type II6. Electron microscopy has revealed the overall shape of proton pumps7, however, an atomic structure has been lacking. Here we present the first structure of a P-type proton pump determined by X-ray crystallography. Ten transmembrane helices and three cytoplasmic domains define...... the functional unit of ATP-coupled proton transport across the plasma membrane, and the structure is locked in a functional state not previously observed in P-type ATPases. The transmembrane domain reveals a large cavity, which is likely to be filled with water, located near the middle of the membrane plane...

  8. MEMS-Based Fuel Reformer with Suspended Membrane Structure

    Science.gov (United States)

    Chang, Kuei-Sung; Tanaka, Shuji; Esashi, Masayoshi

    We report a MEMS-based fuel reformer for supplying hydrogen to micro-fuel cells for portable applications. A combustor and a reforming chamber are fabricated at either side of a suspended membrane structure. This design is used to improve the overall thermal efficiency, which is a critical issue to realize a micro-fuel reformer. The suspended membrane structure design provided good thermal isolation. The micro-heaters consumed 0.97W to maintain the reaction zone of the MEMS-based fuel reformer at 200°C, but further power saving is necessary by improving design and fabrication. The conversion rate of methanol to hydrogen was about 19% at 180°C by using evaporated copper as a reforming catalyst. The catalytic combustion of hydrogen started without any assistance of micro-heaters. By feeding the fuel mixture of an equivalence ratio of 0.35, the temperature of the suspended membrane structure was maintained stable at 100°C with a combustion efficiency of 30%. In future works, we will test a micro-fuel reformer by using a micro-combustor to supply heat.

  9. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  10. Structural basis for alginate secretion across the bacterial outer membrane

    Energy Technology Data Exchange (ETDEWEB)

    Whitney, J.C.; Robinson, H.; Hay, I. D.; Li, C.; Eckford, P. D. W.; Amaya, M. F.; Wood, L. F.; Ohman, D. E.; Bear, C. E.; Rehm, B. H.; Howell, P. L.

    2011-08-09

    Pseudomonas aeruginosa is the predominant pathogen associated with chronic lung infection among cystic fibrosis patients. During colonization of the lung, P. aeruginosa converts to a mucoid phenotype characterized by the overproduction of the exopolysaccharide alginate. Secretion of newly synthesized alginate across the outer membrane is believed to occur through the outer membrane protein AlgE. Here we report the 2.3 {angstrom} crystal structure of AlgE, which reveals a monomeric 18-stranded {beta}-barrel characterized by a highly electropositive pore constriction formed by an arginine-rich conduit that likely acts as a selectivity filter for the negatively charged alginate polymer. Interestingly, the pore constriction is occluded on either side by extracellular loop L2 and an unusually long periplasmic loop, T8. In halide efflux assays, deletion of loop T8 ({Delta}T8-AlgE) resulted in a threefold increase in anion flux compared to the wild-type or {Delta}L2-AlgE supporting the idea that AlgE forms a transport pathway through the membrane and suggesting that transport is regulated by T8. This model is further supported by in vivo experiments showing that complementation of an algE deletion mutant with {Delta}T8-AlgE impairs alginate production. Taken together, these studies support a mechanism for exopolysaccharide export across the outer membrane that is distinct from the Wza-mediated translocation observed in canonical capsular polysaccharide export systems.

  11. Structural Basis for Alginate Secretion Across the Bacterial Outer Membrane

    Energy Technology Data Exchange (ETDEWEB)

    J Whitney; I Hay; C Li; P Eckford; H Robinson; M Amaya; L Wood; D Ohman; C Bear; et al.

    2011-12-31

    Pseudomonas aeruginosa is the predominant pathogen associated with chronic lung infection among cystic fibrosis patients. During colonization of the lung, P. aeruginosa converts to a mucoid phenotype characterized by the overproduction of the exopolysaccharide alginate. Secretion of newly synthesized alginate across the outer membrane is believed to occur through the outer membrane protein AlgE. Here we report the 2.3 {angstrom} crystal structure of AlgE, which reveals a monomeric 18-stranded {beta}-barrel characterized by a highly electropositive pore constriction formed by an arginine-rich conduit that likely acts as a selectivity filter for the negatively charged alginate polymer. Interestingly, the pore constriction is occluded on either side by extracellular loop L2 and an unusually long periplasmic loop, T8. In halide efflux assays, deletion of loop T8 ({Delta}T8-AlgE) resulted in a threefold increase in anion flux compared to the wild-type or {Delta}L2-AlgE supporting the idea that AlgE forms a transport pathway through the membrane and suggesting that transport is regulated by T8. This model is further supported by in vivo experiments showing that complementation of an algE deletion mutant with {Delta}T8-AlgE impairs alginate production. Taken together, these studies support a mechanism for exopolysaccharide export across the outer membrane that is distinct from the Wza-mediated translocation observed in canonical capsular polysaccharide export systems.

  12. The crystal structure of GXGD membrane protease FlaK

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya (Yale-MED)

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  13. The Crystal Structure of GXGD Membrane Protease FlaK

    Energy Technology Data Exchange (ETDEWEB)

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  14. F-BAR family proteins, emerging regulators for cell membrane dynamic changes-from structure to human diseases.

    Science.gov (United States)

    Liu, Suxuan; Xiong, Xinyu; Zhao, Xianxian; Yang, Xiaofeng; Wang, Hong

    2015-05-09

    Eukaryotic cell membrane dynamics change in curvature during physiological and pathological processes. In the past ten years, a novel protein family, Fes/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain proteins, has been identified to be the most important coordinators in membrane curvature regulation. The F-BAR domain family is a member of the Bin/Amphiphysin/Rvs (BAR) domain superfamily that is associated with dynamic changes in cell membrane. However, the molecular basis in membrane structure regulation and the biological functions of F-BAR protein are unclear. The pathophysiological role of F-BAR protein is unknown. This review summarizes the current understanding of structure and function in the BAR domain superfamily, classifies F-BAR family proteins into nine subfamilies based on domain structure, and characterizes F-BAR protein structure, domain interaction, and functional relevance. In general, F-BAR protein binds to cell membrane via F-BAR domain association with membrane phospholipids and initiates membrane curvature and scission via Src homology-3 (SH3) domain interaction with its partner proteins. This process causes membrane dynamic changes and leads to seven important cellular biological functions, which include endocytosis, phagocytosis, filopodium, lamellipodium, cytokinesis, adhesion, and podosome formation, via distinct signaling pathways determined by specific domain-binding partners. These cellular functions play important roles in many physiological and pathophysiological processes. We further summarize F-BAR protein expression and mutation changes observed in various diseases and developmental disorders. Considering the structure feature and functional implication of F-BAR proteins, we anticipate that F-BAR proteins modulate physiological and pathophysiological processes via transferring extracellular materials, regulating cell trafficking and mobility, presenting antigens, mediating extracellular matrix degradation, and transmitting

  15. The Structural Dynamics of the Flavivirus Fusion Peptide–Membrane Interaction

    Science.gov (United States)

    Souza, Theo L. F.; Sousa, Ivanildo P.; Bianconi, M. Lucia; Bernardi, Rafael C.; Pascutti, Pedro G.; Silva, Jerson L.; Gomes, Andre M. O.; Oliveira, Andréa C.

    2012-01-01

    Membrane fusion is a crucial step in flavivirus infections and a potential target for antiviral strategies. Lipids and proteins play cooperative roles in the fusion process, which is triggered by the acidic pH inside the endosome. This acidic environment induces many changes in glycoprotein conformation and allows the action of a highly conserved hydrophobic sequence, the fusion peptide (FP). Despite the large volume of information available on the virus-triggered fusion process, little is known regarding the mechanisms behind flavivirus–cell membrane fusion. Here, we evaluated the contribution of a natural single amino acid difference on two flavivirus FPs, FLAG (98DRGWGNGCGLFGK110) and FLAH (98DRGWGNHCGLFGK110), and investigated the role of the charge of the target membrane on the fusion process. We used an in silico approach to simulate the interaction of the FPs with a lipid bilayer in a complementary way and used spectroscopic approaches to collect conformation information. We found that both peptides interact with neutral and anionic micelles, and molecular dynamics (MD) simulations showed the interaction of the FPs with the lipid bilayer. The participation of the indole ring of Trp appeared to be important for the anchoring of both peptides in the membrane model, as indicated by MD simulations and spectroscopic analyses. Mild differences between FLAG and FLAH were observed according to the pH and the charge of the target membrane model. The MD simulations of the membrane showed that both peptides adopted a bend structure, and an interaction between the aromatic residues was strongly suggested, which was also observed by circular dichroism in the presence of micelles. As the FPs of viral fusion proteins play a key role in the mechanism of viral fusion, understanding the interactions between peptides and membranes is crucial for medical science and biology and may contribute to the design of new antiviral drugs. PMID:23094066

  16. TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

    Science.gov (United States)

    Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

    2016-01-21

    Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. The influence of hypoxia-hypercapnia on the structural state of cellular membranes of rat hepatocytes

    Directory of Open Access Journals (Sweden)

    Світлана Володимирівна Хижняк

    2015-10-01

    Full Text Available The structural and dynamic state of cellular membranes of rat hepatocytes under the influence of hypoxia, hypercapnia and hypothermia factors (artificial hypobiosis was investigated using the method of fluorescent probes. The diverse changes of the structure and physical properties of these membranes (especially of inner mitochondrial membrane were shown. The structural reorganization of the membrane surface area, the decrease of the lipid structural orderliness and conformational modification of proteins occur during artificial hypobiosis

  18. Novel structure design of composite proton exchange membranes with continuous and through-membrane proton-conducting channels

    Science.gov (United States)

    Wang, Hang; Tang, Chenxiao; Zhuang, Xupin; Cheng, Bowen; Wang, Wei; Kang, Weimin; Li, Hongjun

    2017-10-01

    The primary goal of this study is to develop a high-performanced proton exchange membrane with the characteristics of through-membrane and continuous solution blown nanofibers as proton-conducting channels. The curled sulfonated phenolphthalein poly (ether sulfone) and poly (vinylidene fluoride) nanofibers were separately fabricated through the solution blowing process which is a new nanofiber fabricating method with high productivity, then they were fabricated into a sandwich-structured mat. Then this sandwich-structured mat was hot-pressed to form the designed structure using different melting temperatures of the two polymers by melting and making poly (vinylidene fluoride) flow into the phenolphthalein poly (ether sulfone) nanofiber mat. The characteristics of the composite membrane, such as morphology and performance of the membrane, were investigated. The characterization results proved the successful preparation of the membrane structure. Performance results showed that the novel structured membrane with through-membrane nanofibers significantly improved water swelling and methanol permeability, though its conductivity is lower than that of Nafion, the cell performance showed comparable results. Therefore, the novel structure design can be considered as a promising method for preparing of proton exchange membranes.

  19. New penta-saccharide-bearing tripod amphiphiles for membrane protein structure studies

    DEFF Research Database (Denmark)

    Ehsan, Muhammad; Ghani, Lubna; Du, Yang

    2017-01-01

    Integral membrane proteins either alone or as complexes carry out a range of key cellular functions. Detergents are indispensable tools in the isolation of membrane proteins from biological membranes for downstream studies. Although a large number of techniques and tools, including a wide variety...

  20. Iontophoresis as a non-invasive enhancement technique for the administration of drugs across biological membranes

    OpenAIRE

    Tratta, Elena

    2015-01-01

    Iontophoresis, a technique that consists in applying low density current to a membrane, has been widely investigated in order to enhance the permeation of drugs through different biological barriers such as the skin, the buccal mucosa and the sclera in order to obtain a systemic or local (in case of trans-scleral administration) effect without the need of an injection. The aim of this thesis was to investigate the effect of iontophoresis on these three barriers, considering the different s...

  1. Biologically constrained optimization based cell membrane segmentation in C. elegans embryos.

    Science.gov (United States)

    Azuma, Yusuke; Onami, Shuichi

    2017-06-19

    Recent advances in bioimaging and automated analysis methods have enabled the large-scale systematic analysis of cellular dynamics during the embryonic development of Caenorhabditis elegans. Most of these analyses have focused on cell lineage tracing rather than cell shape dynamics. Cell shape analysis requires cell membrane segmentation, which is challenging because of insufficient resolution and image quality. This problem is currently solved by complicated segmentation methods requiring laborious and time consuming parameter adjustments. Our new framework BCOMS (Biologically Constrained Optimization based cell Membrane Segmentation) automates the extraction of the cell shape of C. elegans embryos. Both the segmentation and evaluation processes are automated. To automate the evaluation, we solve an optimization problem under biological constraints. The performance of BCOMS was validated against a manually created ground truth of the 24-cell stage embryo. The average deviation of 25 cell shape features was 5.6%. The deviation was mainly caused by membranes parallel to the focal planes, which either contact the surfaces of adjacent cells or make no contact with other cells. Because segmentation of these membranes was difficult even by manual inspection, the automated segmentation was sufficiently accurate for cell shape analysis. As the number of manually created ground truths is necessarily limited, we compared the segmentation results between two adjacent time points. Across all cells and all cell cycles, the average deviation of the 25 cell shape features was 4.3%, smaller than that between the automated segmentation result and ground truth. BCOMS automated the accurate extraction of cell shapes in developing C. elegans embryos. By replacing image processing parameters with easily adjustable biological constraints, BCOMS provides a user-friendly framework. The framework is also applicable to other model organisms. Creating the biological constraints is a

  2. Structure-based membrane dome mechanism for Piezo mechanosensitivity.

    Science.gov (United States)

    Guo, Yusong R; MacKinnon, Roderick

    2017-12-12

    Mechanosensitive ion channels convert external mechanical stimuli into electrochemical signals for critical processes including touch sensation, balance, and cardiovascular regulation. The best understood mechanosensitive channel, MscL, opens a wide pore, which accounts for mechanosensitive gating due to in-plane area expansion. Eukaryotic Piezo channels have a narrow pore and therefore must capture mechanical forces to control gating in another way. We present a cryo-EM structure of mouse Piezo1 in a closed conformation at 3.7Å-resolution. The channel is a triskelion with arms consisting of repeated arrays of 4-TM structural units surrounding a pore. Its shape deforms the membrane locally into a dome. We present a hypothesis in which the membrane deformation changes upon channel opening. Quantitatively, membrane tension will alter gating energetics in proportion to the change in projected area under the dome. This mechanism can account for highly sensitive mechanical gating in the setting of a narrow, cation-selective pore. © 2017, Guo et al.

  3. Structural biology computing: Lessons for the biomedical research sciences.

    Science.gov (United States)

    Morin, Andrew; Sliz, Piotr

    2013-11-01

    The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields. Copyright © 2013 Wiley Periodicals, Inc.

  4. Role of charged lipids in membrane structures — Insight given by simulations

    DEFF Research Database (Denmark)

    Pöyry, Sanja; Vattulainen, Ilpo

    2016-01-01

    to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane...

  5. Ontological knowledge structure of intuitive biology

    Science.gov (United States)

    Martin, Suzanne Michele

    It has become increasingly important for individuals to understand infections disease, as there has been a tremendous rise in viral and bacterial disease. This research examines systematic misconceptions regarding the characteristics of viruses and bacteria present in individuals previously educated in biological sciences at a college level. 90 pre-nursing students were administered the Knowledge Acquisition Device (KAD) which consists of 100 True/False items that included statements about the possible attributes of four entities: bacteria, virus, amoeba, and protein. Thirty pre-nursing students, who incorrectly stated that viruses were alive, were randomly assigned to three conditions. (1) exposed to information about the ontological nature of viruses, (2) Information about viruses, (3) control. In the condition that addressed the ontological nature of a virus, all of those participants were able to classify viruses correctly as not alive; however any items that required inferences, such as viruses come in male and female forms or viruses breed with each other to make baby viruses were still incorrectly answered by all conditions in the posttest. It appears that functional knowledge, ex. If a virus is alive or dead, or how it is structured, is not enough for an individual to have a full and accurate understanding of viruses. Ontological knowledge information may alter the functional knowledge but underlying inferences remain systematically incorrect.

  6. Structural Biology in the context of EGEE

    CERN Document Server

    García, D; Carazo, J M; Valverde, J R; Moscicki, J; Muraru, A

    2007-01-01

    Electron microscopy (EM) is a crucial technique, which allows Structural Biology researchers to characterize macromolecular assemblies in distinct functional states. Image processing in three dimensional EM (3D-EM) is used by a flourishing community (exemplarized by the EU funded 3D-EM NoE) and is characterized by voluminous data and large computing requirements, making this a problem well suited for Grid computing and the EGEE infrastructure. There are various steps in the 3D-EM refinement process that may benefit from Grid computing. To start with, large numbers of experimental images need to be averaged. Nowadays, typically tens of thousands of images are used, while future studies may routinely employ millions of images. Our group has been developing Xmipp, a package for single-particle 3D-EM image processing. Using Xmipp, the classification of 91,000 ribosome projections into 4 classes took more than 2500 CPU hours using the resources of the MareNostrum supercomputer at the Barcelona Supercomputing Centr...

  7. The Effect of LiCl and Coagulation Bath Temperature on the Structure and Performance of PVDF Membranes

    Directory of Open Access Journals (Sweden)

    Marzieh Sedaghat

    2015-09-01

    Full Text Available Polyvinylidene fluoride (PVDF membranes are widely used in microfiltration and ultrafiltration processes for their excellent mechanical and chemical resistance and thermal stability in comparison with other polymeric membranes. Non-solvent induced phase separation (NIPS is the most important method by which the PVDF membranes are prepared. The structure of the membranes prepared by NIPS method depends on different parameters including the concentration of the polymer solution, polymer molecular weight, the composition and temperature of coagulation bath, type of solvent and the presence of additives in the initial solution. In the present work, the effects of coagulation bath temperature and LiCl content of the dope solution were studied with respect to the structure and performance of PVDF membranes. N-Methyl-2-pyrrolidone and water were used as solvent and coagulation bath, respectively. A set of analytical techniques including: scanning electron microscopy, mechanical test, pure water permeability and mean pore radius of pores was used to characterize the membranes. Moreover, the separation of humic acid, a main biological contaminant in surface water resources, was studied to determine membranes performance. The results show that at constant coagulation bath temperature, presence of LiCl in the dope solution increased the number as well as the mean pore radius of the pores at the surface of membranes and consequently, pure water permeability of the membranes was increased, whereas, the mechanical strength and humic acid rejection of the membranes were dropped. Moreover, at a constant content of LiCl, increasing the coagulation bath temperature decreased the size of macrovoids so that the mechanical strength as well as humic acid rejection of the membranes was increased.

  8. The effects of 7-dehydrocholesterol on the structural properties of membranes

    Science.gov (United States)

    Liu, Yingzhe; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng

    2011-10-01

    Smith-Lemli-Opitz syndrome, a congenital and developmental malformation disease, is typified by abnormal accumulation of 7-dehydrocholesterol (7DHC), the immediate precursor of cholesterol (CHOL), and depletion thereof. Knowledge of the effect of 7DHC on the biological membrane is, however, still fragmentary. In this study, large-scale atomistic molecular dynamics simulations, employing two distinct force fields, have been conducted to elucidate differences in the structural properties of a hydrated dimyristoylphosphatidylcholine bilayer due to CHOL and 7DHC. The present series of results indicate that CHOL and 7DHC possess virtually the same ability to condense and order membranes. Furthermore, the condensing and ordering effects are shown to be strengthened at increasing sterol concentrations.

  9. Recognition of GPCRs by peptide ligands and membrane compartments theory: structural studies of endogenous peptide hormones in membrane environment.

    Science.gov (United States)

    Sankararamakrishnan, Ramasubbu

    2006-04-01

    One of the largest family of cell surface proteins, G-protein coupled receptors (GPCRs) regulate virtually all known physiological processes in mammals. With seven transmembrane segments, they respond to diverse range of extracellular stimuli and represent a major class of drug targets. Peptidergic GPCRs use endogenous peptides as ligands. To understand the mechanism of GPCR activation and rational drug design, knowledge of three-dimensional structure of receptor-ligand complex is important. The endogenous peptide hormones are often short, flexible and completely disordered in aqueous solution. According to "Membrane Compartments Theory", the flexible peptide binds to the membrane in the first step before it recognizes its receptor and the membrane-induced conformation is postulated to bind to the receptor in the second step. Structures of several peptide hormones have been determined in membrane-mimetic medium. In these studies, micelles, reverse micelles and bicelles have been used to mimic the cell membrane environment. Recently, conformations of two peptide hormones have also been studied in receptor-bound form. Membrane environment induces stable secondary structures in flexible peptide ligands and membrane-induced peptide structures have been correlated with their bioactivity. Results of site-directed mutagenesis, spectroscopy and other experimental studies along with the conformations determined in membrane medium have been used to interpret the role of individual residues in the peptide ligand. Structural differences of membrane-bound peptides that belong to the same family but differ in selectivity are likely to explain the mechanism of receptor selectivity and specificity of the ligands. Knowledge of peptide 3D structures in membrane environment has potential applications in rational drug design.

  10. Depression, osteoporosis, serotonin and cell membrane viscosity between biology and philosophical anthropology

    OpenAIRE

    Cocchi, Massimo; Tonello, Lucio; Gabrielli, Fabio; Pregnolato, Massimo

    2011-01-01

    Abstract Due to the relationship between biology and culture, we believe that depression, understood as a cultural and existential phenomenon, has clear markers in molecular biology. We begin from an existential analysis of depression constituting the human condition and then shift to analysis of biological data confirming, according to our judgment, its original (ontological) structure. In this way philosophy is involved at the anthropological level, in as much as it detects the underlying m...

  11. G protein-membrane interactions II: Effect of G protein-linked lipids on membrane structure and G protein-membrane interactions.

    Science.gov (United States)

    Casas, Jesús; Ibarguren, Maitane; Álvarez, Rafael; Terés, Silvia; Lladó, Victoria; Piotto, Stefano P; Concilio, Simona; Busquets, Xavier; López, David J; Escribá, Pablo V

    2017-09-01

    G proteins often bear myristoyl, palmitoyl and isoprenyl moieties, which favor their association with the membrane and their accumulation in G Protein Coupled Receptor-rich microdomains. These lipids influence the biophysical properties of membranes and thereby modulate G protein binding to bilayers. In this context, we showed here that geranylgeraniol, but neither myristate nor palmitate, increased the inverted hexagonal (H II ) phase propensity of phosphatidylethanolamine-containing membranes. While myristate and palmitate preferentially associated with phosphatidylcholine membranes, geranylgeraniol favored nonlamellar-prone membranes. In addition, Gαi 1 monomers had a higher affinity for lamellar phases, while Gβγ and Gαβγ showed a marked preference for nonlamellar prone membranes. Moreover, geranylgeraniol enhanced the binding of G protein dimers and trimers to phosphatidylethanolamine-containing membranes, yet it decreased that of monomers. By contrast, both myristate and palmitate increased the Gαi 1 preference for lamellar membranes. Palmitoylation reinforced the binding of the monomer to PC membranes and myristoylation decreased its binding to PE-enriched bilayer. Finally, binding of dimers and trimers to lamellar-prone membranes was decreased by palmitate and myristate, but it was increased in nonlamellar-prone bilayers. These results demonstrate that co/post-translational G protein lipid modifications regulate the membrane lipid structure and that they influence the physico-chemical properties of membranes, which in part explains why G protein subunits sort to different plasma membrane domains. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Lipophilic indocarbocyanine conjugates for efficient incorporation of enzymes, antibodies and small molecules into biological membranes.

    Science.gov (United States)

    Smith, Weston J; Tran, Huy; Griffin, James I; Jones, Jessica; Vu, Vivian P; Nilewski, Lizanne; Gianneschi, Nathan; Simberg, Dmitri

    2018-04-01

    Decoration of cell membranes with biomolecules, targeting ligands and imaging agents is an emerging strategy to improve functionality of cell-based therapies. Compared to covalent chemistry or genetic expression on the cell surface, lipid painting (i.e., incorporation of lipid-conjugated molecules into the cell bilayer) is a fast, non-damaging and less expensive approach. Previous studies demonstrated excellent incorporation and retention of distearyl indocarbocyanine dye DiI in membranes of cells in vitro and in vivo. In order to exploit the membrane stability of DiI, we synthesized an amino-DiI derivative, to which we subsequently conjugated an antibody (cetuximab), an enzyme (superoxide dismutase), and a small molecule (DyLight 800). Red blood cells have long been used as drug delivery vehicles so they were utilized as a model to study the incorporation of DiI conjugates in the plasma membrane. All the DiI constructs demonstrated fast and efficient ex vivo incorporation in the membrane of mouse RBCs, resulting in millions of exogenous molecules per RBC. Following an intravenous injection into mice, the molecules were detected on circulating RBCs for several days. DiI anchored molecules showed longer residence time in blood and significantly higher area under the curve (AUC) compared to free non-conjugated molecules. Thus, cetuximab, SOD and DyLight painted on RBC showed 5.5-fold, 6.5-fold and 78-fold increase in the AUC, respectively, compared to the non-modified molecules. Lipophilic indocarbocyanine anchors are a promising technology for incorporation of biomolecules and small molecules into biological membranes for in vivo applications. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Liquid membrane extraction techniques for trace metal analysis and speciation in environmental and biological matrices

    Energy Technology Data Exchange (ETDEWEB)

    Ndungu, Kuria

    1999-04-01

    In this thesis, liquid-membrane-based methods for the analysis of trace metal species in samples of environmental and biological origin were developed. By incorporating extracting reagents in the membrane liquid, trace metal ions were selectively separated from humic-rich natural waters and urine samples, prior to their determination using various instrumental techniques. The extractions were performed in closed flow systems thus allowing easy automation of both the sample clean-up and enrichment. An acidic organophosphorus reagent (DEHPA) and a basic tetraalkylammonium reagent (Aliquat-336) were used as extractants in the membrane liquid to selectively extract and enrich cationic and anionic metal species respectively. A speciation method for chromium species was developed that allowed the determination of cationic Cr(III) species and anionic CR(VI) species in natural water samples without the need of a chromatographic separation step prior to their detection. SLM was also coupled on-line to potentiometric stripping analysis providing a fast and sensitive method for analysis of Pb in urine samples. A microporous membrane liquid-liquid extraction (MMLLE) method was developed for the determination of organotin compounds in natural waters that reduced the number of manual steps involved in the LLE of organotin compounds prior to their CC separation. Clean extracts obtained after running unfiltered humic-rich river water samples through the MMLLE flow system allowed selective determination of all the organotin compounds in a single run using GC-MS in the selected ion monitoring mode (SIM) 171 refs, 9 figs, 4 tabs

  14. Structural Biology and Molecular Applications Research

    Science.gov (United States)

    Part of NCI's Division of Cancer Biology's research portfolio, research and development in this area focuses on enabling technologies, models, and methodologies to support basic and applied cancer research.

  15. Calcitonin Forms Oligomeric Pore-Like Structures in Lipid Membranes

    Science.gov (United States)

    Diociaiuti, Marco; Polzi, Laura Zanetti; Valvo, Luisa; Malchiodi-Albedi, Fiorella; Bombelli, Cecilia; Gaudiano, Maria Cristina

    2006-01-01

    Calcitonin is a polypeptidic hormone involved in calcium metabolism in the bone. It belongs to the amyloid protein family, which is characterized by the common propensity to aggregate acquiring a β-sheet conformation and include proteins associated with important neurodegenerative diseases. Here we show for the first time, to our knowledge, by transmission electron microscopy (TEM) that salmon-calcitonin (sCT) forms annular oligomers similar to those observed for β-amyloid and α-sinuclein (Alzheimer's and Parkinson's diseases). We also investigated the interaction between sCT and model membranes, such as liposomes, with particular attention to the effect induced by lipid “rafts” made of cholesterol and GM1. We observed, by TEM immunogold labeling of sCT, that protein binding is favored by the presence of rafts. In addition, we found by TEM that sCT oligomers inserted in the membrane have the characteristic pore-like morphology of the amyloid proteins. Circular dichroism experiments revealed an increase in β-content in sCT secondary structure when the protein was reconstituted in rafts mimicking liposomes. Finally, we showed, by spectrofluorimetry experiments, that the presence of sCT allowed Ca2+ entry in rafts mimicking liposomes loaded with the Ca2+-specific fluorophore Fluo-4. This demonstrates that sCT oligomers have ion-channel activity. Our results are in good agreement with recent electrophysiological studies reporting that sCT forms Ca2+-permeable ion channels in planar model membranes. It has been proposed that, beyond the well-known interaction of the monomer with the specific receptor, the formation of Ca2+ channels due to sCT oligomers could represent an extra source of Ca2+ entry in osteoblasts. Structural and functional data reported here support this hypothesis. PMID:16940475

  16. Hydrological structure and biological productivity of the tropical Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Muraleedharan, U.D.; Muraleedharan, P.M.

    Hydrological structure analyses of regions in the tropical Atlantic Ocean have consistently revealed the existence of a typical tropical structure characterized by a nitrate-depleted mixed layer above the thermocline. The important biological...

  17. Structure of functional Staphylococcus aureus alpha-hemolysin channels in tethered bilayer lipid membranes.

    Science.gov (United States)

    McGillivray, Duncan J; Valincius, Gintaras; Heinrich, Frank; Robertson, Joseph W F; Vanderah, David J; Febo-Ayala, Wilma; Ignatjev, Ilja; Lösche, Mathias; Kasianowicz, John J

    2009-02-18

    We demonstrate a method for simultaneous structure and function determination of integral membrane proteins. Electrical impedance spectroscopy shows that Staphylococcus aureus alpha-hemolysin channels in membranes tethered to gold have the same properties as those formed in free-standing bilayer lipid membranes. Neutron reflectometry provides high-resolution structural information on the interaction between the channel and the disordered membrane, validating predictions based on the channel's x-ray crystal structure. The robust nature of the membrane enabled the precise localization of the protein within 1.1 A. The channel's extramembranous cap domain affects the lipid headgroup region and the alkyl chains in the outer membrane leaflet and significantly dehydrates the headgroups. The results suggest that this technique could be used to elucidate molecular details of the association of other proteins with membranes and may provide structural information on domain organization and stimuli-responsive reorganization for transmembrane proteins in membrane mimics.

  18. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  19. Light- and pH-dependent conformational changes in protein structure induce strong bending of purple membranes--active membranes studied by cryo-SEM.

    Science.gov (United States)

    Rhinow, Daniel; Hampp, Norbert A

    2008-10-16

    Bacteriorhodopsin (BR) undergoes a conformational change during the photocycle and the proton transport through the membrane. For the first time, we could demonstrate by direct imaging of freely suspended native purple membranes (PMs) that the flat disk-like shape of PMs changes dramatically as soon as most of the BRs are in a state characterized by a deprotonated Schiff base. Light-induced shape changes are easily observed with mutated BRs of the BR-D96N type, i.e., all variants which show an increased M 2 lifetime. On the other hand, large-scale shape changes are induced by pH changes with PM containing mutated BRs of the BR-D85T type, where Asp85 is replaced for a neutral amino acid. In such PMs, all BRs are titrated simultaneously and the resulting shape of the membranes depends on the initial shape only. As the majority of PMs in the "flat" state are more or less round disks, the bent membranes often comprise bowl-like and tube-like bent structures. The method presented here enables one to derive size changes of membrane-embedded BRs on the single molecule level from "macroscopic", easily accessible data like the curvature radii observed in cryo-SEM. The potential of BR as a pH-controlled and/or light-controlled microscaled biological actuator needs further consideration.

  20. Structure determination of membrane proteins in their native phospholipid bilayer environment by rotationally aligned solid-state NMR spectroscopy.

    Science.gov (United States)

    Opella, Stanley J

    2013-09-17

    One of the most important topics in experimental structural biology is determining the structures of membrane proteins. These structures represent one-third of all of the information expressed from a genome, distinguished by their locations within the phospholipid bilayer of cells, organelles, or enveloped viruses. Their highly hydrophobic nature and insolubility in aqueous media means that they require an amphipathic environment. They have unique functions in transport, catalysis, channel formation, and signaling. Researchers are particularly interested in G-protein coupled receptors (GPCRs) because they modulate many biological processes, and about half of the approximately 800 of these proteins within the human genome are or can be turned into drug receptors that affect a wide range of diseases. Because of experimental difficulties, researchers have studied membrane proteins using a wide variety of artificial media that mimic membranes, such as mixed organic solvents or detergents. More sophisticated mimics include bilayer discs (bicelles) and the lipid cubic phase (LCP), but both of these contain a very large detergent component, which can disrupt the stability and function of membrane proteins. To have confidence in the resulting structures and their biological functions and to avoid disrupting these delicate proteins, the structures of membrane proteins should be determined in their native environment of liquid crystalline phospholipid bilayers under physiological conditions. This Account describes a recently developed general method for determining the structures of unmodified membrane proteins in phospholipid bilayers by solid-state NMR spectroscopy. Because it relies on the natural, rapid rotational diffusion of these proteins about the bilayer normal, this method is referred to as rotationally aligned (RA) solid-state NMR. This technique elaborates on oriented sample (OS) solid-state NMR, its complementary predecessor. These methods exploit the power of

  1. Ion beam evaluation of silicon carbide membrane structures intended for particle detectors

    Energy Technology Data Exchange (ETDEWEB)

    Pallon, J., E-mail: jan.pallon@nuclear.lu.se [Division of Nuclear Physics, Physics Department, Lund University, Box 118, SE-221 00 Lund (Sweden); Syväjärvi, M. [Linköping University, Department of Physics, Chemistry and Biology, SE-58183 Linköping (Sweden); Graphensic AB, Teknikringen 1F, SE-58330 Linköping (Sweden); Wang, Q. [Sensor System, ACREO Swedish ICT AB, Box 1070, SE-164 25 Kista (Sweden); Yakimova, R.; Iakimov, T. [Linköping University, Department of Physics, Chemistry and Biology, SE-58183 Linköping (Sweden); Graphensic AB, Teknikringen 1F, SE-58330 Linköping (Sweden); Elfman, M.; Kristiansson, P.; Nilsson, E.J.C.; Ros, L. [Division of Nuclear Physics, Physics Department, Lund University, Box 118, SE-221 00 Lund (Sweden)

    2016-03-15

    Thin ion transmission detectors can be used as a part of a telescope detector for mass and energy identification but also as a pre-cell detector in a microbeam system for studies of biological effects from single ion hits on individual living cells. We investigated a structure of graphene on silicon carbide (SiC) with the purpose to explore a thin transmission detector with a very low noise level and having mechanical strength to act as a vacuum window. In order to reach very deep cavities in the SiC wafers for the preparation of the membrane in the detector, we have studied the Inductive Coupled Plasma technique to etch deep circular cavities in 325 μm prototype samples. By a special high temperature process the outermost layers of the etched SiC wafers were converted into a highly conductive graphitic layer. The produced cavities were characterized by electron microscopy, optical microscopy and proton energy loss measurements. The average membrane thickness was found to be less than 40 μm, however, with a slightly curved profile. Small spots representing much thinner membrane were also observed and might have an origin in crystal defects or impurities. Proton energy loss measurement (also called Scanning Transmission Ion Microscopy, STIM) is a well suited technique for this thickness range. This work presents the first steps of fabricating a membrane structure of SiC and graphene which may be an attractive approach as a detector due to the combined properties of SiC and graphene in a monolithic materials structure.

  2. Natural vs synthetic auxin: studies on the interactions between plant hormones and biological membrane lipids.

    Science.gov (United States)

    Flasiński, Michał; Hąc-Wydro, Katarzyna

    2014-08-01

    Analysis of the interactions between two representatives of plant hormones: synthetic (1-naphthaleneacetic acid, NAA) as well as natural (indole-3-acetic acid, IAA) and phospholipids occurring in biological membrane of both plant and animal cells was the subject of present studies. The aim of undertaken experiments was to elucidate the problem of direct influence of these plant growth regulators on phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) in monolayers at the air/water solution interface. The studied phospholipids differ not only as regards the structure of polar head-groups but also in the length of hydrophobic chains as well as their saturation degree. These differences result also in the main properties and functions of these phospholipids in biomembranes. The analysis of the results was based on the characteristics of the surface pressure (π)--area (A) isotherms registered for monolayers spread on the subphase containing plant hormone and as a reference on the surface of pure water. Moreover, as a complementary technique, Brewster angle microscopy was applied for the direct visualization of the investigated surface films. The obtained results revealed that auxins effectively influence phospholipids monolayers, regardless of the lipid structure, at the concentration of 10(-4)M. It was found that for this concentration, the influence of auxins was visibly larger in the case of PCs as compared to PEs. On the other hand, in the case of auxins solution of ≤ 10(-5)M, the observed trend was opposite. Generally, our studies showed that the natural plant hormone (IAA) interacts with the investigated lipid monolayers stronger than its synthetic derivative (NAA). The reason of these differences connects with the steric properties of both auxins; namely, the naphthalene ring of NAA molecule occupies larger space than the indole system of IAA. Therefore molecules of the latter compound penetrate easier into the region of phospholipids׳ polar head

  3. Structure and Nanomechanics of Model Membranes by Atomic Force Microscopy and Spectroscopy: Insights into the Role of Cholesterol and Sphingolipids.

    Science.gov (United States)

    Gumí-Audenis, Berta; Costa, Luca; Carlá, Francesco; Comin, Fabio; Sanz, Fausto; Giannotti, Marina I

    2016-12-19

    Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.

  4. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    An epidemic can also spread faster in neuronal networks than in the other biological networks studied here. Thus, the underlying undirected architecture of a neuronal network possesses certain conformation which is favourable for spreading different entities or information. Now, to explore the topological characteristics that ...

  5. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    from five different classes (neuronal, food web, protein–protein interaction, metabolism and gene regulation) and ..... food webs show good expansion property (see table 1) unlike other biological networks. The distribution of distances ..... tion is very fast on a network having high degree nodes. Later on, it was shown that.

  6. Analysis of a nanochanneled membrane structure through convective gas flow

    Science.gov (United States)

    Grattoni, Alessandro; De Rosa, Enrica; Ferrati, Silvia; Wang, Zongxing; Gianesini, Anna; Liu, Xuewu; Hussain, Fazle; Goodall, Randy; Ferrari, Mauro

    2009-11-01

    Micro- and nano-fluidic devices are under development for a variety of applications including bio-molecular separation, drug delivery, biosensing and cell transplantation. Regulatory approval for the commercialization of these products requires the ability to fabricate a large number of these devices with high reproducibility and precision. Though traditional microscopy and particle rejection characterization techniques provide extremely useful measurements of nano-features, they are expensive and inadequate for quality control purposes. In this study, an agile and non-destructive selection method is presented which combines a predictive theoretical model with experimental analysis of convective nitrogen flow to detect structural defects in complex drug delivery membranes (nDS) combining both micro- and nanochanneled features. The mathematical model developed bridges the fluid dynamics between the micro- and nano-scales. An experimental analysis of gas flow was performed on a total of 250 membranes representing five different channel size configurations. The accuracy and reliability of this test in detecting major and minor defects of various kinds were verified by comparing the experimental results with the theoretical prediction.

  7. Low-Resolution Structure of Detergent-Solubilized Membrane Proteins from Small-Angle Scattering Data.

    Science.gov (United States)

    Koutsioubas, Alexandros

    2017-12-05

    Despite the ever-increasing usage of small-angle scattering as a valuable complementary method in the field of structural biology, applications concerning membrane proteins remain elusive mainly due to experimental challenges and the relative lack of theoretical tools for the treatment of scattering data. This fact adds up to general difficulties encountered also by other established methods (crystallography, NMR) for the study of membrane proteins. Following the general paradigm of ab initio methods for low-resolution restoration of soluble protein structure from small-angle scattering data, we construct a general multiphase model with a set of physical constraints, which, together with an appropriate minimization procedure, gives direct structural information concerning the different components (protein, detergent molecules) of detergent-solubilized membrane protein complexes. Assessment of the method's precision and robustness is evaluated by performing shape restorations from simulated data of a tetrameric α-helical membrane channel (Aquaporin-0) solubilized by n-Dodecyl β-D-Maltoside and from previously published small-angle neutron scattering experimental data of the filamentous hemagglutinin adhesin β-barrel protein transporter solubilized by n-Octyl β-D-glucopyranoside. It is shown that the acquisition of small-angle neutron scattering data at two different solvent contrasts, together with an estimation of detergent aggregation number around the protein, permits the reliable reconstruction of the shape of membrane proteins without the need for any prior structural information. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Bacterial membrane vesicles, an overlooked environmental colloid: Biology, environmental perspectives and applications.

    Science.gov (United States)

    Toyofuku, Masanori; Tashiro, Yosuke; Hasegawa, Yusuke; Kurosawa, Masaharu; Nomura, Nobuhiko

    2015-12-01

    Phospholipid vesicles play important roles in biological systems. Bacteria are one of the most abundant organisms on Earth, and bacterial membrane vesicles (MVs) were first observed 50 years ago. Many bacteria release MVs to the environment that mainly consist of the cell membrane and typically range from 20 to 400 nm in size. Bacterial MVs are involved in several biological functions, such as delivery of cargo, virulence and gene transfer. MVs can be isolated from laboratory culture and directly from the environment, indicating their high abundance in and impact on ecosystems. Many colloidal particles in the environment ranging in size from 1 nm to 1 μm have been reported but not characterized at the molecular level, and MVs remain to be explored. Hence, MVs can be considered terra incognita in environmental colloid research. Although MV biogenesis and biological roles are yet to be fully understood, the accumulation of knowledge has opened new avenues for their applications. Via genetic engineering, the MV yield can be greatly increased, and the components of MVs can be tailored. Recent studies have demonstrated that MVs have promising potential for applications such as drug delivery systems and nanobiocatalysts. For instance, MV vaccines have been extensively studied and have already been approved in Europe. Recent MV studies have evoked great interest in the fields of biology and biotechnology, but fundamental questions, such as their transport in the environment or physicochemical features of MVs, remain to be addressed. In this review, we present the current understanding of bacterial MVs and environmental perspectives and further introduce their applications. Copyright © 2015. Published by Elsevier B.V.

  9. Is the fluid mosaic (and the accompanying raft hypothesis a suitable model to describe fundamental features of biological membranes? What may be missing?

    Directory of Open Access Journals (Sweden)

    Luis Alberto Bagatolli

    2013-11-01

    Full Text Available The structure, dynamics, and stability of lipid bilayers are controlled by thermodynamic forces, leading to overall tensionless membranes with a distinct lateral organization and a conspicuous lateral pressure profile. Bilayers are also subject to built-in curvature-stress instabilities that may be released locally or globally in terms of morphological changes leading to the formation of non-lamellar and curved structures. A key controller of the bilayer’s propensity to form curved structures is the average molecular shape of the different lipid molecules. Via the curvature stress, molecular shape mediates a coupling to membrane-protein function and provides a set of physical mechanisms for formation of lipid domains and laterally differentiated regions in the plane of the membrane. Unfortunately, these relevant physical features of membranes are often ignored in the most popular models for biological membranes. Results from a number of experimental and theoretical studies emphasize the significance of these fundamental physical properties and call for a refinement of the fluid mosaic model (and the accompanying raft hypothesis.

  10. A Coincidence Detection Mechanism Controls PX-BAR Domain-Mediated Endocytic Membrane Remodeling via an Allosteric Structural Switch.

    Science.gov (United States)

    Lo, Wen-Ting; Vujičić Žagar, Andreja; Gerth, Fabian; Lehmann, Martin; Puchkov, Dymtro; Krylova, Oxana; Freund, Christian; Scapozza, Leonardo; Vadas, Oscar; Haucke, Volker

    2017-11-20

    Clathrin-mediated endocytosis occurs by bending and remodeling of the membrane underneath the coat. Bin-amphiphysin-rvs (BAR) domain proteins are crucial for endocytic membrane remodeling, but how their activity is spatiotemporally controlled is largely unknown. We demonstrate that the membrane remodeling activity of sorting nexin 9 (SNX9), a late-acting endocytic PX-BAR domain protein required for constriction of U-shaped endocytic intermediates, is controlled by an allosteric structural switch involving coincident detection of the clathrin adaptor AP2 and phosphatidylinositol-3,4-bisphosphate (PI(3,4)P 2 ) at endocytic sites. Structural, biochemical, and cell biological data show that SNX9 is autoinhibited in solution. Binding to PI(3,4)P 2 via its PX-BAR domain, and concomitant association with AP2 via sequences in the linker region, releases SNX9 autoinhibitory contacts to enable membrane constriction. Our results reveal a mechanism for restricting the latent membrane remodeling activity of BAR domain proteins to allow spatiotemporal coupling of membrane constriction to the progression of the endocytic pathway. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.

    Science.gov (United States)

    Leelananda, Sumudu P; Lindert, Steffen

    2017-10-10

    Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures. The incorporation of experimental restraints in computational methods is becoming increasingly important to more reliably predict protein structure. One such experimental input used in structure prediction and refinement is cryo-EM densities. Recent advances in cryo-EM have arguably revolutionized the field of structural biology. Our previously developed cryo-EM-guided Rosetta-MD protocol has shown great promise in the refinement of soluble protein structures. In this study, we extended cryo-EM density-guided iterative Rosetta-MD to membrane proteins. We also improved the methodology in general by picking models based on a combination of their score and fit-to-density during the Rosetta model selection. By doing so, we have been able to pick models superior to those with the previous selection based on Rosetta score only and we have been able to further improve our previously refined models of soluble proteins. The method was tested with five membrane spanning protein structures. By applying density-guided Rosetta-MD iteratively we were able to refine the predicted structures of these membrane proteins to atomic resolutions. We also showed that the resolution of the density maps determines the improvement and quality of the refined models. By incorporating high-resolution density maps (∼4 Å), we were able to more significantly improve the quality of the models than when

  12. Structural and Electrochemical Analysis of PMMA Based Gel Electrolyte Membranes

    Directory of Open Access Journals (Sweden)

    Chithra M. Mathew

    2015-01-01

    Full Text Available New gel polymer electrolytes containing poly(vinylidene chloride-co-acrylonitrile and poly(methyl methacrylate are prepared by solution casting method. With the addition of 60 wt.% of EC to PVdC-AN/PMMA blend, ionic conductivity value 0.398×10-6 S cm−1 has been achieved. XRD and FT-IR studies have been conducted to investigate the structure and complexation in the polymer gel electrolytes. The FT-IR spectra show that the functional groups C=O and C≡N play major role in ion conduction. Thermal stability of the prepared membranes is found to be about 180°C.

  13. Biodegradability of oily wastewater using rotating biological contactor combined with an external membrane.

    Science.gov (United States)

    Safa, Mahdieh; Alemzadeh, Iran; Vossoughi, Manouchehr

    2014-01-01

    A novel implementation of a hybrid membrane bioreactor (HMBR) has been studied in this paper. It is utilized as combination of rotating biological contractor (RBC) and an external membrane, as a new biological system for oily wastewater treatment. Chemical oxygen demand (COD) and total petroleum hydrocarbon (TPH) as factors of Biodegradability has been evaluated. They are both compared together for different hydraulic retention times (HRTs) and petroleum pollution concentrations in RBC and HMBR. The ratio of TPH to COD of Molasses has been varied between 0.2 to 0.8 at two HRTs of 18 and 24 hours while the temperature, pH and dissolved oxygen were kept in the range of 20-25°C, 6.5-7.5, and 2-3.5 mg/l, respectively. The best TPH removal efficiency (99%) was observed in TPH/COD = 0.6 and HRT = 24 hr in HMBR and Removal efficiency was decreased in the ratios above 0.6 in both bioreactors. The experimental results showed that HMBR had higher treatment efficiency than RBC at all ratios and HRTs.

  14. Biological Activity Alterations of Human Amniotic Membrane Pre and Post Irradiation Tissue Banking.

    Science.gov (United States)

    Nemr, Waleed; Bashandy, A S; Araby, Eman; Khamiss, O

    Innate immunity of Human Amniotic Membrane (HAM) and its highly active secretome that rich with various types of growth factors and anti-inflammatory substances proposed it as a promising material for many medical studies and applications. This study evaluate the biological activity of cultivated HAM pre and post tissue banking process in which freeze-dried HAM was sterilized by 25 KGray (kGy) dose of γ radiation. The HAM's antimicrobial activity, viability, growth of isolated human amniotic epithelial cells (HAECs), hematopoietic stimulation of co-cultivated murine bone marrow cells (mammalian model), scaffold efficiency for fish brain building up (non-mammalian model) and self re-epithelialization after trypsin denuding treatment were examined as supposed biological activity features. Native HAM revealed viability indications and was active to kill all tested microorganisms; 6 bacterial species (3 Gram-positive and 3 Gram-negative) and Candida albicans as a pathogenic fungus. Also, HAM activity promoted colony formation of murine hematopoietic cells, Tilapia nilotica brain fragment building-up and self re-epithelialization after trypsin treatment. In contrary, radiation-based tissue banking of HAM caused HAM cellular death and consequently lacked almost all of examined biological activity features. Viable HAM was featured with biological activity than fixed HAM prepared by irradiation tissue banking.

  15. Kinetics of structural reorganizations in multilamellarphotosynthetic membranes monitored by small-angle neutronscattering

    DEFF Research Database (Denmark)

    Nagy, Gergely; Kovacs, Laszlo; Unnep, Renata

    2013-01-01

    We demonstrate the power of time-resolved small-angle neutron scattering experiments for the investigation of the structure and structural reorganizations of multilamellar photosynthetic membranes. In addition to briefly summarizing our results on thylakoid membranes isolated from higher plants...... and in unicellular organisms, we discuss the advantages and technical and methodological limitations of timeresolved SANS. We present a detailed and more systematical investigation of the kinetics of light-induced structural reorganizations in isolated spinach thylakoid membranes, which show how changes...

  16. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from different domains may vary quite significantly. As there is an interplay between network architecture and dynamics, structure plays an important role in communication and spreading of ...

  17. Composition, structure and mechanical properties define performance of pulmonary surfactant membranes and films

    DEFF Research Database (Denmark)

    Ortiz, Elisa Parra; Perez-Gil, Jesús

    2015-01-01

    The respiratory surface in the mammalian lung is stabilized by pulmonary surfactant, a membrane-based system composed of multiple lipids and specific proteins, the primary function of which is to minimize the surface tension at the alveolar air-liquid interface, optimizing the mechanics of breath......The respiratory surface in the mammalian lung is stabilized by pulmonary surfactant, a membrane-based system composed of multiple lipids and specific proteins, the primary function of which is to minimize the surface tension at the alveolar air-liquid interface, optimizing the mechanics...... of breathing and avoiding alveolar collapse, especially at the end of expiration. The goal of the present review is to summarize current knowledge regarding the structure, lipid-protein interactions and mechanical features of surfactant membranes and films and how these properties correlate with surfactant...... biological function inside the lungs. Surfactant mechanical properties can be severely compromised by different agents, which lead to surfactant inhibition and ultimately contributes to the development of pulmonary disorders and pathologies in newborns, children and adults. A detailed comprehension...

  18. X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes

    DEFF Research Database (Denmark)

    Boscia, Alexander L.; Treece, Bradley W.; Mohammadyani, Dariush

    2014-01-01

    Cardiolipins (CLs) are important biologically for their unique role in biomembranes that couple phosphorylation and electron transport like bacterial plasma membranes, chromatophores, chloroplasts and mitochondria. CLs are often tightly coupled to proteins involved in oxidative phosphorylation. T...

  19. X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes

    NARCIS (Netherlands)

    Boscia, Alexander L.; Treece, Bradley W.; Mohammadyani, Dariush; Klein-Seetharaman, Judith; Braun, Anthony R.; Wassenaar, Tsjerk; Kloesgen, Beate; Tristram-Nagle, Stephani

    2014-01-01

    Cardiolipins (CLs) are important biologically for their unique role in biomembranes that couple phosphorylation and electron transport like bacterial plasma membranes, chromatophores, chloroplasts and mitochondria. CLs are often tightly coupled to proteins involved in oxidative phosphorylation. The

  20. Structure versus stochasticity - The role of molecular crowding and intrinsic disorder in membrane fission.

    Science.gov (United States)

    Snead, Wilton T; Stachowiak, Jeanne C

    2018-04-05

    Cellular membranes must undergo remodeling to facilitate critical functions including membrane trafficking, organelle biogenesis, and cell division. An essential step in membrane remodeling is membrane fission, in which an initially continuous membrane surface is divided into multiple, separate compartments. The established view has been that membrane fission requires proteins with conserved structural features such as helical scaffolds, hydrophobic insertions, and polymerized assemblies. In this review we discuss these structure-based fission mechanisms and highlight recent findings from several groups that support an alternative, structure-independent mechanism of membrane fission. This mechanism relies on lateral collisions among crowded, membrane-bound proteins to generate sufficient steric pressure to drive membrane vesiculation. As a stochastic process, this mechanism contrasts with the paradigm that deterministic protein structures are required to drive fission, raising the prospect that many more proteins may participate in fission than previously thought. Paradoxically, our recent work suggests that intrinsically disordered domains may be among the most potent drivers of membrane fission, owing to their large hydrodynamic radii and substantial chain entropy. This stochastic view of fission also suggests new roles for the structure-based fission proteins. Specifically, we hypothesize that in addition to driving fission directly, the canonical fission machines may facilitate the enrichment and organization of bulky disordered protein domains in order to promote membrane fission by locally amplifying protein crowding. Copyright © 2018. Published by Elsevier Ltd.

  1. Simulating the effect of alcohol on the structure of a membrane.

    Science.gov (United States)

    Kranenburg, Marieke; Smit, Berend

    2004-06-18

    Adsorption of alcohol molecules or other small amphiphilic molecules in the cell membrane can induce significant changes in the structure of the membrane. To understand the molecular mechanisms underlying these structural changes, we developed a mesoscopic membrane model. Molecular simulations on this model nicely reproduce the experimental phase diagrams. We find that alcohol can induce an interdigitated structure in which the normal bilayer structure changes into a monolayer in which the alcohol molecules screen the hydrophobic tails from the water phase. We compute the effect of the chain length of the alcohol on the phase behaviour of the membrane. At low concentrations of alcohol, the membrane has domains of the interdigitated phase that are in coexistence with the normal membrane phase. We use our model to clarify some of the experimental questions related to the structure of the interdigitated phase and put forward a simple model that explains the alcohol chain length dependence of the stability of this interdigitated phase.

  2. High Temperature Membrane with Humidification-Independent Cluster Structure

    Energy Technology Data Exchange (ETDEWEB)

    Lipp, Ludwig [FuelCell Energy, Inc., Danbury, CT (United States)

    2015-07-10

    The objective of this project was to develop high temperature membranes to facilitate the wide-spread deployment of hydrogen fuel cells. High temperature membranes offer significant advantages in PEM system operation, overall capital and operating costs. State-of-the-art Nafion-based membranes are inadequate for the high temperature operation. These conventional membranes become unstable at higher temperatures (90-120°C) and lose their conductivity, particularly at low relative humidity. In this program, alternate materials were developed to enable fabrication of novel high performance composite membranes. FCE’s concept for the multi-component composite membrane, named mC2, has been used in the design of more conductive membranes.

  3. Influence of cholesterol and ceramide VI on the structure of multilamellar lipid membranes at water exchange

    International Nuclear Information System (INIS)

    Ryabova, N. Yu.; Kiselev, M. A.; Balagurov, A. M.

    2010-01-01

    The structural changes in the multilamellar lipid membranes of dipalmitoylphosphatidylcholine (DPPC)/cholesterol and DPPC/ceramide VI binary systems during hydration and dehydration have been studied by neutron diffraction. The effect of cholesterol and ceramide on the kinetics of water exchange in DPPC membranes is characterized. Compared to pure DPPC, membranes of binary systems swell faster during hydration (with a characteristic time of ∼30 min). Both compounds, ceramide VI and cholesterol, similarly affect the hydration of DPPC membranes, increasing the repeat distance due to the bilayer growth. However, in contrast to cholesterol, ceramide significantly reduces the thickness of the membrane water layer. The introduction of cholesterol into a DPPC membrane slows down the change in the parameters of the bilayer internal structure during dehydration. In the DPPC/ceramide VI/cholesterol ternary system (with a molar cholesterol concentration of 40%), cholesterol is partially released from the lamellar membrane structure into the crystalline phase.

  4. Structural biology of G protein-coupled receptors: new opportunities from XFELs and cryoEM.

    Science.gov (United States)

    Ishchenko, Andrii; Gati, Cornelius; Cherezov, Vadim

    2018-03-16

    G protein-coupled receptors mediate cell signaling and regulate the majority of sensory and physiological processes in the human body. Recent breakthroughs in cryo-electron microscopy and X-ray free electron lasers have accelerated structural studies of difficult-to-crystallize receptors and their signaling complexes, and have opened up new opportunities in understanding conformational dynamics and visualizing the process of receptor activation with unprecedented spatial and temporal resolution. Here, we summarize major milestones and challenges associated with the application of these techniques and outline future directions in their development with a focus on membrane protein structural biology. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Physical methods for investigating structural colours in biological systems

    NARCIS (Netherlands)

    Vukusic, P.; Stavenga, D. G.

    2009-01-01

    Many biological systems are known to use structural colour effects to generate aspects of their appearance and visibility. The study of these phenomena has informed an eclectic group of fields ranging, for example, from evolutionary processes in behavioural biology to micro-optical devices in

  6. On the Concept "Microscope": Biology Student Teachers' Cognitive Structure

    Science.gov (United States)

    Kurt, Hakan; Ekici, Gulay; Aktas, Murat; Aksu, Ozlem

    2013-01-01

    The purpose of the current study is to determine biology student teachers' cognitive structures on the concept of microscope. Qualitative research methodology has been applied in the study. The data were collected from biology student teachers. Free word association test and drawing-writing test were used to collect data. The data collected were…

  7. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

    Science.gov (United States)

    Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

    2018-04-01

    Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Exploring community structure in biological networks with random graphs

    Science.gov (United States)

    2014-01-01

    Background Community structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a system’s functional components and the impact of local structures on dynamics at a global scale. Choosing an appropriate community detection algorithm to identify the community structure in an empirical network can be difficult, however, as the many algorithms available are based on a variety of cost functions and are difficult to validate. Even when community structure is identified in an empirical system, disentangling the effect of community structure from other network properties such as clustering coefficient and assortativity can be a challenge. Results Here, we develop a generative model to produce undirected, simple, connected graphs with a specified degrees and pattern of communities, while maintaining a graph structure that is as random as possible. Additionally, we demonstrate two important applications of our model: (a) to generate networks that can be used to benchmark existing and new algorithms for detecting communities in biological networks; and (b) to generate null models to serve as random controls when investigating the impact of complex network features beyond the byproduct of degree and modularity in empirical biological networks. Conclusion Our model allows for the systematic study of the presence of community structure and its impact on network function and dynamics. This process is a crucial step in unraveling the functional consequences of the structural properties of biological systems and uncovering the mechanisms that drive these systems. PMID:24965130

  9. Interaction of nonsteroidal anti-inflammatory drugs with membranes: in vitro assessment and relevance for their biological actions.

    Science.gov (United States)

    Pereira-Leite, Catarina; Nunes, Cláudia; Reis, Salette

    2013-10-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used drugs in the world due to their anti-inflammatory, analgesic and antipyretic properties. Nevertheless, the consumption of these drugs is still associated with the occurrence of a wide spectrum of adverse effects. Regarding the major role of membranes in cellular events, the hypothesis that the biological actions of NSAIDs may be related to their effect at the membrane level has triggered the in vitro assessment of NSAIDs-membrane interactions. The use of membrane mimetic models, cell cultures, a wide range of experimental techniques and molecular dynamics simulations has been providing significant information about drugs partition and location within membranes and also about their effect on diverse membrane properties. These studies have indeed been providing evidences that the effect of NSAIDs at membrane level may be an additional mechanism of action and toxicity of NSAIDs. In fact, the pharmacokinetic properties of NSAIDs are closely related to the ability of these drugs to interact and overcome biological membranes. Moreover, the therapeutic actions of NSAIDs may also result from the indirect inhibition of cyclooxygenase due to the disturbing effect of NSAIDs on membrane properties. Furthermore, increasing evidences suggest that the disordering effects of these drugs on membranes may be in the basis of the NSAIDs-induced toxicity in diverse organ systems. Overall, the study of NSAIDs-membrane interactions has proved to be not only important for the better understanding of their pharmacological actions, but also for the rational development of new approaches to overcome NSAIDs adverse effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. An Error Analysis of Structured Light Scanning of Biological Tissue

    DEFF Research Database (Denmark)

    Jensen, Sebastian Hoppe Nesgaard; Wilm, Jakob; Aanæs, Henrik

    2017-01-01

    This paper presents an error analysis and correction model for four structured light methods applied to three common types of biological tissue; skin, fat and muscle. Despite its many advantages, structured light is based on the assumption of direct reflection at the object surface only....... This assumption is violated by most biological material e.g. human skin, which exhibits subsurface scattering. In this study, we find that in general, structured light scans of biological tissue deviate significantly from the ground truth. We show that a large portion of this error can be predicted with a simple......, statistical linear model based on the scan geometry. As such, scans can be corrected without introducing any specially designed pattern strategy or hardware. We can effectively reduce the error in a structured light scanner applied to biological tissue by as much as factor of two or three....

  11. Neutron scattering for the analysis of biological structures. Brookhaven symposia in biology. Number 27

    Energy Technology Data Exchange (ETDEWEB)

    Schoenborn, B P [ed.

    1976-01-01

    Sessions were included on neutron scattering and biological structure analysis, protein crystallography, neutron scattering from oriented systems, solution scattering, preparation of deuterated specimens, inelastic scattering, data analysis, experimental techniques, and instrumentation. Separate entries were made for the individual papers.

  12. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

  13. INSTRUCT - An integrated structural biology infrastructure for Europe

    Czech Academy of Sciences Publication Activity Database

    Dohnálek, Jan

    2010-01-01

    Roč. 17, 1a (2010), b3 ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. 18.03.2010-20.03.2010, Nové Hrady] R&D Projects: GA ČR GA310/09/1407 EU Projects: European Commission(XE) 31220 - SPINE2-COMPLEXES Institutional research plan: CEZ:AV0Z40500505 Keywords : structural biology * research infrastructure Subject RIV: EE - Microbiology, Virology

  14. Constrained saccharides: a review of structure, biology, and synthesis.

    Science.gov (United States)

    Rodriguez, Jacob; O'Neill, Sloane; Walczak, Maciej A

    2018-03-01

    Review primarily covers from 1995-2018Carbohydrate function, recognized in a multitude of biological processes, provides a precedent for developing carbohydrate surrogates that mimic the structure and function of bioactive compounds. In order to constrain highly flexible oligosaccharides, synthetic tethering techniques like those exemplified by stapled peptides are utilized to varying degrees of success. Naturally occurring constrained carbohydrates, however, exist with noteworthy cytotoxic and chemosensitizing properties. This review highlights the structure, biology, and synthesis of this intriguing class of molecules.

  15. Prevention of calcium-induced membrane structural alterations in erythrocyte membranes by flunarizine

    NARCIS (Netherlands)

    Thomas, Peter G.; Zimmermann, A.G.; Verkleij, A.J.

    1988-01-01

    The calcium antagonist flunarizine is shown to be able to prevent particle aggregation, membrane aggregation and blebbing resulting from elevated calcium concentrations. The anti-ischemic effects of flunarizine may therefore result in part from its ability to directly interfere with calcium-membrane

  16. The NMR structure of human obestatin in membrane-like environments: insights into the structure-bioactivity relationship of obestatin.

    Directory of Open Access Journals (Sweden)

    Begoña O Alén

    Full Text Available The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD, nuclear magnetic resonance (NMR spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1. Other analogues, including human non-amidated obestatin (2 and the fragment peptides (6-23-obestatin (3, (11-23-obestatin (4, and (16-23-obestatin (5 have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS. Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation. Our findings emphasize the importance of both the primary structure (composition and size and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively at both the structural and bioactivity levels.

  17. The NMR structure of human obestatin in membrane-like environments: insights into the structure-bioactivity relationship of obestatin.

    Science.gov (United States)

    Alén, Begoña O; Nieto, Lidia; Gurriarán-Rodríguez, Uxía; Mosteiro, Carlos S; Álvarez-Pérez, Juan C; Otero-Alén, María; Camiña, Jesús P; Gallego, Rosalía; García-Caballero, Tomás; Martín-Pastor, Manuel; Casanueva, Felipe F; Jiménez-Barbero, Jesús; Pazos, Yolanda

    2012-01-01

    The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1). Other analogues, including human non-amidated obestatin (2) and the fragment peptides (6-23)-obestatin (3), (11-23)-obestatin (4), and (16-23)-obestatin (5) have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS). Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation). Our findings emphasize the importance of both the primary structure (composition and size) and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively) at both the structural and bioactivity levels.

  18. Modelling the biological performance of a side-stream membrane bioreactor using ASM1.

    Science.gov (United States)

    Tian, Ke-Jun; Liu, Xin-Ai; Jiang, Tao; Kennedy, M D; Schippers, J C; Vanrolleghem, P A

    2004-01-01

    Membrane bioreactors (MBRs) are attracting global interest but the mathematical modeling of the biological performance of MBRs remains very limited. This study focuses on the modelling of a side-stream MBR system using Activated Sludge Model No. 1 (ASM1), and comparing the results with the modelling of traditional activated sludge processes. ASM1 parameters relevant for the long-term biological behaviour in MBR systems were calibrated (i.e. Y(H) = 0.72gCOD/gCOD, Y(A) = 0.25gCOD/gN, b(H) = 0.25 d(-1), b(A) = 0.080 d(-1) and f(P) = 0.06), and generally agreed with the parameters in traditional activated sludge processes, with the exception that a higher autotrophic biomass decay rate was observed in the MBR. A sensitivity analysis for steady state operation and DO dynamics suggested that the biological performance of the MBR system (the sludge concentration, effluent quality and the DO dynamics) are very sensitive to the parameters(i.e. Y(H), Y(A), b(H), b(A), micro(maxH) and micro(maxA)), and influent wastewater components(X(I), S(S), X(S), S(NH)).

  19. Trans-cis isomerization of lipophilic dyes probing membrane microviscosity in biological membranes and in live cells.

    Science.gov (United States)

    Chmyrov, Volodymyr; Spielmann, Thiemo; Hevekerl, Heike; Widengren, Jerker

    2015-06-02

    Membrane environment and fluidity can modulate the dynamics and interactions of membrane proteins and can thereby strongly influence the function of cells and organisms in general. In this work, we demonstrate that trans-cis isomerization of lipophilic dyes is a useful parameter to monitor packaging and fluidity of biomembranes. Fluorescence fluctuations, generated by trans-cis isomerization of the thiocarbocyanine dye Merocyanine 540 (MC540), were first analyzed by fluorescence correlation spectroscopy (FCS) in different alcohol solutions. Similar isomerization kinetics of MC540 in lipid vesicles could then also be monitored, and the influence of lipid polarity, membrane curvature, and cholesterol content was investigated. While no influence of membrane curvature and lipid polarity could be observed, a clear decrease in the isomerization rates could be observed with increasing cholesterol contents in the vesicle membranes. Finally, procedures to spatially map photoinduced and thermal isomerization rates on live cells by transient state (TRAST) imaging were established. On the basis of these procedures, MC540 isomerization was studied on live MCF7 cells, and TRAST images of the cells at different temperatures were found to reliably detect differences in the isomerization parameters. Our studies indicate that trans-cis isomerization is a useful parameter for probing membrane dynamics and that the TRAST imaging technique can provide spatial maps of photoinduced isomerization as well as both photoinduced and thermal back-isomerization, resolving differences in local membrane microviscosity in live cells.

  20. Structural Biology of Pectin Degradation by Enterobacteriaceae

    Science.gov (United States)

    Abbott, D. Wade; Boraston, Alisdair B.

    2008-01-01

    Pectin is a structural polysaccharide that is integral for the stability of plant cell walls. During soft rot infection, secreted virulence factors from pectinolytic bacteria such as Erwinia spp. degrade pectin, resulting in characteristic plant cell necrosis and tissue maceration. Catabolism of pectin and its breakdown products by pectinolytic bacteria occurs within distinct cellular environments. This process initiates outside the cell, continues within the periplasmic space, and culminates in the cytoplasm. Although pectin utilization is well understood at the genetic and biochemical levels, an inclusive structural description of pectinases and pectin binding proteins by both extracellular and periplasmic enzymes has been lacking, especially following the recent characterization of several periplasmic components and protein-oligogalacturonide complexes. Here we provide a comprehensive analysis of the protein folds and mechanisms of pectate lyases, polygalacturonases, and carbohydrate esterases and the binding specificities of two periplasmic pectic binding proteins from Enterobacteriaceae. This review provides a structural understanding of the molecular determinants of pectin utilization and the mechanisms driving catabolite selectivity and flow through the pathway. PMID:18535148

  1. The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins.

    Science.gov (United States)

    Love, James; Mancia, Filippo; Shapiro, Lawrence; Punta, Marco; Rost, Burkhard; Girvin, Mark; Wang, Da-Neng; Zhou, Ming; Hunt, John F; Szyperski, Thomas; Gouaux, Eric; MacKinnon, Roderick; McDermott, Ann; Honig, Barry; Inouye, Masayori; Montelione, Gaetano; Hendrickson, Wayne A

    2010-09-01

    The New York Consortium on Membrane Protein Structure (NYCOMPS) was formed to accelerate the acquisition of structural information on membrane proteins by applying a structural genomics approach. NYCOMPS comprises a bioinformatics group, a centralized facility operating a high-throughput cloning and screening pipeline, a set of associated wet labs that perform high-level protein production and structure determination by x-ray crystallography and NMR, and a set of investigators focused on methods development. In the first three years of operation, the NYCOMPS pipeline has so far produced and screened 7,250 expression constructs for 8,045 target proteins. Approximately 600 of these verified targets were scaled up to levels required for structural studies, so far yielding 24 membrane protein crystals. Here we describe the overall structure of NYCOMPS and provide details on the high-throughput pipeline.

  2. Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives

    Science.gov (United States)

    Solís-Calero, Christian; Ortega-Castro, Joaquín; Frau, Juan; Muñoz, Francisco

    2015-01-01

    Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease. PMID:25977746

  3. Dynamical and structural properties of lipid membranes in relation to liposomal drug delivery systems

    DEFF Research Database (Denmark)

    Jørgensen, Kent; Høyrup, Lise Pernille Kristine; Pedersen, Tina B.

    2001-01-01

    The structural and dynamical properties of DPPC liposomes containing lipopolymers (PEG-lipids) and charged DPPS lipids have been,studied in relation to the lipid membrane interaction of enzymes and peptides. The results suggest that both the lipid membrane structure and dynamics and in particular...

  4. Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation

    KAUST Repository

    Yu, H.

    2016-09-14

    Membranes with a hierarchical porous structure could be manufactured from a block copolymer blend by pure solvent evaporation. Uniform pores in a 30 nm thin skin layer supported by a macroporous structure were formed. This new process is attractive for membrane production because of its simplicity and the lack of liquid waste.

  5. Impacts of operating conditions and solution chemistry on osmotic membrane structure and performance

    KAUST Repository

    Wong, Mavis C.Y.

    2012-02-01

    Herein, we report on changes in the performance of a commercial cellulose triacetate (CTA) membrane, imparted by varied operating conditions and solution chemistries. Changes to feed and draw solution flow rate did not significantly alter the CTA membrane\\'s water permeability, salt permeability, or membrane structural parameter when operated with the membrane skin layer facing the draw solution (PRO-mode). However, water and salt permeability increased with increasing feed or draw solution temperature, while the membrane structural parameter decreased with increasing draw solution, possibly due to changes in polymer intermolecular interactions. High ionic strength draw solutions may de-swell the CTA membrane via charge neutralization, which resulted in lower water permeability, higher salt permeability, and lower structural parameter. This observed trend was further exacerbated by the presence of divalent cations which tends to swell the polymer to a greater extent. Finally, the calculated CTA membrane\\'s structural parameter was lower and less sensitive to external factors when operated in PRO-mode, but highly sensitive to the same factors when the skin layer faced the feed solution (FO-mode), presumably due to swelling/de-swelling of the saturated porous substructure by the draw solution. This is a first attempt aimed at systematically evaluating the changes in performance of the CTA membrane due to operating conditions and solution chemistry, shedding new insight into the possible advantages and disadvantages of this material in certain applications. © 2011 Elsevier B.V.

  6. Micro-structured membranes for electricity generation by reverse electrodialysis

    NARCIS (Netherlands)

    Güler, E.; Elizen, Rianne; Saakes, Michel; Nijmeijer, Dorothea C.

    2014-01-01

    Reverse electrodialysis (RED) is a technology for extracting salinity gradient power by contacting waters with different salinity, i.e. seawater and river water, through ion exchange membranes. Conventionally, non-conductive spacers are used to separate these ion exchange membranes from each other

  7. Optical manipulation of microparticles and biological structures

    Science.gov (United States)

    Gahagan, Kevin Thomas

    1998-06-01

    We report experimental and theoretical investigations of the trapping of microparticles and biological objects using radiation pressure. Part I of this thesis presents a technique for trapping both low and high index microparticles using a single, stationary focused laser beam containing an optical vortex. Advantages of this vortex trap include the ease of implementation, a lower exposure level for high-index particles compared to a standard Gaussian beam trap, and the ability to isolate individual low-index particles in concentrated dispersions. The vortex trap is modeled using ray-tracing methods and a more precise electromagnetic model, which is accurate for particles less than 10 μm in diameter. We have measured the stable equilibrium position for two low-index particle systems (e.g., hollow glass spheres (HGS) in water, and water droplets in acetophenone (W/A)). The strength of the trap was measured for the HGS system along the longitudinal and transverse directions. We also demonstrate simultaneous trapping of a low and high index particle with a vortex beam. The stability of this dual-particle trap is found to depend on the relative particle size, the divergence angle of the beam, and the depth of the particles within the trapping chamber. Part II presents results from an interdisciplinary and collaborative investigation of an all-optical genetic engineering technique whereby Agrobacterium rhizogenes were inserted through a laser-ablated hole in the cell wall of the plant, Gingko biloba. We describe a protocol which includes the control of osmotic conditions, culturing procedures, viability assays and laser microsurgery. We succeeded in placing up to twelve viable bacteria into a single plant cell using this technique. The bacteria are believed to be slightly heated by the Gaussian beam trap. A numerical model is presented predicting a temperature rise of just a few degrees. Whereas G. biloba and A. rhitogenes were chosen for this study because of Ginkgo

  8. Biological, histological and ultra-structural studies of female mullet ...

    African Journals Online (AJOL)

    Aghomotsegin

    2015-07-29

    Jul 29, 2015 ... This study investigates some biological characters (oocyte diameter, fecundity, histological and ultra structural features) of ... histological and fine structure characteristics, it was possible to understand the functional relationship between .... thick were prepared using glass and diamond knives, and stained.

  9. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

    DEFF Research Database (Denmark)

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk

    2013-01-01

    Improve the System A "systems biology" approach may clarify, for example, how particular proteins determine sensitivity of bacteria to extremes of temperature. Chang et al. (p. 1220) integrated information on protein structure with a model of metabolism, thus associating the protein structure of ...

  10. XFELs open a new era in structural chemical biology

    OpenAIRE

    Fromme, Petra

    2015-01-01

    X-ray crystallography, the workhorse of structural biology, has been revolutionized by the advent of serial femtosecond crystallography using X-ray free electron lasers. Here, the fast pace and history of discoveries are discussed together with current challenges and the method’s great potential to make new structural discoveries, such as the ability to generate molecular movies of biomolecules at work.

  11. Giant plasma membrane vesicles: models for understanding membrane organization.

    Science.gov (United States)

    Levental, Kandice R; Levental, Ilya

    2015-01-01

    The organization of eukaryotic membranes into functional domains continues to fascinate and puzzle cell biologists and biophysicists. The lipid raft hypothesis proposes that collective lipid interactions compartmentalize the membrane into coexisting liquid domains that are central to membrane physiology. This hypothesis has proven controversial because such structures cannot be directly visualized in live cells by light microscopy. The recent observations of liquid-liquid phase separation in biological membranes are an important validation of the raft hypothesis and enable application of the experimental toolbox of membrane physics to a biologically complex phase-separated membrane. This review addresses the role of giant plasma membrane vesicles (GPMVs) in refining the raft hypothesis and expands on the application of GPMVs as an experimental model to answer some of key outstanding problems in membrane biology. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Piezo- and Flexoelectric Membrane Materials Underlie Fast Biological Motors in the Ear.

    Science.gov (United States)

    Breneman, Kathryn D; Rabbitt, Richard D

    2009-01-01

    The mammalian inner ear is remarkably sensitive to quiet sounds, exhibits over 100dB dynamic range, and has the exquisite ability to discriminate closely spaced tones even in the presence of noise. This performance is achieved, in part, through active mechanical amplification of vibrations by sensory hair cells within the inner ear. All hair cells are endowed with a bundle of motile microvilli, stereocilia, located at the apical end of the cell, and the more specialized outer hair cells (OHC's) are also endowed with somatic electromotility responsible for changes in cell length in response to perturbations in membrane potential. Both hair bundle and somatic motors are known to feed energy into the mechanical vibrations in the inner ear. The biophysical origin and relative significance of the motors remains a subject of intense research. Several biological motors have been identified in hair cells that might underlie the motor(s), including a cousin of the classical ATP driven actin-myosin motor found in skeletal muscle. Hydrolysis of ATP, however, is much too slow to be viable at audio frequencies on a cycle-by-cycle basis. Heuristically, the OHC somatic motor behaves as if the OHC lateral wall membrane were a piezoelectric material and the hair bundle motor behaves as if the plasma membrane were a flexoelectric material. We propose these observations from a continuum materials perspective are literally true. To examine this idea, we formulated mathematical models of the OHC lateral wall "piezoelectric" motor and the more ubiquitous "flexoelectric" hair bundle motor. Plausible biophysical mechanisms underlying piezo- and flexoelectricity were established. Model predictions were compared extensively to the available data. The models were then applied to study the power conversion efficiency of the motors. Results show that the material properties of the complex membranes in hair cells provide them with the ability to convert electrical power available in the inner

  13. Antibacterial Membrane with a Bone-Like Structure for Guided Bone Regeneration

    Directory of Open Access Journals (Sweden)

    YuYuan Zhang

    2015-01-01

    Full Text Available An antibacterial membrane with a bone-like structure was developed for guided bone regeneration (GBR by mineralising acellular bovine pericardium (ABP and loading it with the antibiotic minocycline. The bovine pericardium (BP membrane was processed using physical and chemical methods to remove the cellular components and obtain ABP membranes. Then, the ABP membranes were biomimetically mineralised using a calcium phosphate-loaded agarose hydrogel system aided by electrophoresis. Minocycline was adsorbed to the mineralised ABP membrane, and the release profile in vitro was studied. The membranes were characterised through scanning electron microscopy, diffuse reflectance-Fourier transform infrared spectroscopy, and X-ray diffraction. Results showed that the ABP membrane had an asymmetric structure with a layer of densely arranged and irregularly aligned collagen fibrils. Collagen fibrils were calcified with the formation of intrafibrillar and interfibrillar hydroxyapatites similar to the bone structure. Minocycline was incorporated into the mineralised collagen membrane and could be released in vitro. This process endowed the membrane with an antibacterial property. This novel composite membrane offers promising applications in bioactive GBR.

  14. High-resolution NMR reveals secondary structure and folding of amino acid transporter from outer chloroplast membrane.

    Directory of Open Access Journals (Sweden)

    James D Zook

    Full Text Available Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16, an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the (13C, (15N, (2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.

  15. Advances in Structural Biology and the Application to Biological Filament Systems.

    Science.gov (United States)

    Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

    2018-02-27

    Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  16. Structural Diversity and Biological Activities of Cyclic Depsipeptides from Fungi

    OpenAIRE

    Xiaohan Wang; Xiao Gong; Peng Li; Daowan Lai; Ligang Zhou

    2018-01-01

    Cyclic depsipeptides (CDPs) are cyclopeptides in which amide groups are replaced by corresponding lactone bonds due to the presence of a hydroxylated carboxylic acid in the peptide structure. These peptides sometimes display additional chemical modifications, including unusual amino acid residues in their structures. This review highlights the occurrence, structures and biological activities of the fungal CDPs reported until October 2017. About 352 fungal CDPs belonging to the groups of cycli...

  17. Structural models of the membrane anchors of envelope glycoproteins E1 and E2 from pestiviruses

    International Nuclear Information System (INIS)

    Wang, Jimin; Li, Yue; Modis, Yorgo

    2014-01-01

    The membrane anchors of viral envelope proteins play essential roles in cell entry. Recent crystal structures of the ectodomain of envelope protein E2 from a pestivirus suggest that E2 belongs to a novel structural class of membrane fusion machinery. Based on geometric constraints from the E2 structures, we generated atomic models of the E1 and E2 membrane anchors using computational approaches. The E1 anchor contains two amphipathic perimembrane helices and one transmembrane helix; the E2 anchor contains a short helical hairpin stabilized in the membrane by an arginine residue, similar to flaviviruses. A pair of histidine residues in the E2 ectodomain may participate in pH sensing. The proposed atomic models point to Cys987 in E2 as the site of disulfide bond linkage with E1 to form E1–E2 heterodimers. The membrane anchor models provide structural constraints for the disulfide bonding pattern and overall backbone conformation of the E1 ectodomain. - Highlights: • Structures of pestivirus E2 proteins impose constraints on E1, E2 membrane anchors. • Atomic models of the E1 and E2 membrane anchors were generated in silico. • A “snorkeling” arginine completes the short helical hairpin in the E2 membrane anchor. • Roles in pH sensing and E1–E2 disulfide bond formation are proposed for E1 residues. • Implications for E1 ectodomain structure and disulfide bonding pattern are discussed

  18. Structural models of the membrane anchors of envelope glycoproteins E1 and E2 from pestiviruses

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jimin, E-mail: jimin.wang@yale.edu; Li, Yue; Modis, Yorgo, E-mail: yorgo.modis@yale.edu

    2014-04-15

    The membrane anchors of viral envelope proteins play essential roles in cell entry. Recent crystal structures of the ectodomain of envelope protein E2 from a pestivirus suggest that E2 belongs to a novel structural class of membrane fusion machinery. Based on geometric constraints from the E2 structures, we generated atomic models of the E1 and E2 membrane anchors using computational approaches. The E1 anchor contains two amphipathic perimembrane helices and one transmembrane helix; the E2 anchor contains a short helical hairpin stabilized in the membrane by an arginine residue, similar to flaviviruses. A pair of histidine residues in the E2 ectodomain may participate in pH sensing. The proposed atomic models point to Cys987 in E2 as the site of disulfide bond linkage with E1 to form E1–E2 heterodimers. The membrane anchor models provide structural constraints for the disulfide bonding pattern and overall backbone conformation of the E1 ectodomain. - Highlights: • Structures of pestivirus E2 proteins impose constraints on E1, E2 membrane anchors. • Atomic models of the E1 and E2 membrane anchors were generated in silico. • A “snorkeling” arginine completes the short helical hairpin in the E2 membrane anchor. • Roles in pH sensing and E1–E2 disulfide bond formation are proposed for E1 residues. • Implications for E1 ectodomain structure and disulfide bonding pattern are discussed.

  19. A Class of Rigid Linker-bearing Glucosides for Membrane Protein Structural Study

    DEFF Research Database (Denmark)

    Sadaf, Aiman; Mortensen, Jonas S; Capaldi, Stefano

    2016-01-01

    for structural and functional analysis. Despite the availability of a large number of detergents, only a few agents are sufficiently effective at maintaining the integrity of membrane proteins to allow successful crystallization. In the present study, we describe a novel class of synthetic amphiphiles....... Members of this class conferred enhanced stability on target membrane proteins compared to conventional detergents. Because of straightforward synthesis of the novel agents and their favourable effects on a range of membrane proteins, these agents should be of wide applicability to membrane protein......Membrane proteins are amphipathic bio-macromolecules incompatible with the polar environments of aqueous media. Conventional detergents encapsulate the hydrophobic surfaces of membrane proteins allowing them to exist in aqueous solution. Membrane proteins stabilized by detergent micelles are used...

  20. Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology.

    Science.gov (United States)

    Elani, Yuval

    2016-06-15

    The quest to construct artificial cells from the bottom-up using simple building blocks has received much attention over recent decades and is one of the grand challenges in synthetic biology. Cell mimics that are encapsulated by lipid membranes are a particularly powerful class of artificial cells due to their biocompatibility and the ability to reconstitute biological machinery within them. One of the key obstacles in the field centres on the following: how can membrane-based artificial cells be generated in a controlled way and in high-throughput? In particular, how can they be constructed to have precisely defined parameters including size, biomolecular composition and spatial organization? Microfluidic generation strategies have proved instrumental in addressing these questions. This article will outline some of the major principles underpinning membrane-based artificial cells and their construction using microfluidics, and will detail some recent landmarks that have been achieved. © 2016 The Author(s).

  1. Enhancement in biological response of Ag-nano composite polymer membranes using plasma treatment for fabrication of efficient bio materials

    Science.gov (United States)

    Agrawal, Narendra Kumar; Sharma, Tamanna Kumari; Chauhan, Manish; Agarwal, Ravi; Vijay, Y. K.; Swami, K. C.

    2016-05-01

    Biomaterials are nonviable material used in medical devices, intended to interact with biological systems, which are becoming necessary for the development of artificial material for biological systems such as artificial skin diaphragm, valves for heart and kidney, lenses for eye etc. Polymers having novel properties like antibacterial, antimicrobial, high adhesion, blood compatibility and wettability are most suitable for synthesis of biomaterial, but all of these properties does not exist in any natural or artificial polymeric material. Nano particles and plasma treatment can offer these properties to the polymers. Hence a new nano-biomaterial has been developed by modifying the surface and chemical properties of Ag nanocomposite polymer membranes (NCPM) by Argon ion plasma treatment. These membranes were characterized using different techniques for surface and chemical modifications occurred. Bacterial adhesion and wettability were also tested for these membranes, to show direct use of this new class of nano-biomaterial for biomedical applications.

  2. Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function

    Science.gov (United States)

    Horowitz, Scott; Trievel, Raymond C.

    2012-01-01

    Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure. PMID:23048026

  3. Exploring membrane protein structural features by oxidative labeling and mass spectrometry.

    Science.gov (United States)

    Konermann, Lars; Pan, Yan

    2012-10-01

    Despite their biological importance, the structural characterization of integral membrane proteins (IMPs) by x-ray crystallography and NMR spectroscopy remains challenging. Hence, there is a need for complementary approaches that are capable of probing IMP conformational features in a robust fashion. Covalent labeling relies on the principle that solvent accessible regions can be modified by reactive species, whereas buried segments are protected. The readout of the labeling pattern is conducted by mass spectrometry. Hydroxyl radical (·OH) introduces oxidative modifications at amino acid side chains. In this article, the authors discuss the application of ·OH labeling for the structural interrogation of IMPs. Kyte-Doolittle hydropathy analyses are widely used for generating IMP topology models. The validation of these models by mutational techniques is labor intensive. ·OH labeling can readily distinguish transmembrane elements from solvent-exposed loops, thereby providing an alternative topology validation tool. For IMPs with published crystal structures, oxidative modifications can report on functionally relevant dynamic features that are invisible in the static x-ray data. The coupling of pulsed ·OH labeling with rapid mixing techniques represents a novel approach for studying IMP folding kinetics. In conclusion, ·OH labeling is a versatile tool that can provide insights into the structure and dynamics of IMPs.

  4. Present and future of membrane protein structure determination by electron crystallography.

    Science.gov (United States)

    Ubarretxena-Belandia, Iban; Stokes, David L

    2010-01-01

    Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. Macromolecular Crystallography and Structural Biology Databases at NIST.

    Science.gov (United States)

    Gilliland, G L

    2001-01-01

    In the late 1970s, macromolecular crystallography at NIST began with collaboration between NIST and NIH to establish a single-crystal neutron diffractometer. This instrument was constructed and employed to solve a number of crystal structures: bovine ribonuclease A, bovine-ribonuclease-uridine vanadate complex, and porcine insulin. In the mid 1980s a Biomolecular Structure Group was created establishing NIST capabilities in biomolecular singe-crystal x-ray diffraction. The group worked on a variety of structural problems until joining the NIST/UMBI Center for Advanced Research in Biotechnology (CARB) in 1987. Crystallographic studies at CARB were then focused on protein engineering efforts that included among others chymosin, subtilisin BPN', interleukin 1β, and glutathione S-transferase. Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of "hypothetical" proteins to aid in assigning function. In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macro-molecule Crystallization Database in 1989. Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformatics that successfully acquired the Protein Data Bank. The NIST efforts in these activities have focused on data uniformity, establishing and maintaining the physical archive, and working with the NMR community.

  6. An innovative methodology for measurement of stress distribution of inflatable membrane structures

    Science.gov (United States)

    Zhao, Bing; Chen, Wujun; Hu, Jianhui; Chen, Jianwen; Qiu, Zhenyu; Zhou, Jinyu; Gao, Chengjun

    2016-02-01

    The inflatable membrane structure has been widely used in the fields of civil building, industrial building, airship, super pressure balloon and spacecraft. It is important to measure the stress distribution of the inflatable membrane structure because it influences the safety of the structural design. This paper presents an innovative methodology for the measurement and determination of the stress distribution of the inflatable membrane structure under different internal pressures, combining photogrammetry and the force-finding method. The shape of the inflatable membrane structure is maintained by the use of pressurized air, and the internal pressure is controlled and measured by means of an automatic pressure control system. The 3D coordinates of the marking points pasted on the membrane surface are acquired by three photographs captured from three cameras based on photogrammetry. After digitizing the markings on the photographs, the 3D curved surfaces are rebuilt. The continuous membrane surfaces are discretized into quadrilateral mesh and simulated by membrane links to calculate the stress distributions using the force-finding method. The internal pressure is simplified to the external node forces in the normal direction according to the contributory area of the node. Once the geometry x, the external force r and the topology C are obtained, the unknown force densities q in each link can be determined. Therefore, the stress distributions of the inflatable membrane structure can be calculated, combining the linear adjustment theory and the force density method based on the force equilibrium of inflated internal pressure and membrane internal force without considering the mechanical properties of the constitutive material. As the use of the inflatable membrane structure is attractive in the field of civil building, an ethylene-tetrafluoroethylene (ETFE) cushion is used with the measurement model to validate the proposed methodology. The comparisons between the

  7. Structural basis of Sec-independent membrane protein insertion by YidC.

    Science.gov (United States)

    Kumazaki, Kaoru; Chiba, Shinobu; Takemoto, Mizuki; Furukawa, Arata; Nishiyama, Ken-ichi; Sugano, Yasunori; Mori, Takaharu; Dohmae, Naoshi; Hirata, Kunio; Nakada-Nakura, Yoshiko; Maturana, Andrés D; Tanaka, Yoshiki; Mori, Hiroyuki; Sugita, Yuji; Arisaka, Fumio; Ito, Koreaki; Ishitani, Ryuichiro; Tsukazaki, Tomoya; Nureki, Osamu

    2014-05-22

    Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the homologous proteins Oxa1 and Alb3 have the same function in mitochondria and chloroplasts, respectively. In the bacterial cytoplasmic membrane, YidC functions as an independent insertase and a membrane chaperone in cooperation with the translocon SecYEG. Here we present the crystal structure of YidC from Bacillus halodurans, at 2.4 Å resolution. The structure reveals a novel fold, in which five conserved transmembrane helices form a positively charged hydrophilic groove that is open towards both the lipid bilayer and the cytoplasm but closed on the extracellular side. Structure-based in vivo analyses reveal that a conserved arginine residue in the groove is important for the insertion of membrane proteins by YidC. We propose an insertion mechanism for single-spanning membrane proteins, in which the hydrophilic environment generated by the groove recruits the extracellular regions of substrates into the low-dielectric environment of the membrane.

  8. Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering.

    Science.gov (United States)

    Midtgaard, Søren Roi; Darwish, Tamim A; Pedersen, Martin Cramer; Huda, Pie; Larsen, Andreas Haahr; Jensen, Grethe Vestergaard; Kynde, Søren Andreas Røssell; Skar-Gislinge, Nicholas; Nielsen, Agnieszka Janina Zygadlo; Olesen, Claus; Blaise, Mickael; Dorosz, Jerzy Józef; Thorsen, Thor Seneca; Venskutonytė, Raminta; Krintel, Christian; Møller, Jesper V; Frielinghaus, Henrich; Gilbert, Elliot Paul; Martel, Anne; Kastrup, Jette Sandholm; Jensen, Poul Erik; Nissen, Poul; Arleth, Lise

    2018-01-01

    A novel and generally applicable method for determining structures of membrane proteins in solution via small-angle neutron scattering (SANS) is presented. Common detergents for solubilizing membrane proteins were synthesized in isotope-substituted versions for utilizing the intrinsic neutron scattering length difference between hydrogen and deuterium. Individual hydrogen/deuterium levels of the detergent head and tail groups were achieved such that the formed micelles became effectively invisible in heavy water (D 2 O) when investigated by neutrons. This way, only the signal from the membrane protein remained in the SANS data. We demonstrate that the method is not only generally applicable on five very different membrane proteins but also reveals subtle structural details about the sarco/endoplasmatic reticulum Ca 2+ ATPase (SERCA). In all, the synthesis of isotope-substituted detergents makes solution structure determination of membrane proteins by SANS and subsequent data analysis available to nonspecialists. © 2017 Federation of European Biochemical Societies.

  9. Partially Fluorinated Sulfonated Poly(ether amide Fuel Cell Membranes: Influence of Chemical Structure on Membrane Properties

    Directory of Open Access Journals (Sweden)

    Chulsung Bae

    2011-01-01

    Full Text Available A series of fluorinated sulfonated poly (ether amides (SPAs were synthesized for proton exchange membrane fuel cell applications. A polycondensation reaction of 4,4’-oxydianiline, 2-sulfoterephthalic acid monosodium salt, and tetrafluorophenylene dicarboxylic acids (terephthalic and isophthalic or fluoroaliphatic dicarboxylic acids produced SPAs with sulfonation degrees of 80–90%. Controlling the feed ratio of the sulfonated and unsulfonated dicarboxylic acid monomers afforded random SPAs with ion exchange capacities between 1.7 and 2.2 meq/g and good solubility in polar aprotic solvents. Their structures were characterized using NMR and FT IR spectroscopies. Tough, flexible, and transparent films were obtained with dimethylsulfoxide using a solution casting method. Most SPA membranes with 90% sulfonation degree showed high proton conductivity (>100 mS/cm at 80 °C and 100% relative humidity. Among them, two outstanding ionomers (ODA-STA-TPA-90 and ODA-STA-IPA-90 showed proton conductivity comparable to that of Nafion 117 between 40 and 80 °C. The influence of chemical structure on the membrane properties was systematically investigated by comparing the fluorinated polymers to their hydrogenated counterparts. The results suggest that the incorporation of fluorinated moieties in the polymer backbone of the membrane reduces water absorption. High molecular weight and the resulting physical entanglement of the polymers chains played a more important role in improving stability in water, however.

  10. Relating performance of thin-film composite forward osmosis membranes to support layer formation and structure

    KAUST Repository

    Tiraferri, Alberto

    2011-02-01

    Osmotically driven membrane processes have the potential to treat impaired water sources, desalinate sea/brackish waters, and sustainably produce energy. The development of a membrane tailored for these processes is essential to advance the technology to the point that it is commercially viable. Here, a systematic investigation of the influence of thin-film composite membrane support layer structure on forward osmosis performance is conducted. The membranes consist of a selective polyamide active layer formed by interfacial polymerization on top of a polysulfone support layer fabricated by phase separation. By systematically varying the conditions used during the casting of the polysulfone layer, an array of support layers with differing structures was produced. The role that solvent quality, dope polymer concentration, fabric layer wetting, and casting blade gate height play in the support layer structure formation was investigated. Using a 1M NaCl draw solution and a deionized water feed, water fluxes ranging from 4 to 25Lm-2h-1 with consistently high salt rejection (>95.5%) were produced. The relationship between membrane structure and performance was analyzed. This study confirms the hypothesis that the optimal forward osmosis membrane consists of a mixed-structure support layer, where a thin sponge-like layer sits on top of highly porous macrovoids. Both the active layer transport properties and the support layer structural characteristics need to be optimized in order to fabricate a high performance forward osmosis membrane. © 2010 Elsevier B.V.

  11. From crystallography to structural biology, a century of discoveries

    Directory of Open Access Journals (Sweden)

    Montoya, Guillermo

    2015-04-01

    Full Text Available From crystallography, the technique mostly used to study the structure of matter, the field mutated into structural biology, has mutated in life sciences into structural biology, which has been developed as an essential and rather successful area of research to fully understand the workings of cellular pathways. The application of physical approaches to biological systems has been crucial to comprehend the structure and function of the biological components of living organisms. In this assay the author walks the reader through the last century, which has witnessed how this life sciences research area was born and moved towards larger assemblies in the core of crucial biological problems. The influence of research in physics, biochemistry and molecular biology has been key in the successes and large body of seminal results obtained by structural biologists. The author proposes that the future of this area implies the integration of its results at the cellular level apart of using more quantitative approaches to describe biological processes.La cristalografía, la técnica más ampliamente usada para estudiar la estructura de la materia, ha evolucionado en las ciencias de la vida hacia la biología estructural, una exitosa área de investigación encaminada a comprender el funcionamiento de los procesos celulares. La aplicación de aproximaciones físicas a sistemas biológicos es clave para entender la estructura y funcionamiento de los componentes de los organismos. En este artículo el autor ofrece al lector un paseo por la evolución de esta área de conocimiento durante el siglo XX, desde su nacimiento hasta el análisis de grandes complejos macromoleculares, protagonistas importantes en diversos procesos biológicos. La influencia de investigaciones en física, bioquímica y biología molecular ha sido clave para los numerosos éxitos alcanzados por biólogos estructurales. El autor sostiene que el futuro de esta disciplina pasa por la

  12. Structural biological materials: critical mechanics-materials connections.

    Science.gov (United States)

    Meyers, Marc André; McKittrick, Joanna; Chen, Po-Yu

    2013-02-15

    Spider silk is extraordinarily strong, mollusk shells and bone are tough, and porcupine quills and feathers resist buckling. How are these notable properties achieved? The building blocks of the materials listed above are primarily minerals and biopolymers, mostly in combination; the first weak in tension and the second weak in compression. The intricate and ingenious hierarchical structures are responsible for the outstanding performance of each material. Toughness is conferred by the presence of controlled interfacial features (friction, hydrogen bonds, chain straightening and stretching); buckling resistance can be achieved by filling a slender column with a lightweight foam. Here, we present and interpret selected examples of these and other biological materials. Structural bio-inspired materials design makes use of the biological structures by inserting synthetic materials and processes that augment the structures' capability while retaining their essential features. In this Review, we explain this idea through some unusual concepts.

  13. Biological activity of antitumoural MGBG: the structural variable.

    Science.gov (United States)

    Marques, M P M; Gil, F P S C; Calheiros, R; Battaglia, V; Brunati, A M; Agostinelli, E; Toninello, A

    2008-05-01

    The present study aims at determining the structure-activity relationships (SAR's) ruling the biological function of MGBG (methylglyoxal bis(guanylhydrazone)), a competitive inhibitor of S-adenosyl-L-methionine decarboxylase displaying anticancer activity, involved in the biosynthesis of the naturally occurring polyamines spermidine and spermine. In order to properly understand its biochemical activity, MGBG's structural preferences at physiological conditions were ascertained, by quantum mechanical (DFT) calculations.

  14. Structure, composition, and strength of nitrifying membrane-aerated biofilms

    DEFF Research Database (Denmark)

    Pellicer i Nàcher, Carles; Smets, Barth F.

    2014-01-01

    Membrane-aerated biofilm reactors (MABRs) are a novel technology based on the growth of biofilms on oxygen-permeable membranes. Hereby, MABRs combine all the advantages of biofilm growth with a more flexible and efficient control of the oxygen load. In the present work, flow cell operation...... had a higher content of proteins and a lower level of carbohydrates. Staining analyses revealed that the EPS in the stronger biofilm regions had hydrophilic nature and distributed around dense microbial aggregates, whereas it was homogeneously distributed in the weaker strata. Overall, the obtained...

  15. Biological, Histological and Ultra-Structural Studies of Female Mullet ...

    African Journals Online (AJOL)

    Biological, Histological and Ultra-Structural Studies of Female Mullet, Mugil cephalus , Ovaries Collected from Different Habitats during Annual Reproductive Cycle. ... 35 and 52 cm, respectively; whereas, the total number of ripe ova in brackish water fish ranged from 0.57±0.14 to 3.81±0.59 x106 for the same length groups.

  16. Structural valve deterioration in the Mitroflow biological heart valve prosthesis

    DEFF Research Database (Denmark)

    Issa, Issa Farah; Poulsen, Steen Hvitfeldt; Waziri, Farhad

    2018-01-01

    OBJECTIVES: Concern has been raised regarding the long-term durability of the Mitroflow biological heart valve prosthesis. Our aim was to assess the incidence of structural valve degeneration (SVD) for the Mitroflow bioprosthesis in a nationwide study in Denmark including all patients alive in De...

  17. Hyperdry amniotic membrane as a suitable biological dressing material for raw wounds in the oral cavity

    Directory of Open Access Journals (Sweden)

    Makoto Noguchi

    2016-06-01

    Full Text Available Raw wounds in the oral cavity are prone not only to infection but also contraction by scaring and often need a proper dressing to prevent these complications. Autografts using free mucosal and split-skin grafts, which seem biologically ideal, have been used to cover raw wounds in the oral cavity. Those grafts, however, require a separate surgical procedure at donor sites and often cause morbidity associated with delayed healing of the donor site. The amnion has been considered a suitable tissue for allografts, based on its low immunogenicity. It also possesses anti-inflammatory, would –protecting, and scar-reducing properties. Preserved amnions have been used for decades in various clinical fields.  However, there have been some problems in the storage and sterilization of the material. To resolve these problems, we developed hyperdry amniotic membrane (HAM, which can be stored at room temperature for a long period. In my lecture, I will share our clinical experiences of applying HAM into oral surgery, including results of experimental studies on would healing of the oral cavity.

  18. Isolation, Characterization and Biological Properties of Membrane Vesicles Produced by the Swine Pathogen Streptococcus suis.

    Directory of Open Access Journals (Sweden)

    Bruno Haas

    Full Text Available Streptococcus suis, more particularly serotype 2, is a major swine pathogen and an emerging zoonotic agent worldwide that mainly causes meningitis, septicemia, endocarditis, and pneumonia. Although several potential virulence factors produced by S. suis have been identified in the last decade, the pathogenesis of S. suis infections is still not fully understood. In the present study, we showed that S. suis produces membrane vesicles (MVs that range in diameter from 13 to 130 nm and that appear to be coated by capsular material. A proteomic analysis of the MVs revealed that they contain 46 proteins, 9 of which are considered as proven or suspected virulence factors. Biological assays confirmed that S. suis MVs possess active subtilisin-like protease (SspA and DNase (SsnA. S. suis MVs degraded neutrophil extracellular traps, a property that may contribute to the ability of the bacterium to escape the host defense response. MVs also activated the nuclear factor-kappa B (NF-κB signaling pathway in both monocytes and macrophages, inducing the secretion of pro-inflammatory cytokines, which may in turn contribute to increase the permeability of the blood brain barrier. The present study brought evidence that S. suis MVs may play a role as a virulence factor in the pathogenesis of S. suis infections, and given their composition be an excellent candidate for vaccine development.

  19. Degradation of pharmaceuticals from membrane biological reactor sludge with Trametes versicolor.

    Science.gov (United States)

    Llorens-Blanch, Guillem; Badia-Fabregat, Marina; Lucas, Daniel; Rodriguez-Mozaz, Sara; Barceló, Damià; Pennanen, Taina; Caminal, Gloria; Blánquez, Paqui

    2015-02-01

    Emerging contaminants are a wide group of chemical products that are found at low concentrations in the environment. These contaminants can be either natural, e.g., estrogens, or synthetics, such as pesticides and pharmaceuticals, which can enter the environment through the water and sludge from wastewater treatment plants (WWTP). The growth of Trametes versicolor on membrane biological reactor (MBR) sludge in bioslurry systems at the Erlenmeyer scale was assessed and its capacity for removing pharmaceutical and personal care products (PPCPs) was evaluated. The ability of the fungus to remove hydrochlorothiazide (HZT) from liquid media cultures was initially assessed. Consequently, different bioslurry media (complete nutrient, glucose and no-nutrient addition) and conditions (sterile and non-sterile) were tested, and the removal of spiked HZT was monitored under each condition. The highest spiked HZT removal was assessed under non-sterile conditions without nutrient addition (93.2%). Finally, the removal assessment of a broad set of pharmaceuticals was performed in non-spiked bioslurry. Under non-sterile conditions, the fungus was able to completely degrade 12 out of the 28 drugs initially detected in the MBR sludge, achieving an overall degradation of 66.9%. Subsequent microbial analysis showed that the microbial diversity increased after 15 days of treatment, but there was still some T. versicolor in the bioslurry. Results showed that T. versicolor can be used to remove PPCPs in bioslurry systems under non-sterile conditions, without extra nutrients in the media, and in matrices as complex as an MBR sludge.

  20. The performance of double layer structure membrane prepared from flowing coagulant

    Science.gov (United States)

    Mieow Kee, Chan; Xeng, Anthony Leong Chan; Regal, Sasiskala; Singh, Balvinder; Raoo, Preeshaath; Koon Eu, Yap; Sok Choo, Ng

    2017-12-01

    Membrane with double layer structure is favourable as it exhibits smooth surface and macrovoids free structure. However, its’ performance in terms of permeability, porosity and strength has not been studied thoroughly. Additionally, the effect of flowing coagulant on the formation of double layer membrane has not been reported. Thus, the objective of this study is to investigate the performance of double layer membranes, which were prepared using flowing coagulant. Results showed that when the coagulant flow changed from laminar to turbulent, the pure water permeation of the membrane increased. It was due to the higher porosity in the membrane, which prepared by turbulent flow (CA-Turbulent) compared to the membrane which fabricated under laminar condition (CA-Laminar). This can be explained by the rapid solvent-coagulant exchange rate between the polymer solution and the turbulent coagulant. In term of strength, the tensile strength of the CA-Turbulent was ~32 MPa, which was 100% higher compared to CA-Laminar. This may due to the presence of large amount of nodules on its surface, which reduced the surface integrity. In conclusion, flowing coagulant altered the membrane properties and adopting turbulent coagulant flow in membrane fabrication would improve the porosity, surface roughness and the strength of the membrane.

  1. Structural and morphological changes in supramolecular-structured polymer electrolyte membrane fuel cell on addition of phosphoric acid

    Science.gov (United States)

    Hendrana, S.; Pryliana, R. F.; Natanael, C. L.; Rahayu, I.

    2018-03-01

    Phosphoric acid is one agents used in membrane fuel cell to modify ionic conductivity. Therefore, its distribution in membrane is a key parameter to gain expected conductivity. Efforts have been made to distribute phosphoric acid in a supramolecular-structured membrane prepared with a matrix. To achieve even distribution across bulk of the membrane, the inclusion of the polyacid is carried out under pressurized chamber. Image of scanning electron microscopy (SEM) shows better phosphoric acid distribution for one prepared in pressurized state. It also leads in better performing in ionic conductivity. Moreover, data from differential scanning calorimetry (DSC) indicate that the addition of phosphoric acid is prominent in the change of membrane structure, while morphological changes are captured in SEM images.

  2. Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures

    Energy Technology Data Exchange (ETDEWEB)

    Pykäläinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Peränen, Johan; Vihinen, Helena; Jokitalo, Eija; Salminen, Marjo; Ikonen, Elina; Dominguez, Roberto; Lappalainen, Pekka (Helsinki); (Penn)

    2013-05-29

    Bin/amphipysin/Rvs (BAR)-domain proteins sculpt cellular membranes and have key roles in processes such as endocytosis, cell motility and morphogenesis. BAR domains are divided into three subfamilies: BAR- and F-BAR-domain proteins generate positive membrane curvature and stabilize cellular invaginations, whereas I-BAR-domain proteins induce negative curvature and stabilize protrusions. We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane tubulation but promotes the formation of planar membrane sheets. Structural and mutagenesis analyses reveal that the BAR domain of Pinkbar has a relatively flat lipid-binding interface and that it assembles into sheet-like oligomers in crystals and in solution, which may explain its unique membrane-deforming activity.

  3. Donnan dialysis as membrane process for nitrate removal from drinking water: Membrane structure effect

    Directory of Open Access Journals (Sweden)

    S. Ben Hamouda

    2017-02-01

    Full Text Available Nitrates are extremely soluble in water and are considered as the renown pollutants of natural water and water table. Removing them through AMX, AM3, and RPA anion exchange membranes has been studied under donnan dialysis conditions as a function of concentration, pH and the nature of the feed phase. It was observed that the AMX membrane gives the highest nitrate transport efficiency and that the optimal concentration in the selected zone was in 6.2 g/L (0.1 M with 37.9%. It was also observed that the best pH for the concentration of 0.62 g/L is pH 10 with yield of 23%. Results are evaluated by the yield calculated with nitrates concentration detected by molecular absorption spectrometry in 212 nm.

  4. Outer Hair Cell Lateral Wall Structure Constrains the Mobility of Plasma Membrane Proteins.

    Science.gov (United States)

    Yamashita, Tetsuji; Hakizimana, Pierre; Wu, Siva; Hassan, Ahmed; Jacob, Stefan; Temirov, Jamshid; Fang, Jie; Mellado-Lagarde, Marcia; Gursky, Richard; Horner, Linda; Leibiger, Barbara; Leijon, Sara; Centonze, Victoria E; Berggren, Per-Olof; Frase, Sharon; Auer, Manfred; Brownell, William E; Fridberger, Anders; Zuo, Jian

    2015-09-01

    Nature's fastest motors are the cochlear outer hair cells (OHCs). These sensory cells use a membrane protein, Slc26a5 (prestin), to generate mechanical force at high frequencies, which is essential for explaining the exquisite hearing sensitivity of mammalian ears. Previous studies suggest that Slc26a5 continuously diffuses within the membrane, but how can a freely moving motor protein effectively convey forces critical for hearing? To provide direct evidence in OHCs for freely moving Slc26a5 molecules, we created a knockin mouse where Slc26a5 is fused with YFP. These mice and four other strains expressing fluorescently labeled membrane proteins were used to examine their lateral diffusion in the OHC lateral wall. All five proteins showed minimal diffusion, but did move after pharmacological disruption of membrane-associated structures with a cholesterol-depleting agent and salicylate. Thus, our results demonstrate that OHC lateral wall structure constrains the mobility of plasma membrane proteins and that the integrity of such membrane-associated structures are critical for Slc26a5's active and structural roles. The structural constraint of membrane proteins may exemplify convergent evolution of cellular motors across species. Our findings also suggest a possible mechanism for disorders of cholesterol metabolism with hearing loss such as Niemann-Pick Type C diseases.

  5. Outer Hair Cell Lateral Wall Structure Constrains the Mobility of Plasma Membrane Proteins.

    Directory of Open Access Journals (Sweden)

    Tetsuji Yamashita

    2015-09-01

    Full Text Available Nature's fastest motors are the cochlear outer hair cells (OHCs. These sensory cells use a membrane protein, Slc26a5 (prestin, to generate mechanical force at high frequencies, which is essential for explaining the exquisite hearing sensitivity of mammalian ears. Previous studies suggest that Slc26a5 continuously diffuses within the membrane, but how can a freely moving motor protein effectively convey forces critical for hearing? To provide direct evidence in OHCs for freely moving Slc26a5 molecules, we created a knockin mouse where Slc26a5 is fused with YFP. These mice and four other strains expressing fluorescently labeled membrane proteins were used to examine their lateral diffusion in the OHC lateral wall. All five proteins showed minimal diffusion, but did move after pharmacological disruption of membrane-associated structures with a cholesterol-depleting agent and salicylate. Thus, our results demonstrate that OHC lateral wall structure constrains the mobility of plasma membrane proteins and that the integrity of such membrane-associated structures are critical for Slc26a5's active and structural roles. The structural constraint of membrane proteins may exemplify convergent evolution of cellular motors across species. Our findings also suggest a possible mechanism for disorders of cholesterol metabolism with hearing loss such as Niemann-Pick Type C diseases.

  6. Uniform Structure of Eukaryotic Plasma Membrane: Lateral Domains in Plants

    Czech Academy of Sciences Publication Activity Database

    Malínská, Kateřina; Zažímalová, Eva

    2011-01-01

    Roč. 12, č. 2 (2011), s. 148-155 ISSN 1389-2037 R&D Projects: GA MŠk(CZ) LC06034 Institutional research plan: CEZ:AV0Z50380511 Keywords : Plasma membrane * microdomains * lateral segregation Subject RIV: ED - Physiology Impact factor: 2.886, year: 2011

  7. Probing water structure and transport in proton exchange membranes

    NARCIS (Netherlands)

    Ling, X.

    2018-01-01

    Proton exchange membrane fuel cells (PEMFCs) have attracted tremendous attention as alternative energy sources because of their high energy density and practically zero greenhouse gas emission - water is their only direct by-product. Critical to the function of PEMFCs is fast proton and water

  8. Molecular mechanisms of acetylcholine receptor-lipid interactions: from model membranes to human biology.

    Science.gov (United States)

    Baenziger, John E; daCosta, Corrie J B

    2013-03-01

    Lipids are potent modulators of the Torpedo nicotinic acetylcholine receptor. Lipids influence nicotinic receptor function by allosteric mechanisms, stabilizing varying proportions of pre-existing resting, open, desensitized, and uncoupled conformations. Recent structures reveal that lipids could alter function by modulating transmembrane α-helix/α-helix packing, which in turn could alter the conformation of the allosteric interface that links the agonist-binding and transmembrane pore domains-this interface is essential in the coupling of agonist binding to channel gating. We discuss potential mechanisms by which lipids stabilize different conformational states in the context of the hypothesis that lipid-nicotinic receptor interactions modulate receptor function at biological synapses.

  9. Structural basis for the membrane association of ankyrinG via palmitoylation

    Science.gov (United States)

    Fujiwara, Yuichiro; Kondo, Hiroko X.; Shirota, Matsuyuki; Kobayashi, Megumi; Takeshita, Kohei; Nakagawa, Atsushi; Okamura, Yasushi; Kinoshita, Kengo

    2016-04-01

    By clustering various ion channels and transporters, ankyrin-G (AnkG) configures the membrane-excitation platforms in neurons and cardiomyocytes. AnkG itself localizes to specific areas on the plasma membrane via s-palmitoylation of Cys. However, the structural mechanism by which AnkG anchors to the membrane is not understood. In this study, we solved the crystal structures of the reduced and oxidized forms of the AnkG s-palmitoylation domain and used multiple long-term coarse-grained molecular dynamics simulations to analyze their membrane association. Here we report that the membrane anchoring of AnkG was facilitated by s-palmitoylation, defining a stable binding interface on the lipid membrane, and that AnkG without s-palmitoylation also preferred to stay near the membrane but did not have a unique binding interface. This suggests that AnkG in the juxtamembrane region is primed to accept lipid modification at Cys, and once that happens AnkG constitutes a rigid structural base upon which a membrane-excitation platform can be assembled.

  10. Investigation of biological and fouling characteristics of submerged membrane bioreactor process for wastewater treatment by model sensitivity analysis.

    Science.gov (United States)

    Cho, J W; Ahn, K H; Lee, Y H; Lim, B R; Kim, J Y

    2004-01-01

    In this study, a mathematical model for the submerged membrane bioreactor (SMBR) was developed. The activated sludge model No. 1 (ASM1) was modified to be suitable for describing the characteristics of the SMBR, and the resistance-in-series model was integrated into the ASM1 to describe membrane fouling. Using the newly developed model, the biological and fouling characteristics of the submerged membrane bioreactor process for wastewater treatment was investigated by sensitivity analysis. The sensitivity of effluent COD and nitrogen, TSS in the reactor and membrane flux with respect to each parameter (K(h), mu(H), K(S), K(NHH), K(NOH), b(H), Y(H), mu(A), K(NHA), b(A), Y(A), K(m) and alpha) was investigated by model simulation. As a result, the most important factors affecting membrane fouling were hydrolysis rate constant (K(h)) and cross-flow effect coefficient (K(m)). Heterotrophic yield coefficient (Y(H)) had a great influence on effluent quality. Effluent quality was also somewhat sensitive to K(h). Peculiar operating conditions of the SMBR such as long solids retention time (SRT), absolute retention of solids by membrane and high biomass concentration in bioreactor could explain these model simulation results. The model developed in this study would be very helpful to optimize operating conditions as well as design parameters for a SMBR system.

  11. Structural Characterization of Outer Membrane Components of the Type IV Pili System in Pathogenic Neisseria

    NARCIS (Netherlands)

    Jain, Samta; Moscicka, Katarzyna B.; Bos, Martine P.; Pachulec, Emilia; Stuart, Marc C. A.; Keegstra, Wilko; Boekema, Egbert J.; van der Does, Chris; B. Mościcka, K.; Ahmed, Niyaz

    2011-01-01

    Structures of the type IV pili secretin complexes from Neisseria gonorrhoeae and Neisseria meningitidis, embedded in outer membranes were investigated by transmission electron microscopy. Single particle averaging revealed additional domains not observed previously. Secretin complexes of N.

  12. Paramyxovirus membrane fusion: Lessons from the F and HN atomic structures

    International Nuclear Information System (INIS)

    Lamb, Robert A.; Paterson, Reay G.; Jardetzky, Theodore S.

    2006-01-01

    Paramyxoviruses enter cells by fusion of their lipid envelope with the target cell plasma membrane. Fusion of the viral membrane with the plasma membrane allows entry of the viral genome into the cytoplasm. For paramyxoviruses, membrane fusion occurs at neutral pH, but the trigger mechanism that controls the viral entry machinery such that it occurs at the right time and in the right place remains to be elucidated. Two viral glycoproteins are key to the infection process-an attachment protein that varies among different paramyxoviruses and the fusion (F) protein, which is found in all paramyxoviruses. For many of the paramyxoviruses (parainfluenza viruses 1-5, mumps virus, Newcastle disease virus and others), the attachment protein is the hemagglutinin/neuraminidase (HN) protein. In the last 5 years, atomic structures of paramyxovirus F and HN proteins have been reported. The knowledge gained from these structures towards understanding the mechanism of viral membrane fusion is described

  13. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    Science.gov (United States)

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-11-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

  14. Neutron scattering applications in structural biology: now and the future

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J. [Los Alamos National Lab., NM (United States)

    1996-05-01

    Neutrons have an important role to play in structural biology. Neutron crystallography, small-angle neutron scattering and inelastic neutron scattering techniques all contribute unique information on biomolecular structures. In particular, solution scattering techniques give critical information on the conformations and dispositions of the components of complex assemblies under a wide variety of relevant conditions. The power of these methods is demonstrated here by studies of protein/DNA complexes, and Ca{sup 2+}-binding proteins complexed with their regulatory targets. In addition, we demonstrate the utility of a new structural approach using neutron resonance scattering. The impact of biological neutron scattering to date has been constrained principally by the available fluxes at neutron sources and the true potential of these approaches will only be realized with the development of new more powerful neutron sources. (author)

  15. Structural Diversity and Biological Activities of Cyclic Depsipeptides from Fungi

    Directory of Open Access Journals (Sweden)

    Xiaohan Wang

    2018-01-01

    Full Text Available Cyclic depsipeptides (CDPs are cyclopeptides in which amide groups are replaced by corresponding lactone bonds due to the presence of a hydroxylated carboxylic acid in the peptide structure. These peptides sometimes display additional chemical modifications, including unusual amino acid residues in their structures. This review highlights the occurrence, structures and biological activities of the fungal CDPs reported until October 2017. About 352 fungal CDPs belonging to the groups of cyclic tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, and tridecadepsipeptides have been isolated from fungi. These metabolites are mainly reported from the genera Acremonium, Alternaria, Aspergillus, Beauveria, Fusarium, Isaria, Metarhizium, Penicillium, and Rosellina. They are known to exhibit various biological activities such as cytotoxic, phytotoxic, antimicrobial, antiviral, anthelmintic, insecticidal, antimalarial, antitumoral and enzyme-inhibitory activities. Some CDPs (i.e., PF1022A, enniatins and destruxins have been applied as pharmaceuticals and agrochemicals.

  16. Synthesis and structural characterization of a mimetic membrane-anchored prion protein

    OpenAIRE

    Hicks, M R; Gill, A C; Bath, I K; Rullay, A K; Sylvester, I D; Crout, D H; Pinheiro, T J T

    2006-01-01

    During pathogenesis of transmissible spongiform encephalopathies (TSEs) an abnormal form (PrPSc) of the host encoded prion protein (PrPC) accumulates in insoluble fibrils and plaques. The two forms of PrP appear to have identical covalent structures, but differ in secondary and tertiary structure. Both PrPC and PrPSc have glycosylphospatidylinositol (GPI) anchors through which the protein is tethered to cell membranes. Membrane attachment has been suggested to play a role in the conversion of...

  17. Building bridges between cellular and molecular structural biology.

    Science.gov (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  18. Biologically inspired autonomous structural materials with controlled toughening and healing

    Science.gov (United States)

    Garcia, Michael E.; Sodano, Henry A.

    2010-04-01

    The field of structural health monitoring (SHM) has made significant contributions in the field of prognosis and damage detection in the past decade. The advantageous use of this technology has not been integrated into operational structures to prevent damage from propagating or to heal injured regions under real time loading conditions. Rather, current systems relay this information to a central processor or human operator, who then determines a course of action such as altering the mission or scheduling repair maintenance. Biological systems exhibit advanced sensory and healing traits that can be applied to the design of material systems. For instance, bone is the major structural component in vertebrates; however, unlike modern structural materials, bone has many properties that make it effective for arresting the propagation of cracks and subsequent healing of the fractured area. The foremost goal for the development of future adaptive structures is to mimic biological systems, similar to bone, such that the material system can detect damage and deploy defensive traits to impede damage from propagating, thus preventing catastrophic failure while in operation. After sensing and stalling the propagation of damage, the structure must then be repaired autonomously using self healing mechanisms motivated by biological systems. Here a novel autonomous system is developed using shape memory polymers (SMPs), that employs an optical fiber network as both a damage detection sensor and a network to deliver stimulus to the damage site initiating adaptation and healing. In the presence of damage the fiber optic fractures allowing a high power laser diode to deposit a controlled level of thermal energy at the fractured sight locally reducing the modulus and blunting the crack tip, which significantly slows the crack growth rate. By applying a pre-induced strain field and utilizing the shape memory recovery effect, thermal energy can be deployed to close the crack and return

  19. Ultrafiltration of biologically treated domestic wastewater: How membrane properties influence performance

    KAUST Repository

    Filloux, Emmanuelle

    2014-09-01

    In this study, the impact of membrane properties on membrane fouling and permeate water quality was investigated. Short- and long-term laboratory scale experiments using four commercially available hollow fiber UF membranes were performed to study the impact of membrane properties on reversible and irreversible fouling. No significant differences in terms of permeate quality (i.e. biopolymer rejection) were observed over the four tested membranes. It was found that membrane characteristics including pore size, pore distribution and especially materials had a strong impact on the filtration performances in terms of both reversible and irreversible fouling. The short-term filtration tests showed that due to its specific hydrodynamic condition only the inside-out mode UF membrane was subjected to irreversible fouling. These data demonstrate the importance of membrane selection with appropriate operating conditions for optimum performances. The added value of membrane characterization to lab-scale filtration tests for membrane performance was discussed. © 2014 Elsevier B.V. All rights reserved.

  20. Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase.

    Science.gov (United States)

    Barreras, Máximo; Salinas, Silvina R; Abdian, Patricia L; Kampel, Matías A; Ielpi, Luis

    2008-09-05

    Xanthomonas campestris GumK (beta-1,2-glucuronosyltransferase) is a 44-kDa membrane-associated protein that is involved in the biosynthesis of xanthan, an exopolysaccharide crucial for this bacterium's phytopathogenicity. Xanthan also has many important industrial applications. The GumK enzyme is the founding member of the glycosyltransferase family 70 of carbohydrate-active enzymes, which is composed of bacterial glycosyltransferases involved in exopolysaccharide synthesis. No x-ray structures have been reported for this family. To better understand the mechanism of action of the bacterial glycosyltransferases in this family, the x-ray crystal structure of apo-GumK was solved at 1.9 angstroms resolution. The enzyme has two well defined Rossmann domains with a catalytic cleft between them, which is a typical feature of the glycosyltransferase B superfamily. Additionally, the crystal structure of GumK complexed with UDP was solved at 2.28 angstroms resolution. We identified a number of catalytically important residues, including Asp157, which serves as the general base in the transfer reaction. Residues Met231, Met273, Glu272, Tyr292, Met306, Lys307, and Gln310 interact with UDP, and mutation of these residues affected protein activity both in vitro and in vivo. The biological and structural data reported here shed light on the molecular basis for donor and acceptor selectivity in this glycosyltransferase family. These results also provide a rationale to obtain new polysaccharides by varying residues in the conserved alpha/beta/alpha structural motif of GumK.

  1. From protons to OXPHOS supercomplexes and Alzheimer's disease: structure-dynamics-function relationships of energy-transducing membranes.

    Science.gov (United States)

    Seelert, H; Dani, D N; Dante, S; Hauss, T; Krause, F; Schäfer, E; Frenzel, M; Poetsch, A; Rexroth, S; Schwassmann, H J; Suhai, T; Vonck, J; Dencher, N A

    2009-06-01

    By the elucidation of high-resolution structures the view of the bioenergetic processes has become more precise. But in the face of these fundamental advances, many problems are still unresolved. We have examined a variety of aspects of energy-transducing membranes from large protein complexes down to the level of protons and functional relevant picosecond protein dynamics. Based on the central role of the ATP synthase for supplying the biological fuel ATP, one main emphasis was put on this protein complex from both chloroplast and mitochondria. In particular the stoichiometry of protons required for the synthesis of one ATP molecule and the supramolecular organisation of ATP synthases were examined. Since formation of supercomplexes also concerns other complexes of the respiratory chain, our work was directed to unravel this kind of organisation, e.g. of the OXPHOS supercomplex I(1)III(2)IV(1), in terms of structure and function. Not only the large protein complexes or supercomplexes work as key players for biological energy conversion, but also small components as quinones which facilitate the transfer of electrons and protons. Therefore, their location in the membrane profile was determined by neutron diffraction. Physico-chemical features of the path of protons from the generators of the electrochemical gradient to the ATP synthase, as well as of their interaction with the membrane surface, could be elucidated by time-resolved absorption spectroscopy in combination with optical pH indicators. Diseases such as Alzheimer's dementia (AD) are triggered by perturbation of membranes and bioenergetics as demonstrated by our neutron scattering studies.

  2. Membrane Characterization by Microscopic and Scattering Methods: Multiscale Structure

    Directory of Open Access Journals (Sweden)

    Philippe Moulin

    2011-04-01

    Full Text Available Several microscopic and scattering techniques at different observation scales (from atomic to macroscopic were used to characterize both surface and bulk properties of four new flat-sheet polyethersulfone (PES membranes (10, 30, 100 and 300 kDa and new 100 kDa hollow fibers (PVDF. Scanning Electron Microscopy (SEM with “in lens” detection was used to obtain information on the pore sizes of the skin layers at the atomic scale. White Light Interferometry (WLI and Atomic Force Microscopy (AFM using different scales (for WLI: windows: 900 × 900 µm2 and 360 × 360 µm2; number of points: 1024; for AFM: windows: 50 × 50 µm2 and 5 × 5 µm2; number of points: 512 showed that the membrane roughness increases markedly with the observation scale and that there is a continuity between the different scan sizes for the determination of the RMS roughness. High angular resolution ellipsometric measurements were used to obtain the signature of each cut-off and the origin of the scattering was identified as coming from the membrane bulk.

  3. NOVEL NANOCOMPOSITE MEMBRANE STRUCTURES FOR H2 SEPARATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Benny D. Freeman

    2005-03-31

    This report explores possible methods of improving CO{sub 2} selectivity in polymer based membranes. The first method investigated using basic nanoparticles to enhance the solubility of acid gases in nanocomposite membranes, thus enhancing the overall acid gas/light gas selectivity (e.g., CO{sub 2}/H{sub 2}, CO{sub 2}/CH{sub 4}, etc.). The influence of nanoparticle surface chemistry on nanocomposite morphology and transport properties will be determined experimentally in a series of poly(1-trimethylsilyl-1-propyne). Additional factors (e.g., chemical reaction of the particles with the polymers) have been considered, as necessary, during the course of the investigation. The second method investigated using polar polymers such as crosslinked poly(ethylene oxide) and poly(ether-b-amide) to improve CO{sub 2} sorption and thereby increase CO{sub 2} permeability and CO{sub 2}/light gas selectivity. For both types of materials, CO{sub 2} and light gas permeabilities have been characterized. The overall objective was to improve the understanding of materials design strategies to improve acid gas transport properties of membranes.

  4. Databases, Repositories, and Other Data Resources in Structural Biology.

    Science.gov (United States)

    Zheng, Heping; Porebski, Przemyslaw J; Grabowski, Marek; Cooper, David R; Minor, Wladek

    2017-01-01

    Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

  5. Biochar composite membrane for high performance pollutant management: Fabrication, structural characteristics and synergistic mechanisms.

    Science.gov (United States)

    Ghaffar, Abdul; Zhu, Xiaoying; Chen, Baoliang

    2018-02-01

    Biochar, a natural sourced carbon-rich material, has been used commonly in particle shape for carbon sequestration, soil fertility and environmental remediation. Here, we report a facile approach to fabricate freestanding biochar composite membranes for the first time. Wood biochars pyrolyzed at 300 °C and 700 °C were blended with polyvinylidene fluoride (PVdF) in three percentages (10%, 30% and 50%) to construct membranes through thermal phase inversion process. The resultant biochar composite membranes possess high mechanical strength and porous structure with uniform distribution of biochar particles throughout the membrane surface and cross-section. The membrane pure water flux was increased with B300 content (4825-5411 ± 21 L m -2 h -1 ) and B700 content (5823-6895 ± 72 L m -2 h -1 ). The membranes with B300 were more hydrophilic with higher surface free energy (58.84-60.31 mJ m -2 ) in comparison to B700 (56.32-51.91 mJ m -2 ). The biochar composite membranes indicated promising adsorption capacities (47-187 mg g -1 ) to Rhodamine B (RhB) dye. The biochar membranes also exhibited high retention (74-93%) for E. coli bacterial suspensions through filtration. After simple physical cleaning, both the adsorption and sieving capabilities of the biochar composite membranes could be effectively recovered. Synergistic mechanisms of biochar/PVdF in the composite membrane are proposed to elucidate the high performance of the membrane in pollutant management. The multifunctional biochar composite membrane not only effectively prevent the problems caused by directly using biochar particle as sorbent but also can be produced in large scale, indicating great potential for practical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Properties and in vitro biological evaluation of nano-hydroxyapatite/chitosan membranes for bone guided regeneration

    Energy Technology Data Exchange (ETDEWEB)

    Cheng Xianmiao [Research Center for Nano-Biomaterials, Analytical and Testing Center, Sichuan University, 610064 Chengdu (China); Department of Chemistry, Sichuan University, 610064 Chengdu (China); Li Yubao [Research Center for Nano-Biomaterials, Analytical and Testing Center, Sichuan University, 610064 Chengdu (China)], E-mail: nic7504@scu.edu.cn; Zuo Yi; Zhang Li [Research Center for Nano-Biomaterials, Analytical and Testing Center, Sichuan University, 610064 Chengdu (China); Li Jidong [Research Center for Nano-Biomaterials, Analytical and Testing Center, Sichuan University, 610064 Chengdu (China); Department of Chemistry, Sichuan University, 610064 Chengdu (China); Wang Huanan [Research Center for Nano-Biomaterials, Analytical and Testing Center, Sichuan University, 610064 Chengdu (China)

    2009-01-01

    Nano-hydroxyapatite(n-HA)/chitosan(CS) composite membranes were prepared by solvent casting and evaporation methods for the function of guided bone regeneration (GBR). The effect of n-HA content and solvent evaporation temperature on the properties of the composite membranes was studied. The n-HA/CS membranes were analyzed by scanning electron microscopy, Fourier transformed infrared spectroscopy, X-ray diffraction, swelling measurement, mechanical test, cell culture and MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenylte-2H-tetrazolium bromide) assay. The results show that the surface roughness and micropores of the composite membranes increase with the rise of n-HA content, suitable for adhesion, crawl and growth of cells. The hydroxyapatite holds nano size and distributes uniformly in the composite membranes. Chemical bond interaction exists between Ca ions and -OH groups of n-HA and -NH{sub 2} or -OH groups of CS. The n-HA content and solvent evaporation temperature have obvious influence on the swelling ratio, tensile strength and elongation rate of the composite membranes. Cell culture and MTT assays show that n-HA and its content can affect the proliferation of cells. The n-HA/CS composite membranes have no negative effect on the cell morphology, viability and proliferation and possess good biocompatibility. This study makes the n-HA/CS composite membrane be a prospective biodegradable GBR membrane for future applications.

  7. Three-dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication.

    Science.gov (United States)

    Romero-Brey, Inés; Merz, Andreas; Chiramel, Abhilash; Lee, Ji-Young; Chlanda, Petr; Haselman, Uta; Santarella-Mellwig, Rachel; Habermann, Anja; Hoppe, Simone; Kallis, Stephanie; Walther, Paul; Antony, Claude; Krijnse-Locker, Jacomine; Bartenschlager, Ralf

    2012-01-01

    All positive strand RNA viruses are known to replicate their genomes in close association with intracellular membranes. In case of the hepatitis C virus (HCV), a member of the family Flaviviridae, infected cells contain accumulations of vesicles forming a membranous web (MW) that is thought to be the site of viral RNA replication. However, little is known about the biogenesis and three-dimensional structure of the MW. In this study we used a combination of immunofluorescence- and electron microscopy (EM)-based methods to analyze the membranous structures induced by HCV in infected cells. We found that the MW is derived primarily from the endoplasmic reticulum (ER) and contains markers of rough ER as well as markers of early and late endosomes, COP vesicles, mitochondria and lipid droplets (LDs). The main constituents of the MW are single and double membrane vesicles (DMVs). The latter predominate and the kinetic of their appearance correlates with kinetics of viral RNA replication. DMVs are induced primarily by NS5A whereas NS4B induces single membrane vesicles arguing that MW formation requires the concerted action of several HCV replicase proteins. Three-dimensional reconstructions identify DMVs as protrusions from the ER membrane into the cytosol, frequently connected to the ER membrane via a neck-like structure. In addition, late in infection multi-membrane vesicles become evident, presumably as a result of a stress-induced reaction. Thus, the morphology of the membranous rearrangements induced in HCV-infected cells resemble those of the unrelated picorna-, corona- and arteriviruses, but are clearly distinct from those of the closely related flaviviruses. These results reveal unexpected similarities between HCV and distantly related positive-strand RNA viruses presumably reflecting similarities in cellular pathways exploited by these viruses to establish their membranous replication factories.

  8. The synthesis of recombinant membrane proteins in yeast for structural studies.

    Science.gov (United States)

    Routledge, Sarah J; Mikaliunaite, Lina; Patel, Anjana; Clare, Michelle; Cartwright, Stephanie P; Bawa, Zharain; Wilks, Martin D B; Low, Floren; Hardy, David; Rothnie, Alice J; Bill, Roslyn M

    2016-02-15

    Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets. This review focuses on methods that are available for protein production in yeast, which is an important source of recombinant eukaryotic membrane proteins. We provide an overview of approaches to optimize the expression plasmid, host cell and culture conditions, as well as the extraction and purification of functional protein for crystallization trials in preparation for structural studies. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Biological nitrogen removal from plating wastewater by submerged membrane bioreactor packed with granular sulfur.

    Science.gov (United States)

    Moon, Jinyoung; Hwang, Yongwoo; Kim, Junbeum; Kwak, Inho

    Recent toughened water quality standards have necessitated improvements for existing sewer treatment facilities through advanced treatment processes. Therefore, an advanced treatment process that can be installed through simple modification of existing sewer treatment facilities needs to be developed. In this study, a new submerged membrane bioreactor process packed with granular sulfur (MBR-GS) was developed and operated to determine the biological nitrogen removal behaviors of plating wastewater containing a high concentration of NO3(-). Continuous denitrification was carried out at various nitrogen loading rates at 20 °C using synthetic wastewater, which was comprised of NO3(-) and HCO3(-), and actual plating wastewater, which was collected from the effluent water of a plating company called 'H Metals'. High-rate denitrification in synthetic plating wastewater was accomplished at 0.8 kg NO3(-)-N/m(3)·day at a nitrogen loading rate of 0.9 kg NO3(-)-N/m(3)·day. The denitrification rate further increased in actual plating wastewater to 0.91 kg NO3(-)-N/m(3)·day at a nitrogen loading rate of 1.11 kg NO3(-)-N/m(3)·day. Continuous filtration was maintained for up to 30 days without chemical cleaning with a transmembrane pressure in the range of 20 cmHg. Based on stoichiometry, SO4(2-) production and alkalinity consumption could be calculated theoretically. Experimental alkalinity consumption was lower than the theoretical value. This newly proposed MBR-GS process, capable of high-rate nitrogen removal by compulsive flux, is expected to be applicable as an alternative renovation technique for nitrogen treatment of plating wastewater as well as municipal wastewater with a low C/N ratio.

  10. Modeling of the axon membrane skeleton structure and implications for its mechanical properties.

    Directory of Open Access Journals (Sweden)

    Yihao Zhang

    2017-02-01

    Full Text Available Super-resolution microscopy recently revealed that, unlike the soma and dendrites, the axon membrane skeleton is structured as a series of actin rings connected by spectrin filaments that are held under tension. Currently, the structure-function relationship of the axonal structure is unclear. Here, we used atomic force microscopy (AFM to show that the stiffness of the axon plasma membrane is significantly higher than the stiffnesses of dendrites and somata. To examine whether the structure of the axon plasma membrane determines its overall stiffness, we introduced a coarse-grain molecular dynamics model of the axon membrane skeleton that reproduces the structure identified by super-resolution microscopy. Our proposed computational model accurately simulates the median value of the Young's modulus of the axon plasma membrane determined by atomic force microscopy. It also predicts that because the spectrin filaments are under entropic tension, the thermal random motion of the voltage-gated sodium channels (Nav, which are bound to ankyrin particles, a critical axonal protein, is reduced compared to the thermal motion when spectrin filaments are held at equilibrium. Lastly, our model predicts that because spectrin filaments are under tension, any axonal injuries that lacerate spectrin filaments will likely lead to a permanent disruption of the membrane skeleton due to the inability of spectrin filaments to spontaneously form their initial under-tension configuration.

  11. Membrane fusion

    DEFF Research Database (Denmark)

    Bendix, Pól Martin

    2015-01-01

    At Stanford University, Boxer lab, I worked on membrane fusion of small unilamellar lipid vesicles to flat membranes tethered to glass surfaces. This geometry closely resembles biological systems in which liposomes fuse to plasma membranes. The fusion mechanism was studied using DNA zippering...... between complementary strands linked to the two apposing membranes closely mimicking the zippering mechanism of SNARE fusion complexes....

  12. Membrane proteins: functional and structural studies using reconstituted proteoliposomes and 2-D crystals

    Directory of Open Access Journals (Sweden)

    Rigaud J.-L.

    2002-01-01

    Full Text Available Reconstitution of membrane proteins into lipid bilayers is a powerful tool to analyze functional as well as structural areas of membrane protein research. First, the proper incorporation of a purified membrane protein into closed lipid vesicles, to produce proteoliposomes, allows the investigation of transport and/or catalytic properties of any membrane protein without interference by other membrane components. Second, the incorporation of a large amount of membrane proteins into lipid bilayers to grow crystals confined to two dimensions has recently opened a new way to solve their structure at high resolution using electron crystallography. However, reconstitution of membrane proteins into functional proteoliposomes or 2-D crystallization has been an empirical domain, which has been viewed for a long time more like "black magic" than science. Nevertheless, in the last ten years, important progress has been made in acquiring knowledge of lipid-protein-detergent interactions and has permitted to build upon a set of basic principles that has limited the empirical approach of reconstitution experiments. Reconstitution strategies have been improved and new strategies have been developed, facilitating the success rate of proteoliposome formation and 2-D crystallization. This review deals with the various strategies available to obtain proteoliposomes and 2-D crystals from detergent-solubilized proteins. It gives an overview of the methods that have been applied, which may be of help for reconstituting more proteins into lipid bilayers in a form suitable for functional studies at the molecular level and for high-resolution structural analysis.

  13. Modeling and analysis of modular structure in diverse biological networks.

    Science.gov (United States)

    Al-Anzi, Bader; Gerges, Sherif; Olsman, Noah; Ormerod, Christopher; Piliouras, Georgios; Ormerod, John; Zinn, Kai

    2017-06-07

    Biological networks, like most engineered networks, are not the product of a singular design but rather are the result of a long process of refinement and optimization. Many large real-world networks are comprised of well-defined and meaningful smaller modules. While engineered networks are designed and refined by humans with particular goals in mind, biological networks are created by the selective pressures of evolution. In this paper, we seek to define aspects of network architecture that are shared among different types of evolved biological networks. First, we developed a new mathematical model, the Stochastic Block Model with Path Selection (SBM-PS) that simulates biological network formation based on the selection of edges that increase clustering. SBM-PS can produce modular networks whose properties resemble those of real networks. Second, we analyzed three real networks of very different types, and showed that all three can be fit well by the SBM-PS model. Third, we showed that modular elements within the three networks correspond to meaningful biological structures. The networks chosen for analysis were a proteomic network composed of all proteins required for mitochondrial function in budding yeast, a mesoscale anatomical network composed of axonal connections among regions of the mouse brain, and the connectome of individual neurons in the nematode C. elegans. We find that the three networks have common architectural features, and each can be divided into subnetworks with characteristic topologies that control specific phenotypic outputs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Membrane dish analysis: A summary of structural and optical analysis capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Steele, C.R.; Balch, C.D.; Jorgensen, G.J.; Wendelin, T.; Lewandowski, A.

    1991-11-01

    Research at SERI within the Department of Energy`s Solar Thermal Technology Program has focused on the development of membrane dish concentrators for space and terrestrial power applications. As potentially lightweight, inexpensive, high-performance structures, they are excellent candidates for space-deployable energy sources as well as cost-effective terrestrial energy concepts. A thorough engineering research treatment of these types of structures consists primarily of two parts: (1) structural mechanics of the membrane and ring support and (2) analysis and characterization of the concentrator optical performance. It is important to understand the effects of the membrane`s structure and support system on the optical performance of the concentrator. This requires an interface between appropriate structural and optical models. Until recently, such models and the required interface have not existed. This report documents research that has been conducted at SERI in this area. It is a compilation of several papers describing structural models of membrane dish structures and optical models used to predict dish concentrator optical and thermal performance. The structural models were developed under SERI subcontract by Dr. Steele and Dr. Balch of Stanford University. The optical model was developed in-house by SERI staff. In addition, the interface between the models is described. It allows easy and thorough characterization of membrane dish systems from the mechanics to the resulting optical performance. The models described herein have been and continue to be extremely useful to SERI, industry, and universities involved with the modeling and analysis of lightweight membrane concentrators for solar thermal applications.

  15. Structure refinement and membrane positioning of selectively labeled OmpX in phospholipid nanodiscs

    Energy Technology Data Exchange (ETDEWEB)

    Hagn, Franz, E-mail: franz.hagn@tum.de; Wagner, Gerhard, E-mail: gerhard-wagner@hms.harvard.edu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2015-04-15

    NMR structural studies on membrane proteins are often complicated by their large size, taking into account the contribution of the membrane mimetic. Therefore, classical resonance assignment approaches often fail. The large size of phospholipid nanodiscs, a detergent-free phospholipid bilayer mimetic, prevented their use in high-resolution solution-state NMR spectroscopy so far. We recently introduced smaller nanodiscs that are suitable for NMR structure determination. However, side-chain assignments of a membrane protein in nanodiscs still remain elusive. Here, we utilized a NOE-based approach to assign (stereo-) specifically labeled Ile, Leu, Val and Ala methyl labeled and uniformly {sup 15}N-Phe and {sup 15}N-Tyr labeled OmpX and calculated a refined high-resolution structure. In addition, we were able to obtain residual dipolar couplings (RDCs) of OmpX in nanodiscs using Pf1 phage medium for the induction of weak alignment. Back-calculated NOESY spectra of the obtained NMR structures were compared to experimental NOESYs in order to validate the quality of these structures. We further used NOE information between protonated lipid head groups and side-chain methyls to determine the position of OmpX in the phospholipid bilayer. These data were verified by paramagnetic relaxation enhancement (PRE) experiments obtained with Gd{sup 3+}-modified lipids. Taken together, this study emphasizes the need for the (stereo-) specific labeling of membrane proteins in a highly deuterated background for high-resolution structure determination, particularly in large membrane mimicking systems like phospholipid nanodiscs. Structure validation by NOESY back-calculation will be helpful for the structure determination and validation of membrane proteins where NOE assignment is often difficult. The use of protein to lipid NOEs will be beneficial for the positioning of a membrane protein in the lipid bilayer without the need for preparing multiple protein samples.

  16. The potential for biological structure determination with pulsed neutrons

    International Nuclear Information System (INIS)

    Wilson, C.C.

    1994-01-01

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed

  17. Molecular aspects of GAPR-1 interactions with biological and model membranes

    NARCIS (Netherlands)

    van Galen, J.

    2008-01-01

    Golgi-Associated Plant Pathogenesis-Related protein 1 (GAPR-1) is a mammalian protein that belongs to the superfamily of plant pathogenesis related proteins group 1 (PR-1). It is a peripheral membrane protein that strongly associates with the cytosolic leaflet of Golgi membranes and is enriched in

  18. Influence of the membrane structure plan shape on the displacements under point load

    Directory of Open Access Journals (Sweden)

    Milošević Vuk S.

    2016-01-01

    Full Text Available Deformations of membrane structures under external loads are much more prominent compared to other structures and structural materials. External area loads cause large displacements and redistribution of internal tension forces. Point loads have a less significant impact on changes of internal forces, but a more significant role in creation of local deformations. Previous researches have shown the influence of position and intensity of point loads on the deformations of membrane structures. The aim of this research is to investigate the influence of plan shape of the membrane structure on the displacements under point load. The influence of rhombic shaped plans with different diagonal lengths and ratios is explored. The research is conducted on numerical models in the specialized software Sofistik. Models are loaded with point loads in the point where diagonals intersect and the results are compared.

  19. Molecular biology of Neisseria meningitidis class 5 and H. 8 outer membrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Kawula, T.H.

    1987-01-01

    One of the surface structures responsible for inter- and intrastrain antigenic variability in meningococci is the heat-modifiable class 5 (C.5) protein. Neisseria meningitidis strain FAM18 (a meningococcal disease isolate) expressed two different C.5 proteins (C.5a and C.5b) identifiable by sodium dodecyl sulfate polyacrylamide gel electrophoresis. We generated two monoclonal antibodies (MAbs), each specific for one of the identified C.5 proteins. The MAbs, which were bactericidal for variants expressing the appropriate C.5 protein, were used to study C.5 expression changes in FAM18. The H.8 protein is an antigenically conserved outer membrane protein expressed almost exclusively by the pathogenic Neisseria. We have cloned and sequenced an H.8 gene from N. meningitidis FAM18. The predicted H.8 amino acid sequence indicated that the most probable signal peptide processing site matched the consensus prokaryotic lipoprotein processing/modification sequence. We then showed that the H.8 protein could be labeled with {sup 14}C-palmitic acid, confirming that H.8 was a lipoprotein. Processing of the H.8 protein was inhibited by globomycin in E. coli indicating that H.8 was modified by the described lipoprotein processing/modifying pathway described in both gram negative and gram positive genera.

  20. Synthesis, crystal structure and biological activity of novel diester cyclophanes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Pengfei; Yang, Bingqin; Fang, Xianwen; Cheng, Zhao; Yang, Meipan, E-mail: yangbq@nwu.edu.cn [Department of Chemistry, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, Northwest University, Shaanxi (China)

    2012-10-15

    A series of novel diester cyclophanes was synthesized by esterification of 1,2-benzenedicarbonyl chloride with eight different diols under high dilution conditions. The structures of the compounds were verified by elemental analysis, {sup 1}H nuclear magnetic resonance (NMR), IR spectroscopy and high resolution mass spectrometry (HRMS). The crystal structures of two compounds were characterized by single crystal X-ray diffractometry (XRD). All the new cyclophanes were evaluated for biological activities and the results showed that some of these compounds have low antibacterial or antifungal activities (author)

  1. Robust hydrophobic polyurethane fibrous membranes with tunable porous structure for waterproof and breathable application

    Science.gov (United States)

    Gu, Jiatai; Gu, Haihong; Cao, Jin; Chen, Shaojie; Li, Ni; Xiong, Jie

    2018-05-01

    In this work, novel nanofibrous membranes with waterproof and breathable (W&B) performance were successfully fabricated by the combination of electrospinning and surface modification technology. This fibrous membranes consisted of polyurethane (PU), NaCl, and fluoroalkylsilane (FAS). Firstly, The fibrous construction and porous structure of fibrous membranes were regulated by tuning the NaCl concentrations in PU solutions. Then, the obtained PU/NaCl fibrous membranes were further modified with fluoroalkylsilane (FAS) to improve hydrophobic property. The synergistic effect of porous structure and hydrophobicity on waterproof and breathable performance was investigated. Furthermore, the mechanical property of fibrous membranes was deeply analysed on the basis of macromolecule orientation and adhesive structure. Benefiting from the optimized porous structure and hydrophobic modification, the resultant fibrous membranes exhibited excellent waterproof (hydrostatic pressure of 1261 Mbar), breathable (water vapor transmission (WVT) rate of 9.06 kg m-2 d-1 and air permeability of 4.8 mm s-1) performance, as well as high tensile strength (breakage stress of 10.4 MPa), suggesting a promising candidate for various applications, especially in protective clothing.

  2. Depolarization affects lateral microdomain structure of yeast plasma membrane

    Czech Academy of Sciences Publication Activity Database

    Herman, P.; Večeř, J.; Opekarová, Miroslava; Veselá, Petra; Jančíková, I.; Zahumenský, J.; Malínský, Jan

    2015-01-01

    Roč. 282, č. 3 (2015), s. 419-434 ISSN 1742-464X R&D Projects: GA ČR GAP205/12/0720 Institutional support: RVO:68378041 Keywords : gel microdomains * lipid order * transmembrane potential Subject RIV: EA - Cell Biology Impact factor: 4.237, year: 2015

  3. J D Bernal and the genesis of structural biology

    International Nuclear Information System (INIS)

    Caffrey, Martin

    2007-01-01

    I was invited to participate in this Symposium a month or so before the event. At that time however, I knew little about J D Bernal. I vaguely remembered a brief conversation on the topic over a decade ago with Professor Vittorio Luzzati as we ambled around the gardens at the Palace of Varsailles. Vittorio likely knew Bernal through his friend Rosalind Franklin who worked with Bernal at Birbeck College. But beyond that I knew nothing about the man or his science. And so it was most fortunate that Andrew Brown's book J D Bernal: The Sage of Science appeared in 2005 and I was able to call on it. Indeed, much of the material included in this chapter is based on that source and on Dorothy Hodgkin's biographic memoir of J D Bernal, her postgraduate supervisor. Given that this chapter is to be published in a Physics journal I thought it appropriate to provide some background to the theme of my presentation, structural biology. Accordingly, I will begin with an introduction to proteins, one of structural biology's central characters, and to which Bernal devoted much energy and attention. How the molecular structure of a protein determines its activity and function will then be described. Bernal's major contribution in this area was to X-ray crystallography, the primary method by which a protein's structure is determined. The method, and aspects of its development, will be described. I will also make reference to some of Bernal's additional contributions in related fields. Finally, Vincent Casey, the symposium organizer, asked that I comment on how structural biology might impact on society. I will attempt to address that at the close of my presentation

  4. Reconstitutions of mitochondrial inner membrane remodeling.

    Science.gov (United States)

    Barbot, Mariam; Meinecke, Michael

    2016-10-01

    Biological membranes exhibit function-related shapes, leading to a plethora of complex and beautiful cell and cell organellar morphologies. Most if not all of these structures have evolved for a particular physiological reason. The shapes of these structures are formed by physical forces that operate on membranes. To create particular shaped cells and cell organelles, membranes must undergo deformations which are determined by the structure and elasticity of the membrane and this process is most probable driven by proteins, lipids and/or interplay of both Zimmerberg and Kozlov (2006). Therefore, an important question of current cell biology in conjunction with physics and mathematics is to elucidate the functional cause for these different membrane morphologies as well as how they are formed. One of the most peculiar membrane shapes is observed in mitochondria. These organelles are surrounded by two membranes and especially the convoluted inner membrane displays a complex ultra-structure. A molecular understanding of how this membrane is shaped is missing to a large extent. Unlike membrane remodeling in classical curvature-dependent processes like clathrin-mediated endocytosis, mitochondria are most likely shaped by integral membrane proteins. Following, we will review the current knowledge of inner mitochondrial membrane architecture and discuss recent findings and advances in understanding the factors that shape this membrane. We will address pending questions especially with regard to the experimentally challenging nature of investigating membrane bending by hydrophobic integral membrane proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. High-resolution Structures of Protein-Membrane Complexes by Neutron Reflection and MD Simulation: Membrane Association of the PTEN Tumor Suppressor

    Science.gov (United States)

    Lösche, Matthias

    2012-02-01

    The lipid matrix of biomembranes is an in-plane fluid, thermally and compositionally disordered leaflet of 5 nm thickness and notoriously difficult to characterize in structural terms. Yet, biomembranes are ubiquitous in the cell, and membrane-bound proteins are implicated in a variety of signaling pathways and intra-cellular transport. We developed methodology to study proteins associated with model membranes using neutron reflection measurements and showed recently that this approach can resolve the penetration depth and orientation of membrane proteins with ångstrom resolution if their crystal or NMR structure is known. Here we apply this technology to determine the membrane bindung and unravel functional details of the PTEN phosphatase, a key player in the PI3K apoptosis pathway. PTEN is an important regulatory protein and tumor suppressor that performs its phosphatase activity as an interfacial enzyme at the plasma membrane-cytoplasm boundary. Acting as an antagonist to phosphoinositide-3-kinase (PI3K) in cell signaling, it is deleted in many human cancers. Despite its importance in regulating the levels of the phosphoinositoltriphosphate PI(3,4,5)P3, there is little understanding of how PTEN binds to membranes, is activated and then acts as a phosphatase. We investigated the structure and function of PTEN by studying its membrane affinity and localization on in-plane fluid, thermally disordered synthetic membrane models. The membrane association of the protein depends strongly on membrane composition, where phosphatidylserine (PS) and phosphatidylinositol diphosphate (PI(4,5)P2) act synergetically in attracting the enzyme to the membrane surface. Membrane affinities depend strongly on membrane fluidity, which suggests multiple binding sites on the protein for PI(4,5)P2. Neutron reflection measurements show that the PTEN phosphatase ``scoots'' along the membrane surface (penetration PTEN's regulatory C-terminal tail is displaced from the membrane and

  6. Effects of temperature on structure and mechanical properties of alkanethiol coated gold nanoparticle membranes

    Science.gov (United States)

    Salerno, K. Michael; Grest, Gary

    2015-03-01

    Single-nanoparticle-thick membranes have a variety of potential uses due to unique mechanical properties. While these membranes have been studied experimentally and computationally at 300K, the effects of thermal annealing on structure and properties have not been investigated. We present atomistic molecular dynamics simulations that study the effects of temperature on nanoparticle membrane properties. Nanoparticles are made of a gold core coated with organic oligomer ligands. At high grafting density, ligands with CH3 end groups exhibit local crystallinity at 300K while those with COOH end groups orient to form dimers due to electrostatics. Both features influence membrane mechanical properties. As temperature increases ligand crystallinity and COOH affinity are disrupted, and mechanical strength is reduced. Immediately after cooling back to 300K, membranes are weaker and measures of ligand interdigitation and COOH affinity are reduced. Over time, interdigitation and end-group interactions rejuvenate and samples that undergo high-temperature annealing have mechanical properties comparable to the original membranes. The structure/property temperature dependence points to ways that membranes could be tailored for temperature-dependent/resistant properties. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.

  7. The JCSG high-throughput structural biology pipeline.

    Science.gov (United States)

    Elsliger, Marc André; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wooley, John; Wüthrich, Kurt; Wilson, Ian A

    2010-10-01

    The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications.

  8. Development of a stealth carrier system for structural studies of membrane proteins in solution

    DEFF Research Database (Denmark)

    Maric, Selma

    Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial carriers that mimic the native bilayer environment allows for the handling of membrane proteins in solution and enables the use of small-angle scattering techniques for fast...... which can be used for SANS structural analysis of membrane proteins in solution. In combination with the D2O/H2O-based contrast variation method it is demonstrated that it is possible to prepare specifically deuterated analogues of the nanodisc, which give minimal contribution to the neutron scattering...... data when used in 100% D2O. An important challenge in the project was obtaining selective partial deuteration of the nanodisc system necessary for the total matching at 100% D2O. This was achieved through an E. coli based biosynthesis for both deuterated phosphatidylcholines as well as membrane...

  9. Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering

    DEFF Research Database (Denmark)

    Midtgaard, Søren Roi; Darwish, Tamim A.; Pedersen, Martin Cramer

    2018-01-01

    A novel and generally applicable method for determining structures of membrane proteins in solution via small-angle neutron scattering (SANS) is presented. Common detergents for solubilizing membrane proteins were synthesized in isotope-substituted versions for utilizing the intrinsic neutron...... scattering length difference between hydrogen and deuterium. Individual hydrogen/deuterium levels of the detergent head and tail groups were achieved such that the formed micelles became effectively invisible in heavy water (D2 O) when investigated by neutrons. This way, only the signal from the membrane...... protein remained in the SANS data. We demonstrate that the method is not only generally applicable on five very different membrane proteins but also reveals subtle structural details about the sarco/endoplasmatic reticulum Ca2+ ATPase (SERCA). In all, the synthesis of isotope-substituted detergents makes...

  10. Spectrins: a structural platform for stabilization and activation of membrane channels, receptors and transporters.

    Science.gov (United States)

    Machnicka, Beata; Czogalla, Aleksander; Hryniewicz-Jankowska, Anita; Bogusławska, Dżamila M; Grochowalska, Renata; Heger, Elżbieta; Sikorski, Aleksander F

    2014-02-01

    This review focuses on structure and functions of spectrin as a major component of the membrane skeleton. Recent advances on spectrin function as an interface for signal transduction mediation and a number of data concerning interaction of spectrin with membrane channels, adhesion molecules, receptors and transporters draw a picture of multifaceted protein. Here, we attempted to show the current depiction of multitask role of spectrin in cell physiology. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Membrane fission by protein crowding.

    Science.gov (United States)

    Snead, Wilton T; Hayden, Carl C; Gadok, Avinash K; Zhao, Chi; Lafer, Eileen M; Rangamani, Padmini; Stachowiak, Jeanne C

    2017-04-18

    Membrane fission, which facilitates compartmentalization of biological processes into discrete, membrane-bound volumes, is essential for cellular life. Proteins with specific structural features including constricting rings, helical scaffolds, and hydrophobic membrane insertions are thought to be the primary drivers of fission. In contrast, here we report a mechanism of fission that is independent of protein structure-steric pressure among membrane-bound proteins. In particular, random collisions among crowded proteins generate substantial pressure, which if unbalanced on the opposite membrane surface can dramatically increase membrane curvature, leading to fission. Using the endocytic protein epsin1 N-terminal homology domain (ENTH), previously thought to drive fission by hydrophobic insertion, our results show that membrane coverage correlates equally with fission regardless of the hydrophobicity of insertions. Specifically, combining FRET-based measurements of membrane coverage with multiple, independent measurements of membrane vesiculation revealed that fission became spontaneous as steric pressure increased. Further, fission efficiency remained equally potent when helices were replaced by synthetic membrane-binding motifs. These data challenge the view that hydrophobic insertions drive membrane fission, suggesting instead that the role of insertions is to anchor proteins strongly to membrane surfaces, amplifying steric pressure. In line with these conclusions, even green fluorescent protein (GFP) was able to drive fission efficiently when bound to the membrane at high coverage. Our conclusions are further strengthened by the finding that intrinsically disordered proteins, which have large hydrodynamic radii yet lack a defined structure, drove fission with substantially greater potency than smaller, structured proteins.

  12. CO2 Permeability of Biological Membranes and Role of CO2 Channels

    Science.gov (United States)

    Endeward, Volker; Arias-Hidalgo, Mariela; Al-Samir, Samer; Gros, Gerolf

    2017-01-01

    We summarize here, mainly for mammalian systems, the present knowledge of (a) the membrane CO2 permeabilities in various tissues; (b) the physiological significance of the value of the CO2 permeability; (c) the mechanisms by which membrane CO2 permeability is modulated; (d) the role of the intracellular diffusivity of CO2 for the quantitative significance of cell membrane CO2 permeability; (e) the available evidence for the existence of CO2 channels in mammalian and artificial systems, with a brief view on CO2 channels in fishes and plants; and, (f) the possible significance of CO2 channels in mammalian systems. PMID:29064458

  13. Structure and properties of PVDF membrane with PES-C addition via thermally induced phase separation process

    Science.gov (United States)

    Wu, Lishun; Sun, Junfen

    2014-12-01

    Polyvinylidene fluoride (PVDF) membrane and PVDF membrane with phenolphthalein polyethersulfone (PES-C) addition were prepared via thermally induced phase separation (TIPS) method by using diphenyl carbonate (DPC) and dimethyl acetamide (DMAc) as mixed diluents. The effects of coagulation temperature and pre-evaporation time on structure and properties of membranes were studied. The changes of sewage flux in MBR and the attenuation coefficient of sewage flux were investigated. The resistance distributions of PVDF and PVDF/PES-C membranes were compared by resistance analysis. Membrane composition and structure were characterized by ATR-FTIR, TGA, SEM and AFM. The foulant on membranes was analyzed by FTIR. The contact angle of PVDF/PES-C membrane was lower than that of PVDF membrane. A thinner skin layer and a porous cellular support layer formed in PVDF/PES-C membrane and resulted in a higher porosity and pure water flux. The pure water flux and porosity of PVDF/PES-C membrane increased with rising coagulation temperature and decreased with extending pre-evaporation time. The flux attenuation coefficient, the cake layer resistance and internal fouling resistance of PVDF/PES-C membrane in MBR were smaller than those of PVDF membrane in MBR. The FTIR spectrum of foulant on membrane indicated that the foulant on PVDF/PES-C membrane was mostly composed of protein and polysaccharide, while the foulant on pure PVDF membrane included biopolymer clusters besides protein and polysaccharide.

  14. Spontaneous formation of complex structures made from elastic membranes in an aluminum-hydroxide-carbonate system

    Science.gov (United States)

    Kiehl, Micah; Kaminker, Vitaliy; Pantaleone, James; Nowak, Piotr; Dyonizy, Agnieszka; Maselko, Jerzy

    2015-06-01

    A popular playground for studying chemo-hydrodynamic patterns and instabilities is chemical gardens, also known as silicate gardens. In these systems, complex structures spontaneously form, driven by buoyant forces and either osmotic or mechanical pumps. Here, we report on systems that differ somewhat from classical chemical gardens in that the membranes are much more deformable and soluble. These properties lead to structures that self-construct and evolve in new ways. For example, they exhibit the formation of chemical balloons, a new growth mechanism for tubes, and also the homologous shrinking of these tubes. The stretching mechanism for the membranes is probably different than for other systems by involving membrane "self-healing." Other unusual properties are osmosis that sometimes occurs out of the structure and also small plumes that flow away from the structure, sometimes upwards, and sometimes downwards. Mathematical models are given that explain some of the observed phenomena.

  15. Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

    Science.gov (United States)

    Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

    2013-01-01

    Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

  16. Tensegrity I. Cell structure and hierarchical systems biology

    Science.gov (United States)

    Ingber, Donald E.

    2003-01-01

    In 1993, a Commentary in this journal described how a simple mechanical model of cell structure based on tensegrity architecture can help to explain how cell shape, movement and cytoskeletal mechanics are controlled, as well as how cells sense and respond to mechanical forces (J. Cell Sci. 104, 613-627). The cellular tensegrity model can now be revisited and placed in context of new advances in our understanding of cell structure, biological networks and mechanoregulation that have been made over the past decade. Recent work provides strong evidence to support the use of tensegrity by cells, and mathematical formulations of the model predict many aspects of cell behavior. In addition, development of the tensegrity theory and its translation into mathematical terms are beginning to allow us to define the relationship between mechanics and biochemistry at the molecular level and to attack the larger problem of biological complexity. Part I of this two-part article covers the evidence for cellular tensegrity at the molecular level and describes how this building system may provide a structural basis for the hierarchical organization of living systems--from molecule to organism. Part II, which focuses on how these structural networks influence information processing networks, appears in the next issue.

  17. Synthesis, structure and biological properties of active spirohydantoin derivatives

    Directory of Open Access Journals (Sweden)

    Lazić Anita M.

    2016-01-01

    Full Text Available Spirohidantoins represent an pharmacologically important class of heterocycles since many derivatives have been recognized that display interesting activities against a wide range of biological targets. First synthesis of cycloalkanespiro-5-hydantoins was performed by Bucherer and Lieb 1934 by the reaction of cycloalkanone, potassium cyanide and ammonium-carbonate at reflux in a mixture of ethanol and water. QSAR (Quantitative Structure-Activity Relationship studies showed that a wide range of biological activities of spirohydantoin derivatives strongly depend upon their structure. This paper describes different methods of synthesis of spirohydantoin derivatives, their physico-chemical properties and biological activity. It emphasizes the importance of cycloalkanespiro-5-hydantoins with anticonvulsant, antiproliferative, antipsychotic, antimicrobial and antiinflammatory properties as well as their importance in the treatment of diabetes. Numerous spirohydantoin compounds exhibit physiological activity such as serotonin and fibrinogen antagonist, inhibitors of the glycine binding site of the NMDA receptor also, antagonist of leukocyte cell adhesion, acting as allosteric inhibitors of the protein-protein interactions. Some spirohydantoin derivatives have been identified as antitumor agents. Their activity depends on the substituent presented at position N-3 of the hydantoin ring and increases in order alkene > ester > ether. Besides that, compounds that contain two electron withdrawing groups (e.g. fluorine or chlorine on the third and fourth position of the phenyl ring are better antitumor agents than compounds with a single electron withdrawing group. [Projekat Ministarstva nauke Republike Srbije, br. 172013

  18. Microbial community structure characteristics associated membrane fouling in A/O-MBR system.

    Science.gov (United States)

    Gao, Da-Wen; Wen, Zhi-Dan; Li, Bao; Liang, Hong

    2014-02-01

    The study demonstrated the potential relationship between microbial community structure and membrane fouling in an anoxic-oxic membrane bioreactor (A/O-MBR). The results showed that the microbial community structure in biocake was different with aerobic mixture, and the dominant populations were out of sync during the fouling process. Based on microbial community structure and metabolites analysis, the results showed that the succession of microbial community might be the leading factor to the variation of metabolites, and it might be the primary cause of membrane fouling. The rise of Shannon diversity index (H) of the microbial community in A/O-MBR went with the gradually serious membrane fouling. Pareto-Lorenz curve was used to describe the evenness of microbial distribution in A/O-MBR, and the result indicated when community evenness was low, the membrane fouling took place smoothly or slightly, otherwise, high evenness of microbial community would lead to more seriously membrane fouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers.

    Science.gov (United States)

    Dutta, Samit Kumar; Yao, Yong; Marassi, Francesca M

    2017-08-17

    Yersinia pestis the causative agent of plague, is highly pathogenic and poses very high risk to public health. The outer membrane protein Ail (Adhesion invasion locus) is one of the most highly expressed proteins on the cell surface of Y. pestis, and a major target for the development of medical countermeasures. Ail is essential for microbial virulence and is critical for promoting the survival of Y. pestis in serum. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but the protein's activity is influenced by the detergents in these samples, underscoring the importance of the surrounding environment for structure-activity studies. Here we describe the backbone structure of Ail, determined in lipid bilayer nanodiscs, using solution NMR spectroscopy. We also present solid-state NMR data obtained for Ail in membranes containing lipopolysaccharide (LPS), a major component of the bacterial outer membranes. The protein in lipid bilayers, adopts the same eight-stranded β-barrel fold observed in the crystalline and micellar states. The membrane composition, however, appears to have a marked effect on protein dynamics, with LPS enhancing conformational order and slowing down the 15 N transverse relaxation rate. The results provide information about the way in which an outer membrane protein inserts and functions in the bacterial membrane.

  20. Dawning of a new era in TRP channel structural biology by cryo-electron microscopy.

    Science.gov (United States)

    Madej, M Gregor; Ziegler, Christine M

    2018-02-01

    Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins. As one of the most important structural biology methods at present, cryo-EM was awarded in October 2017 with the Nobel Prize in Chemistry. The molecular understanding of Transient-Receptor-Potential (TRP) channels has been boosted tremendously by cryo-EM single-particle analysis. Several near-atomic and atomic structures gave important mechanistic insights, e.g., into ion permeation and selectivity, gating, as well as into the activation of this enigmatic and medically important membrane protein family by various chemical and physical stimuli. Lastly, these structures have set the starting point for the rational design of TRP channel-targeted therapeutics to counteract life-threatening channelopathies. Here, we attempt a brief introduction to the method, review the latest advances in cryo-EM structure determination of TRP channels, and discuss molecular insights into the channel function based on the wealth of TRP channel cryo-EM structures.

  1. Single-particle electron microscopy in the study of membrane protein structure.

    Science.gov (United States)

    De Zorzi, Rita; Mi, Wei; Liao, Maofu; Walz, Thomas

    2016-02-01

    Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Quantitative Modeling of Membrane Transport and Anisogamy by Small Groups Within a Large-Enrollment Organismal Biology Course

    Directory of Open Access Journals (Sweden)

    Eric S. Haag

    2016-12-01

    Full Text Available Quantitative modeling is not a standard part of undergraduate biology education, yet is routine in the physical sciences. Because of the obvious biophysical aspects, classes in anatomy and physiology offer an opportunity to introduce modeling approaches to the introductory curriculum. Here, we describe two in-class exercises for small groups working within a large-enrollment introductory course in organismal biology. Both build and derive biological insights from quantitative models, implemented using spreadsheets. One exercise models the evolution of anisogamy (i.e., small sperm and large eggs from an initial state of isogamy. Groups of four students work on Excel spreadsheets (from one to four laptops per group. The other exercise uses an online simulator to generate data related to membrane transport of a solute, and a cloud-based spreadsheet to analyze them. We provide tips for implementing these exercises gleaned from two years of experience.

  3. Structural Study and Modification of Support Layer for Forward Osmosis Membranes

    KAUST Repository

    Shi, Meixia

    2016-06-01

    Water scarcity is a serious global issue, due to the increasing population and developing economy, and membrane technology is an essential way to address this problem. Forward osmosis (FO) is an emerging membrane process, due to its low energy consumption (not considering the draw solute regeneration). A bottleneck to advance this technology is the design of the support layer for FO membranes to minimize the internal concentration polarization. In this dissertation, we focus on the structural study and modification of the support layer for FO membranes. Firstly, we digitally reconstruct different membrane morphologies in 3D and propose a method for predicting performance in ultrafiltration operations. Membranes with analogous morphologies are later used as substrate for FO membranes. Secondly, we experimentally apply substrates with different potentially suitable morphologies as an FO support layer. We investigate their FO performance after generating a selective polyamide layer on the top, by interfacial polymerization. Among the different substrates we include standard asymmetric porous membranes prepared from homopolymers, such as polysulfone. Additionally block copolymer membrane and Anodisc alumina membrane are chosen based on their exceptional structures, with cylindrical pores at least in part. 3D digitally reconstructed porous substrates, analogous to those investigated for ultrafiltration, are then used to model the performance in FO operation. Finally, we analyze the effect of intermediate layers between the porous substrate and the interfacial polymerized layer. We investigate two materials including chitosan and hydrogel. The main results are the following. Pore-scale modeling for digital membrane generation effectively predicts the velocity profile in different layers of the membrane and the performance in UF experiments. Flow simulations confirm the advantage of finger-like substrates over sponge-like ones, when high water permeance is sought

  4. Removal of selected nitrogenous heterocyclic compounds in biologically pretreated coal gasification wastewater (BPCGW) using the catalytic ozonation process combined with the two-stage membrane bioreactor (MBR).

    Science.gov (United States)

    Zhu, Hao; Han, Yuxing; Ma, Wencheng; Han, Hongjun; Ma, Weiwei

    2017-12-01

    Three identical anoxic-aerobic membrane bioreactors (MBRs) were operated in parallel for 300 consecutive days for raw (R 1 ), ozonated (R 2 ) and catalytic ozonated (R 3 ) biologically pretreated coal gasification wastewater (BPCGW) treatment. The results demonstrated that catalytic ozonation process (COP) applied asa pretreatment remarkably improved the performance of the unsatisfactory single MBR. The overall removal efficiencies of COD, NH 3 -N and TN in R 3 were 92.7%, 95.6% and 80.6%, respectively. In addition, typical nitrogenous heterocyclic compounds (NHCs) of quinoline, pyridine and indole were completely removed in the integrated process. Moreover, COP could alter sludge properties and reshape microbial community structure, thus delaying the occurrence of membrane fouling. Finally, the total cost for this integrated process was estimated to be lower than that of single MBR. The results of this study suggest that COP is a good option to enhance pollutants removal and alleviate membrane fouling in the MBR for BPCGW treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Structure and Biological Activity of Pathogen-like Synthetic Nanomedicines

    Science.gov (United States)

    Lőrincz, Orsolya; Tőke, Enikő R.; Somogyi, Eszter; Horkay, Ferenc; Chandran, Preethi; Douglas, Jack F.; Szebeni, János; Lisziewicz, Julianna

    2011-01-01

    Here we characterize the structure, stability and intracellular mode-of-action of DermaVir nanomedicine that is under clinical development for the treatment of HIV/AIDS. This nanomedicine is comprised of pathogen-like pDNA/PEIm nanoparticles (NPs) having the structure and function resembling spherical viruses that naturally evolved to deliver nucleic acids to the cells. Atomic force microscopy demonstrated spherical 100–200nm NPs with a smooth polymer surface protecting the pDNA in the core. Optical-absorption determined both the NP structural stability and biological activity relevant to their ability to escape from the endosome and release the pDNA at the nucleus. Salt, pH and temperature influence the nanomedicine shelf-life and intracellular stability. This approach facilitates the development of diverse polyplex nanomedicines where the delivered pDNA-expressed antigens induce immune responses to kill infected cells. PMID:21839051

  6. Correlation between Membrane Potential Responses and Tentacle Movement in the Dinoflagellate Noctiluca miliaris(Behavior Biology)

    OpenAIRE

    Kazunori, Oami; Institute of Biological Sciences, University of Tsukuba

    2004-01-01

    Membrane potential responses and tentacle movement of the marine dinoflagellate Noctiluca miliaris were recorded simultaneously and their time relationships were examined. The food-gathering tentacle of Noctiluca exhibited slow extension-flexion movements in association with the spontaneously recurring membrane potential responses termed the tentacle regulating potentials (TRPs). The flexion of the tentacle began during the slow depolarization of the TRPs. The rate of the flexion increased af...

  7. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    International Nuclear Information System (INIS)

    Rønnest, A. K.; Peters, G. H.; Hansen, F. Y.; Taub, H.; Miskowiec, A.

    2016-01-01

    Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic potential within phospholipid membranes imply an enormous electric field of 10 8 –10 9 V m −1 , which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential for DMPG bilayers and found ∼1 V (∼2 ⋅ 10 8 V m −1 ) when in the fluid phase with a monovalent counter-ion and ∼1.4 V (∼2.8 ⋅ 10 8 V m −1 ) when in the gel phase with a divalent counter-ion. The number of water molecules for a fully hydrated DMPG membrane has been estimated to be 9.7 molecules per lipid in the gel phase and 17.5 molecules in the fluid phase, considerably smaller than inferred experimentally for 1,2-dimyristoyl-sn-glycero-3

  8. Biological Activity of Blackcurrant Extracts (Ribes nigrum L. in Relation to Erythrocyte Membranes

    Directory of Open Access Journals (Sweden)

    Dorota Bonarska-Kujawa

    2014-01-01

    Full Text Available Compounds contained in fruits and leaves of blackcurrant (Ribes nigrum L. are known as agents acting preventively and therapeutically on the organism. The HPLC analysis showed they are rich in polyphenol anthocyanins in fruits and flavonoids in leaves, that have antioxidant activity and are beneficial for health. The aim of the research was to determine the effect of blackcurrant fruit and leaf extracts on the physical properties of the erythrocyte membranes and assess their antioxidant properties. The effect of the extracts on osmotic resistance, shape of erythrocytes and hemolytic and antioxidant activity of the extracts were examined with spectrophotometric methods. The FTIR investigation showed that extracts modify the erythrocyte membrane and protect it against free radicals induced by UV radiation. The results show that the extracts do not induce hemolysis and even protect erythrocytes against the harmful action of UVC radiation, while slightly strengthening the membrane and inducing echinocytes. The compounds contained in the extracts do not penetrate into the hydrophobic region, but bind to the membrane surface inducing small changes in the packing arrangement of the polar head groups of membrane lipids. The extracts have a high antioxidant activity. Their presence on the surface of the erythrocyte membrane entails protection against free radicals.

  9. Micro-buckling in the nanocomposite structure of biological materials

    Science.gov (United States)

    Su, Yewang; Ji, Baohua; Hwang, Keh-Chih; Huang, Yonggang

    2012-10-01

    Nanocomposite structure, consisting of hard mineral and soft protein, is the elementary building block of biological materials, where the mineral crystals are arranged in a staggered manner in protein matrix. This special alignment of mineral is supposed to be crucial to the structural stability of the biological materials under compressive load, but the underlying mechanism is not yet clear. In this study, we performed analytical analysis on the buckling strength of the nanocomposite structure by explicitly considering the staggered alignment of the mineral crystals, as well as the coordination among the minerals during the buckling deformation. Two local buckling modes of the nanostructure were identified, i.e., the symmetric mode and anti-symmetric mode. We showed that the symmetric mode often happens at large aspect ratio and large volume fraction of mineral, while the anti-symmetric happens at small aspect ratio and small volume fraction. In addition, we showed that because of the coordination of minerals with the help of their staggered alignment, the buckling strength of these two modes approached to that of the ideally continuous fiber reinforced composites at large aspect ratio given by Rosen's model, insensitive to the existing "gap"-like flaws between mineral tips. Furthermore, we identified a mechanism of buckling mode transition from local to global buckling with increase of aspect ratio, which was attributed to the biphasic dependence of the buckling strength on the aspect ratio. That is, for small aspect ratio, the local buckling strength is smaller than that of global buckling so that it dominates the buckling behavior of the nanocomposite; for comparatively larger aspect ratio, the local buckling strength is higher than that of global buckling so that the global buckling dominates the buckling behavior. We also found that the hierarchical structure can effectively enhance the buckling strength, particularly, this structural design enables

  10. Cryo-focused-ion-beam applications in structural biology.

    Science.gov (United States)

    Rigort, Alexander; Plitzko, Jürgen M

    2015-09-01

    The ability to precisely control the preparation of biological samples for investigations by electron cryo-microscopy is becoming increasingly important for ultrastructural imaging in biology. Precision machining instruments such as the focused ion beam microscope (FIB) were originally developed for applications in materials science. However, today we witness a growing use of these tools in the life sciences mainly due to their versatility, since they can be used both as manipulation and as imaging devices, when complemented with a scanning electron microscope (SEM). The advent of cryo-preparation equipment and accessories made it possible to pursue work on frozen-hydrated biological specimens with these two beam (FIB/SEM) instruments. In structural biology, the cryo-FIB can be used to site-specifically thin vitrified specimens for transmission electron microscopy (TEM) and tomography. Having control over the specimen thickness is a decisive factor for TEM imaging, as the thickness of the object under scrutiny determines the attainable resolution. Besides its use for TEM preparation, the FIB/SEM microscope can be additionally used to obtain three-dimensional volumetric data from biological specimens. The unique combination of an imaging and precision manipulation tool allows sequentially removing material with the ion beam and imaging the milled block faces by scanning with the electron beam, an approach known as FIB/SEM tomography. This review covers both fields of cryo-FIB applications: specimen preparation for TEM cryo-tomography and volume imaging by cryo-FIB/SEM tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Identification of glycan structure alterations on cell membrane proteins in desoxyepothilone B resistant leukemia cells.

    Science.gov (United States)

    Nakano, Miyako; Saldanha, Rohit; Göbel, Anja; Kavallaris, Maria; Packer, Nicolle H

    2011-11-01

    Resistance to tubulin-binding agents used in cancer is often multifactorial and can include changes in drug accumulation and modified expression of tubulin isotypes. Glycans on cell membrane proteins play important roles in many cellular processes such as recognition and apoptosis, and this study investigated whether changes to the glycan structures on cell membrane proteins occur when cells become resistant to drugs. Specifically, we investigated the alteration of glycan structures on the cell membrane proteins of human T-cell acute lymphoblastic leukemia (CEM) cells that were selected for resistance to desoxyepothilone B (CEM/dEpoB). The glycan profile of the cell membrane glycoproteins was obtained by sequential release of N- and O-glycans from cell membrane fraction dotted onto polyvinylidene difluoride membrane with PNGase F and β-elimination respectively. The released glycan alditols were analyzed by liquid chromatography (graphitized carbon)-electrospray ionization tandem MS. The major N-glycan on CEM cell was the core fucosylated α2-6 monosialo-biantennary structure. Resistant CEM/dEpoB cells had a significant decrease of α2-6 linked sialic acid on N-glycans. The lower α2-6 sialylation was caused by a decrease in activity of β-galactoside α2-6 sialyltransferase (ST6Gal), and decreased expression of the mRNA. It is clear that the membrane glycosylation of leukemia cells changes during acquired resistance to dEpoB drugs and that this change occurs globally on all cell membrane glycoproteins. This is the first identification of a specific glycan modification on the surface of drug resistant cells and the mechanism of this downstream effect on microtubule targeting drugs may offer a route to new interventions to overcome drug resistance.

  12. Molecular dynamics simulation studies of transmembrane transport of chemical components in Chinese herbs and the function of platycodin D in a biological membrane

    Directory of Open Access Journals (Sweden)

    Shufang Yang

    2017-04-01

    Conclusion: The Martini force field was successfully applied to the study of the interaction between herbal compounds and a biological membrane. By combining the dynamics equilibrium morphology, the distribution of drugs inside and outside the biomembrane, and the interaction sites of drugs on the DPPC bilayer, factors influencing transmembrane transport of drugs were elucidated and the function of platycodin D in a biological membrane was reproduced.

  13. Serial Femtosecond Crystallography Opens New Avenues for Structural Biology

    Science.gov (United States)

    Coe, Jesse; Fromme, Petra

    2016-01-01

    Free electron lasers (FELs) provide X-ray pulses in the femtosecond time domain with up to 1012 higher photon flux than synchrotrons and open new avenues for the determination of difficult to crystallize proteins, like large complexes and human membrane proteins. While the X-ray pulses are so strong that they destroy any solid material, the crystals diffract before they are destroyed. The most successful application of FELs for biology has been the method of serial femtosecond crystallography (SFX) where nano or microcrystals are delivered to the FEL beam in a stream of their mother liquid at room temperature, which ensures the replenishment of the sample before the next X-ray pulse arrives. New injector technology allows also for the delivery of crystal in lipidic cubic phases or agarose, which reduces the sample amounts for an SFX data set by two orders of magnitude. Time-resolved SFX also allows for analysis of the dynamics of biomolecules, the proof of principle being recently shown for light-induced reactions in photosystem II and photoactive yellow protein. An SFX data sets consist of thousands of single crystal snapshots in random orientations, which can be analyzed now “on the fly” by data analysis programs specifically developed for SFX, but de-novo phasing is still a challenge, that might be overcome by two-color experiments or phasing by shape transforms. PMID:26786767

  14. Review: Serial Femtosecond Crystallography: A Revolution in Structural Biology

    Science.gov (United States)

    Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

    2016-01-01

    Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

  15. Serial femtosecond crystallography: A revolution in structural biology.

    Science.gov (United States)

    Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

    2016-07-15

    Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. Published by Elsevier Inc.

  16. Exploring biological network structure with clustered random networks

    Directory of Open Access Journals (Sweden)

    Bansal Shweta

    2009-12-01

    Full Text Available Abstract Background Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions and the extent of clustering (the tendency for a set of three nodes to be interconnected are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics. Results Here we develop and implement a new Markov chain simulation algorithm to generate simple, connected random graphs that have a specified degree sequence and level of clustering, but are random in all other respects. The implementation of the algorithm (ClustRNet: Clustered Random Networks provides the generation of random graphs optimized according to a local or global, and relative or absolute measure of clustering. We compare our algorithm to other similar methods and show that ours more successfully produces desired network characteristics. Finding appropriate null models is crucial in bioinformatics research, and is often difficult, particularly for biological networks. As we demonstrate, the networks generated by ClustRNet can serve as random controls when investigating the impacts of complex network features beyond the byproduct of degree and clustering in empirical networks. Conclusion ClustRNet generates ensembles of graphs of specified edge structure and clustering. These graphs allow for systematic study of the impacts of connectivity and redundancies on network function and dynamics. This process is a key step in

  17. Structural models of the membrane anchors of envelope glycoproteins E1 and E2 from pestiviruses

    Science.gov (United States)

    Wang, Jimin; Li, Yue; Modis, Yorgo

    2014-01-01

    The membrane anchors of viral envelope proteins play essential roles in cell entry. Recent crystal structures of the ectodomain of envelope protein E2 from a pestivirus suggest that E2 belongs to a novel structural class of membrane fusion machinery. Based on geometric constraints from the E2 structures, we generated atomic models of the E1 and E2 membrane anchors using computational approaches. The E1 anchor contains two amphipathic perimembrane helices and one transmembrane helix; the E2 anchor contains a short helical hairpin stabilized in the membrane by an arginine residue, similar to flaviviruses. A pair of histidine residues in the E2 ectodomain may participate in pH sensing. The proposed atomic models point to Cys987 in E2 as the site of disulfide bond linkage with E1 to form E1–E2 heterodimers. The membrane anchor models provide structural constraints for the disulfide bonding pattern and overall backbone conformation of the E1 ectodomain. PMID:24725935

  18. Nonlinear Shell Modeling of Thin Membranes with Emphasis on Structural Wrinkling

    Science.gov (United States)

    Tessler, Alexander; Sleight, David W.; Wang, John T.

    2003-01-01

    Thin solar sail membranes of very large span are being envisioned for near-term space missions. One major design issue that is inherent to these very flexible structures is the formation of wrinkling patterns. Structural wrinkles may deteriorate a solar sail's performance and, in certain cases, structural integrity. In this paper, a geometrically nonlinear, updated Lagrangian shell formulation is employed using the ABAQUS finite element code to simulate the formation of wrinkled deformations in thin-film membranes. The restrictive assumptions of true membranes, i.e. Tension Field theory (TF), are not invoked. Two effective modeling strategies are introduced to facilitate convergent solutions of wrinkled equilibrium states. Several numerical studies are carried out, and the results are compared with recent experimental data. Good agreement is observed between the numerical simulations and experimental data.

  19. Tuning of Preparational Factors Affecting the Morphological Structure and Gas Separation Property of Asymmetric Polysulfone Membranes

    Science.gov (United States)

    Yuenyao, C.; Ruangdit, S.; Chittrakarn, T.

    2017-09-01

    The aim of this work was to study the effect of preparational factors such as solvent type, evaporation time (ET) and non-solvent additive, on the morphological structure, physical and gas separation properties of the prepared membrane samples by tuning of these parameters. Flat sheet asymmetric polysulfone (PSF) membranes were prepared by the dry/wet phase inversion process combined with the double coagulation bath method. The alteration of the prepared membranes were analyzed through scientific techniques such as Scanning Electron Microscope (SEM) and Dynamic Mechanical Thermal Analysis (DMTA). Furthermore, gas separation performance of membrane samples was measured in term of gas permeation and ideal selectivity of CO2/CH4. Experimental results showed that the change of preparational factors affected to the gas permeation of asymmetric PSF membranes. For example, the selective layer thickness increased with increasing of ET. This lead to increase significantly of ideal selectivity of CO2/CH4. The CO2/CH4 ideal selectivity was also increased with increase of ethanol (non-solvent additive) concentration in casting solution. In summary, the tuning of preparational factors affected to morphological structure, physical and gas separation properties of PSF membranes.

  20. A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions.

    Science.gov (United States)

    Rath, Emma M; Tessier, Dominique; Campbell, Alexander A; Lee, Hong Ching; Werner, Tim; Salam, Noeris K; Lee, Lawrence K; Church, W Bret

    2013-03-27

    Helical membrane proteins are vital for the interaction of cells with their environment. Predicting the location of membrane helices in protein amino acid sequences provides substantial understanding of their structure and function and identifies membrane proteins in sequenced genomes. Currently there is no comprehensive benchmark tool for evaluating prediction methods, and there is no publication comparing all available prediction tools. Current benchmark literature is outdated, as recently determined membrane protein structures are not included. Current literature is also limited to global assessments, as specialised benchmarks for predicting specific classes of membrane proteins were not previously carried out. We present a benchmark server at http://sydney.edu.au/pharmacy/sbio/software/TMH_benchmark.shtml that uses recent high resolution protein structural data to provide a comprehensive assessment of the accuracy of existing membrane helix prediction methods. The server further allows a user to compare uploaded predictions generated by novel methods, permitting the comparison of these novel methods against all existing methods compared by the server. Benchmark metrics include sensitivity and specificity of predictions for membrane helix location and orientation, and many others. The server allows for customised evaluations such as assessing prediction method performances for specific helical membrane protein subtypes.We report results for custom benchmarks which illustrate how the server may be used for specialised benchmarks. Which prediction method is the best performing method depends on which measure is being benchmarked. The OCTOPUS membrane helix prediction method is consistently one of the highest performing methods across all measures in the benchmarks that we performed. The benchmark server allows general and specialised assessment of existing and novel membrane helix prediction methods. Users can employ this benchmark server to determine the most

  1. Impact of the antimicrobial peptide Novicidin on membrane structure and integrity

    DEFF Research Database (Denmark)

    Nielsen, Søren B; Otzen, Daniel Erik

    2010-01-01

    We have studied the impact of an 18-residue cationic antimicrobial peptide Novicidin (Nc) on the structure and integrity of partially anionic lipid membranes using oriented circular dichroism (OCD), quartz crystal microbalance with dissipation (QCM-D), dual polarization interferometry (DPI......), calcein dye leakage and fluorescence spectroscopy. OCD consistently showed that Nc is bound in an alpha-helical, surface bound state over a range of peptide to lipid (P/L) ratios up to approximately 1:15. Realignment of Nc at higher P/L ratios correlates to loss of membrane integrity as shown by Laurdan...... concentration, probably through formation of transient pores or transient disruption of the membrane integrity, followed by more extensive membrane disintegration at higher P/L ratios....

  2. Electrokinetic migration across artificial liquid membranes. New concept for rapid sample preparation of biological fluids.

    Science.gov (United States)

    Pedersen-Bjergaard, Stig; Rasmussen, Knut Einar

    2006-03-24

    Basic drug substances were transported across a thin artificial organic liquid membrane by the application of 300 V d.c. From a 300 microl aqueous donor compartment (containing 10 mM HCl), the drugs migrated through a 200 microm artificial liquid membrane of 2-nitrophenyl octyl ether immobilized in the pores of a polypropylene hollow fiber, and into a 30 microl aqueous acceptor solution of 10 mM HCl inside the lumen of the hollow fiber. The transport was forced by an electrical potential difference sustained over the liquid membrane, resulting in electrokinetic migration of drug substances from the donor compartment to the acceptor solution. Within 5 min of operation at 300 V, pethidine, nortriptyline, methadone, haloperidol, and loperamide were extracted with recoveries in the range 70-79%, which corresponded to enrichments in the range 7.0-7.9. The chemical composition of the organic liquid membrane strongly affected the permeability, and may serve as an efficient tool for controlling the transport selectivity. Water samples, human plasma, and human urine were successfully processed, and in light of the present report, electrokinetic migration across thin artificial liquid membranes may be an interesting tool for future isolation within chemical analysis.

  3. Electrochemical properties of honeycomb-like structured HFBI self-organized membranes on HOPG electrodes.

    Science.gov (United States)

    Yamasaki, Ryota; Takatsuji, Yoshiyuki; Lienemann, Michael; Asakawa, Hitoshi; Fukuma, Takeshi; Linder, Markus; Haruyama, Tetsuya

    2014-11-01

    HFBI (derived from Trichoderma sp.) is a unique structural protein, which forms a self-organized monolayer at both air/water interface and water/solid interfaces in accurate two-dimensional ordered structures. We have taken advantage of the unique functionality of HFBI as a molecular carrier for preparation of ordered molecular phase on solid substrate surfaces. The HFBI molecular carrier can easily form ordered structures; however, the dense molecular layers form an electrochemical barrier between the electrode and solution phase. In this study, the electrochemical properties of HFBI self-organized membrane-covered electrodes were investigated. Wild-type HFBI has balanced positive and negative charges on its surface. Highly oriented pyrolytic graphite (HOPG) electrodes coated with HFBI molecules were investigated electrochemically. To improve the electrochemical properties of this HFBI-coated electrode, the two types of HFBI variants, with oppositely charged surfaces, were prepared genetically. All three types of HFBI-coated HOPG electrode perform electron transfer between the electrode and solution phase through the dense HFBI molecular layer. This is because the HFBI self-organized membrane has a honeycomb-like structure, with penetrating holes. In the cases of HFBI variants, the oppositely charged HFBI membrane phases shown opposite electrochemical behaviors in electrochemical impedance spectroscopy. HFBI is a molecule with a unique structure, and can easily form honeycomb-like structures on solid material surfaces such as electrodes. The molecular membrane phase can be used for electrochemical molecular interfaces. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Development of a stealth carrier system for structural studies of membrane proteins in solution

    DEFF Research Database (Denmark)

    Maric, Selma

    Structural studies of membrane proteins remain a great experimental challenge. Functional reconstitution into artificial carriers that mimic the native bilayer environment allows for the handling of membrane proteins in solution and enables the use of small-angle scattering techniques for fast...... and reliable structural analysis. The difficulty with this approach is that the carrier discs contribute to the measured scattering intensity in a highly non-trivial fashion, making subsequent data analysis challenging. This thesis presents the development of a specifically deuterated, stealth nanodisc system...

  5. Super-resolution optical microscopy for studying membrane structure and dynamics.

    Science.gov (United States)

    Sezgin, Erdinc

    2017-07-12

    Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.

  6. Natural Products at Work: Structural Insights into Inhibition of the Bacterial Membrane Protein MraY.

    Science.gov (United States)

    Koppermann, Stefan; Ducho, Christian

    2016-09-19

    Natural(ly) fit: The X-ray crystal structure of the bacterial membrane protein MraY in complex with its natural product inhibitor muraymycin D2 is discussed. MraY catalyzes one of the membrane-associated steps in peptidoglycan biosynthesis and, therefore, represents a promising target for novel antibiotics. Structural insights derived from the protein-inhibitor complex might now pave the way for the development of new antimicrobial drugs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Laser-matter structuration of optical and biological materials

    Energy Technology Data Exchange (ETDEWEB)

    Hallo, L., E-mail: hallo@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Mezel, C., E-mail: candice.mezel@cea.fr [CELIA, Universite Bordeaux 1 (France); CEA Le Ripault, 37260 Monts (France); Guillemot, F., E-mail: fabien.guillemot@inserm.fr [UMR 577 INSERM, Universite Bordeaux 2 (France); Chimier, B., E-mail: chimier@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Bourgeade, A., E-mail: antoine.bourgeade@cea.fr [CEA-CESTA, Le Barp (France); Regan, C., E-mail: regan@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Duchateau, G., E-mail: duchateau@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Souquet, A., E-mail: agnes.souquet@inserm.fr [UMR 577 INSERM, Universite Bordeaux 2 (France); Hebert, D., E-mail: david.hebert@cea.fr [CEA-CESTA, Le Barp (France)

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer In this study we model nanomaterial structuring. Black-Right-Pointing-Pointer The laser energy deposition is discussed first. Black-Right-Pointing-Pointer Full and approximate models are discussed. Black-Right-Pointing-Pointer Dynamic material response is addressed via hydrodynamics. Black-Right-Pointing-Pointer Sild effects are accounted for - Abstract: Interaction of ultrafast laser, i.e. from the femtosecond (fs) to the nanosecond (ns) regime, with initially transparent matter may produce very high energy density hot spots in the bulk as well as at the material surface, depending on focusing conditions. In the fs regime, absorption is due to ionisation of the dielectric, which enables absorption process to begin, and then hydrodynamic to take place. In the ns regime both absorption and hydrodynamic are coupled to each other, which complexifies considerably the comprehension but matter structuration looks similar. A numerical tool including solution of 3D Maxwell equations and a rate equation for free electrons is first compared to some available simple models of laser energy absorption. Then, subsequent material deformation, i.e. structuration, is determined by solving hydrodynamic equations, including or not solid behaviour. We show that nature of the final structures strongly depends on the amount of deposited energy and on the shape of the absorption zone. Then we address some problems related to laser-matter structuration of optical and biological materials in the fs, ps and ns regimes.

  8. Characterizing the structure of lipodisq nanoparticles for membrane protein spectroscopic studies.

    Science.gov (United States)

    Zhang, Rongfu; Sahu, Indra D; Liu, Lishan; Osatuke, Anna; Comer, Raven G; Dabney-Smith, Carole; Lorigan, Gary A

    2015-01-01

    Membrane protein spectroscopic studies are challenging due to the difficulty introduced in preparing homogenous and functional hydrophobic proteins incorporated into a lipid bilayer system. Traditional membrane mimics such as micelles or liposomes have proved to be powerful in solubilizing membrane proteins for biophysical studies, however, several drawbacks have limited their applications. Recently, a nanosized complex termed lipodisq nanoparticles was utilized as an alternative membrane mimic to overcome these caveats by providing a homogeneous lipid bilayer environment. Despite all the benefits that lipodisq nanoparticles could provide to enhance the biophysical studies of membrane proteins, structural characterization in different lipid compositions that closely mimic the native membrane environment is still lacking. In this study, the formation of lipodisq nanoparticles using different weight ratios of POPC/POPG lipids to SMA polymers was characterized via solid-state nuclear magnetic resonance (SSNMR) spectroscopy and dynamic light scattering (DLS). A critical weight ratio of (1/1.25) for the complete solubilization of POPC/POPG vesicles has been observed and POPC/POPG vesicles turned clear instantaneously upon the addition of the SMA polymer. The size of lipodisq nanoparticles formed from POPC/POPG lipids at this weight ratio of (1/1.25) was found to be about 30 nm in radius. We also showed that upon the complete solubilization of POPC/POPG vesicles by SMA polymers, the average size of the lipodisq nanoparticles is weight ratio dependent, when more SMA polymers were introduced, smaller lipodisq nanoparticles were obtained. The results of this study will be helpful for a variety of biophysical experiments when specific size of lipid disc is required. Further, this study will provide a proper path for researchers working on membrane proteins to obtain pertinent structure and dynamic information in a physiologically relevant membrane mimetic environment

  9. Data publication with the structural biology data grid supports live analysis

    NARCIS (Netherlands)

    Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung I.; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Fromme, J. Christopher; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercé; Sliz, Piotr

    2016-01-01

    Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology

  10. Development of miniaturized sorbent membrane funnel-based spray platform for biological analysis.

    Science.gov (United States)

    Yeung, Hoi Sze; Chen, Xiangfeng; Li, Wan; Wang, Ze; Wong, Y L Elaine; Chan, T-W Dominic

    2015-03-17

    In this work, a miniaturized solid-phase extraction (SPE) platform, called sorbent membrane funnel, which permits in situ cleanup prior to membrane funnel-based spray analysis was developed. The fabrication of funnel and the mounting of SPE sorbent were simple and straightforward by a homemade punching system. Using different sorbents, the SPE sorbent funnel has been successfully applied in spray analysis of drug molecules spiked in human plasma, trypsin digested solution of bovine serum albumin in the presence of high concentration of chaotropic reagents, and phosphopeptides in the tryptic digested solution of casein. The results demonstrated that SPE sorbent attached membrane funnels can be a useful tool in common metabolomic and proteomic applications.

  11. Sphingomyelinase D activity in model membranes: structural effects of in situ generation of ceramide-1-phosphate.

    Directory of Open Access Journals (Sweden)

    Roberto P Stock

    Full Text Available The toxicity of Loxosceles spider venom has been attributed to a rare enzyme, sphingomyelinase D, which transforms sphingomyelin to ceramide-1-phosphate. The bases of its inflammatory and dermonecrotic activity, however, remain unclear. In this work the effects of ceramide-1-phosphate on model membranes were studied both by in situ generation of this lipid using a recombinant sphingomyelinase D from the spider Loxosceles laeta and by pre-mixing it with sphingomyelin and cholesterol. The systems of choice were large unilamellar vesicles for bulk studies (enzyme kinetics, fluorescence spectroscopy and dynamic light scattering and giant unilamellar vesicles for fluorescence microscopy examination using a variety of fluorescent probes. The influence of membrane lateral structure on the kinetics of enzyme activity and the consequences of enzyme activity on the structure of target membranes containing sphingomyelin were examined. The findings indicate that: 1 ceramide-1-phosphate (particularly lauroyl ceramide-1-phosphate can be incorporated into sphingomyelin bilayers in a concentration-dependent manner and generates coexistence of liquid disordered/solid ordered domains, 2 the activity of sphingomyelinase D is clearly influenced by the supramolecular organization of its substrate in membranes and, 3 in situ ceramide-1-phosphate generation by enzymatic activity profoundly alters the lateral structure and morphology of the target membranes.

  12. Sphingomyelinase D activity in model membranes: structural effects of in situ generation of ceramide-1-phosphate.

    Science.gov (United States)

    Stock, Roberto P; Brewer, Jonathan; Wagner, Kerstin; Ramos-Cerrillo, Blanca; Duelund, Lars; Jernshøj, Kit Drescher; Olsen, Lars Folke; Bagatolli, Luis A

    2012-01-01

    The toxicity of Loxosceles spider venom has been attributed to a rare enzyme, sphingomyelinase D, which transforms sphingomyelin to ceramide-1-phosphate. The bases of its inflammatory and dermonecrotic activity, however, remain unclear. In this work the effects of ceramide-1-phosphate on model membranes were studied both by in situ generation of this lipid using a recombinant sphingomyelinase D from the spider Loxosceles laeta and by pre-mixing it with sphingomyelin and cholesterol. The systems of choice were large unilamellar vesicles for bulk studies (enzyme kinetics, fluorescence spectroscopy and dynamic light scattering) and giant unilamellar vesicles for fluorescence microscopy examination using a variety of fluorescent probes. The influence of membrane lateral structure on the kinetics of enzyme activity and the consequences of enzyme activity on the structure of target membranes containing sphingomyelin were examined. The findings indicate that: 1) ceramide-1-phosphate (particularly lauroyl ceramide-1-phosphate) can be incorporated into sphingomyelin bilayers in a concentration-dependent manner and generates coexistence of liquid disordered/solid ordered domains, 2) the activity of sphingomyelinase D is clearly influenced by the supramolecular organization of its substrate in membranes and, 3) in situ ceramide-1-phosphate generation by enzymatic activity profoundly alters the lateral structure and morphology of the target membranes.

  13. Integral Membrane Proteins and Bilayer Proteomics

    OpenAIRE

    Whitelegge, Julian P.

    2013-01-01

    Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary and quaternary structure, as well as the dynamics that accompany function...

  14. Integral membrane proteins and bilayer proteomics.

    Science.gov (United States)

    Whitelegge, Julian P

    2013-03-05

    Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary, and quaternary structures as well as the dynamics that accompany functional cycles and catalysis.

  15. Elastic membranes in confinement.

    Science.gov (United States)

    Bostwick, J B; Miksis, M J; Davis, S H

    2016-07-01

    An elastic membrane stretched between two walls takes a shape defined by its length and the volume of fluid it encloses. Many biological structures, such as cells, mitochondria and coiled DNA, have fine internal structure in which a membrane (or elastic member) is geometrically 'confined' by another object. Here, the two-dimensional shape of an elastic membrane in a 'confining' box is studied by introducing a repulsive confinement pressure that prevents the membrane from intersecting the wall. The stage is set by contrasting confined and unconfined solutions. Continuation methods are then used to compute response diagrams, from which we identify the particular membrane mechanics that generate mitochondria-like shapes. Large confinement pressures yield complex response diagrams with secondary bifurcations and multiple turning points where modal identities may change. Regions in parameter space where such behaviour occurs are then mapped. © 2016 The Author(s).

  16. Structures and physical properties of gaseous metal cationized biological ions.

    Science.gov (United States)

    Burt, Michael B; Fridgen, Travis D

    2012-01-01

    Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

  17. Physico-mechanical and structural properties of eggshell membrane gelatin- chitosan blend edible films

    DEFF Research Database (Denmark)

    Mohammadi, Reza; Mohammadifar, Mohammad Amin; Rouhi, Milad

    2018-01-01

    This study investigated the physico-mechanical and structural properties of composite edible films based on eggshell membrane gelatin (G) and chitosan (Ch) (75G:25Ch, 50G:50Ch, 25G:75Ch). The results demonstrated that the addition of Ch increased elongation at break significantly (p< 0.05), but r......This study investigated the physico-mechanical and structural properties of composite edible films based on eggshell membrane gelatin (G) and chitosan (Ch) (75G:25Ch, 50G:50Ch, 25G:75Ch). The results demonstrated that the addition of Ch increased elongation at break significantly (p... interactions introduced by the addition of chitosan to eggshell membrane gelatin as new resources could improve the films’ functional properties....

  18. Sphingomyelinase D activity in model membranes: structural effects of in situ generation of ceramide-1-phosphate

    DEFF Research Database (Denmark)

    Stock, Roberto; Brewer, Jonathan R.; Wagner, Kerstin

    2012-01-01

    The toxicity of Loxosceles spider venom has been attributed to a rare enzyme, sphingomyelinase D, which transforms sphingomyelin to ceramide-1-phosphate. The bases of its inflammatory and dermonecrotic activity, however, remain unclear. In this work the effects of ceramide-1-phosphate on model...... membranes were studied both by in situ generation of this lipid using a recombinant sphingomyelinase D from the spider Loxosceles laeta and by pre-mixing it with sphingomyelin and cholesterol. The systems of choice were large unilamellar vesicles for bulk studies (enzyme kinetics, fluorescence spectroscopy...... and dynamic light scattering) and giant unilamellar vesicles for fluorescence microscopy examination using a variety of fluorescent probes. The influence of membrane lateral structure on the kinetics of enzyme activity and the consequences of enzyme activity on the structure of target membranes containing...

  19. Unconventional transport routes of soluble and membrane proteins and their role in developmental biology

    Czech Academy of Sciences Publication Activity Database

    Pompa, A.; De Marchis, F.; Pallotta, M. T.; Benitez-Alfonso, Y.; Jones, A.; Schipper, K.; Moreau, K.; Žárský, Viktor; Di Sansebastiano, G. P.; Bellucci, M.

    2017-01-01

    Roč. 18, č. 4 (2017), č. článku 703. E-ISSN 1422-0067 Institutional support: RVO:61389030 Keywords : Autophagy * Exosomes * Intercellular channels * Leaderless proteins * Protein secretion * Trafficking mechanisms * Unconventional secretion Subject RIV: EA - Cell Biology OBOR OECD: Developmental biology Impact factor: 3.226, year: 2016

  20. Effect of non-solvent additives on the morphology, pore structure, and direct contact membrane distillation performance of PVDF-CTFE hydrophobic membranes.

    Science.gov (United States)

    Zheng, Libing; Wu, Zhenjun; Zhang, Yong; Wei, Yuansong; Wang, Jun

    2016-07-01

    Four common types of additives for polymer membrane preparation including organic macromolecule and micromolecule additives, inorganic salts and acids, and the strong non-solvent H2O were used to prepare poly (vinylidene fluoride-co-chlorotrifluoroethylene) (PVDF-CTFE) hydrophobic flat-sheet membranes. Membrane properties including morphology, porosity, hydrophobicity, pore size and pore distribution were investigated, and the permeability was evaluated via direct contact membrane distillation (DCMD) of 3.5g/L NaCl solution in a DCMD configuration. Both inorganic and organic micromolecule additives were found to slightly influence membrane hydrophobicity. Polyethylene glycol (PEG), organic acids, LiCl, MgCl2, and LiCl/H2O mixtures were proved to be effective additives to PVDF-CTFE membranes due to their pore-controlling effects and the capacity to improve the properties and performance of the resultant membranes. The occurrence of a pre-gelation process showed that when organic and inorganic micromolecules were added to PVDF-CTFE solution, the resultant membranes presented a high interconnectivity structure. The membrane prepared with dibutyl phthalate (DBP) showed a nonporous surface and symmetrical cross-section. When H2O and LiCl/H2O mixtures were also used as additives, they were beneficial for solid-liquid demixing, especially when LiCl/H2O mixed additives were used. The membrane prepared with 5% LiCl+2% H2O achieved a flux of 24.53kg/(m(2)·hr) with 99.98% salt rejection. This study is expected to offer a reference not only for PVDF-CTFE membrane preparation but also for other polymer membranes. Copyright © 2016. Published by Elsevier B.V.

  1. The Chemical Potential of Plasma Membrane Cholesterol: Implications for Cell Biology.

    Science.gov (United States)

    Ayuyan, Artem G; Cohen, Fredric S

    2018-02-27

    Cholesterol is abundant in plasma membranes and exhibits a variety of interactions throughout the membrane. Chemical potential accounts for thermodynamic consequences of molecular interactions, and quantifies the effective concentration (i.e., activity) of any substance participating in a process. We have developed, to our knowledge, the first method to measure cholesterol chemical potential in plasma membranes. This was accomplished by complexing methyl-β-cyclodextrin with cholesterol in an aqueous solution and equilibrating it with an organic solvent containing dissolved cholesterol. The chemical potential of cholesterol was thereby equalized in the two phases. Because cholesterol is dilute in the organic phase, here activity and concentration were equivalent. This equivalence allowed the amount of cholesterol bound to methyl-β-cyclodextrin to be converted to cholesterol chemical potential. Our method was used to determine the chemical potential of cholesterol in erythrocytes and in plasma membranes of nucleated cells in culture. For erythrocytes, the chemical potential did not vary when the concentration was below a critical value. Above this value, the chemical potential progressively increased with concentration. We used standard cancer lines to characterize cholesterol chemical potential in plasma membranes of nucleated cells. This chemical potential was significantly greater for highly metastatic breast cancer cells than for nonmetastatic breast cancer cells. Chemical potential depended on density of the cancer cells. A method to alter and fix the cholesterol chemical potential to any value (i.e., a cholesterol chemical potential clamp) was also developed. Cholesterol content did not change when cells were clamped for 24-48 h. It was found that the level of activation of the transcription factor STAT3 increased with increasing cholesterol chemical potential. The cholesterol chemical potential may regulate signaling pathways. Copyright © 2018. Published by

  2. Complete flexural vibration band gaps in membrane-like lattice structures

    International Nuclear Information System (INIS)

    Yu Dianlong; Liu Yaozong; Qiu Jing; Wang Gang; Zhao Honggang

    2006-01-01

    The propagation of flexural vibration in the periodical membrane-like lattice structure is studied. The band structure calculated with the plane wave expansion method indicates the existence of complete gaps. The frequency response function of a finite periodic structure is simulated with finite element method. Frequency ranges with vibration attenuation are in good agreement with the gaps found in the band structure. Much larger attenuations are found in the complete gaps comparing to those directional ones. The existence of complete flexural vibration gaps in such a lattice structure provides a new idea for vibration control of thin plates

  3. Effect of Melatonin and Cholesterol on the Structure of DOPC and DPPC Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Drolle, E [University of Waterloo, Canada; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Hoopes, M I [University of Waterloo, Canada; Choi, Y [University of Waterloo, Canada; Katsaras, John [ORNL; Karttunen, M [University of Waterloo, Canada; Leonenko, Z [University of Waterloo, Canada

    2013-01-01

    The cell membrane plays an important role in the molecular mechanism of amyloid toxicity associated with Alzheimer's disease. The membrane's chemical composition and the incorporation of small molecules, such as melatonin and cholesterol, can alter its structure and physical properties, thereby affecting its interaction with amyloid peptides. Both melatonin and cholesterol have been recently linked to amyloid toxicity. Melatonin has been shown to have a protective role against amyloid toxicity. However, the underlying molecular mechanism of this protection is still not well understood, and cholesterol's role remains controversial. We used small-angle neutron diffraction (SAND) from oriented lipid multi-layers, small-angle neutron scattering (SANS) from unilamellar vesicles experiments andMolecular Dynamics (MD) simulations to elucidate non-specific interactions of melatonin and cholesterol with 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoyl-snglycero-3-phosphocholine (DPPC) model membranes. We conclude that melatonin decreases the thickness of both model membranes by disordering the lipid hydrocarbon chains, thus increasing membrane fluidity. This result is in stark contrast to the much accepted ordering effect induced by cholesterol, which causes membranes to thicken.

  4. Crosslinked copolyazoles with a zwitterionic structure for organic solvent resistant membranes

    KAUST Repository

    Chisca, Stefan

    2015-01-01

    The preparation of crosslinked membranes with a zwitterionic structure based on a facile reaction between a newly synthesized copolyazole with free OH groups and (3-glycidyloxypropyl)trimethoxysilane (GPTMS) is reported. The new OH-functionalized copolyazole is soluble in common organic solvents, such as tetrahydrofuran (THF), dimethylsulfoxide (DMSO), N,N′-dimethylformamide (DMF) and N-methyl-2-pyrrolidone (NMP) and can be easily processed by phase inversion. After crosslinking with GPTMS, the membranes acquire high solvent resistance. We show the membrane performance and the influence of the crosslinking reaction conditions on the thermal stability, surface polarity, pore morphology, and solvent resistance. By using UV-spectroscopy we monitored the solvent resistance of the membranes in four aggressive solvents (THF, DMSO, DMF and NMP) for 30 days. After this time, only minor changes (less than 2%) were detected for membranes subjected to a crosslinking reaction for 6 hours or longer. Our data suggest that the novel crosslinked membranes can be used for industrial applications in wide harsh environments in the presence of organic solvents.

  5. Electrospun PCL/gelatin composite nanofiber structures for effective guided bone regeneration membranes.

    Science.gov (United States)

    Ren, Ke; Wang, Yi; Sun, Tao; Yue, Wen; Zhang, Hongyu

    2017-09-01

    Guided bone regeneration (GBR) membranes have been proved of great benefit for bone tissue engineering due to the improvement of cell attachment and proliferation. To develop GBR membranes with better biocompatibility and more proper degradation ability, here we fabricated polycaprolactone (PCL, polymer)/gelatin (protein) hybrid nanofibrous GBR membranes via electrospinning, followed by crosslinking with genipin. Acetic acid (HAc) was utilized to resolve the phase separation of PCL and gelatin, therefore homogeneous PCL/gelatin hybrid nanofibers with different ratios were successfully prepared. FTIR, XPS, TGA, DSC results proved that the proportion of PCL and gelatin in the as-spun nanofiber membranes could be simply adjusted by changing the weight ratio of PCL and gelatin in the spinning solution. SEM and AFM images demonstrated that all the nanofibers possessed uniform and smooth structures both in two dimension (2D) and three dimension (3D). The mechanical tests showed that these nanofibers exhibited appropriate tensile and strength properties, which were suitable for bone tissue engineering. CCK-8 and SEM images revealed that all the membranes were biocompatible to MC3T3-e1 cells. In addition, the in vitro osteogenesis characterizations, alizarin red in normal medium and osteogenesis medium, indicated that the nanofibers could promote bone formation. Therefore, all these results could suggest that our design of electrospun polymer/protein nanofiber membranes was effective for guided bone regeneration. Copyright © 2017. Published by Elsevier B.V.

  6. Nanoclay-Directed Structure and Morphology in PVDF Electrospun Membranes

    Directory of Open Access Journals (Sweden)

    Kyunghwan Yoon

    2014-01-01

    Full Text Available The incorporation of organically modified Lucentite nanoclay dramatically modifies the structure and morphology of the PVDF electrospun fibers. In a molecular level, the nanoclay preferentially stabilizes the all-trans conformation of the polymer chain, promoting an α to β transformation of the crystalline phase. The piezoelectric properties of the β-phase carry great promise for energy harvest applications. At a larger scale, the nanoclay facilitates the formation of highly uniform, bead-free fibers. Such an effect can be attributed to the enhanced conductivity and viscoelasticity of the PVDF-clay suspension. The homogenous distribution of the directionally aligned nanoclays imparts advanced mechanical properties to the nanofibers.

  7. Dimensional and Structural Control of Silica Aerogel Membranes for Miniaturized Motionless Gas Pumps.

    Science.gov (United States)

    Zhao, Shanyu; Jiang, Bo; Maeder, Thomas; Muralt, Paul; Kim, Nayoung; Matam, Santhosh Kumar; Jeong, Eunho; Han, Yen-Lin; Koebel, Matthias M

    2015-08-26

    With growing public interest in portable electronics such as micro fuel cells, micro gas total analysis systems, and portable medical devices, the need for miniaturized air pumps with minimal electrical power consumption is on the rise. Thus, the development and downsizing of next-generation thermal transpiration gas pumps has been investigated intensively during the last decades. Such a system relies on a mesoporous membrane that generates a thermomolecular pressure gradient under the action of an applied temperature bias. However, the development of highly miniaturized active membrane materials with tailored porosity and optimized pumping performance remains a major challenge. Here we report a systematic study on the manufacturing of aerogel membranes using an optimized, minimal-shrinkage sol-gel process, leading to low thermal conductivity and high air conductance. This combination of properties results in superior performance for miniaturized thermomolecular air pump applications. The engineering of such aerogel membranes, which implies pore structure control and chemical surface modification, requires both chemical processing know-how and a detailed understanding of the influence of the material properties on the spatial flow rate density. Optimal pumping performance was found for devices with integrated membranes with a density of 0.062 g cm(-3) and an average pore size of 142.0 nm. Benchmarking of such low-density hydrophobic active aerogel membranes gave an air flow rate density of 3.85 sccm·cm(-2) at an operating temperature of 400 °C. Such a silica aerogel membrane based system has shown more than 50% higher pumping performance when compared to conventional transpiration pump membrane materials as well as the ability to withstand higher operating temperatures (up to 440 °C). This study highlights new perspectives for the development of miniaturized thermal transpiration air pumps while offering insights into the fundamentals of molecular pumping in

  8. A lightweight, biological structure with tailored stiffness: The feather vane.

    Science.gov (United States)

    Sullivan, Tarah N; Pissarenko, Andreï; Herrera, Steven A; Kisailus, David; Lubarda, Vlado A; Meyers, Marc A

    2016-09-01

    The flying feathers of birds are keratinous appendages designed for maximum performance with a minimum weight penalty. Thus, their design contains ingenious combinations of components that optimize lift, stiffness, aerodynamics, and damage resistance. This design involves two main parts: a central shaft that prescribes stiffness and lateral vanes which allows for the capture of air. Within the feather vane, barbs branch from the shaft and barbules branch from barbs, forming a flat surface which ensures lift. Microhooks at the end of barbules hold barbs tightly together, providing the close-knit, unified structure of the feather vane and enabling a repair of the structure through the reattachment of un-hooked junctions. Both the shaft and barbs are lightweight biological structures constructed of keratin using the common motif of a solid shell and cellular interior. The cellular core increases the resistance to buckling with little added weight. Here we analyze the detailed structure of the feather barb and, for the first time, explain its flexural stiffness in terms of the mechanics of asymmetric foam-filled beams subjected to bending. The results are correlated and validated with finite element modeling. We compare the flexure of single barbs as well as arrays of barbs and find that the interlocking adherence of barbs to one another enables a more robust structure due to minimized barb rotation during deflection. Thus, the flexure behavior of the feather vane can be tailored by the adhesive hooking between barbs, creating a system that mitigates damage. A simplified three-dimensional physical model for this interlocking mechanism is constructed by additive manufacturing. The exceptional architecture of the feather vane will motivate the design of bioinspired structures with tailored and unique properties ranging from adhesives to aerospace materials. Despite its importance to bird flight, literature characterizing the feather vane is extremely limited. The feather

  9. The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope.

    Directory of Open Access Journals (Sweden)

    Haijiao Xu

    Full Text Available The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm -200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.

  10. Nano-scale structure in membranes in relation to enzyme action - computer simulation vs. experiment

    DEFF Research Database (Denmark)

    Høyrup, P.; Jørgensen, Kent; Mouritsen, O.G.

    2002-01-01

    lengths are in the nano-meter range. The nano-scale structure is believed to be important for controlling the activity of enzymes, specifically phospholipases, which act at bilayer membranes. We propose here a lattice-gas statistical mechanical model with appropriate dynamics to account for the non...

  11. Solution Structure and Membrane Interaction of the Cytoplasmic Tail of HIV-1 gp41 Protein.

    Science.gov (United States)

    Murphy, R Elliot; Samal, Alexandra B; Vlach, Jiri; Saad, Jamil S

    2017-11-07

    The cytoplasmic tail of gp41 (gp41CT) remains the last HIV-1 domain with an unknown structure. It plays important roles in HIV-1 replication such as mediating envelope (Env) intracellular trafficking and incorporation into assembling virions, mechanisms of which are poorly understood. Here, we present the solution structure of gp41CT in a micellar environment and characterize its interaction with the membrane. We show that the N-terminal 45 residues are unstructured and not associated with the membrane. However, the C-terminal 105 residues form three membrane-bound amphipathic α helices with distinctive structural features such as variable degree of membrane penetration, hydrophobic and basic surfaces, clusters of aromatic residues, and a network of cation-π interactions. This work fills a major gap by providing the structure of the last segment of HIV-1 Env, which will provide insights into the mechanisms of Gag-mediated Env incorporation as well as the overall Env mobility and conformation on the virion surface. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Non-linear membrane finite-element analysis for lightweight structure enveloppe design

    OpenAIRE

    Muttin, Frédéric; Adés, Claude; Cousin, Philippe; Pallu de la Barrière, Philippe

    1994-01-01

    International audience; Lightweight and textile structures can be modelized by means of the small strains and great displacements non-linear membrane model. Two kinds of finite-element solvers, named explicit and implicit, have been implemented in a software program for a PC computer. Numerical tests and results applied to sail design are presented.

  13. Understanding the structure and performance of self-assembled triblock terpolymer membranes

    KAUST Repository

    Pendergast, MaryTheresa M.

    2013-10-01

    Nanoporous membranes represent a possible route towards more precise particle and macromolecular separations, which are of interest across many industries. Here, we explored membranes with vertically-aligned nanopores formed from a poly(isoprene-. b-styrene-. b-4 vinyl pyridine) (ISV) triblock terpolymer via a hybrid self-assembly/nonsolvent induced phase separation process (S-NIPS). ISV concentration, solvent composition, and evaporation time in the S-NIPS process were varied to tailor ordering of the selective layer and produce enhanced water permeability. Here, water permeability was doubled over previous versions of ISV membranes. This was achieved by increasing volatile solvent concentration, thereby decreasing the evaporation period required for self-assembly. Fine-tuning was required, however, since overly-rapid evaporation did not yield the desired pore structure. Transport models, used to relate the in-. situ structure to the performance of these materials, revealed narrowing of pores and blocking by the dense region below. It was shown that these vertically aligned nanoporous membranes compare favorably with commercial ultrafiltration membranes formed by NIPS and track-etching processes, which suggests that there is practical value in further developing and optimizing these materials for specific industrial separations. © 2013 Elsevier B.V.

  14. Structure and interaction with lipid membrane models of Semliki Forest virus fusion peptide.

    Science.gov (United States)

    Agopian, A; Quetin, M; Castano, S

    2016-11-01

    Semliki Forest virus (SFV) is a well-characterized alphavirus that infects cells via endocytosis and an acid-triggered fusion step using class II fusion proteins. Membrane fusion is mediated by the viral spike protein, a heterotrimer of two transmembrane subunits, E1 and E2, and a peripheral protein, E3. Sequence analysis of the E1 ectodomain of a number of alphaviruses demonstrated the presence of a highly conserved hydrophobic domain on the E1 ectodomain. This sequence was proposed to be the fusion peptide of SFV and is believed to be the domain of E1 that interacts with the target membrane and triggers fusion. Here, we investigate the structure and the interaction with lipid membrane models of 76 YQCKVYTGVYPFMWGGAYCFC 96 sequence from SFV, named SFV21, using optical method (ellipsometry) and vibrational spectroscopiy approaches (Polarization Modulation infra-Red Reflection Absorption Spectroscopy, PMIRRAS, and polarized ATR-FTIR). We demonstrate a structural flexibility of SFV21 sequence whether the lateral pressure and the lipid environment. In a lipid environment that mimics eukaryotic cell membranes, a conformational transition from an α-helix to a β-sheet is induced in the presence of lipid by increasing the peptide to lipid ratio, which leads to important perturbations in the membrane organisation. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Structure and formation of egg membranes in Aedes aegypti. (L. ) (Diptera:Culicidae)

    Energy Technology Data Exchange (ETDEWEB)

    Mathew, G.; Rai, K.S.

    1975-01-01

    An ultrastructural study of mosquito ovarioles reveals that both the vitelline membrane and the endochorion are secreted by the follicular epithelium. The presecretory phase is characterized by the hypertrophy of endoplasmic reticulum and Golgi complex in the follicle cells. Synthesis of vitelline membrane precursors begins immediately after yolk protein uptake by micropinocytosis. Secretory droplets are budded off Golgi cisternae and released into the follicle cell--oocyte interface by exocytosis. The vitelline membrane first appears as dense plaques which eventually fuse to form a single homogeneous layer. Two types of secretory material are identified in the follicle cells prior to the formation of the endochorion. Golgi cisternae bud off small droplets similar in size and appearance to the precursors of the vitelline membrane. These migrate to the apical surface and accumulate between surface folds in the plasma membrane. The second type is a fibrous material formed in endoplasmic reticulum. When fully secreted, the endochorion is a 2-layered structure. The lower layer is comprised of pillar-like structures alternating with fibrous mesh-like areas. The pillars are formed by the coalescence of droplets released from Golgi, while the mesh-like areas presumably arise from the fibrous material. The outer layer is also fibrous. The follicle cells degenerate once the endochorion is laid down. endochorion is laid down.

  16. Membrane Biophysics

    CERN Document Server

    Ashrafuzzaman, Mohammad

    2013-01-01

    Physics, mathematics and chemistry all play a vital role in understanding the true nature and functioning of biological membranes, key elements of living processes. Besides simple spectroscopic observations and electrical measurements of membranes we address in this book the phenomena of coexistence and independent existence of different membrane components using various theoretical approaches. This treatment will be helpful for readers who want to understand biological processes by applying both simple observations and fundamental scientific analysis. It provides a deep understanding of the causes and effects of processes inside membranes, and will thus eventually open new doors for high-level pharmaceutical approaches towards fighting membrane- and cell-related diseases.

  17. Advances in structural and functional analysis of membrane proteins by electron crystallography.

    Science.gov (United States)

    Wisedchaisri, Goragot; Reichow, Steve L; Gonen, Tamir

    2011-10-12

    Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Different Structures of PVA Nano fibrous Membrane for Sound Absorption Application

    International Nuclear Information System (INIS)

    Mohrova, J.; Kalinova, K.

    2012-01-01

    The thin nano fibrous layer has different properties in the field of sound absorption in comparison with porous fibrous material which works on a principle of friction of air particles in contact with walls of pores. In case of the thin nano fibrous layer, which represents a sound absorber here, the energy of sonic waves is absorbed by the principle of membrane resonance. The structure of the membrane can play an important role in the process of converting the sonic energy to a different energy type. The vibration system acts differently depending on the presence of smooth fibers in the structure, amount of partly merged fibers, or structure of polymer foil as extreme. Polyvinyl alcohol (PVA) was used as a polymer because of its good water solubility. It is possible to influence the structure of nano fibrous layer during the production process thanks to this property of polyvinyl alcohol.

  19. Data acquisition and analysis at the Structural Biology Center

    International Nuclear Information System (INIS)

    Westbrook, M.L.; Coleman, T.A.; Daly, R.T.; Pflugrath, J.W.

    1996-01-01

    The Structural Biology Center (SBC), a national user facility for macromolecular crystallography located at Argonne National Laboratory's Advanced Photon Source, is currently being built and commissioned. SBC facilities include a bending-magnet beamline, an insertion-device beamline, laboratory and office space adjacent to the beamlines, and associated instrumentation, experimental apparatus, and facilities. SBC technical facilities will support anomalous dispersion phasing experiments, data collection from microcrystals, data collection from crystals with large molecular structures and rapid data collection from multiple related crystal structures for protein engineering and drug design. The SBC Computing Systems and Software Engineering Group is tasked with developing the SBC Control System, which includes computing systems, network, and software. The emphasis of SBC Control System development has been to provide efficient and convenient beamline control, data acquisition, and data analysis for maximal facility and experimenter productivity. This paper describes the SBC Control System development, specifically data acquisition and analysis at the SBC, and the development methods used to meet this goal

  20. The E. coli Single Protein Production (cSPP) System for Production and Structural Analysis of Membrane Proteins

    OpenAIRE

    Mao, Lili; Vaiphei, S. Thangminlal; Shimazu, Tsutomu; Schneider, William M.; Tang, Yuefeng; Mani, Rajeswari; Roth, Monica J.; Montelione, Gaetano T.; Inouye, Masayori

    2009-01-01

    At present, only 0.9% of PDB-deposited structures are of membrane proteins in spite of the fact that membrane proteins constitute approximately 30% of total proteins in most genomes from bacteria to humans. Here we address some of the major bottlenecks in the structural studies of membrane proteins and discuss the ability of the new technology, the Single-Protein Production (SPP) system, to help solve these bottlenecks.

  1. Synthetic Biology Tools for the Membrane – Targeted Localisation and Elucidation of Protein Interactions

    DEFF Research Database (Denmark)

    Wendel, Sofie; Seppala, Susanna; Nørholm, Morten

    2014-01-01

    -­‐based method for easy detection of surface display using GFP-­‐nanobodies (1). We fused a GFP-­‐nanobody to the E. coli outer membrane anchor LppOmpA, resulting in surface display of the nanobody. Addition of free GFP to the whole cells resulted in binding of GFP to the cells via the nanobody, as shown...

  2. Model Biological Membranes and Possibilities of Application of Electrochemical Impedance Spectroscopy for Their Characterization

    Czech Academy of Sciences Publication Activity Database

    Skalová, Štěpánka; Vyskočil, V.; Barek, J.; Navrátil, Tomáš

    2018-01-01

    Roč. 30, č. 2 (2018), s. 207-219 ISSN 1040-0397 R&D Projects: GA ČR(CZ) GA17-05387S; GA ČR GA17-03868S Institutional support: RVO:61388955 Keywords : Electrochemical impedance spectroscopy (EIS) * Liposomes * Model membrane * Phospholipid bilayer * Planar lipid bilayer * Supported lipid bilayers * Tethered lipid bilayers Subject RIV: CG - Electrochemistry OBOR OECD: Electrochemistry (dry cells, batteries, fuel cells, corrosion metals, electrolysis) Impact factor: 2.851, year: 2016

  3. The normative structure of mathematization in systematic biology.

    Science.gov (United States)

    Sterner, Beckett; Lidgard, Scott

    2014-06-01

    We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. Copyright © 2014. Published by Elsevier Ltd.

  4. Structural Diversity and Biological Activities of the Cyclodipeptides from Fungi

    Directory of Open Access Journals (Sweden)

    Xiaohan Wang

    2017-11-01

    Full Text Available Cyclodipeptides, called 2,5-diketopiperazines (2,5-DKPs, are obtained by the condensation of two amino acids. Fungi have been considered to be a rich source of novel and bioactive cyclodipeptides. This review highlights the occurrence, structures and biological activities of the fungal cyclodipeptides with the literature covered up to July 2017. A total of 635 fungal cyclodipeptides belonging to the groups of tryptophan-proline, tryptophan-tryptophan, tryptophan–Xaa, proline–Xaa, non-tryptophan–non-proline, and thio-analogs have been discussed and reviewed. They were mainly isolated from the genera of Aspergillus and Penicillium. More and more cyclodipeptides have been isolated from marine-derived and plant endophytic fungi. Some of them were screened to have cytotoxic, phytotoxic, antimicrobial, insecticidal, vasodilator, radical scavenging, antioxidant, brine shrimp lethal, antiviral, nematicidal, antituberculosis, and enzyme-inhibitory activities to show their potential applications in agriculture, medicinal, and food industry.

  5. Structure, Function, and Biology of the Enterococcus faecalis Cytolysin

    Directory of Open Access Journals (Sweden)

    Daria Van Tyne

    2013-04-01

    Full Text Available Enterococcus faecalis is a Gram-positive commensal member of the gut microbiota of a wide range of organisms. With the advent of antibiotic therapy, it has emerged as a multidrug resistant, hospital-acquired pathogen. Highly virulent strains of E. faecalis express a pore-forming exotoxin, called cytolysin, which lyses both bacterial and eukaryotic cells in response to quorum signals. Originally described in the 1930s, the cytolysin is a member of a large class of lanthionine-containing bacteriocins produced by Gram-positive bacteria. While the cytolysin shares some core features with other lantibiotics, it possesses unique characteristics as well. The current understanding of cytolysin biosynthesis, structure/function relationships, and contribution to the biology of E. faecalis are reviewed, and opportunities for using emerging technologies to advance this understanding are discussed.

  6. Helium Ion Microscopy of proton exchange membrane fuel cell electrode structures

    OpenAIRE

    Chiriaev, Serguei; Dam Madsen, Nis; Rubahn, Horst-Günter; Andersen, Shuang Ma

    2017-01-01

    Characterization of composite materials with microscopy techniques is an essential route to understanding their properties and degradation mechanisms, though the observation with a suitable type of microscopy is not always possible. In this work, we present proton exchange membrane fuel cell electrode interface structure dependence on ionomer content, systematically studied by Helium Ion Microscopy (HIM). A special focus was on acquiring high resolution images of the electrode structure and a...

  7. Structural feature extraction protocol for classifying reversible membrane binding protein domains.

    Science.gov (United States)

    Källberg, Morten; Lu, Hui

    2009-01-01

    Machine learning based classification protocols for automated function annotation of protein structures have in many instances proven superior to simpler sequence based procedures. Here we present an automated method for extracting features from protein structures by construction of surface patches to be used in such protocols. The utility of the developed patch-growing procedure is exemplified by its ability to identify reversible membrane binding domains from the C1, C2, and PH families.

  8. Mathematical Modeling of Hollow-Fiber Membrane System in Biological Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    Jian PENG

    2006-02-01

    Full Text Available A set of mathematical models were derived based on the bio-kinetics and material balance principles to describe the performance of membrane system in this research. A synthetic wastewater and a meat packing wastewater were processed through a lab-scale membrane bioreactor system to generate experimental data for calibration and verification of the derived models. For the synthetic wastewater treatment, a high and stable Total Organic Carbon (TOC removal was achieved with volumetric organic loading from 0.2 to 24.2 kg TOC/m3ƒ(d. It was found that the derived system models fit the experimental data well. The bio-kinetic coefficients of k, Ks, Y and kd in the models were found to be 0.16 d-1, 1.0 mg/L, 1.75 mg Mixed Liquor Volatile Suspended Solids (MLVSS/mg TOC and 0.11 d-1, respectively. For the meat packing wastewater treatment, the bio-kinetic coefficients of k, Ks, Y and kd were found to be 0.48 d-1, 56.3 mg/L, 0.53 mg MLVSS/mg COD and 0.04 d-1, respectively. F/M ratio of 0.08 was found to be the proper operating condition for the system. Based on the proposed system models, the optimum MLSS concentration and F/M ratio can be computed to yield minimum cost of a membrane bioreactor system without excess biomass production.

  9. 2H NMR evidence for antibiotic-induced cholesterol immobilization in biological model membranes

    International Nuclear Information System (INIS)

    Dufourc, E.J.; Smith, I.C.

    1985-01-01

    The interaction of the polyene antibiotic filipin with membrane sterols has been studied by deuterium nuclear magnetic resonance of the molecular probes [2,2,3,4,4,6- 2 H6]cholesterol and 1-myristoyl-2-[4',4',14',14',14'- 2 H5]myristoyl-sn-glycero-3-phospho- choline. At physiological temperatures, there is evidence of filipin-induced cholesterol immobilization in the membrane. The 2 H NMR spectra of cholesterol show two domains in which ordering and dynamics are very different. In one of these, cholesterol is static on the 2 H NMR time scale, whereas in the other it undergoes rapid axially symmetric motions similar to those it exhibits in the drug-free membrane; this indicates that the jumping frequency of cholesterol between the labile and immobilized domains is less than 10(5) s -1 . The distribution of cholesterol between these two sites is temperature dependent. In contrast to cholesterol, the phospholipids sense only one type of environment, at both the top and center of the bilayer, indicating that cholesterol acts as a screen, preventing the lipids from direct interaction with the antibiotic. At low temperature, the ordering of the lipid in the presence of cholesterol does not change upon filipin addition, whereas at elevated temperatures the local ordering of both the lipid and the labile cholesterol is significantly lower than that in the absence of the drug

  10. Energetics and molecular biology of active transport in bacterial membrane vesicles.

    Science.gov (United States)

    Kaback, H R; Ramos, S; Robertson, D E; Stroobant, P; Tokuda, H

    1977-01-01

    Bacterial membrane vesicles retain the same sidedness as the membrane in the intact cell and catalyze active transport of many solutes by a respiration-dependent mechanism that does not involve the generation of utilization of ATP or other high-energy phosphate compounds. In E. coli vesicles, most of these transport systems are coupled to an electrochemical gradient of protons (deltamuH+, interior negative and alkaline) generated primarily by the oxidation of D-lactate or reduced phenazine methosulfate via a membrane-bound respiratory chain. Oxygen or, under appropriate conditions, fumarate or nitrate can function as terminal electron acceptors, and the site at which deltamuH+ is generated is located before cytochrome b1 in the respiratory chain. Certain (N-dansyl)aminoalkyl-beta-D-galactopyranosides (Dns-gal) and N(2-nitro-4-azidophenyl)aminoalkyl 1-thio-beta-D-galactopyranosides (APG) are competitive inhibitors of lactose transport but are not transported themselves. Various fluorescence techniques, direct binding assays, and photoinactivation studies demonstrate that the great bulk of the lac carrier protein (ca. 95%) does not bind ligand in the absence of energy-coupling. Upon generation of a deltamuH+ (interior negative and alkaline), binding of Dns-gal and APG-dependent photoinactivation are observed. The data indicate that energy is coupled to the initial step in the transport process, and suggest that the lac carrier protein may be negatively charged.

  11. Core/Shell Structured Magnetic Nanoparticles for Biological Applications

    International Nuclear Information System (INIS)

    Park, Jeong Chan; Jung, Myung Hwan

    2013-01-01

    Magnetic nanoparticles have been widely used for biomedical applications, such as magnetic resonance imaging (MRI), hyperthermia, drug delivery and cell signaling. The surface modification of the nanomaterials is required for biomedical use to give physiogical stability, surface reactivity and targeting properties. Among many approaches for the surface modification with materials, such as polymers, organic ligands and metals, one of the most attractive ways is using metals. The fabrication of metal-based, monolayer-coated magnetic nanoparticles has been intensively studied. However, the synthesis of metal-capped magnetic nanoparticles with monodispersities and controllable sizes is still challenged. Recently, gold-capped magnetic nanoparticles have been reported to increase stability and to provide biocompatibility. Magnetic nanoparticle with gold coating is an attractive system, which can be stabilized in biological conditions and readily functionalized in biological conditions and readily functionalized through well-established surface modification (Au-S) chemistry. The Au coating offers plasmonic properties to magnetic nanoparticles. This makes the magnetic/Au core/shell combinations interesting for magnetic and optical applications. Herein, the synthesis and characterization of gold capped-magnetic core structured nanomaterials with different gold sources, such as gold acetate and chloroauric acid have been reported. The core/shell nanoparticles were transferred from organic to aqueous solutions for biomedical applications. Magnetic core/shell structured nanoparticles have been prepared and transferred from organic phase to aqueous solutions. The resulting Au-coated magnetic core nanoparticles might be an attractive system for biomedical applications, which are needed both magnetic resonance imaging and optical imaging

  12. Mitochondrial membranes with mono- and divalent salt: changes induced by salt ions on structure and dynamics

    DEFF Research Database (Denmark)

    Pöyry, Sanja; Róg, Tomasz; Karttunen, Mikko

    2009-01-01

    , and membrane electrostatic potential. The changes induced by salt are more prominent in dynamical properties related to ion binding and formation of ion-lipid complexes and lipid aggregates, as rotational diffusion of lipids is slowed down by ions, especially in the case of CaCl(2). In the same spirit, lateral......We employ atomistic simulations to consider how mono- (NaCl) and divalent (CaCl(2)) salt affects properties of inner and outer membranes of mitochondria. We find that the influence of salt on structural properties is rather minute, only weakly affecting lipid packing, conformational ordering...

  13. Effect of ionizing radiations of lymphocyte membranes. Part of a coordinated programme on cell membrane probes as biological indicators in radiation accidents

    International Nuclear Information System (INIS)

    Ojeda, S.F.

    1981-06-01

    A study of the effects of low doses of irradiation on membrane receptors of lymphoid cells indicated that doses as low as 10 rads induced detectable changes in the antigen receptors of cell surfaces. Lymphoid cells from mice or rabbit lymph nodes, or circulating lymphocytes from human volunteers were irradiated and studied for their ability to bind antisera against the IgG membrane receptors. The isolated lymphoid cells were x-irradiated, and tested versus non-irradiated controls. They were incubated at 37 0 C for different times, and IgG-positive cells stained by the direct or indirect immunofluorescence technique. The percentage of IgG-positive cells was reduced by low-dose irradiation, and proved dose -and temperature-dependent. The disappearance phenomenon depends on the microtubular structure, metabolic energy, and levels of C-AMP. Only the reappearance phase is temperature-dependent and not affected by the drugs tested. The phenomenon is dose-rate dependent, showing greater sensitivity at lower dose/rates. Experiments using anti-Fc and anti-Fab portions of the surface molecule, appear to confirm a partial internatlization of the surface molecule as cause (at least in rabbit cells). Similar experiments with human cells did not show a differential effect. Human T-cells and FC receptors of Mast cells did, however, indicate that these surface molecules are also modified by irradiation

  14. An evaluation of detergents for NMR structural studies of membrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Krueger-Koplin, Ray D.; Sorgen, Paul L.; Krueger-Koplin, Suzanne T.; Rivera-Torres, Ivan O.; Cahill, Sean M. [Albert Einstein College of Medicine, Biochemistry Department (United States); Hicks, David B. [Sinai School of Medicine, Department of Pharmacology and Biological Chemistry, Mt (United States); Grinius, Leo [Cincinnati State Technical College (United States); Krulwich, Terry A. [Sinai School of Medicine, Department of Pharmacology and Biological Chemistry, Mt (United States); Girvin, Mark E. [Albert Einstein College of Medicine, Biochemistry Department (United States)

    2004-01-15

    Structural information on membrane proteins lags far behind that on soluble proteins, in large part due to difficulties producing homogeneous, stable, structurally relevant samples in a membrane-like environment. In this study 25 membrane mimetics were screened using 2D {sup 1}H-{sup 15}N heteronuclear single quantum correlation NMR experiments to establish sample homogeneity and predict fitness for structure determination. A single detergent, 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-RAC-(1-glycerol)] (LPPG), yielded high quality NMR spectra with sample lifetimes greater than one month for the five proteins tested - R. sphaeroides LH1 {alpha} and {beta} subunits, E. coli and B. pseudofirmus OF4 ATP synthase c subunits, and S. aureus small multidrug resistance transporter - with 1, 2, or 4 membrane spanning {alpha}-helices, respectively. Site-specific spin labeling established interhelical distances in the drug transporter and genetically fused dimers of c subunits in LPPG consistent with in vivo distances. Optical spectroscopy showed that LH1 {beta} subunits form native-like complexes with bacteriochlorphyll a in LPPG. All the protein/micelle complexes were estimated to exceed 100 kDaltons by translational diffusion measurements. However, analysis of {sup 15}N transverse, longitudinal and {sup 15}N{l_brace}{sup 1}H{r_brace} nuclear Overhauser effect relaxation measurements yielded overall rotational correlation times of 8 to 12 nsec, similar to a 15-20 kDalton protein tumbling isotropically in solution, and consistent with the high quality NMR data observed.

  15. Structural and functional properties of hydration and confined water in membrane interfaces.

    Science.gov (United States)

    Disalvo, E A; Lairion, F; Martini, F; Tymczyszyn, E; Frías, M; Almaleck, H; Gordillo, G J

    2008-12-01

    The scope of the present review focuses on the interfacial properties of cell membranes that may establish a link between the membrane and the cytosolic components. We present evidences that the current view of the membrane as a barrier of permeability that contains an aqueous solution of macromolecules may be replaced by one in which the membrane plays a structural and functional role. Although this idea has been previously suggested, the present is the first systematic work that puts into relevance the relation water-membrane in terms of thermodynamic and structural properties of the interphases that cannot be ignored in the understanding of cell function. To pursue this aim, we introduce a new definition of interphase, in which the water is organized in different levels on the surface with different binding energies. Altogether determines the surface free energy necessary for the structural response to changes in the surrounding media. The physical chemical properties of this region are interpreted in terms of hydration water and confined water, which explain the interaction with proteins and could affect the modulation of enzyme activity. Information provided by several methodologies indicates that the organization of the hydration states is not restricted to the membrane plane albeit to a region extending into the cytoplasm, in which polar head groups play a relevant role. In addition, dynamic properties studied by cyclic voltammetry allow one to deduce the energetics of the conformational changes of the lipid head group in relation to the head-head interactions due to the presence of carbonyls and phosphates at the interphase. These groups are, apparently, surrounded by more than one layer of water molecules: a tightly bound shell, that mostly contributes to the dipole potential, and a second one that may be displaced by proteins and osmotic stress. Hydration water around carbonyl and phosphate groups may change by the presence of polyhydroxylated compounds

  16. Using the Cambridge structure database of organic and organometalic compounds in structure biology

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich

    2010-01-01

    Roč. 17, 1a (2010), b24-b26 ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. Nové Hrady, 18.03.2010-20.03.2010] R&D Projects: GA AV ČR IAA500500701; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505 Keywords : organic chemistry * Cambridge Structure Data base * molecular structure Subject RIV: CD - Macromolecular Chemistry http://xray.cz/ms/bul2010-1a/friday2.pdf

  17. Harvesting and cryo-cooling crystals of membrane proteins grown in lipidic mesophases for structure determination by macromolecular crystallography.

    Science.gov (United States)

    Li, Dianfan; Boland, Coilín; Aragao, David; Walsh, Kilian; Caffrey, Martin

    2012-09-02

    refined and implemented in the Membrane Structural and Functional Biology (MS&FB) Group, and are described in detail in this JoVE article (Figure 4). Examples are given of situations where crystals are successfully harvested and cryo-cooled. We also provide examples of cases where problems arise that lead to the irretrievable loss of crystals and describe how these problems can be avoided. In this article the Viewer is provided with step-by-step instructions for opening glass sandwich crystallization wells, for harvesting and for cryo-cooling crystals of membrane proteins growing in cubic and in sponge phases.

  18. Electricity and mechanics of biomembrane systems: Flexoelectricity in living membranes

    International Nuclear Information System (INIS)

    Petrov, Alexander G.

    2006-01-01

    Flexoelectricity provides a reciprocal relationship between electricity and mechanics in membranes, i.e., between membrane curvature and polarization. Experimental evidence of biomembrane flexoelectricity (including direct and converse flexoelectric effect) is reviewed. Biological implications of flexoelectricity in membrane transport, membrane contact, mechanosensitivity, electromotility and hearing are underlined. Flexoelectricity enables membrane structures to function like soft micro- and nano-machines, sensors and actuators, thus providing important input to molecular electronics applications

  19. Electricity and mechanics of biomembrane systems: Flexoelectricity in living membranes

    Energy Technology Data Exchange (ETDEWEB)

    Petrov, Alexander G. [Biomolecular Layers Department, Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee, 1784 Sofia (Bulgaria)]. E-mail: director@issp.bas.bg

    2006-05-24

    Flexoelectricity provides a reciprocal relationship between electricity and mechanics in membranes, i.e., between membrane curvature and polarization. Experimental evidence of biomembrane flexoelectricity (including direct and converse flexoelectric effect) is reviewed. Biological implications of flexoelectricity in membrane transport, membrane contact, mechanosensitivity, electromotility and hearing are underlined. Flexoelectricity enables membrane structures to function like soft micro- and nano-machines, sensors and actuators, thus providing important input to molecular electronics applications.

  20. Electricity and mechanics of biomembrane systems: flexoelectricity in living membranes.

    Science.gov (United States)

    Petrov, Alexander G

    2006-05-24

    Flexoelectricity provides a reciprocal relationship between electricity and mechanics in membranes, i.e., between membrane curvature and polarization. Experimental evidence of biomembrane flexoelectricity (including direct and converse flexoelectric effect) is reviewed. Biological implications of flexoelectricity in membrane transport, membrane contact, mechanosensitivity, electromotility and hearing are underlined. Flexoelectricity enables membrane structures to function like soft micro- and nano-machines, sensors and actuators, thus providing important input to molecular electronics applications.

  1. Development of Pd Alloy Hydrogen Separation Membranes with Dense/Porous Hybrid Structure for High Hydrogen Perm-Selectivity

    Directory of Open Access Journals (Sweden)

    Jae-Yun Han

    2014-01-01

    Full Text Available For the commercial applications of hydrogen separation membranes, both high hydrogen selectivity and permeability (i.e., perm-selectivity are required. However, it has been difficult to fabricate thin, dense Pd alloy composite membranes on porous metal support that have a pore-free surface and an open structure at the interface between the Pd alloy films and the metal support in order to obtain the required properties simultaneously. In this study, we fabricated Pd alloy hydrogen separation membranes with dense/porous hybrid structure for high hydrogen perm-selectivity. The hydrogen selectivity of this membrane increased owing to the dense and pore-free microstructure of the membrane surface. The hydrogen permeation flux also was remarkably improved by the formation of an open microstructure with numerous open voids at the interface and by an effective reduction in the membrane thickness as a result of the porous structure formed within the Pd alloy films.

  2. Revealing the membrane-bound structure of neurokinin A using neutron diffraction

    Science.gov (United States)

    Darkes, Malcolm J. M.; Hauss, Thomas; Dante, Silvia; Bradshaw, Jeremy P.

    2000-03-01

    Neurokinin A (or substance K) belongs to the tachykinin family, a group of small amphipathic peptides that bind to specific membrane-embedded, G-protein coupled receptors. The agonist/receptor complex is quaternary in nature because the receptor binding sites are thought to be located within the lipid bilayer and because the role of water cannot be ignored. The cell membrane acts as a solvent to accumulate peptide and an inducer of peptide secondary structure. The three-dimensional shape that the peptide assumes when associated to the cell membrane will be an important parameter with regards to the receptor selectivity and affinity. Neutron diffraction measurements were carried out in order to define the location of the N-terminus of the peptide in synthetic phospholipid multi-bilayer stacks.

  3. Structure and orientation study of Ebola fusion peptide inserted in lipid membrane models.

    Science.gov (United States)

    Agopian, Audrey; Castano, Sabine

    2014-01-01

    The fusion peptide of Ebola virus comprises a highly hydrophobic sequence located downstream from the N-terminus of the glycoprotein GP2 responsible for virus-host membrane fusion. The internal fusion peptide of GP2 inserts into membranes of infected cell to mediate the viral and the host cell membrane fusion. Since the sequence length of Ebola fusion peptide is still not clear, we study in the present work the behavior of two fusion peptides of different lengths which were named EBO17 and EBO24 referring to their amino acid length. The secondary structure and orientation of both peptides in lipid model systems made of DMPC:DMPG:cholesterol:DMPE (6:2:5:3) were investigated using PMIRRAS and polarized ATR spectroscopy coupled with Brewster angle microscopy. The infrared results showed a structural flexibility of both fusion peptides which are able to transit reversibly from an α-helix to antiparallel β-sheets. Ellipsometry results corroborate together with isotherm measurements that EBO peptides interacting with lipid monolayer highly affected the lipid organization. When interacting with a single lipid bilayer, at low peptide content, EBO peptides insert as mostly α-helices mainly perpendicular into the lipid membrane thus tend to organize the lipid acyl chains. Inserted in multilamellar vesicles at higher peptide content, EBO peptides are mostly in β-sheet structures and induce a disorganization of the lipid chain order. In this paper, we show that the secondary structure of the Ebola fusion peptide is reversibly flexible between α-helical and β-sheet conformations, this feature being dependent on its concentration in lipids, eventually inducing membrane fusion. © 2013.

  4. Epileptic seizures induce structural and functional alterations on brain tissue membranes.

    Science.gov (United States)

    Turker, Sevgi; Severcan, Mete; Ilbay, Gul; Severcan, Feride

    2014-12-01

    Epilepsy is characterized by disruption of balance between cerebral excitation and inhibition, leading to recurrent and unprovoked convulsions. Studies are still underway to understand mechanisms lying epileptic seizures with the aim of improving treatment strategies. In this context, the research on brain tissue membranes gains importance for generation of epileptic activities. In order to provide additional information for this field, we have investigated the effects of pentylenetetrazol-induced and audiogenetically susceptible epileptic seizures on structure, content and function of rat brain membrane components using Fourier transform infrared (FT-IR) spectroscopy. The findings have shown that both two types of epileptic seizures stimulate the variations in the molecular organization of membrane lipids, which have potential to influence the structures in connection with functions of membrane proteins. Moreover, less fluid lipid structure and a decline in content of lipids obtained from the ratio of CH3 asym/lipid, CH2 asym/lipid, CO/lipid, and olefinicCH/lipid and the areas of the PO2 symmetric and asymmetric modes were observed. Moreover, based on IR data the changes in the conformation of proteins were predicted by neural network (NN) analysis, and displayed as an increase in random coil despite a decrease in beta sheet. Depending on spectral parameters, we have successfully differentiated treated samples from the control by principal component analysis (PCA) and cluster analysis. In summary, FT-IR spectroscopy may offer promising attempt to identify compositional, structural and functional alterations in brain tissue membranes resulting from epileptic activities. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Fouling in Membrane Distillation, Osmotic Distillation and Osmotic Membrane Distillation

    Directory of Open Access Journals (Sweden)

    Mourad Laqbaqbi

    2017-03-01

    Full Text Available Various membrane separation processes are being used for seawater desalination and treatment of wastewaters in order to deal with the worldwide water shortage problem. Different types of membranes of distinct morphologies, structures and physico-chemical characteristics are employed. Among the considered membrane technologies, membrane distillation (MD, osmotic distillation (OD and osmotic membrane distillation (OMD use porous and hydrophobic membranes for production of distilled water and/or concentration of wastewaters for recovery and recycling of valuable compounds. However, the efficiency of these technologies is hampered by fouling phenomena. This refers to the accumulation of organic/inorganic deposits including biological matter on the membrane surface and/or in the membrane pores. Fouling in MD, OD and OMD differs from that observed in electric and pressure-driven membrane processes such electrodialysis (ED, membrane capacitive deionization (MCD, reverse osmosis (RO, nanofiltration (NF, ultrafiltration (UF, microfiltration (MF, etc. Other than pore blockage, fouling in MD, OD and OMD increases the risk of membrane pores wetting and reduces therefore the quantity and quality of the produced water or the concentration efficiency of the process. This review deals with the observed fouling phenomena in MD, OD and OMD. It highlights different detected fouling types (organic fouling, inorganic fouling and biofouling, fouling characterization techniques as well as various methods of fouling reduction including pretreatment, membrane modification, membrane cleaning and antiscalants application.

  6. Plasma lipid pattern and red cell membrane structure in β-thalassemia patients in Jakarta

    Directory of Open Access Journals (Sweden)

    Seruni K.U. Freisleben

    2011-08-01

    Full Text Available Background: Over the last 10 years, we have investigated thalassemia patients in Jakarta to obtain a comprehensive picture of iron overload, oxidative stress, and cell damage.Methods: In blood samples from 15 transfusion-dependent patients (group T, 5 non-transfused patients (group N and 10 controls (group C, plasma lipids and lipoproteins, lipid-soluble vitamin E, malondialdehyde (MDA and thiol status were measured. Isolated eryhtrocyte membranes were investigated with electron paramagnetic resonance (EPR spectroscopy using doxyl-stearic acid and maleimido-proxyl spin lables. Data were analyzed statistically with ANOVA.Results: Plasma triglycerides were higher and cholesterol levels were lower in thalassemic patients compared to controls. Vitamin E, group C: 21.8 vs T: 6.2 μmol/L and reactive thiols (C: 144 vs. T: 61 μmol/L were considerably lower in transfused patients, who exert clear signs of oxidative stress (MDA, C: 1.96 vs T: 9.2 μmol/L and of tissue cell damage, i.e., high transaminases plasma levels. Non-transfused thalassemia patients have slight signs of oxidative stress, but no significant indication of cell damage. Erythrocyte membrane parameters from EPR spectroscopy differ considerably between all groups. In transfusion-dependent patients the structure of the erythrocyte membrane and the gradients of polarity and fluidity are destroyed in lipid domains; binding capacity of protein thiols in the membrane is lower and immobilized.Conclusion: In tranfusion-dependent thalassemic patients, plasma lipid pattern and oxidative stress are associated with structural damage of isolated erythrocyte membranes as measured by EPR spectroscopy with lipid and proteinthiol spin labels. (Med J Indones 2011; 20:178-84Keywords: electron paramagnetic resonance spectroscopy, erythrocyte membrane, lipoproteins, oxidative stress, thalassemia, plasma lipids.

  7. Structure/property relationships in polymer membranes for water purification and energy applications

    Science.gov (United States)

    Geise, Geoffrey

    Providing sustainable supplies of purified water and energy is a critical global challenge for the future, and polymer membranes will play a key role in addressing these clear and pressing global needs for water and energy. Polymer membrane-based processes dominate the desalination market, and polymer membranes are crucial components in several rapidly developing power generation and storage applications that rely on membranes to control rates of water and/or ion transport. Much remains unknown about the influence of polymer structure on intrinsic water and ion transport properties, and these relationships must be developed to design next generation polymer membrane materials. For desalination applications, polymers with simultaneously high water permeability and low salt permeability are desirable in order to prepare selective membranes that can efficiently desalinate water, and a tradeoff relationship between water/salt selectivity and water permeability suggests that attempts to prepare such materials should rely on approaches that do more than simply vary polymer free volume. One strategy is to functionalize hydrocarbon polymers with fixed charge groups that can ionize upon exposure to water, and the presence of charged groups in the polymer influences transport properties. Additionally, in many emerging energy applications, charged polymers are exposed to ions that are very different from sodium and chloride. Specific ion effects have been observed in charged polymers, and these effects must be understood to prepare charged polymers that will enable emerging energy technologies. This presentation discusses research aimed at further understanding fundamental structure/property relationships that govern water and ion transport in charged polymer films considered for desalination and electric potential field-driven applications that can help address global needs for clean water and energy.

  8. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications.

    Science.gov (United States)

    Hiruma-Shimizu, Kazumi; Shimizu, Hiroki; Thompson, Gary S; Kalverda, Arnout P; Patching, Simon G

    2015-01-01

    Detergents are amphiphilic compounds that have crucial roles in the extraction, purification and stabilization of integral membrane proteins and in experimental studies of their structure and function. One technique that is highly dependent on detergents for solubilization of membrane proteins is solution-state NMR spectroscopy, where detergent micelles often serve as the best membrane mimetic for achieving particle sizes that tumble fast enough to produce high-resolution and high-sensitivity spectra, although not necessarily the best mimetic for a biomembrane. For achieving the best quality NMR spectra, detergents with partial or complete deuteration can be used, which eliminate interfering proton signals coming from the detergent itself and also eliminate potential proton relaxation pathways and strong dipole-dipole interactions that contribute line broadening effects. Deuterated detergents have also been used to solubilize membrane proteins for other experimental techniques including small angle neutron scattering and single-crystal neutron diffraction and for studying membrane proteins immobilized on gold electrodes. This is a review of the properties, chemical synthesis and applications of detergents that are currently commercially available and/or that have been synthesized with partial or complete deuteration. Specifically, the detergents are sodium dodecyl sulphate (SDS), lauryldimethylamine-oxide (LDAO), n-octyl-β-D-glucoside (β-OG), n-dodecyl-β-D-maltoside (DDM) and fos-cholines including dodecylphosphocholine (DPC). The review also considers effects of deuteration, detergent screening and guidelines for detergent selection. Although deuterated detergents are relatively expensive and not always commercially available due to challenges associated with their chemical synthesis, they will continue to play important roles in structural and functional studies of membrane proteins, especially using solution-state NMR.

  9. Membrane undulations in a structured fluid: Universal dynamics at intermediate length and time scales.

    Science.gov (United States)

    Granek, Rony; Diamant, Haim

    2018-01-05

    The dynamics of membrane undulations inside a viscous solvent is governed by distinctive, anomalous, power laws. Inside a viscoelastic continuous medium these universal behaviors are modified by the specific bulk viscoelastic spectrum. Yet, in structured fluids the continuum limit is reached only beyond a characteristic correlation length. We study the crossover to this asymptotic bulk dynamics. The analysis relies on a recent generalization of the hydrodynamic interaction in structured fluids, which shows a slow spatial decay of the interaction toward the bulk limit. For membranes which are weakly coupled to the structured medium we find a wide crossover regime characterized by different, universal, dynamic power laws. We discuss various systems for which this behavior is relevant, and delineate the time regime over which it may be observed.

  10. Structure and distribution of the Bacillus thuringiensis Cry4Ba toxin in lipid membranes

    Energy Technology Data Exchange (ETDEWEB)

    Puntheeranurak, Theeraporn [Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz (Austria); Laboratory of Molecular Biophysics, Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakornpathom 73170 (Thailand); Stroh, Cordula [Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz (Austria); Zhu Rong [Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz (Austria); Angsuthanasombat, Chanan [Laboratory of Molecular Biophysics, Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakornpathom 73170 (Thailand); Hinterdorfer, Peter [Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz (Austria)]. E-mail: peter.hinterdorfer@jku.at

    2005-11-15

    Bacillus thuringiensis Cry {delta}-endotoxins cause death of susceptible insect larvae by forming lytic pores in the midgut epithelial cell membranes. The 65 kDa trypsin activated Cry4Ba toxin was previously shown to be capable of permeabilizing liposomes and forming ionic channels in receptor-free planar lipid bilayers. Here, magnetic ACmode (MACmode) atomic force microscopy (AFM) was used to characterize the lateral distribution and the native molecular structure of the Cry4Ba toxin in the membrane. Liposome fusion and the Langmuir-Blodgett technique were employed for supported lipid bilayer preparations. The toxin preferentially inserted in a self-assembled structure, rather than as a single monomeric molecule. In addition, the spontaneous insertion into receptor-free lipid bilayers lead to formation of characteristic pore-like structures with four-fold symmetry, suggesting that tetramers are the preferred oligomerization state of this toxin.

  11. Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

    KAUST Repository

    Xue, Zheng

    2014-07-15

    Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community. © 2014 © 2014 Taylor & Francis.

  12. Structure and distribution of the Bacillus thuringiensis Cry4Ba toxin in lipid membranes

    International Nuclear Information System (INIS)

    Puntheeranurak, Theeraporn; Stroh, Cordula; Zhu Rong; Angsuthanasombat, Chanan; Hinterdorfer, Peter

    2005-01-01

    Bacillus thuringiensis Cry δ-endotoxins cause death of susceptible insect larvae by forming lytic pores in the midgut epithelial cell membranes. The 65 kDa trypsin activated Cry4Ba toxin was previously shown to be capable of permeabilizing liposomes and forming ionic channels in receptor-free planar lipid bilayers. Here, magnetic ACmode (MACmode) atomic force microscopy (AFM) was used to characterize the lateral distribution and the native molecular structure of the Cry4Ba toxin in the membrane. Liposome fusion and the Langmuir-Blodgett technique were employed for supported lipid bilayer preparations. The toxin preferentially inserted in a self-assembled structure, rather than as a single monomeric molecule. In addition, the spontaneous insertion into receptor-free lipid bilayers lead to formation of characteristic pore-like structures with four-fold symmetry, suggesting that tetramers are the preferred oligomerization state of this toxin

  13. Structure determination of an integral membrane protein at room temperature from crystals in situ

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Hu, Nien-Jen; Choudhury, Hassanul Ghani [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Kyoto University, Kyoto 606-8501 (Japan); Beis, Konstantinos [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE (United Kingdom); Imperial College London, London SW7 2AZ (United Kingdom); Rutherford Appleton Laboratory, Oxfordshire OX11 0FA (United Kingdom)

    2015-05-14

    The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines.

  14. Structure determination of an integral membrane protein at room temperature from crystals in situ

    International Nuclear Information System (INIS)

    Axford, Danny; Foadi, James; Hu, Nien-Jen; Choudhury, Hassanul Ghani; Iwata, So; Beis, Konstantinos; Evans, Gwyndaf; Alguel, Yilmaz

    2015-01-01

    The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated. The structure determination of an integral membrane protein using synchrotron X-ray diffraction data collected at room temperature directly in vapour-diffusion crystallization plates (in situ) is demonstrated. Exposing the crystals in situ eliminates manual sample handling and, since it is performed at room temperature, removes the complication of cryoprotection and potential structural anomalies induced by sample cryocooling. Essential to the method is the ability to limit radiation damage by recording a small amount of data per sample from many samples and subsequently assembling the resulting data sets using specialized software. The validity of this procedure is established by the structure determination of Haemophilus influenza TehA at 2.3 Å resolution. The method presented offers an effective protocol for the fast and efficient determination of membrane-protein structures at room temperature using third-generation synchrotron beamlines

  15. Anti-deformed Polyacrylonitrile/Polysulfone Composite Membrane with Binary Structures for Effective Air Filtration.

    Science.gov (United States)

    Zhang, Shichao; Liu, Hui; Yin, Xia; Yu, Jianyong; Ding, Bin

    2016-03-01

    Airborne particle filtration proposed for fibers requires their assembly into porous structures with small pore size and low packing density. The ability to maintain structural stability upon deformation stress in service is essential to ensure a highly porous packing material that functions reliably; however, it has proven extremely challenging. Here, we report a strategy to create anti-deformed poly(ethylene oxide)@polyacrylonitrile/polysulfone (PEO@PAN/PSU) composite membranes with binary structures for effective air filtration by combining multijet electrospinning and physical bonding process. Our approach allows the ambigenous fiber framework including thin PAN nanofibers and fluffy PSU microfibers, through which run interpenetrating PEO bonding structures, to assemble into stable filtration medium with tunable pore size and packing density by facilely optimizing the bimodal fiber construction and benefiting from the PEO inspiration. With the integrated features of small pore size, high porosity, and robust mechanical properties (8.2 MPa), the resultant composite membrane exhibits high filtration efficiency of 99.992%, low pressure drop of 95 Pa, and desirable quality factor of 0.1 Pa(-1); more significantly, it successfully gets rid of the potential safety hazards caused by unexpected structural collapsing under service stress. The synthesis of PEO@PAN/PSU medium would not only make it a promising candidate for PM2.5 governance but also provide a versatile strategy to design and develop stable porous membranes for various applications.

  16. Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

    Science.gov (United States)

    Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

    2012-06-06

    Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. The Effect of Knowledge Linking Levels in Biology Lessons upon Students' Knowledge Structure

    Science.gov (United States)

    Wadouh, Julia; Liu, Ning; Sandmann, Angela; Neuhaus, Birgit J.

    2014-01-01

    Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in…

  18. The Learning of Biology: A Structural Basis for Future Research

    Science.gov (United States)

    Murray, Darrel L.

    1977-01-01

    This article reviews recent research studies and experiences relating the learning theories of Ausubel to biology instruction. Also some suggestions are made for future research on the learning of biology. (MR)

  19. Polyphenols from Bee Pollen: Structure, Absorption, Metabolism and Biological Activity

    Directory of Open Access Journals (Sweden)

    Anna Rzepecka-Stojko

    2015-12-01

    Full Text Available Bee pollen constitutes a natural source of antioxidants such as phenolic acids and flavonoids, which are responsible for its biological activity. Research has indicated the correlation between dietary polyphenols and cardioprotective, hepatoprotective, anti-inflammatory, antibacterial, anticancerogenic, immunostimulating, antianaemic effects, as well as their beneficial influence on osseous tissue. The beneficial effects of bee pollen on health result from the presence of phenolic acids and flavonoids which possess anti-inflammatory properties, phytosterol and linolenic acid which play an anticancerogenic role, and polysaccharides which stimulate immunological activity. Polyphenols are absorbed in the alimentary tract, metabolised by CYP450 enzymes, and excreted with urine and faeces. Flavonoids and phenolic acids are characterised by high antioxidative potential, which is closely related to their chemical structure. The high antioxidant potential of phenolic acids is due to the presence and location of hydroxyl groups, a carboxyl group in the immediate vicinity of ortho-diphenolic substituents, and the ethylene group between the phenyl ring and the carboxyl group. As regards flavonoids, essential structural elements are hydroxyl groups at the C5 and C7 positions in the A ring, and at the C3′ and C4′ positions in the B ring, and a hydroxyl group at the C3 position in the C ring. Furthermore, both, the double bond between C2 and C3, and a ketone group at the C4 position in the C ring enhance the antioxidative potential of these compounds. Polyphenols have an ideal chemical structure for scavenging free radicals and for creating chelates with metal ions, which makes them effective antioxidants in vivo.

  20. From structure of the complex to understanding of the biology

    Energy Technology Data Exchange (ETDEWEB)

    Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

  1. Membrane Protein Structure Determination Using Crystallography and Lipidic Mesophases - Recent Advances and Successes

    Science.gov (United States)

    Caffrey, Martin; Li, Dianfan; Dukkipati, Abhiram

    2012-01-01

    The crystal structure of the β2-adrenergic receptor in complex with an agonist and its cognate G protein has just recently been solved. It is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signalling event across the membrane and sets in motion a series of G protein-directed intracellular responses. The structure was determined using crystals of the ternary complex grown in a rationally designed lipidic mesophase by the so-called in meso method. The method is proving to be particularly useful in the G protein-coupled receptor field where the structures of thirteen distinct receptor types have been solved in the past five years. In addition to receptors, the method has proven useful with a wide variety of integral membrane protein classes that include bacterial and eukaryotic rhodopsins, a light harvesting complex II (LHII), photosynthetic reaction centers, cytochrome oxidases, β-barrels, an exchanger, and an integral membrane peptide. This attests to the versatility and range of the method and supports the view that the in meso method should be included in the arsenal of the serious membrane structural biologist. For this to happen however, the reluctance in adopting it attributable, in part, to the anticipated difficulties associated with handling the sticky, viscous cubic mesophase in which crystals grow must be overcome. Harvesting and collecting diffraction data with the mesophase-grown crystals is also viewed with some trepidation. It is acknowledged that there are challenges associated with the method. Over the years, we have endeavored to establish how the method works at a molecular level and to make it user-friendly. To these ends, tools for handling the mesophase in the pico- to nano-liter volume range have been developed for highly efficient crystallization screening in manual and robotic modes. Methods have been implemented for evaluating the functional

  2. Structural and dynamical insights into the membrane-bound α-synuclein.

    Directory of Open Access Journals (Sweden)

    Neha Jain

    Full Text Available Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES, which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (∼ 15 Å layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could

  3. Intramolecular energy transfer at donor-acceptor interactions in model and biological membranes

    International Nuclear Information System (INIS)

    Umarova, Fatima T.

    2011-01-01

    Intramolecular triplet-triplet energy transfer between molecules of sensibilisator and photochrome for registration of protein interactions in the membrane preparation of Na,K-ATPase was investigated. Erythrosinithiocyanate (ERITC) was used as the triplet label of sensibilisator, and 4-acetoamido-4 -isothiocyanatostilbene-2,2 disullfonic acid (SITS) was used as the photochrome label. Na,K-ATPase preparations were covalently bound with ERITC in active centre of enzyme, and SITS molecules were covalently bound by NH2-groups. In model system, in chymotrypsinogene molecule, SITS and ERITC labels were used also. The cis-trans-isomerization of SITS was initiated by triplet-triplet energy transfer from light excited ERITC molecule to photochrome. The kinetics of isomerization was recorded by the SITS fluorescence measurements. The constant of rate of triplet-triplet energy transfer from ERITC to cis-isomers of SITS in Na,K-ATPase was determined as (3-7)x10 3 M -1 s -1 , and in model system it equals 1x 10 7 M 1 s -1 . The value of energy transfer between loos molecules of erythrosine and SITS in buffer solution equaled to 7x10 7 M -1 s -1 . This drop of R m y in the membrane preparation of Na,K-ATPase at 10 4 reflected the decrease in the frequency of label collisions caused by the increase in the media viscosity and steric hindrances. (author)

  4. Supramolecular structures of peptide assemblies in membranes by neutron off-plane scattering: method of analysis.

    Science.gov (United States)

    Yang, L; Weiss, T M; Harroun, T A; Heller, W T; Huang, H W

    1999-11-01

    In a previous paper (Yang et al., Biophys. J. 75:641-645, 1998), we showed a simple, efficient method of recording the diffraction patterns of supramolecular peptide assemblies in membranes where the samples were prepared in the form of oriented multilayers. Here we develop a method of analysis based on the diffraction theory of two-dimensional liquids. Gramicidin was used as a prototype model because its pore structure in membrane in known. At full hydration, the diffraction patterns of alamethicin and magainin are similar to gramicidin except in the scale of q (the momentum transfer of scattering), clearly indicating that both alamethicin and magainin form pores in membranes but of different sizes. When the hydration of the multilayer samples was decreased while the bilayers were still fluid, the in-plane positions of the membrane pores became correlated from one bilayer to the next. We believe that this is a new manifestation of the hydration force. The effect is most prominent in magainin patterns, which are used to demonstrate the method of analysis. When magainin samples were further dehydrated or cooled, the liquid-like diffraction turned into crystal-like patterns. This discovery points to the possibility of investigating the supramolecular structures with high-order diffraction.

  5. Structure of the membrane anchor of pestivirus glycoprotein E(rns, a long tilted amphipathic helix.

    Directory of Open Access Journals (Sweden)

    Daniel Aberle

    2014-02-01

    Full Text Available E(rns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the E(rns membrane contact, processing and secretion.

  6. Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix

    Science.gov (United States)

    Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S.; Meyers, Gregor

    2014-01-01

    Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the Erns membrane contact, processing and secretion. PMID:24586172

  7. Structure of the membrane anchor of pestivirus glycoprotein E(rns), a long tilted amphipathic helix.

    Science.gov (United States)

    Aberle, Daniel; Muhle-Goll, Claudia; Bürck, Jochen; Wolf, Moritz; Reißer, Sabine; Luy, Burkhard; Wenzel, Wolfgang; Ulrich, Anne S; Meyers, Gregor

    2014-02-01

    E(rns) is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the E(rns) membrane contact, processing and secretion.

  8. The effect of natural and synthetic fatty acids on membrane structure, microdomain organization, cellular functions and human health.

    Science.gov (United States)

    Ibarguren, Maitane; López, David J; Escribá, Pablo V

    2014-06-01

    This review deals with the effects of synthetic and natural fatty acids on the biophysical properties of membranes, and on their implication on cell function. Natural fatty acids are constituents of more complex lipids, like triacylglycerides or phospholipids, which are used by cells to store and obtain energy, as well as for structural purposes. Accordingly, natural and synthetic fatty acids may modify the structure of the lipid membrane, altering its microdomain organization and other physical properties, and provoking changes in cell signaling. Therefore, by modulating fatty acids it is possible to regulate the structure of the membrane, influencing the cell processes that are reliant on this structure and potentially reverting pathological cell dysfunctions that may provoke cancer, diabetes, hypertension, Alzheimer's and Parkinson's disease. The so-called Membrane Lipid Therapy offers a strategy to regulate the membrane composition through drug administration, potentially reverting pathological processes by re-adapting cell membrane structure. Certain fatty acids and their synthetic derivatives are described here that may potentially be used in such therapies, where the cell membrane itself can be considered as a target to combat disease. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Structural characterization of Bacillus subtilis membrane protein Bmr: an in silico approach.

    Science.gov (United States)

    Nargotra, Amit; Rukmankesh; Ali, Shakir; Koul, Surrinder

    2014-01-01

    Efflux pump--a membrane protein belonging to Major Facilitator (MF) family and associated with Multi Drug Resistance (MDR) has been a major factor in drug resistance of bacteria. In the era when no new effective antibiotic had been reported for years, the detailed study of these membrane proteins became imperative in order to improve the efficacy of existing drugs. The Bacillus subtilis membrane protein Bmr belongs to the super family of major facilitator proteins and is one of the first-discovered bacterial multidrug-efflux transporters. Development of Bmr inhibitors (B. subtilis) for least resistance, better drug sustainability and effective cellular activity requires three dimensional structure of this protein which has not yet been determined. In this communication structural characterization of this important efflux pump has been attempted using in silico approaches. The modeled structure of Bmr has been found to have 12 main helical segments interspersed by loops of variable lengths at regular intervals with both N- and C-termini on the same side of membrane. Docking of the known inhibitor reserpine on to the predicted structure of Bmr and its mutants signified the importance of the residues Phe143, Val286 and Phe306 in the interaction with the ligand. Besides this, the role of Arg313 and Phe309 in the H-bond formation and π-π interaction respectively, with reserpine was the new significant finding based on the interaction studies. The structure elucidation of Bmr and the role of these residues in binding to the ligand are expected to have a great impact on the efflux pump inhibition studies around the world and hence in the efficiency of the existing antibiotic drugs.

  10. Fiber Temperature Sensor Based on Micro-mechanical Membranes and Optical Interference Structure

    International Nuclear Information System (INIS)

    Liu Yueming; Tian Weijian; Hua Jing

    2011-01-01

    A novel fiber temperature sensor is presented theoretically and experimentally in this paper. Its working principle is based on Optical Fabry-Perot interference structure that is formed between a polished optical fiber end and micro-mechanical Bi-layered membranes. When ambient temperature is varying, Bi-layered membranes will be deflected and the length of Fabry-Perot cavity will be changed correspondingly. By detecting the reflecting optical intensity from the Fabry-Perot cavity, the ambient temperature can be measured. Using finite element software ANSYS, the sensor structure was optimized based on optical Interference theory and Bi-layered membranes thermal expansion theory, and theoretical characteristics was simulated by computer software. In the end, using optical fiber 2x2 coupler and photo-electrical detector, the fabricated sample sensor was tested successfully by experiment that demonstrating above theoretical analysis and simulation results. This sensor has some favorable features, such as: micro size owing to its micro-mechanical structure, high sensitivity owing to its working Fabry-Perot interference cavity structure, and optical integration character by using optical fiber techniques.

  11. Structure Prediction of Outer Membrane Protease Protein of Salmonella typhimurium Using Computational Techniques

    Directory of Open Access Journals (Sweden)

    Rozina Tabassum

    2016-03-01

    Full Text Available Salmonella typhimurium, a facultative gram-negative intracellular pathogen belonging to family Enterobacteriaceae, is the most frequent cause of human gastroenteritis worldwide. PgtE gene product, outer membrane protease emerges important in the intracellular phases of salmonellosis. The pgtE gene product of S. typhimurium was predicted to be capable of proteolyzing T7 RNA polymerase and localize in the outer membrane of these gram negative bacteria. PgtE product of S. enterica and OmpT of E. coli, having high sequence similarity have been revealed to degrade macrophages, causing salmonellosis and other diseases. The three-dimensional structure of the protein was not available through Protein Data Bank (PDB creating lack of structural information about E protein. In our study, by performing Comparative model building, the three dimensional structure of outer membrane protease protein was generated using the backbone of the crystal structure of Pla of Yersinia pestis, retrieved from PDB, with MODELLER (9v8. Quality of the model was assessed by validation tool PROCHECK, web servers like ERRAT and ProSA are used to certify the reliability of the predicted model. This information might offer clues for better understanding of E protein and consequently for developmet of better therapeutic treatment against pathogenic role of this protein in salmonellosis and other diseases.

  12. Effective high-throughput overproduction of membrane proteins in Escherichia coli.

    NARCIS (Netherlands)

    Gordon, E.; Horsefield, R.; Swarts, H.G.P.; Pont, J.J.H.H.M. de; Neutze, R.; Snijder, A.

    2008-01-01

    Structural biology is increasingly reliant on elevated throughput methods for protein production. In particular, development of efficient methods of heterologous production of membrane proteins is essential. Here, we describe the heterologous overproduction of 24 membrane proteins from the human

  13. Fluorescent probes for detecting cholesterol-rich ordered membrane microdomains: entangled relationships between structural analogies in the membrane and functional homologies in the cell

    Directory of Open Access Journals (Sweden)

    Gérald Gaibelet

    2017-02-01

    Full Text Available This review addresses the question of fluorescent detection of ordered membrane (micro domains in living (cultured cells, with a “practical” point of view since the situation is much more complicated than for studying model membranes. We first briefly recall the bases of model membrane structural organization involving liquid-ordered and -disordered phases, and the main features of their counterparts in cell membranes that are the various microdomains. We then emphasize the utility of the fluorescent probes derived from cholesterol, and delineate the respective advantages, limitations and drawbacks of the existing ones. In particular, besides their intra-membrane behavior, their relevant characteristics should integrate their different cellular fates for membrane turn-over, trafficking and metabolism, in order to evaluate and improve their efficiency for in-situ probing membrane microdomains in the cell physiology context. Finally, at the present stage, it appears that Bdp-Chol and Pyr-met-Chol display well complementary properties, allowing to use them in combination to improve the reliability of the current experimental approaches. But the field is still open, and there remains much work to perform in this research area.

  14. Structural diversity and biological significance of lipoteichoic acid in Gram-positive bacteria: focusing on beneficial probiotic lactic acid bacteria.

    Science.gov (United States)

    Shiraishi, Tsukasa; Yokota, Shinichi; Fukiya, Satoru; Yokota, Atsushi

    2016-01-01

    Bacterial cell surface molecules are at the forefront of host-bacterium interactions. Teichoic acids are observed only in Gram-positive bacteria, and they are one of the main cell surface components. Teichoic acids play important physiological roles and contribute to the bacterial interaction with their host. In particular, lipoteichoic acid (LTA) anchored to the cell membrane has attracted attention as a host immunomodulator. Chemical and biological characteristics of LTA from various bacteria have been described. However, most of the information concerns pathogenic bacteria, and information on beneficial bacteria, including probiotic lactic acid bacteria, is insufficient. LTA is structurally diverse. Strain-level structural diversity of LTA is suggested to underpin its immunomodulatory activities. Thus, the structural information on LTA in probiotics, in particular strain-associated diversity, is important for understanding its beneficial roles associated with the modulation of immune response. Continued accumulation of structural information is necessary to elucidate the detailed physiological roles and significance of LTA. In this review article, we summarize the current state of knowledge on LTA structure, in particular the structure of LTA from lactic acid bacteria. We also describe the significance of structural diversity and biological roles of LTA.

  15. Study of the aerobic biological treatment of slaughterhouse wastewater by membrane process

    International Nuclear Information System (INIS)

    Ben yahmed, Nesrine

    2011-01-01

    The objective of this work is to study the performance of aerobic treatment of slaughterhouse wastewater by a side-stream membrane bioreactor (MBR) with semi-frontal filtration and to evaluate the sludge production generated by this system treatment. The MBR was fed with a flow rate of 5 L/d. The wastewater used in this study was collected from the WWTP Ellouhoum following pretreatment operations. They are characterized by an average total COD concentration of approximately 2 g/L. The mass load applied to the system was 0.18 g COD/gVSS.d. The results show that COD and total nitrogen removal efficiencies are respectively estimated at 90.66 pour cent and 92.86 pour cent. Treatment with MBR also allows a total elimination of TSS, fecal coliforms and pathogens. With a total biomass recycling, low sludge yield (Yobs) of 0.106 gTSS/g COD eliminated was obtained.

  16. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of catalytic ultrasound oxidation and membrane bioreactor.

    Science.gov (United States)

    Jia, Shengyong; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Hou, Baolin

    2015-01-01

    Laboratorial scale experiments were conducted to investigate a novel system integrating catalytic ultrasound oxidation (CUO) with membrane bioreactor (CUO-MBR) on advanced treatment of biologically pretreated coal gasification wastewater. Results indicated that CUO with catalyst of FeOx/SBAC (sewage sludge based activated carbon (SBAC) which loaded Fe oxides) represented high efficiencies in eliminating TOC as well as improving the biodegradability. The integrated CUO-MBR system with low energy intensity and high frequency was more effective in eliminating COD, BOD5, TOC and reducing transmembrane pressure than either conventional MBR or ultrasound oxidation integrated MBR. The enhanced hydroxyl radical oxidation, facilitation of substrate diffusion and improvement of cell enzyme secretion were the mechanisms for CUO-MBR performance. Therefore, the integrated CUO-MBR was the promising technology for advanced treatment in engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Toxin studies using an integrated biophysical and structural biology approach.

    Energy Technology Data Exchange (ETDEWEB)

    Last, Julie A.; Schroeder, Anne E.; Slade, Andrea Lynn; Sasaki, Darryl Yoshio; Yip, Christopher M. (University of Toronto, Toronto, Ontario, Canada); Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA)

    2005-03-01

    Clostridial neurotoxins, such as botulinum and tetanus, are generally thought to invade neural cells through a process of high affinity binding mediated by gangliosides, internalization via endosome formation, and subsequent membrane penetration of the catalytic domain activated by a pH drop in the endosome. This surface recognition and internalization process is still not well understood with regard to what specific membrane features the toxins target, the intermolecular interactions between bound toxins, and the molecular conformational changes that occur as a result of pH lowering. In an effort to elucidate the mechanism of tetanus toxin binding and permeation through the membrane a simple yet representative model was developed that consisted of the ganglioside G{sub tlb} incorporated in a bilayer of cholesterol and DPPC (dipalmitoylphosphatidyl choline). The bilayers were stable over time yet sensitive towards the binding and activity of whole toxin. A liposome leakage study at constant pH as well as with a pH gradient, to mimic the processes of the endosome, was used to elucidate the effect of pH on the toxin's membrane binding and permeation capability. Topographic imaging of the membrane surface, via in situ tapping mode AFM, provided nanoscale characterization of the toxin's binding location and pore formation activity.

  18. Effects of the Membrane Action of Tetralin on the Functional and Structural Properties of Artificial and Bacterial Membranes

    NARCIS (Netherlands)

    SIKKEMA, J; POOLMAN, B; KONINGS, WN; DEBONT, JAM

    Tetralin is toxic to bacterial cells at concentrations below 100-mu-mol/liter. To assess the inhibitory action of tetralin on bacterial membranes, a membrane model system, consisting of proteoliposomes in which beef heart cytochrome c oxidase was reconstituted as the proton motive force-generating

  19. Comprehensive report of the overall activities of the contract during the past three years. [Physical properties of biological membranes

    Energy Technology Data Exchange (ETDEWEB)

    Keith, A.D.

    1976-01-01

    The research accomplishments carried out during the last three years of support by ERDA are outlined. These entail various experiments that were carried out using spin labels to uncover information about the physical properties of biological membranes. A second general approach that was developed by this laboratory during that period was the use of paramagnetic broadening agents as an approach to explore certain restricted areas of cell and cellular systems through the use of spin labels. By utilization of this approach it is possible to remove the spin label signal from heterogeneous environments from all zones except a particular one. The third general area of accomplishment during this interval was the initiation of a class of spin labels which we call surface labels. These labels are designed to label the aqueous hydrocarbon interface of one side of a membrane enclosure. This approach is still new to us and its full potential is not yet developed, but we believe it is a profitable approach; it overcomes a number of the criticisms that have been leveled at spin labels over the years. A list of publications is included that report findings in detail.

  20. Physico-mechanical and structural properties of eggshell membrane gelatin- chitosan blend edible films.

    Science.gov (United States)

    Mohammadi, Reza; Mohammadifar, Mohammad Amin; Rouhi, Milad; Kariminejad, Mohaddeseh; Mortazavian, Amir Mohammad; Sadeghi, Ehsan; Hasanvand, Sara

    2018-02-01

    This study investigated the physico-mechanical and structural properties of composite edible films based on eggshell membrane gelatin (G) and chitosan (Ch) (75G:25Ch, 50G:50Ch, 25G:75Ch). The results demonstrated that the addition of Ch increased elongation at break significantly (pfilm. The water solubility and water vapor permeability of the 50G:50Ch film decreased significantly compared to plain films (100G:0Ch and 0G:100Ch) and other composite films (pfilms; it revealed a homogenous and compact structure in 75G:25Ch and 50G:50 Ch. Also, the chemical interactions introduced by the addition of chitosan to eggshell membrane gelatin as new resources could improve the films' functional properties. Copyright © 2017. Published by Elsevier B.V.