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Sample records for acyl chain dynamics

  1. Comparison of the lipid acyl chain dynamics between small and large unilamellar vesicles.

    PubMed Central

    Lepore, L S; Ellena, J F; Cafiso, D S

    1992-01-01

    13C NMR spin-lattice relaxation (T1) rates and 13C-1H nuclear Overhauser effects (NOEs) were measured in an identical fashion in two lipid preparations having dramatically different curvatures. The T1 times that were obtained at four magnetic field strengths were fit along with the NOEs to simple models for lipid molecular dynamics. The results indicate that phospholipid chain ordering and dynamics are virtually identical in small and large unilamellar vesicles at the time scales sampled by these 13C-NMR studies. The order parameters and reorientational correlation times that characterize the amplitudes and rates of internal acyl chain motions were equal within experimental error for the methylene segments in the middle of the chains. The only significant differences in order parameters and correlation times between the two vesicle types were small and appeared at the ends of the acyl chains. At the carbonyl end the order was slightly higher in small vesicles than large vesicles, and at the methyl end the order was slightly lower for small vesicles. This indicates that in the more planar systems the acyl chains exhibit a slightly flatter order profile than in more highly curved membranes. The use of the same experimental approach in both small and large vesicle systems provided a more reliable and accurate assessment of the effect of curvature on molecular order than has been previously obtained. PMID:1504247

  2. Insights into Medium-chain Acyl-CoA Dehydrogenase Structure by Molecular Dynamics Simulations.

    PubMed

    Bonito, Cátia A; Leandro, Paula; Ventura, Fátima V; Guedes, Rita C

    2016-08-01

    The medium-chain acyl-CoA dehydrogenase (MCAD) is a mitochondrial enzyme that catalyzes the first step of mitochondrial fatty acid β-oxidation (mFAO) pathway. Its deficiency is the most common genetic disorder of mFAO. Many of the MCAD disease-causing variants, including the most common p.K304E variant, show loss of function due to protein misfolding. Herein, we used molecular dynamics simulations to provide insights into the structural stability and dynamic behavior of MCAD wild-type (MCADwt) and validate a structure that would allow reliable new studies on its variants. Our results revealed that in both proteins the flavin adenine dinucleotide (FAD) has an important structural role on the tetramer stability and also in maintaining the volume of the enzyme catalytic pockets. We confirmed that the presence of substrate changes the dynamics of the catalytic pockets and increases FAD affinity. A comparison between the porcine MCADwt (pMCADwt) and human MCADwt (hMCADwt) structures revealed that both proteins are essentially similar and that the reversion of the double mutant E376G/T255E of hMCAD enzyme does not affect the structure of the protein neither its behavior in simulation. Our validated hMCADwt structure is crucial for complementing and accelerating the experimental studies aiming for the discovery and development of potential stabilizers of MCAD variants as candidates for the treatment of MCAD deficiency (MCADD).

  3. Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order.

    PubMed

    Chiantia, Salvatore; London, Erwin

    2012-12-05

    A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholine (PC) in the inner leaflet and sphingomyelin (SM) in the outer leaflet. The coupling of both lateral diffusion and membrane order was monitored as a function of PC and SM acyl chain structure. The presence in the outer leaflet of brain SM, which decreased outer-leaflet lateral diffusion, had little effect upon lateral diffusion in inner leaflets composed of dioleoyl PC (i.e., diffusion was only weakly coupled in the two leaflets) but did greatly reduce lateral diffusion in inner leaflets composed of PC with one saturated and one oleoyl acyl chain (i.e., diffusion was strongly coupled in these cases). In addition, reduced outer-leaflet diffusion upon introduction of outer-leaflet milk SM or a synthetic C24:0 SM, both of which have long interdigitating acyl chains, also greatly reduce diffusion of inner leaflets composed of dioleoyl PC, indicative of strong coupling. Strikingly, several assays showed that the ordering of the outer leaflet induced by the presence of SM was not reflected in increased lipid order in the inner leaflet, i.e., there was no detectable coupling between inner and outer leaflet membrane order. We propose a model for how lateral diffusion can be coupled in opposite leaflets and discuss how this might impact membrane function.

  4. Fatty Acyl Chains of Mycobacterium marinum Lipooligosaccharides

    PubMed Central

    Rombouts, Yoann; Alibaud, Laeticia; Carrère-Kremer, Séverine; Maes, Emmanuel; Tokarski, Caroline; Elass, Elisabeth; Kremer, Laurent; Guérardel, Yann

    2011-01-01

    We have recently established the fine structure of the glycan backbone of lipooligosaccharides (LOS-I to LOS-IV) isolated from Mycobacterium marinum, a close relative of Mycobacterium tuberculosis. These studies culminated with the description of an unusual terminal N-acylated monosaccharide that confers important biological functions to LOS-IV, such as macrophage activation, that may be relevant to granuloma formation. It was, however, also suggested that the lipid moiety was required for LOSs to exert their immunomodulatory activity. Herein, using highly purified LOSs from M. marinum, we have determined through a combination of mass spectrometric and NMR techniques, the structure and localization of the fatty acids composing the lipid moiety. The occurrence of two distinct polymethyl-branched fatty acids presenting specific localizations is consistent with the presence of two highly related polyketide synthases (Pks5 and Pks5.1) in M. marinum and presumably involved in the synthesis of these fatty acyl chains. In addition, a bioinformatic search permitted us to identify a set of enzymes potentially involved in the biosynthesis or transfer of these lipids to the LOS trehalose unit. These include MMAR_2343, a member of the Pap (polyketide-associated protein) family, that acylates trehalose-based glycolipids in M. marinum. The participation of MMAR_2343 to LOS assembly was demonstrated using a M. marinum mutant carrying a transposon insertion in the MMAR_2343 gene. Disruption of MMAR_2343 resulted in a severe LOS breakdown, indicating that MMAR_2343, hereafter designated PapA4, fulfills the requirements for LOS acylation and assembly. PMID:21803773

  5. Metabolic Glycoengineering with N-Acyl Side Chain Modified Mannosamines.

    PubMed

    Wratil, Paul R; Horstkorte, Rüdiger; Reutter, Werner

    2016-08-08

    In metabolic glycoengineering (MGE), cells or animals are treated with unnatural derivatives of monosaccharides. After entering the cytosol, these sugar analogues are metabolized and subsequently expressed on newly synthesized glycoconjugates. The feasibility of MGE was first discovered for sialylated glycans, by using N-acyl-modified mannosamines as precursor molecules for unnatural sialic acids. Prerequisite is the promiscuity of the enzymes of the Roseman-Warren biosynthetic pathway. These enzymes were shown to tolerate specific modifications of the N-acyl side chain of mannosamine analogues, for example, elongation by one or more methylene groups (aliphatic modifications) or by insertion of reactive groups (bioorthogonal modifications). Unnatural sialic acids are incorporated into glycoconjugates of cells and organs. MGE has intriguing biological consequences for treated cells (aliphatic MGE) and offers the opportunity to visualize the topography and dynamics of sialylated glycans in vitro, ex vivo, and in vivo (bioorthogonal MGE).

  6. The membrane interaction of amphiphilic model peptides affects phosphatidylserine headgroup and acyl chain order and dynamics. Application of the phospholipid headgroup electrometer concept to phosphatidylserine

    SciTech Connect

    de Kroon, A.I.P.M.; Killian, J.A.; de Gier, J.; de Kruijff, B. )

    1991-01-29

    Deuterium nuclear magnetic resonance ({sup 2}H NMR) was used to study the interaction of amphiphilic model peptides with model membranes consisting of 1,2-dioleoyl-sn-glycero-3-phospho-L-serine deuterated either at the {beta}-position of the serine moiety ((2-{sup 2}H)DOPS) or at the 11-position of the acyl chains ((11,11-{sup 2}H{sub 2})DOPS). The peptides are derived from the sequences H-Ala-Met-Leu-Trp-Ala-OH and H-Arg-Met-Leu-Trp-Ala-OH and contain a positive charge of +1 or +2 at the amino terminus or one positive charge at each end of the molecule. Upon titration of dispersions of DOPS with the peptides, the divalent peptides show a similar extent of binding to the DOPS bilyers, which is larger than that of the single charged peptide. Under these conditions the values of the quadrupolar splitting of both (2-{sup 2}H)DOPS and (11,11-{sup 2}H{sub 2})DOPS are decreased, indicating that the peptides reduce the order of both the DOPS headgroup and the acyl chains. The extent of the decrease depends on the amount of peptide bound and on the position of the charged moieties in the peptide molecule. Titrations of DOPS with poly(L-lysine){sub 100}, which were included for reasons of comparison, reveal increased {Delta}v{sub q} values. When the peptide-lipid titrations are carried out without applying a freeze-thaw procedure to achieve full equilibration, two-component {sup 2}H NMR spectra occur. The apparently limited accessibility of the lipid to the peptides under these circumstances is discussed in relation to the ability of the peptides to exhibit transbilayer movement. {sup 2}H spin-lattice relaxation time T1 measurements demonstrate a decrease of the rates of motion of both headgroup and acyl chains of DOPS in the presence of the peptides.

  7. Sphingomyelin interfacial behavior: the impact of changing acyl chain composition.

    PubMed Central

    Li, X M; Smaby, J M; Momsen, M M; Brockman, H L; Brown, R E

    2000-01-01

    Sphingomyelins (SMs) containing homogeneous acyl chains with 12, 14, 16, 18, 24, or 26 carbons were synthesized and characterized using an automated Langmuir-type film balance. Surface pressure was monitored as a function of lipid molecular area at constant temperatures between 10 degrees C and 30 degrees C. SM containing lauroyl (12:0) acyl chains displayed only liquid-expanded behavior. Increasing the length of the saturated acyl chain (e.g., 14:0, 16:0, or 18:0) resulted in liquid-expanded to condensed two-dimensional phase transitions at many temperatures in the 10-30 degrees C range. Similar behavior was observed for SMs with lignoceroyl (24:0) or (cerotoyl) 26:0 acyl chains, but isotherms showed only condensed behavior at 10 and 15 degrees C. Insights into the physico-mechanical in-plane interactions occurring within the different SM phases and accompanying changes in SM phase state were provided by analyzing the interfacial area compressibility moduli. At similar surface pressures, SM fluid phases were less compressible than those of phosphatidylcholines with similar chain structures. The area per molecule and compressibility of SM condensed phases depended upon the length of the saturated acyl chain and upon spreading temperature. Spreading of SMs with very long saturated acyl chains at temperatures 30-35 degrees below T(m) resulted in condensed films with lower in-plane compressibilities, but consistently larger cross-sectional molecular areas than the condensed phases achieved by spreading at temperatures only 10-20 degrees below T(m). This behavior is discussed in terms of the enhancement of SM lateral aggregation by temperature reduction, a common approach used during domain isolation from biomembranes. PMID:10733971

  8. Acyl chain conformations in phospholipid bilayers: a comparative study of docosahexaenoic acid and saturated fatty acids.

    PubMed

    Feller, Scott E

    2008-05-01

    A variety of experimental methods indicate unique biophysical properties of membranes containing the highly polyunsaturated omega-3 fatty acid, docosahexaenoic acid (DHA). In the following we review the atomically detailed picture of DHA acyl chains structure and dynamics that has emerged from computational studies of this system in our lab. A comprehensive approach, beginning with ab-initio quantum chemical studies of model compounds representing segments of DHA and ending with large scale classical molecular dynamics simulations of DHA-containing bilayers, is described with particular attention paid to contrasting the properties of DHA with those of saturated fatty acids. Connection with experiment is made primarily through comparison with Nuclear Magnetic Resonance (NMR) studies, particularly those that probe details of the chain structure and dynamics. Our computational results suggest that low torsional energy barriers, comparable to kT at physiological conditions, for the rotatable bonds in the DHA chain are the key to the differences observed between polyunsaturated and saturated acyl chains.

  9. Characterization of Lipid A Variants by Energy-Resolved Mass Spectrometry: Impact of Acyl Chains

    NASA Astrophysics Data System (ADS)

    Crittenden, Christopher M.; Akin, Lucas D.; Morrison, Lindsay J.; Trent, M. Stephen; Brodbelt, Jennifer S.

    2016-12-01

    Lipid A molecules consist of a diglucosamine sugar core with a number of appended acyl chains that vary in their length and connectivity. Because of the challenging nature of characterizing these molecules and differentiating between isomeric species, an energy-resolved MS/MS strategy was undertaken to track the fragmentation trends and map genealogies of product ions originating from consecutive cleavages of acyl chains. Generalizations were developed based on the number and locations of the primary and secondary acyl chains as well as variations in preferential cleavages arising from the location of the phosphate groups. Secondary acyl chain cleavage occurs most readily for lipid A species at the 3' position, followed by primary acyl chain fragmentation at both the 3' and 3 positions. In the instances of bisphosphorylated lipid A variants, phosphate loss occurs readily in conjunction with the most favorable primary and secondary acyl chain cleavages.

  10. Effects of Nanoparticle Morphology and Acyl Chain Length on Spontaneous Lipid Transfer Rates

    SciTech Connect

    Xia, Yan; Li, Ming; Charubin, Kamil; Liu, Ying; Heberle, Frederick A.; Katsaras, John; Jing, Benxin; Zhu, Yingxi; Nieh, Mu-Ping

    2015-11-05

    In this paper, we report on studies of lipid transfer rates between different morphology nanoparticles and lipids with different length acyl chains. The lipid transfer rate of dimyristoylphosphatidylcholine (di-C14, DMPC) in discoidal “bicelles” (0.156 h–1) is 2 orders of magnitude greater than that of DMPC vesicles (ULVs) (1.1 × 10–3 h–1). For both bicellar and ULV morphologies, increasing the acyl chain length by two carbons [going from di-C14 DMPC to di-C16, dipalmitoylphosphatidylcholine (DPPC)] causes lipid transfer rates to decrease by more than 2 orders of magnitude. Results from small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and fluorescence correlation spectroscopy (FCS) are in good agreement. Finally, the present studies highlight the importance of lipid dynamic processes taking place in different morphology biomimetic membranes.

  11. Effects of Nanoparticle Morphology and Acyl Chain Length on Spontaneous Lipid Transfer Rates

    DOE PAGES

    Xia, Yan; Li, Ming; Charubin, Kamil; ...

    2015-11-05

    In this paper, we report on studies of lipid transfer rates between different morphology nanoparticles and lipids with different length acyl chains. The lipid transfer rate of dimyristoylphosphatidylcholine (di-C14, DMPC) in discoidal “bicelles” (0.156 h–1) is 2 orders of magnitude greater than that of DMPC vesicles (ULVs) (1.1 × 10–3 h–1). For both bicellar and ULV morphologies, increasing the acyl chain length by two carbons [going from di-C14 DMPC to di-C16, dipalmitoylphosphatidylcholine (DPPC)] causes lipid transfer rates to decrease by more than 2 orders of magnitude. Results from small angle neutron scattering (SANS), differential scanning calorimetry (DSC), and fluorescence correlationmore » spectroscopy (FCS) are in good agreement. Finally, the present studies highlight the importance of lipid dynamic processes taking place in different morphology biomimetic membranes.« less

  12. A Cerulenin Insensitive Short Chain 3-Ketoacyl-Acyl Carrier Protein Synthase in Spinacia oleracea Leaves

    PubMed Central

    Jaworski, Jan G.; Clough, Richard C.; Barnum, Susan R.

    1989-01-01

    A cerulenin insensitive 3-ketoacyl-acyl carrier protein synthase has been assayed in extracts of spinach (Spinacia oleracea) leaf. The enzyme was active in the 40 to 80% ammonium sulfate precipitate of whole leaf homogenates and catalyzed the synthesis of acetoacetyl-acyl carrier protein. This condensation reaction was five-fold faster than acetyl-CoA:acyl carrier protein transacylase, and the initial rates of acyl-acyl carrier protein synthesis were independent of the presence of cerulenin. In the presence of fatty acid synthase cofactors and 100 micromolar cerulenin, the principal fatty acid product of de novo synthesis was butyric and hexanoic acids. Using conformationally sensitive native polyacrylamide gel electrophoresis for separation, malonyl-, acetyl-, butyryl-, hexanoyl, and long chain acyl-acyl carrier proteins could be detected by immunoblotting and autoradiography. In the presence of 100 micromolar cerulenin, the accumulation of butyryl- and hexanoyl-acyl carrier protein was observed, with no detectable long chain acyl-acyl carrier proteins or fatty acids being produced. In the absence of cerulenin, the long chain acyl-acyl carrier proteins also accumulated. Images Figure 2 Figure 3 PMID:16666765

  13. Acyl chain length and charge effect on Tamoxifen-lipid model membrane interactions

    NASA Astrophysics Data System (ADS)

    Bilge, Duygu; Kazanci, Nadide; Severcan, Feride

    2013-05-01

    Tamoxifen (TAM), which is an antiestrogenic agent, is widely used during chemotherapy of breast, pancreas, brain and liver cancers. In this study, TAM and model membrane interactions in the form of multilamellar vesicles (MLVs) were studied for lipids containing different acyl chain length and different charge status as a function of different TAM (1, 6, 9 and 15 mol%) concentrations. Zwitterionic lipids namely dipalmitoyl phosphatidylcholine (DPPC), and dimyristoylphosphatidylcholine (DMPC) lipids were used to see the acyl chain length effect and anionic dipalmitoyl phosphtidylglycerol (DPPG) lipid was used to see the charge effect. For this purpose Fourier transform-infrared (FTIR) spectroscopic and differential scanning calorimetric (DSC) techniques have been conducted. For zwitterionic lipid, concentration dependent different action of TAM was observed both in the gel and liquid crystalline phases by significantly increasing the lipid order and decreasing the dynamics for 1 mol% TAM, while decreasing the lipid order and increasing the dynamics of the lipids for higher concentrations (6, 9 and 15 mol%). However, different than neutral lipids, the dynamics and disorder of DPPG liposome increased for all TAM concentrations. The interactions between TAM and head group of multilamellar liposomes was monitored by analyzing the Cdbnd O stretching and PO2- antisymmetric double bond stretching bands. Increasing Tamoxifen concentrations led to a dehydration around these functional groups in the polar part of the lipids. DSC studies showed that for all types of lipids, TAM eliminates the pre-transition, shifts the main phase transition to lower temperatures and broadened the phase transition curve. The results indicate that not the acyl chain length but the charge status of the polar head group induces different effects on lipid membranes order and dynamics.

  14. Understanding Acyl Chain and Glycerolipid Metabolism in Plants

    SciTech Connect

    Ohlrogge, John B.

    2013-11-05

    Progress is reported in these areas: acyl-editing in initial eukaryotic lipid assembly in soybean seeds; identification and characterization of two Arabidopsis thaliana lysophosphatidyl acyltransferases with preference for lysophosphatidylethanolamine; and characterization and subcellular distribution of lysolipid acyl transferase activity of pea leaves.

  15. Defluoridation potential of jute fibers grafted with fatty acyl chain

    NASA Astrophysics Data System (ADS)

    Manna, Suvendu; Saha, Prosenjit; Roy, Debasis; Sen, Ramkrishna; Adhikari, Basudam

    2015-11-01

    Waterborne fluoride is usually removed from water by coagulation, adsorption, ion exchange, electro dialysis or reverse osmosis. These processes are often effective over narrow pH ranges, release ions considered hazardous to human health or produce large volumes of toxic sludge that are difficult to handle and dispose. Although plant matters have been shown to remove waterborne fluoride, they suffer from poor removal efficiency. Following from the insight that interaction between microbial carbohydrate biopolymers and anionic surfaces is often facilitated by lipids, an attempt has been made to enhance fluoride adsorption efficiency of jute by grafting the lignocellulosic fiber with fatty acyl chains found in vegetable oils. Fluoride removal efficiency of grafted jute was found to be comparable or higher than those of alternative defluoridation processes. Infrared and X-ray photoelectron spectroscopic evidence indicated that hydrogen bonding, protonation and C-F bonding were responsible for fluoride accumulation on grafted jute. Adsorption based on grafted jute fibers appears to be an economical, sustainable and eco-friendly alternative technique for removing waterborne fluoride.

  16. The dependence of lipid asymmetry upon phosphatidylcholine acyl chain structure[S

    PubMed Central

    Son, Mijin; London, Erwin

    2013-01-01

    Lipid asymmetry, the difference in inner and outer leaflet lipid composition, is an important feature of biomembranes. By utilizing our recently developed MβCD-catalyzed exchange method, the effect of lipid acyl chain structure upon the ability to form asymmetric membranes was investigated. Using this approach, SM was efficiently introduced into the outer leaflet of vesicles containing various phosphatidylcholines (PC), but whether the resulting vesicles were asymmetric (SM outside/PC inside) depended upon PC acyl chain structure. Vesicles exhibited asymmetry using PC with two monounsaturated chains of >14 carbons; PC with one saturated and one unsaturated chain; and PC with phytanoyl chains. Vesicles were most weakly asymmetric using PC with two 14 carbon monounsaturated chains or with two polyunsaturated chains. To define the origin of this behavior, transverse diffusion (flip-flop) of lipids in vesicles containing various PCs was compared. A correlation between asymmetry and transverse diffusion was observed, with slower transverse diffusion in vesicles containing PCs that supported lipid asymmetry. Thus, asymmetric vesicles can be prepared using a wide range of acyl chain structures, but fast transverse diffusion destroys lipid asymmetry. These properties may constrain acyl chain structure in asymmetric natural membranes to avoid short or overly polyunsaturated acyl chains. PMID:23093551

  17. Revised nomenclature for the mammalian long-chain acyl-CoA synthetase gene family.

    PubMed

    Mashek, Douglas G; Bornfeldt, Karin E; Coleman, Rosalind A; Berger, Johannes; Bernlohr, David A; Black, Paul; DiRusso, Concetta C; Farber, Steven A; Guo, Wen; Hashimoto, Naohiro; Khodiyar, Varsha; Kuypers, Frans A; Maltais, Lois J; Nebert, Daniel W; Renieri, Alessandra; Schaffer, Jean E; Stahl, Andreas; Watkins, Paul A; Vasiliou, Vasilis; Yamamoto, Tokuo T

    2004-10-01

    By consensus, the acyl-CoA synthetase (ACS) community, with the advice of the human and mouse genome nomenclature committees, has revised the nomenclature for the mammalian long-chain acyl-CoA synthetases. ACS is the family root name, and the human and mouse genes for the long-chain ACSs are termed ACSL1,3-6 and Acsl1,3-6, respectively. Splice variants of ACSL3, -4, -5, and -6 are cataloged. Suggestions for naming other family members and for the nonmammalian acyl-CoA synthetases are made.

  18. Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase

    PubMed Central

    Vance, Steven; Tkachenko, Olga; Thomas, Ben; Bassuni, Mona; Hong, Hui; Nietlispach, Daniel; Broadhurst, William

    2016-01-01

    Type I modular polyketide synthases (PKSs) produce polyketide natural products by passing a growing acyl substrate chain between a series of enzyme domains housed within a gigantic multifunctional polypeptide assembly. Throughout each round of chain extension and modification reactions, the substrate stays covalently linked to an acyl carrier protein (ACP) domain. In the present study we report on the solution structure and dynamics of an ACP domain excised from MLSA2, module 9 of the PKS system that constructs the macrolactone ring of the toxin mycolactone, cause of the tropical disease Buruli ulcer. After modification of apo ACP with 4′-phosphopantetheine (Ppant) to create the holo form, 15N nuclear spin relaxation and paramagnetic relaxation enhancement (PRE) experiments suggest that the prosthetic group swings freely. The minimal chemical shift perturbations displayed by Ppant-attached C3 and C4 acyl chains imply that these substrate-mimics remain exposed to solvent at the end of a flexible Ppant arm. By contrast, hexanoyl and octanoyl chains yield much larger chemical shift perturbations, indicating that they interact with the surface of the domain. The solution structure of octanoyl-ACP shows the Ppant arm bending to allow the acyl chain to nestle into a nonpolar pocket, whereas the prosthetic group itself remains largely solvent exposed. Although the highly reduced octanoyl group is not a natural substrate for the ACP from MLSA2, similar presentation modes would permit partner enzyme domains to recognize an acyl group while it is bound to the surface of its carrier protein, allowing simultaneous interactions with both the substrate and the ACP. PMID:26920023

  19. Altered ceramide acyl chain length and ceramide synthase gene expression in Parkinson’s disease.

    PubMed

    Abbott, Sarah K; Li, Hongyun; Muñoz, Sonia Sanz; Knoch, Bianca; Batterham, Marijka; Murphy, Karen E; Halliday, Glenda M; Garner, Brett

    2014-04-01

    Genetic studies have provided increasing evidence that ceramide homeostasis plays a role in neurodegenerative diseases including Parkinson’s disease (PD). It is known that the relative amounts of different ceramide molecular species, as defined by their fatty acyl chain length, regulate ceramide function in lipid membranes and in signaling pathways. In the present study we used a comprehensive sphingolipidomic case-control approach to determine the effects of PD on ceramide composition in postmortem brain tissue from the anterior cingulate cortex (a region with significant PD pathology) and the occipital cortex (spared in PD), also assessing mRNA expression of the major ceramide synthase genes that regulate ceramide acyl chain composition in the same tissue using quantitative PCR. In PD anterior cingulate cortex but not occipital cortex, total ceramide and sphingomyelin levels were reduced from control levels by 53% (P < 0.001) and 42% (P < 0.001), respectively. Of the 13 ceramide and 15 sphingomyelin molecular lipid species identified and quantified, there was a significant shift in the ceramide acyl chain composition toward shorter acyl chain length in the PD anterior cingulate cortex. This PD-associated change in ceramide acyl chain composition was accompanied by an upregulation of ceramide synthase-1 gene expression, which we consider may represent a response to reduced ceramide levels. These data suggest a significant shift in ceramide function in lipid membranes and signaling pathways occurs in regions with PD pathology. Identifying the regulatory mechanisms precipitating this change may provide novel targets for future therapeutics.

  20. Carbohydrate Conformation and Lipid Condensation in Monolayers Containing Glycosphingolipid Gb3: Influence of Acyl Chain Structure

    PubMed Central

    Watkins, Erik B.; Gao, Haifei; Dennison, Andrew J.C.; Chopin, Nathalie; Struth, Bernd; Arnold, Thomas; Florent, Jean-Claude; Johannes, Ludger

    2014-01-01

    Globotriaosylceramide (Gb3), a glycosphingolipid found in the plasma membrane of animal cells, is the endocytic receptor of the bacterial Shiga toxin. Using x-ray reflectivity (XR) and grazing incidence x-ray diffraction (GIXD), lipid monolayers containing Gb3 were investigated at the air-water interface. XR probed Gb3 carbohydrate conformation normal to the interface, whereas GIXD precisely characterized Gb3’s influence on acyl chain in-plane packing and area per molecule (APM). Two phospholipids, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), were used to study Gb3 packing in different lipid environments. Furthermore, the impact on monolayer structure of a naturally extracted Gb3 mixture was compared to synthetic Gb3 species with uniquely defined acyl chain structures. XR results showed that lipid environment and Gb3 acyl chain structure impact carbohydrate conformation with greater solvent accessibility observed for smaller phospholipid headgroups and long Gb3 acyl chains. In general, GIXD showed that Gb3 condensed phospholipid packing resulting in smaller APM than predicted by ideal mixing. Gb3’s capacity to condense APM was larger for DSPC monolayers and exhibited different dependencies on acyl chain structure depending on the lipid environment. The interplay between Gb3-induced changes in lipid packing and the lipid environment’s impact on carbohydrate conformation has broad implications for glycosphingolipid macromolecule recognition and ligand binding. PMID:25185550

  1. Structural Basis for Substrate Fatty Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase

    SciTech Connect

    McAndrew, Ryan P.; Wang, Yudong; Mohsen, Al-Walid; He, Miao; Vockley, Jerry; Kim, Jung-Ja P.

    2008-08-26

    Very-long-chain acyl-CoA dehydrogenase (VLCAD) is a member of the family of acyl-CoA dehydrogenases (ACADs). Unlike the other ACADs, which are soluble homotetramers, VLCAD is a homodimer associated with the mitochondrial membrane. VLCAD also possesses an additional 180 residues in the C terminus that are not present in the other ACADs. We have determined the crystal structure of VLCAD complexed with myristoyl-CoA, obtained by co-crystallization, to 1.91-{angstrom} resolution. The overall fold of the N-terminal {approx}400 residues of VLCAD is similar to that of the soluble ACADs including medium-chain acyl-CoA dehydrogenase (MCAD). The novel C-terminal domain forms an {alpha}-helical bundle that is positioned perpendicular to the two N-terminal helical domains. The fatty acyl moiety of the bound substrate/product is deeply imbedded inside the protein; however, the adenosine pyrophosphate portion of the C14-CoA ligand is disordered because of partial hydrolysis of the thioester bond and high mobility of the CoA moiety. The location of Glu-422 with respect to the C2-C3 of the bound ligand and FAD confirms Glu-422 to be the catalytic base. In MCAD, Gln-95 and Glu-99 form the base of the substrate binding cavity. In VLCAD, these residues are glycines (Gly-175 and Gly-178), allowing the binding channel to extend for an additional 12{angstrom} and permitting substrate acyl chain lengths as long as 24 carbons to bind. VLCAD deficiency is among the more common defects of mitochondrial {beta}-oxidation and, if left undiagnosed, can be fatal. This structure allows us to gain insight into how a variant VLCAD genotype results in a clinical phenotype.

  2. Long Chain N-acyl Homoserine Lactone Production by Enterobacter sp. Isolated from Human Tongue Surfaces

    PubMed Central

    Yin, Wai-Fong; Purmal, Kathiravan; Chin, Shenyang; Chan, Xin-Yue; Chan, Kok-Gan

    2012-01-01

    We report the isolation of N-acyl homoserine lactone-producing Enterobacter sp. isolate T1-1 from the posterior dorsal surfaces of the tongue of a healthy individual. Spent supernatants extract from Enterobacter sp. isolate T1-1 activated the biosensor Agrobacterium tumefaciens NTL4(pZLR4), suggesting production of long chain AHLs by these isolates. High resolution mass spectrometry analysis of these extracts confirmed that Enterobacter sp. isolate T1-1 produced a long chain N-acyl homoserine lactone, namely N-dodecanoyl-homoserine lactone (C12-HSL). To the best of our knowledge, this is the first isolation of Enterobacter sp., strain T1-1 from the posterior dorsal surface of the human tongue and N-acyl homoserine lactones production by this bacterium. PMID:23202161

  3. Genetics Home Reference: short-chain acyl-CoA dehydrogenase deficiency

    MedlinePlus

    ... Download PDF Open All Close All Description Short-chain acyl-CoA dehydrogenase (SCAD) deficiency is a condition that prevents the body from converting certain fats into energy, especially during periods without food (fasting). Signs and symptoms of SCAD deficiency may ...

  4. Cationic amphiphiles with fatty acyl chain asymmetry of coconut oil deliver genes selectively to mouse lung.

    PubMed

    Chandrashekhar, Voshavar; Srujan, Marepally; Prabhakar, Rairala; Reddy, Rakesh C; Sreedhar, Bojja; Rentam, Kiran K R; Kanjilal, Sanjit; Chaudhuri, Arabinda

    2011-03-16

    Recent structure-activity studies have revealed a dramatic influence of hydrophobic chain asymmetry in enhancing gene delivery efficacies of synthetic cationic amphiphiles (Nantz, M. H. et al. Mol. Pharmaceutics2010, 7, 786-794; Koynova, R. et al. Mol. Pharmaceutics2009, 6, 951-958). The present findings demonstrate for the first time that such a transfection enhancing influence of asymmetric hydrocarbon chains observed in pure synthetic cationic amphiphiles also works for cationic amphiphiles designed with natural, asymmetric fatty acyl chains of a food-grade oil. Herein, we demonstrate that cationic amphiphiles designed with the natural fatty acyl chain asymmetry of food-grade coconut oil are less cytotoxic and deliver genes selectively to mouse lung. Despite lauroyl chains being the major fatty acyl chains of coconut oil, both the in vitro and In vivo gene transfer efficiencies of such cationic amphiphiles were found to be remarkably superior (>4-fold) to those of their pure dilauroyl analogue. Mechanistic studies involving the technique of fluorescence resonance energy transfer (FRET) revealed higher biomembrane fusibility of the cationic liposomes of the coconut amphiphiles than that of the symmetric dilauroyl analogue. AFM study revealed pronounced fusogenic nonlamellar structures of the liposomes of coconut amphiphiles. Findings in the FRET and cellular uptake study, taken together, support the notion that the higher cellular uptake resulting from the more fusogenic nature of the liposomes of coconut amphiphiles 1 are likely to play a dominant role in making the coconut amphiphiles transfection competent.

  5. Role of long-chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling.

    PubMed Central

    Faergeman, N J; Knudsen, J

    1997-01-01

    The intracellular concentration of free unbound acyl-CoA esters is tightly controlled by feedback inhibition of the acyl-CoA synthetase and is buffered by specific acyl-CoA binding proteins. Excessive increases in the concentration are expected to be prevented by conversion into acylcarnitines or by hydrolysis by acyl-CoA hydrolases. Under normal physiological conditions the free cytosolic concentration of acyl-CoA esters will be in the low nanomolar range, and it is unlikely to exceed 200 nM under the most extreme conditions. The fact that acetyl-CoA carboxylase is active during fatty acid synthesis (Ki for acyl-CoA is 5 nM) indicates strongly that the free cytosolic acyl-CoA concentration is below 5 nM under these conditions. Only a limited number of the reported experiments on the effects of acyl-CoA on cellular functions and enzymes have been carried out at low physiological concentrations in the presence of the appropriate acyl-CoA-buffering binding proteins. Re-evaluation of many of the reported effects is therefore urgently required. However, the observations that the ryanodine-senstitive Ca2+-release channel is regulated by long-chain acyl-CoA esters in the presence of a molar excess of acyl-CoA binding protein and that acetyl-CoA carboxylase, the AMP kinase kinase and the Escherichia coli transcription factor FadR are affected by low nanomolar concentrations of acyl-CoA indicate that long-chain acyl-CoA esters can act as regulatory molecules in vivo. This view is further supported by the observation that fatty acids do not repress expression of acetyl-CoA carboxylase or Delta9-desaturase in yeast deficient in acyl-CoA synthetase. PMID:9173866

  6. A severe genotype with favourable outcome in very long chain acyl-CoA dehydrogenase deficiency

    PubMed Central

    Touma, E; Rashed, M; Vianey-Saban, C; Sakr, A; Divry, P; Gregersen, N; Andresen, B

    2001-01-01

    A patient with very long chain acyl-CoA dehydrogenase (VLCAD) deficiency is reported. He had a severe neonatal presentation and cardiomyopathy. He was found to be homozygous for a severe mutation with no residual enzyme activity. Tandem mass spectrometry on dried blood spots revealed increased long chain acylcarnitines. VLCAD enzyme activity was severely decreased to 2% of control levels. Dietary management consisted of skimmed milk supplemented with medium chain triglycerides and L-carnitine. Outcome was good and there was no acute recurrence.

 PMID:11124787

  7. A specific acyl-ACP thioesterase implicated in medium-chain fatty acid production in immature cotyledons of Umbellularia californica.

    PubMed

    Pollard, M R; Anderson, L; Fan, C; Hawkins, D J; Davies, H M

    1991-02-01

    Umbellularia californica (California Bay) seeds accumulate 10:0 and 12:0 as principal reserve fatty acyl groups. An in vitro fatty acid synthesis system from the developing cotyledons produces chiefly 10:0 and 12:0, in approximately the same proportions as the intact tissue. The kinetics of acyl thioester and free fatty acid formation in this system suggest that a medium-chain specific acyl-acyl-carrier protein (ACP) hydrolysis mechanism is responsible for the preponderance of medium-chain products. A crude extract of the developing cotyledons exhibits hydrolytic activity toward acyl-ACPs, with marked preference for 12:0-ACP and 18:1-ACP in the test series 6:0, 8:0, 10:0, 11:0, 12:0, 14:0, 16:0, and 18:1-ACPs. Partial purification of the 12:0-ACP hydrolytic activity has resulted in its separation from the 18:1-ACP hydrolase(s) and the 12:0-coenzyme A hydrolase(s) that are also present, thereby demonstrating its specificity for the 12-carbon acyl chain length and the ACP derivative. During cotyledon development, as the proportion of medium-chain to other fatty acyl groups increases, the extractable yield of this activity also increases substantially. Collectively these results suggest a role for this 12-ACP thioesterase in medium-chain production in vivo.

  8. Syntheses of Papyracillic Acids: Application of the Tandem Chain Extension-Acylation Reaction

    PubMed Central

    Mazzone, Jennifer R.; Zercher, Charles K.

    2012-01-01

    A synthetic approach to the papyracillic acid family of natural products has been developed. The spiroacetal core is rapidly assembled through an unprecedented zinc carbenoid-mediated tandem chain extension-acylation reaction. Subsequent functional group manipulation provided access to papyracillic acid B and 4-epi-papyracillic acid C. The successful preparation of these molecules resulted in the clarification of structural assignments of members of this family of natural products. PMID:23013246

  9. Effect of salicylic acid and diclofenac on the medium-chain and long-chain acyl-CoA formation in the liver and brain of mouse.

    PubMed

    Kasuya, Fumiyo; Kazumi, Maya; Tatsuki, Takao; Suzuki, Risa

    2009-07-01

    Medium-chain and long-chain acyl-CoA esters are key metabolites in fatty acid metabolism. Effects of salicylic acid on the in vivo formation of acyl-CoAs in mouse liver and brain were investigated. Further, inhibition of the medium-chain and long-chain acyl-CoA synthetases by salicylic acid and diclofenac was determined in mouse liver and brain mitochondria. Acyl-CoA esters were analyzed by liquid chromatography-tandem mass spectrometry. The amounts of medium-chain acyl-CoAs (C(6), C(8) and C(10)) were less than long-chain acyl-CoAs (C(16:0), C(18:0), C(18:1) and C(20:4)) in both liver and brain. The administration of salicylic acid decreased the levels of both the medium-chain (C(6), C(8) and C(10)) and long-chain acyl-CoAs (C(16:0), C(18:0), C(18:1) and C(20:4)) in liver. In brain, however, only long-chain acyl-CoAs were decreased. The level of salicylyl-CoA detected in brain was about 12% of that in liver. Salicylic acid had a strong inhibitory activity (IC(50) = 0.1 mm) for the liver mitochondrial formation of hexanoyl-CoA from hexanoic acid, whereas diclofenac was weak (IC(50) = 4.4 mm). In contrast, diclofenac (IC(50) = 1.4 mm) inhibited the liver mitochondrial long-chain acyl-CoA synthetases more potently than salicylic acid (IC(50) = 25.5 mm). Similar inhibitory activities for the acyl-CoA synthetases were obtained in the case of the brain and liver mitochondria, except for the weak inhibition of brain medium-chain acyl-CoA synthetases by salicylic acid (IC(50) = 1.8 mm). These findings suggest that salicylic acid and diclofenac exhibit different mechanisms of inhibition of fatty acid metabolism depending on the length of the acyl chain and tissues, and they may contribute to the further understanding of the toxic effects associated with these drugs.

  10. Hepatic fatty acid uptake is regulated by the sphingolipid acyl chain length

    PubMed Central

    Park, Woo-Jae; Park, Joo-Won; Merrill, Alfred H.; Storch, Judith; Pewzner-Jung, Yael; Futerman, Anthony H.

    2015-01-01

    Ceramide synthase 2 (CerS2) null mice cannot synthesize very-long acyl chain (C22-C24) ceramides resulting in significant alterations in the acyl chain composition of sphingolipids. We now demonstrate that hepatic triacylglycerol (TG) levels are reduced in liver but not in adipose tissue or skeletal muscle in the CerS2 null mouse, both before and after feeding with a high fat diet (HFD), where no weight gain was observed and large hepatic nodules appeared. Uptake of both BODIPY-palmitate and [3H]-palmitate were also abrogated in hepatocytes and liver. The role of a number of key proteins involved in fatty acid uptake was examined, including FATP5, CD36/FAT, FABPpm and cytoplasmic FABP1. Levels of FATP5 and FABP1 were decreased in CerS2 null mouse liver, whereas CD36/FAT levels were significantly elevated and CD36/FAT was also mislocalized upon insulin treatment. Moreover, treatment of hepatocytes with C22-C24-ceramides down-regulated CD36/FAT levels. Infection of CerS2 null mice with recombinant adeno-associated virus (rAAV)-CerS2 restored normal TG levels and corrected the mislocalization of CD36/FAT, but had no effect on the intracellular localization or levels of FATP5 or FABP1. Together, these results demonstrate that hepatic fatty acid uptake via CD36/FAT can be regulated by altering the acyl chain composition of sphingolipids. PMID:25241943

  11. Characterization of acyl chain position in unsaturated phosphatidylcholines using differential mobility-mass spectrometry[S

    PubMed Central

    Maccarone, Alan T.; Duldig, Jackson; Mitchell, Todd W.; Blanksby, Stephen J.; Duchoslav, Eva; Campbell, J. Larry

    2014-01-01

    Glycerophospholipids (GPs) that differ in the relative position of the two fatty acyl chains on the glycerol backbone (i.e., sn-positional isomers) can have distinct physicochemical properties. The unambiguous assignment of acyl chain position to an individual GP represents a significant analytical challenge. Here we describe a workflow where phosphatidylcholines (PCs) are subjected to ESI for characterization by a combination of differential mobility spectrometry and MS (DMS-MS). When infused as a mixture, ions formed from silver adduction of each phospholipid isomer {e.g., [PC (16:0/18:1) + Ag]+ and [PC (18:1/16:0) + Ag]+} are transmitted through the DMS device at discrete compensation voltages. Varying their relative amounts allows facile and unambiguous assignment of the sn-positions of the fatty acyl chains for each isomer. Integration of the well-resolved ion populations provides a rapid method (< 3 min) for relative quantification of these lipid isomers. The DMS-MS results show excellent agreement with established, but time-consuming, enzymatic approaches and also provide superior accuracy to methods that rely on MS alone. The advantages of this DMS-MS method in identification and quantification of GP isomer populations is demonstrated by direct analysis of complex biological extracts without any prior fractionation. PMID:24939921

  12. Alteration of the specificity and regulation of fatty acid synthesis of Escherichia coli by expression of a plant medium-chain acyl-acyl carrier protein thioesterase.

    PubMed

    Voelker, T A; Davies, H M

    1994-12-01

    The expression of a plant (Umbellularia californica) medium-chain acyl-acyl carrier protein (ACP) thioesterase (BTE) cDNA in Escherichia coli results in a very high level of extractable medium-chain-specific hydrolytic activity but causes only a minor accumulation of medium-chain fatty acids. BTE's full impact on the bacterial fatty acid synthase is apparent only after expression in a strain deficient in fatty acid degradation, in which BTE increases the total fatty acid output of the bacterial cultures fourfold. Laurate (12:0), normally a minor fatty acid component of E. coli, becomes predominant, is secreted into the medium, and can accumulate to a level comparable to the total dry weight of the bacteria. Also, large quantities of 12:1, 14:0, and 14:1 are made. At the end of exponential growth, the pathway of saturated fatty acids is almost 100% diverted by BTE to the production of free medium-chain fatty acids, starving the cells for saturated acyl-ACP substrates for lipid biosynthesis. This results in drastic changes in membrane lipid composition from predominantly 16:0 to 18:1. The continued hydrolysis of medium-chain ACPs by the BTE causes the bacterial fatty acid synthase to produce fatty acids even when membrane production has ceased in stationary phase, which shows that the fatty acid synthesis rate can be uncoupled from phospholipid biosynthesis and suggests that acyl-ACP intermediates might normally act as feedback inhibitors for fatty acid synthase. As the fatty acid synthesis is increasingly diverted to medium chains with the onset of stationary phase, the rate of C12 production increases relative to C14 production. This observation is consistent with activity of the BTE on free acyl-ACP pools, as opposed to its interaction with fatty acid synthase-bound substrates.

  13. Cardiac Hypertrophy in Mice with Long-Chain Acyl-CoA Dehydrogenase (LCAD) or Very Long-Chain Acyl-CoA Dehydrogenase (VLCAD) Deficiency

    PubMed Central

    Cox, Keith B.; Liu, Jian; Tian, Liqun; Barnes, Stephen; Yang, Qinglin; Wood, Philip A.

    2009-01-01

    Cardiac hypertrophy is a common finding in human patients with inborn errors of long-chain fatty acid oxidation. Mice with either very long-chain acyl-CoA dehydrogenase deficiency (VLCAD−/−) or long-chain acyl-CoA dehydrogenase deficiency (LCAD−/−) develop cardiac hypertrophy. Cardiac hypertrophy, initially measured using heart/body weight ratios, was manifested most severely in LCAD−/− male mice. VLCAD−/− mice, as a group, showed a mild increase in normalized cardiac mass (8.8% hypertrophy compared to all wild-type [WT] mice). In contrast, LCAD−/− mice as a group showed more severe cardiac hypertrophy (32.2% increase compared to all WT mice). Based on a clear male predilection, we investigated the role of dietary plant estrogenic compounds commonly found in mouse diets due to soy or alfalfa components providing natural phytoestrogens or isoflavones in cardioprotection of LCAD−/− mice. Male LCAD−/− mice fed an isoflavone-free test diet had more severe cardiac hypertrophy (58.1% hypertrophy compared to WT mice fed the same diet. There were no significant differences in the female groups fed any of the diets. Echocardiography measurement performed on male LCAD deficient mice fed a standard diet at ~3 months of age confirmed the substantial cardiac hypertrophy in these mice compared with WT controls. Left ventricular wall thickness of interventricular septum and posterior wall was remarkably increased in LCAD−/− mice compared with that of WT controls. Accordingly, the calculated LV mass after normalization to body weight was increased about 40% in the LCAD−/− mice compared with WT mice. In summary, we found that metabolic cardiomyopathy, expressed as hypertrophy, developed in mice due to either VLCAD deficiency or LCAD deficiency; however, LCAD deficiency was the most profound and appeared to be attenuated either by endogenous estrogen in females or phytoestrogens in the diet as isoflavones in males. PMID:19736549

  14. Accumulation of medium-chain, saturated fatty acyl moieties in seed oils of transgenic Camelina sativa.

    PubMed

    Hu, Zhaohui; Wu, Qian; Dalal, Jyoti; Vasani, Naresh; Lopez, Harry O; Sederoff, Heike W; Qu, Rongda

    2017-01-01

    With its high seed oil content, the mustard family plant Camelina sativa has gained attention as a potential biofuel source. As a bioenergy crop, camelina has many advantages. It grows on marginal land with low demand for water and fertilizer, has a relatively short life cycle, and is stress tolerant. As most other crop seed oils, camelina seed triacylglycerols (TAGs) consist of mostly long, unsaturated fatty acyl moieties, which is not desirable for biofuel processing. In our efforts to produce shorter, saturated chain fatty acyl moieties in camelina seed oil for conversion to jet fuel, a 12:0-acyl-carrier thioesterase gene, UcFATB1, from California bay (Umbellularia californica Nutt.) was expressed in camelina seeds. Up to 40% of short chain laurate (C12:0) and myristate (C14:0) were present in TAGs of the seed oil of the transgenics. The total oil content and germination rate of the transgenic seeds were not affected. Analysis of positions of these two fatty acyl moieties in TAGs indicated that they were present at the sn-1 and sn-3 positions, but not sn-2, on the TAGs. Suppression of the camelina KASII genes by RNAi constructs led to higher accumulation of palmitate (C16:0), from 7.5% up to 28.5%, and further reduction of longer, unsaturated fatty acids in seed TAGs. Co-transformation of camelina with both constructs resulted in enhanced accumulation of all three medium-chain, saturated fatty acids in camelina seed oils. Our results show that a California bay gene can be successfully used to modify the oil composition in camelina seed and present a new biological alternative for jet fuel production.

  15. Accumulation of medium-chain, saturated fatty acyl moieties in seed oils of transgenic Camelina sativa

    PubMed Central

    Dalal, Jyoti; Vasani, Naresh; Lopez, Harry O.; Sederoff, Heike W.

    2017-01-01

    With its high seed oil content, the mustard family plant Camelina sativa has gained attention as a potential biofuel source. As a bioenergy crop, camelina has many advantages. It grows on marginal land with low demand for water and fertilizer, has a relatively short life cycle, and is stress tolerant. As most other crop seed oils, camelina seed triacylglycerols (TAGs) consist of mostly long, unsaturated fatty acyl moieties, which is not desirable for biofuel processing. In our efforts to produce shorter, saturated chain fatty acyl moieties in camelina seed oil for conversion to jet fuel, a 12:0-acyl-carrier thioesterase gene, UcFATB1, from California bay (Umbellularia californica Nutt.) was expressed in camelina seeds. Up to 40% of short chain laurate (C12:0) and myristate (C14:0) were present in TAGs of the seed oil of the transgenics. The total oil content and germination rate of the transgenic seeds were not affected. Analysis of positions of these two fatty acyl moieties in TAGs indicated that they were present at the sn-1 and sn-3 positions, but not sn-2, on the TAGs. Suppression of the camelina KASII genes by RNAi constructs led to higher accumulation of palmitate (C16:0), from 7.5% up to 28.5%, and further reduction of longer, unsaturated fatty acids in seed TAGs. Co-transformation of camelina with both constructs resulted in enhanced accumulation of all three medium-chain, saturated fatty acids in camelina seed oils. Our results show that a California bay gene can be successfully used to modify the oil composition in camelina seed and present a new biological alternative for jet fuel production. PMID:28212406

  16. Actinobacterial Acyl Coenzyme A Synthetases Involved in Steroid Side-Chain Catabolism

    PubMed Central

    Casabon, Israël; Swain, Kendra; Crowe, Adam M.

    2014-01-01

    Bacterial steroid catabolism is an important component of the global carbon cycle and has applications in drug synthesis. Pathways for this catabolism involve multiple acyl coenzyme A (CoA) synthetases, which activate alkanoate substituents for β-oxidation. The functions of these synthetases are poorly understood. We enzymatically characterized four distinct acyl-CoA synthetases from the cholate catabolic pathway of Rhodococcus jostii RHA1 and the cholesterol catabolic pathway of Mycobacterium tuberculosis. Phylogenetic analysis of 70 acyl-CoA synthetases predicted to be involved in steroid metabolism revealed that the characterized synthetases each represent an orthologous class with a distinct function in steroid side-chain degradation. The synthetases were specific for the length of alkanoate substituent. FadD19 from M. tuberculosis H37Rv (FadD19Mtb) transformed 3-oxo-4-cholesten-26-oate (kcat/Km = 0.33 × 105 ± 0.03 × 105 M−1 s−1) and represents orthologs that activate the C8 side chain of cholesterol. Both CasGRHA1 and FadD17Mtb are steroid-24-oyl-CoA synthetases. CasG and its orthologs activate the C5 side chain of cholate, while FadD17 and its orthologs appear to activate the C5 side chain of one or more cholesterol metabolites. CasIRHA1 is a steroid-22-oyl-CoA synthetase, representing orthologs that activate metabolites with a C3 side chain, which accumulate during cholate catabolism. CasI had similar apparent specificities for substrates with intact or extensively degraded steroid nuclei, exemplified by 3-oxo-23,24-bisnorchol-4-en-22-oate and 1β(2′-propanoate)-3aα-H-4α(3″-propanoate)-7aβ-methylhexahydro-5-indanone (kcat/Km = 2.4 × 105 ± 0.1 × 105 M−1 s−1 and 3.2 × 105 ± 0.3 × 105 M−1 s−1, respectively). Acyl-CoA synthetase classes involved in cholate catabolism were found in both Actinobacteria and Proteobacteria. Overall, this study provides insight into the physiological roles of acyl-CoA synthetases in steroid catabolism and

  17. Medium-chain acyl-CoA dehydrogenase deficiency in children with non-ketotic hypoglycemia and low carnitine levels.

    PubMed

    Stanley, C A; Hale, D E; Coates, P M; Hall, C L; Corkey, B E; Yang, W; Kelley, R I; Gonzales, E L; Williamson, J R; Baker, L

    1983-11-01

    Three children in two families presented in early childhood with episodes of illness associated with fasting which resembled Reye's syndrome: coma, hypoglycemia, hyperammonemia, and fatty liver. One child died with cerebral edema during an episode. Clinical studies revealed an absence of ketosis on fasting (plasma beta-hydroxybutyrate less than 0.4 mmole/liter) despite elevated levels of free fatty acids (2.6-4.2 mmole/liter) which suggested that hepatic fatty acid oxidation was impaired. Urinary dicarboxylic acids were elevated during illness or fasting. Total carnitine levels were low in plasma (18-25 mumole/liter), liver (200-500 nmole/g), and muscle (500-800 nmole/g); however, treatment with L-carnitine failed to correct the defect in ketogenesis. Studies on ketone production from fatty acid substrates by liver tissue in vitro showed normal rates from short-chain fatty acids, but very low rates from all medium and long-chain fatty acid substrates. These results suggested that the defect was in the mid-portion of the intramitochondrial beta-oxidation pathway at the medium-chain acyl-CoA dehydrogenase step. A new assay for the electron transfer flavoprotein-linked acyl-CoA dehydrogenases was used to test this hypothesis. This assay follows the decrease in electron transfer flavoprotein fluorescence as it is reduced by acyl-CoA-acyl-CoA dehydrogenase complex. Results with octanoyl-CoA as substrate indicated that patients had less than 2.5% normal activity of medium-chain acyl-CoA dehydrogenase. The activities of short-chain and isovaleryl acyl-CoA dehydrogenases were normal; the activity of long-chain acyl-CoA dehydrogenase was one-third normal. These results define a previously unrecognized inherited metabolic disorder of fatty acid oxidation due to deficiency of medium-chain acyl-CoA dehydrogenase.

  18. Structural identification of skin ceramides containing ω-hydroxy acyl chains using mass spectrometry.

    PubMed

    Wu, Zhexue; Shon, Jong Cheol; Kim, Jong Yei; Cho, Yunhi; Liu, Kwang-Hyeon

    2016-10-01

    The stratum corneum (SC) acts as a barrier that protects organisms against the environment and from transepidermal water loss. It consists of corneocytes embedded in a matrix of lipid metabolites (ceramides, cholesterol, and free fatty acids). Of these lipids, ceramides are sphingolipids consisting of sphingoid bases, linked to fatty acyl chains. Typical fatty acid acyl chains are composed of α-hydroxy fatty acids (A), esterified ω-hydroxy fatty acids (EO), non-hydroxy fatty acids (N), and ω-hydroxy fatty acids (O). Of these, O-type ceramides are ester-linked via their ω-hydroxyl group to proteins in the cornified envelope and can be released and extracted following mild alkaline hydrolysis. Tandem mass spectrometry (MS/MS) analysis of O-type ceramides using chip-based direct infusion nanoelectrospray-ion trap mass spectrometry generated the characteristic fragmentation pattern of both acyl and sphingoid units, suggesting that this method could be applied to the structural identification of O-type ceramides. Based on the MS/MS fragmentation patterns of O-type ceramides, comprehensive fragmentation schemes are proposed. In addition, we have also developed a method for identifying and profiling O-type ceramides in the mouse and guinea pig SC. This information may be used to identify O-type ceramides in the SC of animal skin.

  19. Acyl chain composition and coexisting fluid phases in lipid bilayers

    NASA Astrophysics Data System (ADS)

    Gu, Yongwen; Bradley, Miranda; Mitchell, Drake

    2011-10-01

    At room temperature phospholipid bilayers enriched in sphingolipids and cholesterol may form a solid phase as well as two coexisting fluid phases. These are the standard fluid phase, or the liquid-disordered phase, ld, and the liquid-ordered phase, lo, which is commonly associated with lipid rafts. Ternary mixtures of palmitoyl-oleoyl-phosphocholine (POPC; 16:0,18:1 PC), sphingomyelin (SPM), and cholesterol (Chol) form coexisting lo, ld and solid phases over a wide range of molar ratios. We are examining the ability of two fluorescent probes to detect these 2 phases: NBD linked to di-16:0 PE which partitions strongly into the lo phase and NBD linked to di-18:1 PE which partitions strongly into the ld phase. We are also examining the effect of the highly polyunsaturated phospholipid stearoyl-docosahexanoyl-phosphocholine (SDPC; 18:0, 22:6 PC) on the ternary phase diagram of POPC/SPM/Chol with particular focus on the functionally important lo/ld coexistence region. We report on the fluorescence lifetime and anisotropy decay dynamics of these two fluorescent probes.

  20. Characterization of a novel long-chain acyl-CoA thioesterase from Alcaligenes faecalis.

    PubMed

    Shahi, Puja; Kumar, Ish; Sharma, Ritu; Sanger, Shefali; Jolly, Ravinder S

    2006-06-01

    A novel long-chain acyl-CoA thioesterase from Alcaligenes faecalis has been isolated and characterized. The protein was extracted from the cells with 1 m NaCl, which required 1.5-fold, single-step purification to yield near-homogeneous preparations. In solution, the protein exists as homomeric aggregates, of mean diameter 21.6 nm, consisting of 22-kDa subunits. MS/MS data for peptides obtained by trypsin digestion of the thiosterase did not match any peptide from Escherichia coli thioesterases or any other thioesterases in the database. The thioesterase was associated exclusively with the surface of cells as revealed by ultrastructural studies using electron microscopy and immunogold labeling. It hydrolyzed saturated and unsaturated fatty acyl-CoAs of C12 to C18 chain length with Vmax and Km of 3.58-9.73 micromol x min(-1) x (mg protein)(-1) and 2.66-4.11 microm, respectively. A catalytically important histidine residue is implicated in the active site of the enzyme. The thioesterase was active and stable over a wide range of temperature and pH. Maximum activity was observed at 65 degrees C and pH 10.5, and varied between 60% and 80% at temperatures of 25-70 degrees C and pH 6.5-10. The thioesterase also hydrolyzed p-nitrophenyl esters of C2 to C12 chain length, but substrate competition experiments demonstrated that the long-chain acyl-CoAs are better substrates for thioesterase than p-nitrophenyl esters. When assayed at 37 and 20 degrees C, the affinity and catalytic efficiency of the thioesterase for palmitoleoyl-CoA and cis-vaccenoyl-CoA were reduced approximately twofold at the lower temperature, but remained largely unaltered for palmitoyl-CoA.

  1. Acyl-chain remodeling of dioctanoyl-phosphatidylcholine in Saccharomyces cerevisiae mutant defective in de novo and salvage phosphatidylcholine synthesis

    SciTech Connect

    Kishino, Hideyuki; Eguchi, Hiroki; Takagi, Keiko; Horiuchi, Hiroyuki; Fukuda, Ryouichi; Ohta, Akinori

    2014-03-07

    Highlights: • Dioctanoyl-PC (diC8PC) supported growth of a yeast mutant defective in PC synthesis. • diC8PC was converted to PC species containing longer acyl residues in the mutant. • Both acyl residues of diC8PC were replaced by longer fatty acids in vitro. • This system will contribute to the elucidation of the acyl chain remodeling of PC. - Abstract: A yeast strain, in which endogenous phosphatidylcholine (PC) synthesis is controllable, was constructed by the replacement of the promoter of PCT1, encoding CTP:phosphocholine cytidylyltransferase, with GAL1 promoter in a double deletion mutant of PEM1 and PEM2, encoding phosphatidylethanolamine methyltransferase and phospholipid methyltransferase, respectively. This mutant did not grow in the glucose-containing medium, but the addition of dioctanoyl-phosphatidylcholine (diC8PC) supported its growth. Analyses of the metabolism of {sup 13}C-labeled diC8PC ((methyl-{sup 13}C){sub 3}-diC8PC) in this strain using electrospray ionization tandem mass spectrometry revealed that it was converted to PC species containing acyl residues of 16 or 18 carbons at both sn-1 and sn-2 positions. In addition, both acyl residues of (methyl-{sup 13}C){sub 3}-diC8PC were replaced with 16:1 acyl chains in the in vitro reaction using the yeast cell extract in the presence of palmitoleoyl-CoA. These results indicate that PC containing short acyl residues was remodeled to those with acyl chains of physiological length in yeast.

  2. Acyl-CoA dehydrogenase 9 (ACAD 9) is the long-chain acyl-CoA dehydrogenase in human embryonic and fetal brain.

    PubMed

    Oey, N A; Ruiter, J P N; Ijlst, L; Attie-Bitach, T; Vekemans, M; Wanders, R J A; Wijburg, F A

    2006-07-21

    We recently reported the expression and activity of several fatty acid oxidation enzymes in human embryonic and fetal tissues including brain and spinal cord. Liver and heart showed expression of both very long-chain acyl-CoA dehydrogenase (VLCAD) and long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) mRNA. However, while mRNA expression of LCHAD could be clearly detected in the retina and spinal cord, expression of VLCAD mRNA was low to undetectable in these tissues. Nevertheless, abundant acyl-CoA dehydrogenase (ACAD) activity was detected with palmitoyl-CoA as substrate in fetal central nervous tissue. These conflicting data suggested the presence of a different long-chain ACAD in human embryonic and fetal brain. In this study, using in situ hybridization as well as enzymatic studies, we identified acyl-CoA dehydrogenase 9 (ACAD 9) as the long-chain ACAD in human embryonic and fetal central nervous tissue. Until now, no clinical signs and symptoms of central nervous system involvement have been reported in VLCAD deficiency. A novel long-chain FAO defect, i.e., ACAD 9 deficiency with only central nervous system involvement, could, if not lethal during intra uterine development, easily escape proper diagnosis, since probably no classical signs and symptoms of FAO deficiency will be observed. Screening for ACAD 9 deficiency in patients with undefined neurological symptoms and/or impairment in neurological development of unknown origin is necessary to establish if ACAD 9 deficiency exists as a separate disease entity.

  3. Continuous recording of long-chain acyl-coenzyme a synthetase activity using fluorescently labeled bovine serum albumin.

    PubMed

    Demant, E J; Nystrøm, B T

    2001-08-01

    The fluorescence-based long-chain fatty acid probe BSA-HCA (bovine serum albumin labeled with 7-hydroxycoumarin-4-acetic acid) is shown to respond to binding of long-chain acyl-CoA thioesters by quenching of the 450 nm fluorescence emission. As determined by spectrofluorometric titration, binding affinities for palmitoyl-, stearoyl-, and oleoyl-CoA (Kd = 0.2-0.4 microM) are 5-10 times lower than those for the corresponding nonesterified fatty acids. In the presence of detergent (Chaps, Triton X-100, n-octylglucoside) above the critical micelle concentration, acyl-CoA partitions from BSA-HCA and into the detergent micelles. This allows BSA-HCA to be used as a fluorescent probe for continuous recording of fatty acid concentrations in detergent solution with little interference from acyl-CoA. Using a calibration of the fluorescence signal with fatty acids in the C14 to C20 chain-length range, fatty acid consumption by Pseudomonas fragi and rat liver microsomal acyl-CoA synthetase activities are measured down to 0.05 microM/min with a data sampling rate of 10 points per second. This new method provides a very promising spectrofluorometric approach to the study of acyl-CoA synthetase reaction kinetics at physiologically relevant (nM) aqueous phase concentrations of fatty acid substrates and at a time resolution that cannot be obtained in isotopic sampling or enzyme-coupled assays.

  4. Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency: diagnosis by acylcarnitine analysis in blood.

    PubMed Central

    Van Hove, J L; Zhang, W; Kahler, S G; Roe, C R; Chen, Y T; Terada, N; Chace, D H; Iafolla, A K; Ding, J H; Millington, D S

    1993-01-01

    Medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency is a disorder of fatty acid catabolism, with autosomal recessive inheritance. The disease is characterized by episodic illness associated with potentially fatal hypoglycemia and has a relatively high frequency. A rapid and reliable method for the diagnosis of MCAD deficiency is highly desirable. Analysis of specific acylcarnitines was performed by isotope-dilution tandem mass spectrometry on plasma or whole blood samples from 62 patients with MCAD deficiency. Acylcarnitines were also analyzed in 42 unaffected relatives of patients with MCAD deficiency and in other groups of patients having elevated plasma C8 acylcarnitine, consisting of 32 receiving valproic acid, 9 receiving medium-chain triglyceride supplement, 4 having multiple acyl-coenzyme A dehydrogenase deficiency, and 8 others with various etiologies. Criteria for the unequivocal diagnosis of MCAD deficiency by acylcarnitine analysis are an elevated C8-acylcarnitine concentration (> 0.3 microM), a ratio of C8/C10 acylcarnitines of > 5, and lack of elevated species of chain length > C10. These criteria were not influenced by clinical state, carnitine treatment, or underlying genetic mutation, and no false-positive or false-negative results were obtained. The same criteria were also successfully applied to profiles from neonatal blood spots retrieved from the original Guthrie cards of eight patients. Diagnosis of MCAD deficiency can therefore be made reliably through the analysis of acylcarnitines in blood, including presymptomatic neonatal recognition. Tandem mass spectrometry is a convenient method for fast and accurate determination of all relevant acylcarnitine species. PMID:8488845

  5. Functional reconstitution of the Mycobacterium tuberculosis long-chain acyl-CoA carboxylase from multiple acyl-CoA subunits.

    PubMed

    Bazet Lyonnet, Bernardo; Diacovich, Lautaro; Gago, Gabriela; Spina, Lucie; Bardou, Fabienne; Lemassu, Anne; Quémard, Annaïk; Gramajo, Hugo

    2017-02-21

    Mycobacterium tuberculosis produces a large number of structurally diverse lipids that have been implicated in the pathogenicity, persistence and antibiotic resistance of this organism. Most building blocks involved in the biosynthesis of all these lipids are generated by acyl-CoA carboxylases (ACCase) whose subunit composition and physiological roles have not yet been clearly established. A rather controversial data in the literature refers to the exact protein composition and substrate specificity of the enzyme complex that produces the long-chain α-carboxy-acyl-CoAs; one of the substrates involved in the last step of condensation mediated by the polyketide synthase Pks13 to synthesize mature mycolic acids. Here we have successfully reconstituted the so called long-chain acyl-CoA carboxylase complex (LCC) from its purified components: the α-subunit AccA3, the ε-subunit AccE5 and the two β-subunits AccD4 and AccD5, and demonstrated that the four subunits are essential for its LCC activity. Furthermore, we also showed by substrate competition experiments and the use of a specific inhibitor of the AccD5 subunit, that its role in the carboxylation of the long acyl-CoAs, as part of the LCC complex, was structural rather than catalytic. Moreover, AccD5 was also able to carboxylate its natural substrates, acetyl-CoA and propionyl-CoA, in the context of the LCC enzyme complex. Thus, the supercomplex formed by these four subunits has the potential to generate the main substrates, malonyl-CoA, methylmalonyl-CoA and α-carboxy-C24-26 -CoA, used as condensing units for the biosynthesis of all the lipids present in this pathogen. This article is protected by copyright. All rights reserved.

  6. Crystallization of the C-terminal domain of the mouse brain cytosolic long-chain acyl-CoA thioesterase

    PubMed Central

    Serek, Robert; Forwood, Jade K.; Hume, David A.; Martin, Jennifer L.; Kobe, Bostjan

    2006-01-01

    The mammalian long-chain acyl-CoA thioesterase, the enzyme that catalyses the hydrolysis of acyl-CoAs to free fatty acids, contains two fused 4HBT (4-­hydroxybenzoyl-CoA thioesterase) motifs. The C-terminal domain of the mouse long-chain acyl-CoA thioesterase (Acot7) has been expressed in bacteria and crystallized. The crystals were obtained by vapour diffusion using PEG 2000 MME as precipitant at pH 7.0 and 290 K. The crystals have the symmetry of space group R32 (unit-cell parameters a = b = 136.83, c = 99.82 Å, γ = 120°). Two molecules are expected in the asymmetric unit. The crystals diffract to 2.4 Å resolution using the laboratory X-ray source and are suitable for crystal structure determination. PMID:16511283

  7. Ceramide acyl chain length markedly influences miscibility with palmitoyl sphingomyelin in bilayer membranes.

    PubMed

    Westerlund, Bodil; Grandell, Pia-Maria; Isaksson, Y Jenny E; Slotte, J Peter

    2010-07-01

    Ceramides are precursors of major sphingolipids and can be important cellular effectors. The biological effects of ceramides have been suggested to stem from their biophysical effects on membrane structure affecting the lateral and transbilayer organization of other membrane components. In this study we investigated the effect of acyl chain composition in ceramides (C4-C24:1) on their miscibility with N-palmitoyl-sphingomyelin (PSM) using differential scanning calorimetry. We found that short-chain (C4 and C8) ceramides induced phase separation and lowered the T (m) and enthalpy of the PSM endotherm. We conclude that short-chain ceramides were more miscible in the fluid-phase than in the gel-phase PSM bilayers. Long-chain ceramides induced apparent heterogeneity in the bilayers. The main PSM endotherm decreased in cooperativity and enthalpy with increasing ceramide concentration. New ceramide-enriched components could be seen in the thermograms at all ceramide concentrations above X (Cer) = 0.05. These broad components had higher T (m) values than pure PSM. C24:1 ceramide exhibited complex behavior in the PSM bilayers. The miscibility of C24:1 ceramide with PSM at low (X (Cer) = 0.05-0.10) concentrations was exceptionally good according to the cooperativity of the transition. At higher concentrations, multiple components were detected, which might have arisen from interdigitated gel-phases formed by this very asymmetric ceramide. The results of this study indicate that short-chain and long-chain ceramides have very different effects on the sphingomyelin bilayers. There also seems to be a correlation between their miscibility in binary systems and the effect of ceramides of different hydrophobic length on sphingomyelin-rich domains in multicomponent membranes.

  8. Lipid transfer between phosphatidylcholine vesicles and human erythrocytes: exponential decrease in rate with increasing acyl chain length.

    PubMed

    Ferrell, J E; Lee, K J; Huestis, W H

    1985-06-04

    The rate of phospholipid transfer from sonicated phospholipid vesicles to human erythrocytes has been studied as a function of membrane concentration and lipid acyl chain composition. Phospholipid transfer exhibits saturable first-order kinetics with respect to both cell and vesicle membrane concentrations. This kinetic behavior is consistent either with transfer during transient contact between cell and vesicle surfaces (but only if the fraction of the cell surface susceptible to such interaction is small) or with transfer of monomers through the aqueous phase. The acyl chain composition of the transferred phospholipid affects the transfer kinetics profoundly; for homologous saturated phosphatidylcholines, the rate of transfer decreases exponentially with increasing acyl chain length. This behavior is consistent with passage of phospholipid monomers through a polar phase, which might be the bulk aqueous phase( as in the monomer transfer model) or the hydrated head-group regions of a cell-vesicle complex (transient collision model). Collisional transfer also predicts that intercell transfer of phospholipids should be slow compared to cell-vesicle transfer, as surface charge and steric effects should prevent close apposition of donor and acceptor membranes. This is not found; dilauroylphosphatidylcholine transfers rapidly between red cells. Thus, the observed relationship between acyl chain length and intermembrane phospholipid transfer rates likely reflects the energetics of monomer transfer through the aqueous phase.

  9. Genomic analysis of branched chain fatty acid and acyl sugar production in Solanum pennellii and Nicotiana benthamiana

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Acyl sugars are extracellular epidermal lipids that are exuded from glandular trichomes and coat the aerial organs of many species in the Solanaceae. These highly viscous surfactants, which often contain branched-chain fatty acids (BCFA), play an important defensive role against pest and insects. ...

  10. Unsaturated acyl chains dramatically enhanced cellular uptake by direct translocation of a minimalist oligo-arginine lipopeptide.

    PubMed

    Swiecicki, J-M; Di Pisa, M; Lippi, F; Chwetzoff, S; Mansuy, C; Trugnan, G; Chassaing, G; Lavielle, S; Burlina, F

    2015-10-07

    The recurring issue with cell penetrating peptides is how to increase direct translocation vs. endocytosis, to avoid premature degradation. Acylation by a cis unsaturated chain (C22:6) of a short cationic peptide provides a new rational design to favour diffuse cytosolic and dense Golgi localisations.

  11. ACX3, a Novel Medium-Chain Acyl-Coenzyme A Oxidase from Arabidopsis

    PubMed Central

    Froman, Byron E.; Edwards, Patricia C.; Bursch, Adam G.; Dehesh, Katayoon

    2000-01-01

    In a database search for homologs of acyl-coenzyme A oxidases (ACX) in Arabidopsis, we identified a partial genomic sequence encoding an apparently novel member of this gene family. Using this sequence information we then isolated the corresponding full-length cDNA from etiolated Arabidopsis cotyledons and have characterized the encoded recombinant protein. The polypeptide contains 675 amino acids. The 34 residues at the amino terminus have sequence similarity to the peroxisomal targeting signal 2 of glyoxysomal proteins, including the R-[I/Q/L]-X5-HL-XL-X15-22-C consensus sequence, suggesting a possible microsomal localization. Affinity purification of the encoded recombinant protein expressed in Escherichia coli followed by enzymatic assay, showed that this enzyme is active on C8:0- to C14:0-coenzyme A with maximal activity on C12:0-coenzyme A, indicating that it has medium-chain-specific activity. These data indicate that the protein reported here is different from previously characterized classes of ACX1, ACX2, and short-chain ACX (SACX), both in sequence and substrate chain-length specificity profile. We therefore, designate this new gene AtACX3. The temporal and spatial expression patterns of AtACX3 during development and in various tissues were similar to those of the AtSACX and other genes expressed in glyoxysomes. Currently available database information indicates that AtACX3 is present as a single copy gene. PMID:10859203

  12. Crystallization of the C-terminal domain of the mouse brain cytosolic long-chain acyl-CoA thioesterase

    SciTech Connect

    Serek, Robert; Forwood, Jade K.; Hume, David A.; Martin, Jennifer L.; Kobe, Bostjan

    2006-02-01

    The C-terminal domain of the mouse long-chain acyl-CoA thioesterase has been expressed in bacteria and crystallized by vapour diffusion. The crystals diffract to 2.4 Å resolution. The mammalian long-chain acyl-CoA thioesterase, the enzyme that catalyses the hydrolysis of acyl-CoAs to free fatty acids, contains two fused 4HBT (4-hydroxybenzoyl-CoA thioesterase) motifs. The C-terminal domain of the mouse long-chain acyl-CoA thioesterase (Acot7) has been expressed in bacteria and crystallized. The crystals were obtained by vapour diffusion using PEG 2000 MME as precipitant at pH 7.0 and 290 K. The crystals have the symmetry of space group R32 (unit-cell parameters a = b = 136.83, c = 99.82 Å, γ = 120°). Two molecules are expected in the asymmetric unit. The crystals diffract to 2.4 Å resolution using the laboratory X-ray source and are suitable for crystal structure determination.

  13. Determination of individual long-chain fatty acyl-CoA esters in heart and skeletal muscle.

    PubMed

    Molaparast-Saless, F; Shrago, E; Spennetta, T L; Donatello, S; Kneeland, L M; Nellis, S H; Liedtke, A J

    1988-05-01

    A method has been developed for determination of individual long-chain fatty acyl-CoA esters from heart and skeletal muscle using high performance liquid chromatography (HPLC). The esters were extracted from freeze-clamped tissue of pig and rat hearts and rat skeletal muscle for analysis on a radially compressed C18 5mu reverse-phase column. Nine peaks in the extract with carbon chain lengths from C12 to C20 that subsequently disappeared on alkaline hydrolysis were identified. The major acyl-CoA peaks were 14:1, 18:2, 16:0 and 18:1 and additionally in rat heart 18:0. Total long-chain acyl-CoA esters obtained by summation of the individual molecular species was 11.34 +/- 1.48 nmol/g wet wt. pig heart; 14.51 +/- 2.11 nmol/g wet wt. in rat heart, and 4.35 +/- 0.71 nmol/g wet wt. in rat skeletal muscle. These values were approximately 132% of those obtained using a separate procedure that measured total CoA by HPLC after alkaline hydrolysis of the esters. The described method demonstrates the quantitation of individual acyl-CoA species in muscle tissue. Therefore, it has a number of advantages in that it permits information to be obtained on the individual molecular species under various nutritional and metabolic conditions.

  14. A hydrophobic loop in acyl-CoA binding protein is functionally important for binding to palmitoyl-coenzyme A: a molecular dynamics study.

    PubMed

    Vallejo, Diego F G; Grigera, J Raúl; Costabel, Marcelo D

    2008-04-01

    Acyl-CoA binding protein (ACBP) plays a key role in lipid metabolism, interacting via a partly unknown mechanism with high affinity with long chain fatty acyl-CoAs (LCFA-CoAs). At present there is no study of the microscopic way ligand binding is accomplished. We analyzed this process by molecular dynamics (MDs) simulations. We proposed a computational model of ligand, able to reproduce some evidence from nuclear magnetic resonance (NMR) data, quantitative time resolved fluorometry and X-ray crystallography. We found that a hydrophobic loop, not in the active site, is important for function. Besides, multiple sequence alignment shows hydrophobicity (and not the residues itselves) conservation.

  15. Purification and Characterization of a Novel Pumpkin Short-Chain Acyl-Coenzyme A Oxidase with Structural Similarity to Acyl-Coenzyme A Dehydrogenases

    PubMed Central

    De Bellis, Luigi; Gonzali, Silvia; Alpi, Amedeo; Hayashi, Hiroshi; Hayashi, Makoto; Nishimura, Mikio

    2000-01-01

    A novel pumpkin (Cucurbita pepo) short-chain acyl-coenzyme A (CoA) oxidase (ACOX) was purified to homogeneity by hydrophobic-interaction, hydroxyapatite, affinity, and anion-exchange chromatography. The purified enzyme is a tetrameric protein, consisting of apparently identical 47-kD subunits. The protein structure of this oxidase differs from other plant and mammalian ACOXs, but is similar to the protein structure of mammalian mitochondrial acyl-CoA dehydrogenase (ACDH) and the recently identified plant mitochondrial ACDH. Subcellular organelle separation by sucrose density gradient centrifugation revealed that the enzyme is localized in glyoxysomes, whereas no immunoreactive bands of similar molecular weight were detected in mitochondrial fractions. The enzyme selectively catalyzes the oxidation of CoA esters of fatty acids with 4 to 10 carbon atoms, and exhibits the highest activity on C-6 fatty acids. Apparently, the enzyme has no activity on CoA esters of branched-chain or dicarboxylic fatty acids. The enzyme is slightly inhibited by high concentrations of substrate and it is not inhibited by Triton X-100 at concentrations up to 0.5% (v/v). The characteristics of this novel ACOX enzyme are discussed in relation to other ACOXs and ACDHs. PMID:10806249

  16. Effect of ceramide acyl chain length on skin permeability and thermotropic phase behavior of model stratum corneum lipid membranes.

    PubMed

    Janůšová, Barbora; Zbytovská, Jarmila; Lorenc, Petr; Vavrysová, Helena; Palát, Karel; Hrabálek, Alexandr; Vávrová, Kateřina

    2011-03-01

    Stratum corneum ceramides play an essential role in the barrier properties of skin. However, their structure-activity relationships are poorly understood. We investigated the effects of acyl chain length in the non-hydroxy acyl sphingosine type (NS) ceramides on the skin permeability and their thermotropic phase behavior. Neither the long- to medium-chain ceramides (8-24 C) nor free sphingosine produced any changes of the skin barrier function. In contrast, the short-chain ceramides decreased skin electrical impedance and increased skin permeability for two marker drugs, theophylline and indomethacin, with maxima in the 4-6C acyl ceramides. The thermotropic phase behavior of pure ceramides and model stratum corneum lipid membranes composed of ceramide/lignoceric acid/cholesterol/cholesterol sulfate was studied by differential scanning calorimetry and infrared spectroscopy. Differences in thermotropic phase behavior of these lipids were found: those ceramides that had the greatest impact on the skin barrier properties displayed the lowest phase transitions and formed the least dense model stratum corneum lipid membranes at 32°C. In conclusion, the long hydrophobic chains in the NS-type ceramides are essential for maintaining the skin barrier function. However, this ability is not shared by their short-chain counterparts despite their having the same polar head structure and hydrogen bonding ability.

  17. Acyl chain preference and inhibitor identification of Moraxella catarrhalis LpxA: Insight through crystal structure and computational studies.

    PubMed

    Pratap, Shivendra; Kesari, Pooja; Yadav, Ravi; Dev, Aditya; Narwal, Manju; Kumar, Pravindra

    2017-03-01

    Lipopolysaccharide (LPS) is an important surface component and a potential virulence factor in the pathogenesis of Gram-negative bacteria. UDP-N-acetylglucosamine acyltransferase (LpxA) enzyme catalyzes the first reaction of LPS biosynthesis, reversible transfer of R-3-hydroxy-acyl moiety from donor R-3-hydroxy-acyl-acyl carrier protein to the 3' hydroxyl position of UDP-N-acetyl-glucosamine. LpxA enzyme's essentiality in bacterial survival and absence of any homologous protein in humans makes it a promising target for anti-bacterial drug development. Herein, we present the crystal structure of Moraxella catarrhalis LpxA (McLpxA). We propose that L171 is responsible for limiting the acyl chain length in McLpxA to 10C or 12C. The study reveals the plausible interactions between the highly conserved clusters of basic residues at the C-terminal end of McLpxA and acidic residues of acyl carrier protein (ACP). Furthermore, the crystal structure of McLpxA was used to screen potential inhibitors from NCI open database using various computational approaches viz. pharmacophore mapping, virtual screening and molecular docking. Molecules Mol212032, Mol609399 and Mol152546 showed best binding affinity with McLpxA among all screened molecules. These molecules mimic the substrate-LpxA binding interactions.

  18. Chain Dynamics in Magnetorheological Suspensions

    NASA Technical Reports Server (NTRS)

    Gast, A. P.; Furst, E. M.

    1999-01-01

    Magnetorheological (MR) suspensions are composed of colloidal particles which acquire dipole moments when subjected to an external magnetic field. At sufficient field strengths and concentrations, the dipolar particles rapidly aggregate to form long chains. Subsequent lateral cross-linking of the dipolar chains is responsible for a rapid liquid-to-solid-like rheological transition. The unique, magnetically-activated rheological properties of MR suspensions make them ideal for interfacing mechanical systems to electronic controls. Additionally, the ability to experimentally probe colloidal suspensions interacting through tunable anisotropic potentials is of fundamental interest. Our current experimental work has focused on understanding the fluctuations of dipolar chains. It has been proposed by Halsey and Toor (HT) that the strong Landau-Peierls thermal fluctuations of dipolar chains could be responsible for long-range attractions between chains. Such interactions will govern the long-time relaxation of MR suspensions. We have synthesized monodisperse neutrally buoyant MR suspensions by density matching stabilized ferrofluid emulsion droplets with D2O. This allows us to probe the dynamics of the dipolar chains using light scattering without gravitational, interfacial, and polydispersity effects to resolve the short-wavelength dynamics of the dipolar chains. We used diffusing wave spectroscopy to measure these dynamics. The particle displacements at short times that show an independence to the field strength, but at long times exhibit a constrained, sub-diffusive motion that slows as the dipole strength is increased. The experiments are in good qualitative agreement with Brownian dynamics simulations of dipolar chains. Although there have been several important and detailed studies of the structure and interactions in MR suspensions, there has not been conclusive evidence that supports or contradicts the HT model prediction that long-range interactions exist between

  19. Retrospective study of the medium-chain acyl-CoA dehydrogenase deficiency in Portugal.

    PubMed

    Ventura, F V; Leandro, P; Luz, A; Rivera, I A; Silva, M F B; Ramos, R; Rocha, H; Lopes, A; Fonseca, H; Gaspar, A; Diogo, L; Martins, E; Leão-Teles, E; Vilarinho, L; Tavares de Almeida, I

    2014-06-01

    Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the commonest genetic defect of mitochondrial fatty acid β-oxidation. About 60% of MCADD patients are homozygous for the c.985A>G (p.Lys329Glu) mutation in the ACADM gene (G985 allele). Herein, we present the first report on the molecular and biochemical spectrum of Portuguese MCADD population. From the 109 patients studied, 83 were diagnosed after inclusion of MCADD in the national newborn screening, 8 following the onset of symptoms and 18 through segregation studies. Gypsy ancestry was identified in 85/109 patients. The G985 allele was found in homozygosity in 102/109 patients, in compound heterozygosity in 6/109 and was absent in one patient. Segregation studies in the Gypsy families showed that 93/123 relatives were carriers of the G985 allele, suggesting its high prevalence in this ethnic group. Additionally, three new substitutions-c.218A>G (p.Tyr73Cys), c.503A>T (p.Asp168Val) and c.1205G>T (p.Gly402Val)-were identified. Despite the particularity of the MCADD population investigated, the G985 allele was found in linkage disequilibrium with H1(112) haplotype. Furthermore, two novel haplotypes, H5(212) and H6(122) were revealed.

  20. Medium chain acyl-CoA dehydrogenase deficiency detected among Hispanics by New Jersey newborn screening.

    PubMed

    Anderson, Sharon; Botti, Christina; Li, Bo; Millonig, James H; Lyon, Elaine; Millson, Alison; Karabin, Suzanne S M; Brooks, Susan Sklower

    2012-09-01

    In the follow-up of New Jersey newborn screens suggestive of medium chain acyl-CoA dehydrogenase deficiency (MCADD) during a 30-month period, we identified five patients of Hispanic American ethnicity. With information provided by the New Jersey Department of Health and Human Services Newborn Screening program we calculated an overall cumulative incidence of approximately 7.20/100,000 for MCADD; 7.58/100,000 among Hispanic Americans and 7.08/100,000 among non-Hispanic Americans. Among the five Hispanic American infants who screened positive, a common variant (c.443G>A [p.R148K]) was identified which accounted for 30% of the alleles; c.799G>A (p.G267R) and c.985A>G (p.K329E) each accounted for an additional 20%; and a novel variant c.302G>A (p.G101E) was identified in one patient. Although treated prospectively during interim illnesses to prevent unwanted sequelae; till date, none of the patients carrying the c.443G>A variant have been symptomatic.

  1. Enzymatic Transesterification of Kraft Lignin with Long Acyl Chains in Ionic Liquids.

    PubMed

    Hulin, Lise; Husson, Eric; Bonnet, Jean-Pierre; Stevanovic, Tatjana; Sarazin, Catherine

    2015-09-09

    Valorization of lignin is essential for the economic viability of the biorefinery concept. For example, the enhancement of lignin hydrophobicity by chemical esterification is known to improve its miscibility in apolar polyolefin matrices, thereby helping the production of bio-based composites. To this end and due to its many reactive hydroxyl groups, lignin is a challenging macromolecular substrate for biocatalyzed esterification in non-conventional media. The present work describes for the first time the lipase-catalyzed transesterification of Kraft lignin in ionic liquids (ILs). Three lipases, three 1-butyl-3-methylimidazolium based ILs and ethyl oleate as long chain acyl donor were selected. Best results were obtained with a hydrophilic/hydrophobic binary IL system (1-butyl-3-methylimidazolium trifluoromethanesulfonate/1-butyl-3-methylimidazolium hexafluoro- phosphate, 1/1 v/v) and the immobilized lipase B from Candida antarctica (CALB) that afforded a promising transesterification yield (ca. 30%). Similar performances were achieved by using 1-butyl-3-methylimidazolium hexafluorophosphate as a coating agent for CALB rather than as a co-solvent in 1-butyl-3-methylimidazolium trifluoromethane-sulfonate thus limiting the use of hydrophobic IL. Structural characterization of lignin oleate was performed by spectroscopic studies (FTIR and ¹H-NMR). The synthesized lignin oleate exhibited interesting thermal and textural properties, different from those of the original Kraft lignin.

  2. Diametric Stereocontrol in Dynamic Catalytic Reduction of Racemic Acyl Phosphonates: Divergence from α-Keto Ester Congeners

    PubMed Central

    Corbett, Michael T.; Johnson, Jeffrey S.

    2013-01-01

    An unexpected dichotomy was observed in the Ru-catalyzed asymmetric transfer hydrogenation of acyl phosphonates: reduction proceeded from the opposite face relative to that observed in the analogous reduction of α-keto esters. The first highly selective catalytic hydrogenation of acyl phosphonates was utilized in the dynamic kinetic resolution of α-aryl acyl phosphonates providing β-stereogenic α-hydroxy phosphonic acid derivatives. PMID:23297694

  3. Concentrations of long-chain acyl-acyl carrier proteins during fatty acid synthesis by chloroplasts isolated from pea (Pisum sativum), safflower (Carthamus tinctoris), and amaranthus (Amaranthus lividus) leaves

    SciTech Connect

    Roughan, G.; Nishida, I. )

    1990-01-01

    Fatty acid synthesis from (1-14C)acetate by chloroplasts isolated from peas and amaranthus was linear for at least 15 min, whereas incorporation of the tracer into long-chain acyl-acyl carrier protein (ACP) did not increase after 2-3 min. When reactions were transferred to the dark after 3-5 min, long-chain acyl-ACPs lost about 90% of their radioactivity and total fatty acids retained all of theirs. Half-lives of the long-chain acyl-ACPs were estimated to be 10-15 s. Concentrations of palmitoyl-, stearoyl-, and oleoyl-ACP as indicated by equilibrium labeling during steady-state fatty acid synthesis, ranged from 0.6-1.1, 0.2-0.7, and 0.4-1.6 microM, respectively, for peas and from 1.6-1.9, 1.3-2.6, and 0.6-1.4 microM, respectively, for amaranthus. These values are based on a chloroplast volume of 47 microliters/mg chlorophyll and varied according to the mode of the incubation. A slow increase in activity of the fatty acid synthetase in safflower chloroplasts resulted in long-chain acyl-ACPs continuing to incorporate labeled acetate for 10 min. Upon re-illumination following a dark break, however, both fatty acid synthetase activity and acyl-ACP concentrations increased very rapidly. Palmitoyl-ACP was present at concentrations up to 2.5 microM in safflower chloroplasts, whereas those of stearoyl- and oleoyl-ACPs were in the lower ranges measured for peas. Acyl-ACPs were routinely separated from extracts of chloroplasts that had been synthesising long-chain fatty acids from labeled acetate by a minor modification of the method of Mancha et al. The results compared favorably with those obtained using alternative analytical methods such as adsorption to filter paper and partition chromatography on silicic acid columns.

  4. Enhanced production of branched-chain fatty acids by replacing β-ketoacyl-(acyl-carrier-protein) synthase III (FabH).

    PubMed

    Jiang, Wen; Jiang, Yanfang; Bentley, Gayle J; Liu, Di; Xiao, Yi; Zhang, Fuzhong

    2015-08-01

    Branched-chain fatty acids (BCFAs) are important precursors for the production of advanced biofuels with improved cold-flow properties. Previous efforts in engineering type II fatty acid synthase (FAS) for BCFA production suffered from low titers and/or the co-production of a large amount of straight-chain fatty acids (SCFAs), making it nearly impossible for further conversion of BCFAs to branched biofuels. Synthesis of both SCFAs and BCFAs requires FabH, the only β-ketoacyl-(acyl-carrier-protein) synthase in Escherichia coli that catalyzes the initial condensation reaction between malonyl-ACP and a short-chain acyl-CoA. In this study, we demonstrated that replacement of the acetyl-CoA-specific E. coli FabH with a branched-chain-acyl-CoA-specific FabH directed the flux to the synthesis of BCFAs, resulting in a significant enhancement in BCFA titer compared to a strain containing both acetyl-CoA- and branched-chain-acyl-CoA-specific FabHs. We further demonstrated that the composition of BCFAs can be tuned by engineering the upstream pathway to control the supply of different branched-chain acyl-CoAs, leading to the production either even-chain-iso-, odd-chain-iso-, or odd-chain-anteiso-BCFAs separately. Overall, the top-performing strain from this study produced BCFAs at 126 mg/L, comprising 52% of the total free fatty acids.

  5. Novel inhibitory action of tunicamycin homologues suggests a role for dynamic protein fatty acylation in growth cone-mediated neurite extension

    PubMed Central

    1994-01-01

    In neuronal growth cones, the advancing tips of elongating axons and dendrites, specific protein substrates appear to undergo cycles of posttranslational modification by covalent attachment and removal of long-chain fatty acids. We show here that ongoing fatty acylation can be inhibited selectively by long-chain homologues of the antibiotic tunicamycin, a known inhibitor of N-linked glycosylation. Tunicamycin directly inhibits transfer of palmitate to protein in a cell-free system, indicating that tunicamycin inhibition of protein palmitoylation reflects an action of the drug separate from its previously established effects on glycosylation. Tunicamycin treatment of differentiated PC12 cells or dissociated rat sensory neurons, under conditions in which protein palmitoylation is inhibited, produces a prompt cessation of neurite elongation and induces a collapse of neuronal growth cones. These growth cone responses are rapidly reversed by washout of the antibiotic, even in the absence of protein synthesis, or by addition of serum. Two additional lines of evidence suggest that the effects of tunicamycin on growth cones arise from its ability to inhibit protein long-chain acylation, rather than its previously established effects on protein glycosylation and synthesis. (a) The abilities of different tunicamycin homologues to induce growth cone collapse very systematically with the length of the fatty acyl side- chain of tunicamycin, in a manner predicted and observed for the inhibition of protein palmitoylation. Homologues with fatty acyl moieties shorter than palmitic acid (16 hydrocarbons), including potent inhibitors of glycosylation, are poor inhibitors of growth cone function. (b) The tunicamycin-induced impairment of growth cone function can be reversed by the addition of excess exogenous fatty acid, which reverses the inhibition of protein palmitoylation but has no effect on the inhibition of protein glycosylation. These results suggest an important role for

  6. Screening for medium chain acyl-CoA dehydrogenase deficiency using electrospray ionisation tandem mass spectrometry

    PubMed Central

    Clayton, P.; Doig, M.; Ghafari, S.; Meaney, C.; Taylor, C.; Leonard, J.; Morris, M.; Johnson, A.

    1998-01-01

    OBJECTIVE—To establish criteria for the diagnosis of medium chain acyl-CoA dehydrogenase (MCAD) deficiency in the UK population using a method in which carnitine species eluted from blood spots are butylated and analysed by electrospray ionisation tandem mass spectrometry (ESI-MS/MS).
DESIGN—Four groups were studied: (1) 35 children, aged 4 days to 16.2 years, with proven MCAD deficiency (mostly homozygous for the A985G mutation, none receiving carnitine supplements); (2) 2168control children; (3) 482 neonates; and (4) 15 MCAD heterozygotes.
RESULTS—All patients with MCAD deficiency had an octanoylcarnitine concentration ([C8-Cn]) > 0.38 µM and no accumulation of carnitine species > C10 or < C6. Among the patients with MCAD deficiency, the [C8-Cn] was significantly lower in children > 10 weeks old and in children with carnitine depletion (free carnitine < 20 µM). Neonatal blood spots from patients with MCAD deficiency had a [C8-Cn] > 1.5 µM, whereas in heterozygotes and other normal neonates the [C8-Cn] was < 1.0 µM. In contrast, the blood spot [C8-Cn] in eight of 27 patients with MCAD deficiency > 10 weeks old fell within the same range as five of 15 MCAD heterozygotes (0.38-1.0 µM). However, the free carnitine concentrations were reduced (< 20 µM) in the patients with MCAD deficiency but normal in the heterozygotes.
CONCLUSIONS—Criteria for the diagnosis of MCAD deficiency using ESI-MS/MS must take account of age and carnitine depletion. If screening is undertaken at 7-10 days, the number of false positive and negative results should be negligible. Because there have been no instances of death or neurological damage following diagnosis of MCAD deficiency in our patient group, a strong case can be made for neonatal screening for MCAD deficiency in the UK.

 PMID:9797589

  7. Unusual Heme Iron-Lipid Acyl Chain Coordination in Escherichia coli Flavohemoglobin

    PubMed Central

    D'Angelo, Paola; Lucarelli, Debora; della Longa, Stefano; Benfatto, Maurizio; Hazemann, Jean Louis; Feis, Alessandro; Smulevich, Giulietta; Ilari, Andrea; Bonamore, Alessandra; Boffi, Alberto

    2004-01-01

    Escherichia coli flavohemoglobin is endowed with the notable property of binding specifically unsaturated and/or cyclopropanated fatty acids both as free acids or incorporated into a phospholipid molecule. Unsaturated or cyclopropanated fatty acid binding to the ferric heme results in a spectral change observed in the visible absorption, resonance Raman, extended x-ray absorption fine spectroscopy (EXAFS), and x-ray absorption near edge spectroscopy (XANES) spectra. Resonance Raman spectra, measured on the flavohemoglobin heme domain, demonstrate that the lipid (linoleic acid or total lipid extracts)-induced spectral signals correspond to a transition from a five-coordinated (typical of the ligand-free protein) to a hexacoordinated, high spin heme iron. EXAFS and XANES measurements have been carried out both on the lipid-free and on the lipid-bound protein to assign the nature of ligand in the sixth coordination position of the ferric heme iron. EXAFS data analysis is consistent with the presence of a couple of atoms in the sixth coordination position at 2.7 Å in the lipid-bound derivative (bonding interaction), whereas a contribution at 3.54 Å (nonbonding interaction) can be singled out in the lipid-free protein. This last contribution is assigned to the CD1 carbon atoms of the distal LeuE11, in full agreement with crystallographic data on the lipid-free protein at 1.6 Å resolution obtained in the present work. Thus, the contributions at 2.7 Å distance from the heme iron are assigned to a couple of carbon atoms of the lipid acyl chain, possibly corresponding to the unsaturated carbons of the linoleic acid. PMID:15189885

  8. Acylation of Glucagon-Like Peptide-2: Interaction with Lipid Membranes and In Vitro Intestinal Permeability

    PubMed Central

    Trier, Sofie; Linderoth, Lars; Bjerregaard, Simon; Andresen, Thomas Lars; Rahbek, Ulrik Lytt

    2014-01-01

    Background Acylation of peptide drugs with fatty acid chains has proven beneficial for prolonging systemic circulation as well as increasing enzymatic stability without disrupting biological potency. Acylation has furthermore been shown to increase interactions with the lipid membranes of mammalian cells. The extent to which such interactions hinder or benefit delivery of acylated peptide drugs across cellular barriers such as the intestinal epithelia is currently unknown. The present study investigates the effect of acylating peptide drugs from a drug delivery perspective. Purpose We hypothesize that the membrane interaction is an important parameter for intestinal translocation, which may be used to optimize the acylation chain length for intestinal permeation. This work aims to characterize acylated analogues of the intestinotrophic Glucagon-like peptide-2 by systematically increasing acyl chain length, in order to elucidate its influence on membrane interaction and intestinal cell translocation in vitro. Results Peptide self-association and binding to both model lipid and cell membranes was found to increase gradually with acyl chain length, whereas translocation across Caco-2 cells depended non-linearly on chain length. Short and medium acyl chains increased translocation compared to the native peptide, but long chain acylation displayed no improvement in translocation. Co-administration of a paracellular absorption enhancer was found to increase translocation irrespective of acyl chain length, whereas a transcellular enhancer displayed increased synergy with the long chain acylation. Conclusions These results show that membrane interactions play a prominent role during intestinal translocation of an acylated peptide. Acylation benefits permeation for shorter and medium chains due to increased membrane interactions, however, for longer chains insertion in the membrane becomes dominant and hinders translocation, i.e. the peptides get ‘stuck’ in the cell

  9. Ceramides with a pentadecasphingosine chain and short acyls have strong permeabilization effects on skin and model lipid membranes.

    PubMed

    Školová, Barbora; Janůšová, Barbora; Vávrová, Kateřina

    2016-02-01

    The composition and organization of stratum corneum lipids play an essential role in skin barrier function. Ceramides represent essential components of this lipid matrix; however, the importance of the individual structural features in ceramides is not fully understood. To probe the structure-permeability relationships in ceramides, we prepared analogs of N-lignoceroylsphingosine with shortened sphingosine (15 and 12 carbons) and acyl chains (2, 4 and 6 carbons) and studied their behavior in skin and in model lipid membranes. Ceramide analogs with pentadecasphingosine (15C) chains were more barrier-perturbing than 12C- and 18C-sphingosine ceramides; the greatest effects were found with 4 to 6C acyls (up to 15 times higher skin permeability compared to an untreated control and up to 79 times higher permeability of model stratum corneum lipid membranes compared to native very long-chain ceramides). Infrared spectroscopy using deuterated lipids and X-ray powder diffraction showed surprisingly similar behavior of the short ceramide membranes in terms of lipid chain order and packing, phase transitions and domain formation. The high- and low-permeability membranes differed in their amide I band shape and lamellar organization. These skin and membrane permeabilization properties of some short ceramides may be explored, for example, for the rational design of permeation enhancers for transdermal drug delivery.

  10. α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase: Exploration of Conformational Constraints in the Acyl Side Chain

    PubMed Central

    Duncan, Katharine K.; Otrubova, Katerina; Boger, Dale L.

    2014-01-01

    A series of α-ketooxazoles containing heteroatoms embedded within conformational constraints in the C2 acyl side chain of 2 (OL-135) were synthesized and evaluated as inhibitors of fatty acid amide hydrolase (FAAH). The studies reveal that the installation of a heteroatom (O) in the conformational constraint is achievable, although the potency of these novel derivatives is reduced slightly relative to 2 and the analogous 1,2,3,4-tetrahydronaphthalene series. Interestingly, both enantiomers (R and S) of the candidate inhibitors bearing a chiral center adjacent to the electrophilic carbonyl were found to effectively inhibit FAAH. PMID:24690529

  11. The Length of the Bound Fatty Acid Influences the Dynamics of the Acyl Carrier Protein and the Stability of the Thioester Bond†

    PubMed Central

    2009-01-01

    Acyl carrier proteins involved in fatty acid biosynthesis have been shown to exhibit a high degree of conformational flexibility, in that they are able to sequester fatty acid intermediates between 4 and 18 carbons in length. This flexibility has been observed in X-ray and NMR structures of acyl carrier proteins attached to different fatty acids. NMR studies comparing decanoyl-ACP and stearoyl-ACP indicated that ACP exhibits more dynamic motions when bound to longer fatty acids. We have used complementary chemical and NMR methods as an approach to improving our understanding of the effect of fatty acid length on the dynamics of acyl carrier protein. A chemical assay of the accessibility of the acyl thioester to solvent revealed a positive correlation between chain length and rate of hydrolysis. Surprisingly, this linear correlation was biphasic, with accelerated hydrolysis observed for fatty acids longer than 15 carbons. To further understand the motions associated with this acceleration, we collected 15N relaxation dispersion data for 14:0-, 15:0-, and 16:0-ACP. The greatest dispersions were exhibited by residues that form the entrance to the fatty acid binding pocket. In addition, these dispersions were observed to increase with the length of the fatty acid. Because the exchange rates derived from fitting the data to a two-state model varied from residue to residue, a more complex motional model appears to be required to adequately explain the dynamics. Thus, acyl-ACP offers an interesting system for future investigations of complex protein motions on the micro- and millisecond time scales. PMID:20014832

  12. Two Predicted Transmembrane Domains Exclude Very Long Chain Fatty acyl-CoAs from the Active Site of Mouse Wax Synthase

    PubMed Central

    Kawelke, Steffen; Feussner, Ivo

    2015-01-01

    Wax esters are used as coatings or storage lipids in all kingdoms of life. They are synthesized from a fatty alcohol and an acyl-CoA by wax synthases. In order to get insights into the structure-function relationships of a wax synthase from Mus musculus, a domain swap experiment between the mouse acyl-CoA:wax alcohol acyltransferase (AWAT2) and the homologous mouse acyl-CoA:diacylglycerol O-acyltransferase 2 (DGAT2) was performed. This showed that the substrate specificity of AWAT2 is partially determined by two predicted transmembrane domains near the amino terminus of AWAT2. Upon exchange of the two domains for the respective part of DGAT2, the resulting chimeric enzyme was capable of incorporating up to 20% of very long acyl chains in the wax esters upon expression in S. cerevisiae strain H1246. The amount of very long acyl chains in wax esters synthesized by wild type AWAT2 was negligible. The effect was narrowed down to a single amino acid position within one of the predicted membrane domains, the AWAT2 N36R variant. Taken together, we provide first evidence that two predicted transmembrane domains in AWAT2 are involved in determining its acyl chain length specificity. PMID:26714272

  13. Phospholipid profiling identifies acyl chain elongation as a ubiquitous trait and potential target for the treatment of lung squamous cell carcinoma

    PubMed Central

    Marien, Eyra; Meister, Michael; Muley, Thomas; del Pulgar, Teresa Gomez; Derua, Rita; Spraggins, Jeffrey M.; Van de Plas, Raf; Vanderhoydonc, Frank; Machiels, Jelle; Binda, Maria Mercedes; Dehairs, Jonas; Willette-Brown, Jami; Hu, Yinling; Dienemann, Hendrik; Thomas, Michael; Schnabel, Philipp A.; Caprioli, Richard M.; Lacal, Juan Carlos; Waelkens, Etienne; Swinnen, Johannes V.

    2016-01-01

    Lung cancer is the leading cause of cancer death. Beyond first line treatment, few therapeutic options are available, particularly for squamous cell carcinoma (SCC). Here, we have explored the phospholipidomes of 30 human SCCs and found that they almost invariably (in 96.7% of cases) contain phospholipids with longer acyl chains compared to matched normal tissues. This trait was confirmed using in situ 2D-imaging MS on tissue sections and by phospholipidomics of tumor and normal lung tissue of the L-IkkαKA/KA mouse model of lung SCC. In both human and mouse, the increase in acyl chain length in cancer tissue was accompanied by significant changes in the expression of acyl chain elongases (ELOVLs). Functional screening of differentially expressed ELOVLs by selective gene knockdown in SCC cell lines followed by phospholipidomics revealed ELOVL6 as the main elongation enzyme responsible for acyl chain elongation in cancer cells. Interestingly, inhibition of ELOVL6 drastically reduced colony formation of multiple SCC cell lines in vitro and significantly attenuated their growth as xenografts in vivo in mouse models. These findings identify acyl chain elongation as one of the most common traits of lung SCC discovered so far and pinpoint ELOVL6 as a novel potential target for cancer intervention. PMID:26862848

  14. Pre-exercise medium-chain triglyceride application prevents acylcarnitine accumulation in skeletal muscle from very-long-chain acyl-CoA-dehydrogenase-deficient mice.

    PubMed

    Primassin, Sonja; Tucci, Sara; Herebian, Diran; Seibt, Annette; Hoffmann, Lars; ter Veld, Frank; Spiekerkoetter, Ute

    2010-06-01

    Dietary modification with medium-chain triglyceride (MCT) supplementation is one crucial way of treating children with long-chain fatty acid oxidation disorders. Recently, supplementation prior to exercise has been reported to prevent muscular pain and rhabdomyolysis. Systematic studies to determine when MCT supplementation is most beneficial have not yet been undertaken. We studied the effects of an MCT-based diet compared with MCT administration only prior to exercise in very-long-chain acyl-CoA dehydrogenase (VLCAD) knockout (KO) mice. VLCAD KO mice were fed an MCT-based diet in same amounts as normal mouse diet containing long-chain triglycerides (LCT) and were exercised on a treadmill. Mice fed a normal LCT diet received MCT only prior to exercise. Acylcarnitine concentration, free carnitine concentration, and acyl-coenzyme A (CoA) oxidation capacity in skeletal muscle as well as hepatic lipid accumulation were determined. Long-chain acylcarnitines significantly increased in VLCAD-deficient skeletal muscle with an MCT diet compared with an LCT diet with MCT bolus prior to exercise, whereas an MCT bolus treatment significantly decreased long-chain acylcarnitines after exercise compared with an LCT diet. C8-carnitine was significantly increased in skeletal muscle after MCT bolus treatment and exercise compared with LCT and long-term MCT treatment. Increased hepatic lipid accumulation was observed in long-term MCT-treated KO mice. MCT seems most beneficial when given in a single dose directly prior to exercise to prevent acylcarnitine accumulation. In contrast, continuous MCT treatment produces a higher skeletal muscle content of long-chain acylcarnitines after exercise and increases hepatic lipid storage in VLCAD KO mice.

  15. Chlamydia trachomatis growth and development requires the activity of host Long-chain Acyl-CoA Synthetases (ACSLs)

    PubMed Central

    Recuero-Checa, Maria A.; Sharma, Manu; Lau, Constance; Watkins, Paul A.; Gaydos, Charlotte A.; Dean, Deborah

    2016-01-01

    The obligate-intracellular pathogen Chlamydia trachomatis (Ct) has undergone considerable genome reduction with consequent dependence on host biosynthetic pathways, metabolites and enzymes. Long-chain acyl-CoA synthetases (ACSLs) are key host-cell enzymes that convert fatty acids (FA) into acyl-CoA for use in metabolic pathways. Here, we show that the complete host ACSL family [ACSL1 and ACSL3–6] translocates into the Ct membrane-bound vacuole, termed inclusion, and remains associated with membranes of metabolically active forms of Ct throughout development. We discovered that three different pharmacologic inhibitors of ACSL activity independently impede Ct growth in a dose-dependent fashion. Using an FA competition assay, host ACSLs were found to activate Ct branched-chain FAs, suggesting that one function of the ACSLs is to activate Ct FAs and host FAs (recruited from the cytoplasm) within the inclusion. Because the ACSL inhibitors can deplete lipid droplets (LD), we used a cell line where LD synthesis was switched off to evaluate whether LD deficiency affects Ct growth. In these cells, we found no effect on growth or on translocation of ACSLs into the inclusion. Our findings support an essential role for ACSL activation of host-cell and bacterial FAs within the inclusion to promote Ct growth and development, independent of LDs. PMID:26988341

  16. Clear correlation of genotype with disease phenotype in very-long-chain acyl-CoA dehydrogenase deficiency.

    PubMed Central

    Andresen, B S; Olpin, S; Poorthuis, B J; Scholte, H R; Vianey-Saban, C; Wanders, R; Ijlst, L; Morris, A; Pourfarzam, M; Bartlett, K; Baumgartner, E R; deKlerk, J B; Schroeder, L D; Corydon, T J; Lund, H; Winter, V; Bross, P; Bolund, L; Gregersen, N

    1999-01-01

    Very-long-chain acyl-CoA dehydrogenase (VLCAD) catalyzes the initial rate-limiting step in mitochondrial fatty acid beta-oxidation. VLCAD deficiency is clinically heterogenous, with three major phenotypes: a severe childhood form, with early onset, high mortality, and high incidence of cardiomyopathy; a milder childhood form, with later onset, usually with hypoketotic hypoglycemia as the main presenting feature, low mortality, and rare cardiomyopathy; and an adult form, with isolated skeletal muscle involvement, rhabdomyolysis, and myoglobinuria, usually triggered by exercise or fasting. To examine whether these different phenotypes are due to differences in the VLCAD genotype, we investigated 58 different mutations in 55 unrelated patients representing all known clinical phenotypes and correlated the mutation type with the clinical phenotype. Our results show a clear relationship between the nature of the mutation and the severity of disease. Patients with the severe childhood phenotype have mutations that result in no residual enzyme activity, whereas patients with the milder childhood and adult phenotypes have mutations that may result in residual enzyme activity. This clear genotype-phenotype relationship is in sharp contrast to what has been observed in medium-chain acyl-CoA dehydrogenase deficiency, in which no correlation between genotype and phenotype can be established. PMID:9973285

  17. Chlamydia trachomatis growth and development requires the activity of host Long-chain Acyl-CoA Synthetases (ACSLs).

    PubMed

    Recuero-Checa, Maria A; Sharma, Manu; Lau, Constance; Watkins, Paul A; Gaydos, Charlotte A; Dean, Deborah

    2016-03-18

    The obligate-intracellular pathogen Chlamydia trachomatis (Ct) has undergone considerable genome reduction with consequent dependence on host biosynthetic pathways, metabolites and enzymes. Long-chain acyl-CoA synthetases (ACSLs) are key host-cell enzymes that convert fatty acids (FA) into acyl-CoA for use in metabolic pathways. Here, we show that the complete host ACSL family [ACSL1 and ACSL3-6] translocates into the Ct membrane-bound vacuole, termed inclusion, and remains associated with membranes of metabolically active forms of Ct throughout development. We discovered that three different pharmacologic inhibitors of ACSL activity independently impede Ct growth in a dose-dependent fashion. Using an FA competition assay, host ACSLs were found to activate Ct branched-chain FAs, suggesting that one function of the ACSLs is to activate Ct FAs and host FAs (recruited from the cytoplasm) within the inclusion. Because the ACSL inhibitors can deplete lipid droplets (LD), we used a cell line where LD synthesis was switched off to evaluate whether LD deficiency affects Ct growth. In these cells, we found no effect on growth or on translocation of ACSLs into the inclusion. Our findings support an essential role for ACSL activation of host-cell and bacterial FAs within the inclusion to promote Ct growth and development, independent of LDs.

  18. Enrichment of hydroxylated C24- and C26-acyl-chain sphingolipids mediates PIN2 apical sorting at trans-Golgi network subdomains

    PubMed Central

    Wattelet-Boyer, Valérie; Brocard, Lysiane; Jonsson, Kristoffer; Esnay, Nicolas; Joubès, Jérôme; Domergue, Frédéric; Mongrand, Sébastien; Raikhel, Natasha; Bhalerao, Rishikesh P.; Moreau, Patrick; Boutté, Yohann

    2016-01-01

    The post-Golgi compartment trans-Golgi Network (TGN) is a central hub divided into multiple subdomains hosting distinct trafficking pathways, including polar delivery to apical membrane. Lipids such as sphingolipids and sterols have been implicated in polar trafficking from the TGN but the underlying mechanisms linking lipid composition to functional polar sorting at TGN subdomains remain unknown. Here we demonstrate that sphingolipids with α-hydroxylated acyl-chains of at least 24 carbon atoms are enriched in secretory vesicle subdomains of the TGN and are critical for de novo polar secretory sorting of the auxin carrier PIN2 to apical membrane of Arabidopsis root epithelial cells. We show that sphingolipid acyl-chain length influences the morphology and interconnections of TGN-associated secretory vesicles. Our results uncover that the sphingolipids acyl-chain length links lipid composition of TGN subdomains with polar secretory trafficking of PIN2 to apical membrane of polarized epithelial cells. PMID:27681606

  19. Differential effects of cholesterol on acyl chain order in erythrocyte membranes as a function of depth from the surface. An electron paramagnetic resonance (EPR) spin label study.

    PubMed

    Cassera, M B; Silber, A M; Gennaro, A M

    2002-10-16

    The purpose of this work is to analyze the effects of cholesterol modulation on acyl chain ordering in the membrane of human erythrocytes as a function of depth from the surface. Partial cholesterol depletion was achieved by incubation of erythrocytes with liposomes containing saturated phospholipids, or with methyl-beta-cyclodextrin (MbetaCD). Cholesterol enrichment was achieved by incubation with liposomes formed by phospholipids/cholesterol, or with the complex MbetaCD/cholesterol. Acyl chain order was studied with electron paramagnetic resonance spectroscopy (EPR) using spin labels that sense the lipid bilayer at different depths. It is shown that the increase in cholesterol stiffens acyl chains but decreases the interaction among lipid headgroups, while cholesterol depletion causes the opposite behavior. It is likely that the observed cholesterol effects are related to those stabilizing the cholesterol-rich detergent-insoluble membrane domains (rafts), recently shown to exist in erythrocytes.

  20. Carbon and Acyl Chain Flux during Stress-induced Triglyceride Accumulation by Stable Isotopic Labeling of the Polar Microalga Coccomyxa subellipsoidea C169.

    PubMed

    Allen, James W; DiRusso, Concetta C; Black, Paul N

    2017-01-06

    Deriving biofuels and other lipoid products from algae is a promising future technology directly addressing global issues of atmospheric CO2 balance. To better understand the metabolism of triglyceride synthesis in algae, we examined their metabolic origins in the model species, Coccomyxa subellipsoidea C169, using stable isotopic labeling. Labeling patterns arising from [U-(13)C]glucose, (13)CO2, or D2O supplementation were analyzed by GC-MS and/or LC-MS over time courses during nitrogen starvation to address the roles of catabolic carbon recycling, acyl chain redistribution, and de novo fatty acid (FA) synthesis during the expansion of the lipid bodies. The metabolic origin of stress-induced triglyceride was found to be a continuous 8:2 ratio between de novo synthesized FA and acyl chain transfer from pre-stressed membrane lipids with little input from lipid remodeling. Membrane lipids were continually synthesized with associated acyl chain editing during nitrogen stress, in contrast to an overall decrease in total membrane lipid. The incorporation rates of de novo synthesized FA into lipid classes were measured over a time course of nitrogen starvation. The synthesis of triglycerides, phospholipids, and galactolipids followed a two-stage pattern where nitrogen starvation resulted in a 2.5-fold increase followed by a gradual decline. Acyl chain flux into membrane lipids was dominant in the first stage followed by triglycerides. These data indicate that the level of metabolic control that determines acyl chain flux between membrane lipids and triglycerides during nitrogen stress relies primarily on the Kennedy pathway and de novo FA synthesis with limited, defined input from acyl editing reactions.

  1. Structural basis for selective recognition of acyl chains by the membrane-associated acyltransferase PatA

    PubMed Central

    Albesa-Jové, David; Svetlíková, Zuzana; Tersa, Montse; Sancho-Vaello, Enea; Carreras-González, Ana; Bonnet, Pascal; Arrasate, Pedro; Eguskiza, Ander; Angala, Shiva K.; Cifuente, Javier O.; Korduláková, Jana; Jackson, Mary; Mikušová, Katarína; Guerin, Marcelo E.

    2016-01-01

    The biosynthesis of phospholipids and glycolipids are critical pathways for virtually all cell membranes. PatA is an essential membrane associated acyltransferase involved in the biosynthesis of mycobacterial phosphatidyl-myo-inositol mannosides (PIMs). The enzyme transfers a palmitoyl moiety from palmitoyl–CoA to the 6-position of the mannose ring linked to 2-position of inositol in PIM1/PIM2. We report here the crystal structures of PatA from Mycobacterium smegmatis in the presence of its naturally occurring acyl donor palmitate and a nonhydrolyzable palmitoyl–CoA analog. The structures reveal an α/β architecture, with the acyl chain deeply buried into a hydrophobic pocket that runs perpendicular to a long groove where the active site is located. Enzyme catalysis is mediated by an unprecedented charge relay system, which markedly diverges from the canonical HX4D motif. Our studies establish the mechanistic basis of substrate/membrane recognition and catalysis for an important family of acyltransferases, providing exciting possibilities for inhibitor design. PMID:26965057

  2. Structural basis for selective recognition of acyl chains by the membrane-associated acyltransferase PatA.

    PubMed

    Albesa-Jové, David; Svetlíková, Zuzana; Tersa, Montse; Sancho-Vaello, Enea; Carreras-González, Ana; Bonnet, Pascal; Arrasate, Pedro; Eguskiza, Ander; Angala, Shiva K; Cifuente, Javier O; Korduláková, Jana; Jackson, Mary; Mikušová, Katarína; Guerin, Marcelo E

    2016-03-11

    The biosynthesis of phospholipids and glycolipids are critical pathways for virtually all cell membranes. PatA is an essential membrane associated acyltransferase involved in the biosynthesis of mycobacterial phosphatidyl-myo-inositol mannosides (PIMs). The enzyme transfers a palmitoyl moiety from palmitoyl-CoA to the 6-position of the mannose ring linked to 2-position of inositol in PIM1/PIM2. We report here the crystal structures of PatA from Mycobacterium smegmatis in the presence of its naturally occurring acyl donor palmitate and a nonhydrolyzable palmitoyl-CoA analog. The structures reveal an α/β architecture, with the acyl chain deeply buried into a hydrophobic pocket that runs perpendicular to a long groove where the active site is located. Enzyme catalysis is mediated by an unprecedented charge relay system, which markedly diverges from the canonical HX4D motif. Our studies establish the mechanistic basis of substrate/membrane recognition and catalysis for an important family of acyltransferases, providing exciting possibilities for inhibitor design.

  3. Fatty Acid Oxidation Mediated by Acyl-CoA Synthetase Long Chain 3 Is Required for Mutant KRAS Lung Tumorigenesis.

    PubMed

    Padanad, Mahesh S; Konstantinidou, Georgia; Venkateswaran, Niranjan; Melegari, Margherita; Rindhe, Smita; Mitsche, Matthew; Yang, Chendong; Batten, Kimberly; Huffman, Kenneth E; Liu, Jingwen; Tang, Ximing; Rodriguez-Canales, Jaime; Kalhor, Neda; Shay, Jerry W; Minna, John D; McDonald, Jeffrey; Wistuba, Ignacio I; DeBerardinis, Ralph J; Scaglioni, Pier Paolo

    2016-08-09

    KRAS is one of the most commonly mutated oncogenes in human cancer. Mutant KRAS aberrantly regulates metabolic networks. However, the contribution of cellular metabolism to mutant KRAS tumorigenesis is not completely understood. We report that mutant KRAS regulates intracellular fatty acid metabolism through Acyl-coenzyme A (CoA) synthetase long-chain family member 3 (ACSL3), which converts fatty acids into fatty Acyl-CoA esters, the substrates for lipid synthesis and β-oxidation. ACSL3 suppression is associated with depletion of cellular ATP and causes the death of lung cancer cells. Furthermore, mutant KRAS promotes the cellular uptake, retention, accumulation, and β-oxidation of fatty acids in lung cancer cells in an ACSL3-dependent manner. Finally, ACSL3 is essential for mutant KRAS lung cancer tumorigenesis in vivo and is highly expressed in human lung cancer. Our data demonstrate that mutant KRAS reprograms lipid homeostasis, establishing a metabolic requirement that could be exploited for therapeutic gain.

  4. Strategies for Correcting Very Long Chain Acyl-CoA Dehydrogenase Deficiency*

    PubMed Central

    Tenopoulou, Margarita; Chen, Jie; Bastin, Jean; Bennett, Michael J.; Ischiropoulos, Harry; Doulias, Paschalis-Thomas

    2015-01-01

    Very long acyl-CoA dehydrogenase (VLCAD) deficiency is a genetic pediatric disorder presenting with a spectrum of phenotypes that remains for the most part untreatable. Here, we present a novel strategy for the correction of VLCAD deficiency by increasing mutant VLCAD enzymatic activity. Treatment of VLCAD-deficient fibroblasts, which express distinct mutant VLCAD protein and exhibit deficient fatty acid β-oxidation, with S-nitroso-N-acetylcysteine induced site-specific S-nitrosylation of VLCAD mutants at cysteine residue 237. Cysteine 237 S-nitrosylation was associated with an 8–17-fold increase in VLCAD-specific activity and concomitant correction of acylcarnitine profile and β-oxidation capacity, two hallmarks of the disorder. Overall, this study provides biochemical evidence for a potential therapeutic modality to correct β-oxidation deficiencies. PMID:25737446

  5. Molecular dynamics simulations of class C beta-lactamase from Citrobacter freundii: insights into the base catalyst for acylation.

    PubMed

    Díaz, Natalia; Suárez, Dimas; Sordo, Tomás L

    2006-01-17

    Herein, we present results from molecular dynamics (MD) simulations of the class C beta-lactamase from Citrobacter freundii and its Michaelis complex with aztreonam. Four different configurations of the active site were modeled in aqueous solution, and their relative stability was estimated by means of quantum mechanical energy calculations. For the free enzyme, the energetically most stable configurations present a neutral Lys67 residue or an anionic Tyr150 side chain. Our calculations predict that these two configurations are quite close in terms of free energy, the anionic Tyr150 state being favored by approximately 1 kcal/mol. In contrast, for the noncovalent complex formed between the C. freundii enzyme and aztreonam, the energetic analyses predict that the configuration with the neutral Lys67 residue is much more stable than the anionic Tyr150 one (approximately 20 kcal/mol). Moreover, the MD simulations reveal that the neutral Lys67 state results in a proper enzyme-aztreonam orientation for nucleophilic attack and in a very stable contact between the nucleophilic hydroxyl group of Ser64 and the neutral amino side chain of Lys67. Thus, both the computed free energies and the structural analyses support the assignation of Lys67 as the base catalyst for the acylation step in the native form of the C. freundii enzyme.

  6. Medium-chain triglycerides impair lipid metabolism and induce hepatic steatosis in very long-chain acyl-CoA dehydrogenase (VLCAD)-deficient mice.

    PubMed

    Tucci, Sara; Primassin, Sonja; Ter Veld, Frank; Spiekerkoetter, Ute

    2010-09-01

    A medium-chain-triglyceride (MCT)-based diet is mainstay of treatment in very-long-chain acyl-CoA dehydrogenase deficiency (VLCADD), a long-chain fatty acid beta-oxidation defect. Beneficial effects have been reported with an MCT-bolus prior to exercise. Little is known about the impact of a long-term MCT diet on hepatic lipid metabolism. Here we investigate the effects of MCT-supplementation on liver and blood lipids in the murine model of VLCADD. Wild-type (WT) and VLCAD-knock-out (KO) mice were fed (1) a long-chain triglyceride (LCT)-diet over 5weeks, (2) an MCT diet over 5 weeks and (3) an LCT diet plus MCT-bolus. Blood and liver lipid content were determined. Expression of genes regulating lipogenesis was analyzed by RT-PCR. Under the LCT diet, VLCAD-KO mice accumulated significantly higher blood cholesterol concentrations compared to WT mice. The MCT-diet induced severe hepatic steatosis, significantly higher serum free fatty acids and impaired hepatic lipid mobilization in VLCAD-KO mice. Expression at mRNA level of hepatic lipogenic genes was up-regulated. The long-term MCT diet stimulates lipogenesis and impairs hepatic lipid metabolism in VLCAD-KO mice. These results suggest a critical reconsideration of a long-term MCT-modified diet in human VLCADD. In contrast, MCT in situations of increased energy demand appears to be a safer treatment alternative.

  7. The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View

    SciTech Connect

    Pontes, Frederico J.; Rusu, Victor H.; Soares, Thereza A.; Lins, Roberto D.

    2012-05-24

    Lipopolysaccharides (LPS) are the main constituent of the outer bacterial membrane of Gram-negative bacteria. Lipid-A is the structural region of LPS that interacts with the innate immune system and induces inflammatory responses. It is formed by a phosphorylated β-d-glucosaminyl-(1→6)-α-N-glucosamine disaccharide backbone containing ester-linked and amide-linked long-chain fatty acids, which may vary in length and number depending on the bacterial strains and the environment. Phenotypical variation (i.e., number of acyl chains), cation type, and temperature influence the phase transition, aggregate structure, and endotoxic activity of Lipid-A. We have applied an extension of the GROMOS force field 45a4 carbohydrate parameter set to investigate the behavior of hexa- and pentaacylated Lipid-A of Pseudomonas aeruginosa at two temperatures (300 and 328 K) and in the presence of mono- and divalent cations (represented by Ca2+ and Na+, respectively) through molecular dynamics simulations. The distinct phase of Lipid-A aggregates was characterized by structural properties, deuterium order parameters, the molecular shape of the lipid units (conical versus cylindrical), and molecular packing. Our results show that Na+ ions induce a transition from the lamellar to nonlamellar phase. In contrast, the bilayer integrity is maintained in the presence of Ca2+ ions. Through these findings, we present microscopic insights on the influence of different cations on the molecular behavior of Lipid-A associated with the lamellar to nonlamellar transition.

  8. Genetics Home Reference: very long-chain acyl-CoA dehydrogenase deficiency

    MedlinePlus

    ... metabolize) a group of fats called very long-chain fatty acids. These fatty acids are found in foods and the body's fat tissues. Fatty acids are a major source of energy for the heart and muscles. During periods of fasting, ... of this enzyme, very long-chain fatty acids are not metabolized properly. As a ...

  9. Genetics Home Reference: medium-chain acyl-CoA dehydrogenase deficiency

    MedlinePlus

    ... down (metabolize) a group of fats called medium-chain fatty acids. These fatty acids are found in foods and the body's fat tissues. Fatty acids are a major source of energy for the heart and muscles. During periods of fasting, ... of this enzyme, medium-chain fatty acids are not metabolized properly. As a ...

  10. Protoxenicins A and B, Cytotoxic Long-Chain Acylated Xenicanes from the Soft Coral Protodendron repens.

    PubMed

    Urda, Carlos; Fernández, Rogelio; Pérez, Marta; Rodríguez, Jaime; Jiménez, Carlos; Cuevas, Carmen

    2017-03-24

    Two new xenicanes, named protoxenicins A (1) and B (2), were isolated from an organic extract of the soft coral Protodendron repens, collected off the coast of Okuza (Tanzania), being the first chemical study of an organism belonging to this genus. Their planar structures were determined by 1D and 2D NMR and HRESIMS techniques, while the relative configurations were elucidated by comparison of their chemical shifts and coupling constants with the literature values of their congeners, as well as by ROESY experiments, chemical derivatization, and molecular mechanics calculations. This is the first report of a xenicin acylated with a long saturated fatty acid. Furthermore, the absolute configuration of the stereogenic centers of the cyclononane ring and at C-1 in 1 was determined by Mosher's method. Protoxenicin B (2) is present in solution as a mixture of two conformers in a 2:1 ratio deduced by (1)H NMR. Both xenicanes display significant cytotoxic activity against a panel of different tumor cell lines.

  11. Characterization of carnitine and fatty acid metabolism in the long-chain acyl-CoA dehydrogenase-deficient mouse

    PubMed Central

    van Vlies, Naomi; Tian, Liqun; Overmars, Henk; Bootsma, Albert H.; Kulik, Willem; Wanders, Ronald J. A.; Wood, Philip A.; Vaz, Frédéric M.

    2004-01-01

    In the present paper, we describe a novel method which enables the analysis of tissue acylcarnitines and carnitine biosynthesis intermediates in the same sample. This method was used to investigate the carnitine and fatty acid metabolism in wild-type and LCAD−/− (long-chain acyl-CoA dehydrogenase-deficient) mice. In agreement with previous results in plasma and bile, we found accumulation of the characteristic C14:1-acylcarnitine in all investigated tissues from LCAD−/− mice. Surprisingly, quantitatively relevant levels of 3-hydroxyacylcarnitines were found to be present in heart, muscle and brain in wild-type mice, suggesting that, in these tissues, long-chain 3-hydroxyacyl-CoA dehydrogenase is rate-limiting for mitochondrial β-oxidation. The 3-hydroxyacylcarnitines were absent in LCAD−/− tissues, indicating that, in this situation, the β-oxidation flux is limited by the LCAD deficiency. A profound deficiency of acetylcarnitine was observed in LCAD−/− hearts, which most likely corresponds with low cardiac levels of acetyl-CoA. Since there was no carnitine deficiency and only a marginal elevation of potentially cardiotoxic acylcarnitines, we conclude from these data that the cardiomyopathy in the LCAD−/− mouse is caused primarily by a severe energy deficiency in the heart, stressing the important role of LCAD in cardiac fatty acid metabolism in the mouse. PMID:15535801

  12. Long-chain bases of sphingolipids are transported into cells via the acyl-CoA synthetases

    PubMed Central

    Narita, Tomomi; Naganuma, Tatsuro; Sase, Yurie; Kihara, Akio

    2016-01-01

    Transport of dietary lipids into small-intestinal epithelial cells is pathologically and nutritionally important. However, lipid uptake remains an almost unexplored research area. Although we know that long-chain bases (LCBs), constituents of sphingolipids, can enter into cells efficiently, the molecular mechanism of LCB uptake is completely unclear. Here, we found that the yeast acyl-CoA synthetases (ACSs) Faa1 and Faa4 are redundantly involved in LCB uptake. In addition to fatty acid-activating activity, transporter activity toward long-chain fatty acids (LCFAs) has been suggested for ACSs. Both LCB and LCFA transports were largely impaired in faa1Δ faa4Δ cells. Furthermore, LCB and LCFA uptakes were mutually competitive. However, the energy dependency was different for their transports. Sodium azide/2-deoxy-D-glucose treatment inhibited import of LCFA but not that of LCB. Furthermore, the ATP-AMP motif mutation FAA1 S271A largely impaired the metabolic activity and LCFA uptake, while leaving LCB import unaffected. These results indicate that only LCFA transport requires ATP. Since ACSs do not metabolize LCBs as substrates, Faa1 and Faa4 are likely directly involved in LCB transport. Furthermore, we revealed that ACSs are also involved in LCB transport in mammalian cells. Thus, our findings provide strong support for the hypothesis that ACSs directly transport LCFAs. PMID:27136724

  13. Hepatic expression of long-chain acyl-CoA synthetase 3 is upregulated in hyperlipidemic hamsters.

    PubMed

    Wu, Minhao; Liu, Haiyan; Chen, Wei; Fujimoto, Yasuyuki; Liu, Jingwen

    2009-11-01

    Members of the mammalian long-chain acyl-CoA synthetase (ACSL) family are key enzymes for cellular fatty acid metabolism that catalyze the initial step in activation of long-chain fatty acids. However, the specificity of individual isoforms of ACSL to the lipid metabolic process is not well studied. In addition, the regulation of expression of individual ACSL isoforms under hyperlipidemic conditions is largely unknown. We cloned the hamster ACSL3 cDNA coding region and generated specific antibodies recognizing the ACSL3 protein. We next observed the changes in ACSL3 mRNA and protein expression in hamsters fed a standard chow diet or a high fat and high cholesterol (HFHC) diet. HFHC feeding significantly increased ACSL3 mRNA and protein expression in liver and to a lesser extent in muscle but not in adipose, brain, heart, or testis. Additionally, ACSL3 mRNA abundance was differentially regulated by the nutritional status in different tissues with liver, muscle, and adipose being the most sensitive tissues. Importantly, the hepatic ACSL3 mRNA expression pattern in response to fasting and refeeding in hyperlipidemic hamsters differed from that observed in normal chow-fed hamsters. Together, these results provide the first in vivo evidence of altered regulation of hepatic ACSL3 expression under hyperlipidemic conditions and suggest important regulatory roles for this enzyme in lipid metabolism.

  14. Surface active molecules: preparation and properties of long chain n-acyl-l-alpha-amino-omega-guanidine alkyl acid derivatives.

    PubMed

    Infante, R; Dominguez, J G; Erra, P; Julia, R; Prats, M

    1984-12-01

    Synopsis A new route for the synthesis of long chain N(alpha)-acyl-l-alpha-amino-omega-guamdine alkyl acid derivatives, with cationic or amphoteric character has been established. The general formula of these compounds is shown below. A physico-chemical and antimicrobial study of these products as a function of the alkyl ester or sodium salt (R), the straight chain length of the fatty acid residue (x) and the number of carbons between the omega-guanidine and omega-carboxyl group (n) has been investigated. The water solubility, surface tension, critical micelle concentration (c.m.c.) and minimum inhibitory concentration (MIC) against Gram-positive and Gram-negative bacteria (including Pseudomonas) has been determined. Dicyclohexylcarbodiimide has been used to condense fatty acids and alpha-amino-omega-guanidine alkyl acids. In these conditions protection of the omega-guanidine group is not necessary. The main characteristic of this synthetic procedure is the use of very mild experimental conditions (temperature, pH) to form the amide linkage which leads to pure optical compounds in high yield in the absence of electrolytes. The results show that some structural modifications, particularly the protection of the carboxyl group, promote variations of the surfactant and antimicrobial properties. Only those molecules with the blocked carboxyl group (cationic molecules, where R = Me, Et or Pr) showed a good surfactant and antimicrobial activity. When the carboxyl group was unprotected (amphoteric molecules, where R = Na(+)) the resulting compounds were inactive.

  15. Anesthetic agents in patients with very long-chain acyl-coenzyme A dehydrogenase deficiency: a literature review.

    PubMed

    Redshaw, Charlotte; Stewart, Catherine

    2014-11-01

    Very long-chain acyl-coenzyme A dehydrongenase deficiency (VLCADD) is a rare disorder of fatty acid metabolism that renders sufferers susceptible to hypoglycemia, liver failure, cardiomyopathy, and rhabdomyolysis. The literature about the management of these patients is hugely conflicting, suggesting that both propofol and volatile anesthesia should be avoided. We have reviewed the literature and have concluded that the source papers do not support the statements that volatile anesthetic agents are unsafe. The reports on rhabdomyolysis secondary to anesthesia appear to be due to inadequate supply of carbohydrate not volatile agents. Catabolism must be avoided with minimal fasting, glucose infusions based on age and weight, and attenuation of emotional and physical stress. General anesthesia appears to be protective of stress-induced catabolism and may offer benefits in children and anxious patients over regional anesthesia. Propofol has not been demonstrated to be harmful in VLCADD but is presented in an emulsion containing very long-chain fatty acids which can cause organ lipidosis and itself can inhibit mitochondrial fatty acid metabolism. It is therefore not recommended. Suxamethonium-induced myalgia may mimic symptoms of rhabdomyolysis and cause raised CK therefore should be avoided. Opioids, NSAIDS, regional anesthesia, and local anesthetic techniques have all been used without complication.

  16. Sunflower (Helianthus annuus) long-chain acyl-coenzyme A synthetases expressed at high levels in developing seeds.

    PubMed

    Aznar-Moreno, Jose A; Venegas Calerón, Mónica; Martínez-Force, Enrique; Garcés, Rafael; Mullen, Robert; Gidda, Satinder K; Salas, Joaquín J

    2014-03-01

    Long chain fatty acid synthetases (LACSs) activate the fatty acid chains produced by plastidial de novo biosynthesis to generate acyl-CoA derivatives, important intermediates in lipid metabolism. Oilseeds, like sunflower, accumulate high levels of triacylglycerols (TAGs) in their seeds to nourish the embryo during germination. This requires that sunflower seed endosperm supports very active glycerolipid synthesis during development. Sunflower seed plastids produce large amounts of fatty acids, which must be activated through the action of LACSs, in order to be incorporated into TAGs. We cloned two different LACS genes from developing sunflower endosperm, HaLACS1 and HaLACS2, which displayed sequence homology with Arabidopsis LACS9 and LACS8 genes, respectively. These genes were expressed at high levels in developing seeds and exhibited distinct subcellular distributions. We generated constructs in which these proteins were fused to green fluorescent protein and performed transient expression experiments in tobacco cells. The HaLACS1 protein associated with the external envelope of tobacco chloroplasts, whereas HaLACS2 was strongly bound to the endoplasmic reticulum. Finally, both proteins were overexpressed in Escherichia coli and recovered as active enzymes in the bacterial membranes. Both enzymes displayed similar substrate specificities, with a very high preference for oleic acid and weaker activity toward stearic acid. On the basis of our findings, we discuss the role of these enzymes in sunflower oil synthesis.

  17. The adjuvant activity of fatty acid esters. The role of acyl chain length and degree of saturation.

    PubMed Central

    Bomford, R

    1981-01-01

    Water-in-oil emulsions of metabolizable fatty acid esters, with the non-toxic surfactant Pluronic L122 as emulsifying agent, potentiated the humoral response to bovine serum albumin and staphylococcal toxoid in the mouse. Adjuvant activity was increased by changing the chemical nature of the esters as follows: (i) using a series of ethyl esters, adjuvant activity appeared when the acyl chain length of the fatty acid component was 16 or greater; (ii) isobutyl and isopropyl esters of palmitic acid (C16:0) were superior to ethyl; (iii) the ethyl esters of oleic (C18:1) and linoleic (C18:2) acids were better than stearic (C18:0). Since emulsions prepared with longer chain saturated esters are very viscous or solid at room temperature, and unsaturated esters are chemically reactive, emulsions were prepared with differing proportions of ethyl caprate (C10:0) and butyl stearate. At a ratio of 9:1 the emulsions possessed the low viscosity of ethyl caprate, but gained the adjuvant activity of butyl stearate. 125I-labelled BSA was retained in the footpad to a significantly greater extent than with a caprate emulsion, but reasons are given for believing that slow release of antigen is not the only mechanism of adjuvant activity. The ester emulsions caused more acute but less chronic local inflammation (footpad swelling) than Freund's incomplete adjuvant. PMID:7275184

  18. Only One of the Five Ralstonia solanacearum Long-Chain 3-Ketoacyl-Acyl Carrier Protein Synthase Homologues Functions in Fatty Acid Synthesis

    PubMed Central

    Cheng, Juanli; Ma, Jincheng; Lin, Jinshui; Fan, Zhen-Chuan; Cronan, John E.

    2012-01-01

    Ralstonia solanacearum, a major phytopathogenic bacterium, causes a bacterial wilt disease in diverse plants. Although fatty acid analyses of total membranes of R. solanacearum showed that they contain primarily palmitic (C16:0), palmitoleic (C16:1) and cis-vaccenic (C18:1) acids, little is known regarding R. solanacearum fatty acid synthesis. The R. solanacearum GMI1000 genome is unusual in that it contains four genes (fabF1, fabF2, fabF3, and fabF4) annotated as encoding 3-ketoacyl-acyl carrier protein synthase II homologues and one gene (fabB) annotated as encoding 3-ketoacyl-acyl carrier protein synthase I. We have analyzed this puzzling apparent redundancy and found that only one of these genes, fabF1, encoded a long-chain 3-ketoacyl-acyl carrier protein synthase, whereas the other homologues did not play roles in R. solanacearum fatty acid synthesis. Mutant strains lacking fabF1 are nonviable, and thus, FabF1 is essential for R. solanacearum fatty acid biosynthesis. Moreover, R. solanacearum FabF1 has the activities of both 3-ketoacyl-acyl carrier protein synthase II and 3-ketoacyl-acyl carrier protein synthase I. PMID:22194290

  19. Only one of the five Ralstonia solanacearum long-chain 3-ketoacyl-acyl carrier protein synthase homologues functions in fatty acid synthesis.

    PubMed

    Cheng, Juanli; Ma, Jincheng; Lin, Jinshui; Fan, Zhen-Chuan; Cronan, John E; Wang, Haihong

    2012-03-01

    Ralstonia solanacearum, a major phytopathogenic bacterium, causes a bacterial wilt disease in diverse plants. Although fatty acid analyses of total membranes of R. solanacearum showed that they contain primarily palmitic (C(16:0)), palmitoleic (C(16:1)) and cis-vaccenic (C(18:1)) acids, little is known regarding R. solanacearum fatty acid synthesis. The R. solanacearum GMI1000 genome is unusual in that it contains four genes (fabF1, fabF2, fabF3, and fabF4) annotated as encoding 3-ketoacyl-acyl carrier protein synthase II homologues and one gene (fabB) annotated as encoding 3-ketoacyl-acyl carrier protein synthase I. We have analyzed this puzzling apparent redundancy and found that only one of these genes, fabF1, encoded a long-chain 3-ketoacyl-acyl carrier protein synthase, whereas the other homologues did not play roles in R. solanacearum fatty acid synthesis. Mutant strains lacking fabF1 are nonviable, and thus, FabF1 is essential for R. solanacearum fatty acid biosynthesis. Moreover, R. solanacearum FabF1 has the activities of both 3-ketoacyl-acyl carrier protein synthase II and 3-ketoacyl-acyl carrier protein synthase I.

  20. Influence of the degree of unsaturation of the acyl side chain upon the interaction of analogues of 1-arachidonoylglycerol with monoacylglycerol lipase and fatty acid amide hydrolase.

    PubMed

    Vandevoorde, Séverine; Saha, Bijali; Mahadevan, Anu; Razdan, Raj K; Pertwee, Roger G; Martin, Billy R; Fowler, Christopher J

    2005-11-11

    Little is known as to the structural requirements of the acyl side chain for interaction of acylglycerols with monoacylglycerol lipase (MAGL), the enzyme chiefly responsible for the metabolism of the endocannabinoid 2-arachidonoylglycerol (2-AG) in the brain. In the present study, a series of twelve analogues of 1-AG (the more stable regioisomer of 2-AG) were investigated with respect to their ability to inhibit the metabolism of 2-oleoylglycerol by cytosolic and membrane-bound MAGL. In addition, the ability of the compounds to inhibit the hydrolysis of anandamide by fatty acid amide hydrolase (FAAH) was investigated. For cytosolic MAGL, compounds with 20 carbon atoms in the acyl chain and 2-5 unsaturated bonds inhibited the hydrolysis of 2-oleoylglycerol with similar potencies (IC50 values in the range 5.1-8.2 microM), whereas the two compounds with a single unsaturated bond were less potent (IC50 values 19 and 21 microM). The fully saturated analogue 1-monoarachidin did not inhibit the enzyme, whereas the lower side chain analogues 1-monopalmitin and 1-monomyristin inhibited the enzyme with IC50 values of 12 and 32 microM, respectively. The 22-carbon chain analogue of 1-AG was also potent (IC50 value 4.5 microM). Introduction of an alpha-methyl group for the C20:4, C20:3, and C22:4 compounds did not affect potency in a consistent manner. For the FAAH and the membrane-bound MAGL, there was no obvious relationship between the degree of unsaturation of the acyl side chain and the ability to inhibit the enzymes. It is concluded that increasing the number of unsaturated bonds on the acyl side chain of 1-AG from 1 to 5 has little effect on the affinity of acylglycerols for cytosolic MAGL.

  1. Acyl-CoA Dehydrogenases: Dynamic History of Protein Family Evolution

    PubMed Central

    Mohsen, Al-Walid

    2014-01-01

    The acyl-CoA dehydrogenases (ACADs) are enzymes that catalyze the α,β-dehydrogenation of acyl-CoA esters in fatty acid and amino acid catabolism. Eleven ACADs are now recognized in the sequenced human genome, and several homologs have been reported from bacteria, fungi, plants, and nematodes. We performed a systematic comparative genomic study, integrating homology searches with methods of phylogenetic reconstruction, to investigate the evolutionary history of this family. Sequence analyses indicate origin of the family in the common ancestor of Archaea, Bacteria, and Eukaryota, illustrating its essential role in the metabolism of early life. At least three ACADs were already present at that time: ancestral glutaryl-CoA dehydrogenase (GCD), isovaleryl-CoA dehydrogenase (IVD), and ACAD10/11. Two gene duplications were unique to the eukaryotic domain: one resulted in the VLCAD and ACAD9 paralogs and another in the ACAD10 and ACAD11 paralogs. The overall patchy distribution of specific ACADs across the tree of life is the result of dynamic evolution that includes numerous rounds of gene duplication and secondary losses, interdomain lateral gene transfer events, alteration of cellular localization, and evolution of novel proteins by domain acquisition. Our finding that eukaryotic ACAD species are more closely related to bacterial ACADs is consistent with endosymbiotic origin of ACADs in eukaryotes and further supported by the localization of all nine previously studied ACADs in mitochondria. PMID:19639238

  2. Fatty acid transport by vectorial acylation in mammals: roles played by different isoforms of rat long-chain acyl-CoA synthetases.

    PubMed

    Tong, Fumin; Black, Paul N; Coleman, Rosalind A; DiRusso, Concetta C

    2006-03-01

    Mammals express multiple isoforms of acyl-CoA synthetase (ACSL1 and ACSL3-6) in various tissues. These enzymes are essential for fatty acid metabolism providing activated intermediates for complex lipid synthesis, protein modification, and beta-oxidation. Yeast in contrast express four major ACSLs, which have well-defined functions. Two, Faa1p and Faa4p, are specifically required for fatty acid transport by vectorial acylation. Four ACSLs from the rat were expressed in a yeast faa1delta faa4delta strain and their roles in fatty acid transport and trafficking characterized. All four restored ACS activity yet varied in substrate preference. ACSL1, 4, and 6 were able to rescue fatty acid transport activity and triglyceride synthesis. ACSL5, however, was unable to facilitate fatty acid transport despite conferring robust oleoyl-CoA synthetase activity. This is the first study evaluating the role of the mammalian ACSLs in fatty acid transport and supports a role for ACSL1, 4, and 6 in transport by vectorial acylation.

  3. Interfacial interactions of ceramide with dimyristoylphosphatidylcholine: impact of the N-acyl chain.

    PubMed

    Holopainen, J M; Brockman, H L; Brown, R E; Kinnunen, P K

    2001-02-01

    The mixing behavior of dimyristoylphosphatidylcholine (DMPC) with either N-palmitoyl-sphingosine (C16:0-ceramide) or N-nervonoyl-sphingosine (C24:1-ceramide) was examined using monomolecular films. While DMPC forms highly elastic liquid-expanded monolayers, both neat C16:0-ceramide and C24:1-ceramide yield stable solid condensed monomolecular films with small areas and low interfacial elasticity. Compression isotherms of mixed C16:0-ceramide/DMPC films exhibit an apparent condensation upon increasing X(cer16:0) at all surface pressures. The average area isobars, coupled with the lack of a liquid-expanded to condensed phase transition as X(cer16:0) is increased, are indicative of immiscibility of the lipids at all surface pressures. In contrast, isobars for C24:1-ceramide/DMPC mixtures show surface pressure-dependent apparent condensation or expansion and surface pressure-area isotherms show a composition and surface pressure-dependent phase transition. This suggests miscibility, albeit non-ideal, of C24:1-ceramide and DMPC in both liquid and condensed surface phases. The above could be verified by fluorescence microscopy of the monolayers and measurements of surface potential, which revealed distinctly different domain morphologies and surface potential values for the DMPC/C16:0- and DMPC/C24:1-ceramide monolayers. Taken together, whereas C16:0-ceramide and DMPC form immiscible pseudo-compounds, C24:1-ceramide and DMPC are partially miscible in both the liquid-expanded and condensed phases, and a composition and lateral pressure-dependent two-phase region is evident between the liquid-expanded and condensed regimes. Our results provide novel understanding of the regulation of membrane properties by ceramides and raise the possibility that ceramides with different acyl groups could serve very different functions in cells, relating to their different physicochemical properties.

  4. Interfacial interactions of ceramide with dimyristoylphosphatidylcholine: impact of the N-acyl chain.

    PubMed Central

    Holopainen, J M; Brockman, H L; Brown, R E; Kinnunen, P K

    2001-01-01

    The mixing behavior of dimyristoylphosphatidylcholine (DMPC) with either N-palmitoyl-sphingosine (C16:0-ceramide) or N-nervonoyl-sphingosine (C24:1-ceramide) was examined using monomolecular films. While DMPC forms highly elastic liquid-expanded monolayers, both neat C16:0-ceramide and C24:1-ceramide yield stable solid condensed monomolecular films with small areas and low interfacial elasticity. Compression isotherms of mixed C16:0-ceramide/DMPC films exhibit an apparent condensation upon increasing X(cer16:0) at all surface pressures. The average area isobars, coupled with the lack of a liquid-expanded to condensed phase transition as X(cer16:0) is increased, are indicative of immiscibility of the lipids at all surface pressures. In contrast, isobars for C24:1-ceramide/DMPC mixtures show surface pressure-dependent apparent condensation or expansion and surface pressure-area isotherms show a composition and surface pressure-dependent phase transition. This suggests miscibility, albeit non-ideal, of C24:1-ceramide and DMPC in both liquid and condensed surface phases. The above could be verified by fluorescence microscopy of the monolayers and measurements of surface potential, which revealed distinctly different domain morphologies and surface potential values for the DMPC/C16:0- and DMPC/C24:1-ceramide monolayers. Taken together, whereas C16:0-ceramide and DMPC form immiscible pseudo-compounds, C24:1-ceramide and DMPC are partially miscible in both the liquid-expanded and condensed phases, and a composition and lateral pressure-dependent two-phase region is evident between the liquid-expanded and condensed regimes. Our results provide novel understanding of the regulation of membrane properties by ceramides and raise the possibility that ceramides with different acyl groups could serve very different functions in cells, relating to their different physicochemical properties. PMID:11159444

  5. Coordinated supply chain dynamic production planning model

    NASA Astrophysics Data System (ADS)

    Chandra, Charu; Grabis, Janis

    2001-10-01

    Coordination of different and often contradicting interests of individual supply chain members is one of the important issues in supply chain management because the individual members can not succeed without success of the supply chain and vice versa. This paper investigates a supply chain dynamic production planning problem with emphasis on coordination. A planning problem is formally described using a supply chain kernel, which defines supply chain configuration, management policies, available resources and objectives both at supply chain or macro and supply chain member or micro levels. The coordinated model is solved in order to balance decisions made at the macro and micro levels and members' profitability is used as the coordination criterion. The coordinated model is used to determine inventory levels and production capacity across the supply chain. Application of the coordinated model distributes costs burden uniformly among supply chain members and preserves overall efficiency of the supply chain. Influence of the demand series uncertainty is investigated. The production planning model is a part of the integrated supply chain decision modeling system, which is shared among the supply chain members across the Internet.

  6. Arabidopsis CER8 encodes LONG-CHAIN ACYL-COA SYNTHETASE 1 (LACS1) that has overlapping functions with LACS2 in plant wax and cutin synthesis.

    PubMed

    Lü, Shiyou; Song, Tao; Kosma, Dylan K; Parsons, Eugene P; Rowland, Owen; Jenks, Matthew A

    2009-08-01

    Plant cuticle is an extracellular lipid-based matrix of cutin and waxes, which covers aerial organs and protects them from many forms of environmental stress. We report here the characterization of CER8/LACS1, one of nine Arabidopsis long-chain acyl-CoA synthetases thought to activate acyl chains. Mutations in LACS1 reduced the amount of wax in all chemical classes on the stem and leaf, except in the very long-chain fatty acid (VLCFA) class wherein acids longer than 24 carbons (C(24)) were elevated more than 155%. The C(16) cutin monomers on lacs1 were reduced by 37% and 22%, whereas the C(18) monomers were increased by 28% and 20% on stem and leaf, respectively. Amounts of wax and cutin on a lacs1-1 lacs2-3 double mutant were much lower than on either parent, and lacs1-1 lacs2-3 had much higher cuticular permeability than either parent. These additive effects indicate that LACS1 and LACS2 have overlapping functions in both wax and cutin synthesis. We demonstrated that LACS1 has synthetase activity for VLCFAs C(20)-C(30), with highest activity for C(30) acids. LACS1 thus appears to function as a very long-chain acyl-CoA synthetase in wax metabolism. Since C(16) but not C(18) cutin monomers are reduced in lacs1, and C(16) acids are the next most preferred acid (behind C(30)) by LACS1 in our assays, LACS1 also appears to be important for the incorporation of C(16) monomers into cutin polyester. As such, LACS1 defines a functionally novel acyl-CoA synthetase that preferentially modifies both VLCFAs for wax synthesis and long-chain (C(16)) fatty acids for cutin synthesis.

  7. Structure of a Specialized Acyl Carrier Protein Essential for Lipid A Biosynthesis with Very Long-chain Fatty Acids in Open and Closed Conformations

    SciTech Connect

    Ramelot, Theresa A.; Rossi, Paolo M.; Forouhar, Farhad; Lee, Hsiau-Wei; Yang, Yunhuang; Ni, Shuisong; Unser, Sarah; Lew, Scott; Seetharaman, Jayaraman; Xiao, Rong; Acton, Thomas; Everett, John K.; Prestegard, James H.; Hunt, John F.; Montelione, Gaetano; Kennedy, Michael A.

    2012-09-18

    The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.

  8. Elevated Temperature Enhances Short to Medium Chain Acyl Homoserine Lactone Production by Black Band Disease Associated Vibrios.

    PubMed

    Bhedi, Chinmayee D; Prevatte, Carson W; Lookadoo, Maggie S; Waikel, Patricia A; Gillevet, Patrick M; Sikaroodi, Masoumeh; Campagna, Shawn R; Richardson, Laurie L

    2017-01-29

    Black band disease (BBD) of corals is a horizontally migrating, pathogenic, polymicrobial mat community which is active above a temperature threshold of 27.5°C on the reef. Bacterial isolates from BBD, the surface mucopolysaccharide layer (SML) of healthy corals, and SML of healthy areas of BBD infected corals were tested for production of short to medium chain acyl homoserine lactones (AHLs) using the Chromobacterium violaceum CV026 reporter strain. Of 110 bacterial isolates tested, 19 produced AHLs and 15 of these were from BBD. Eight AHLs were identified using LC-MS/MS, with 3OHC4 the most commonly produced, followed by C6. AHL-producing isolates exposed to three temperatures (24°, 27°, 30°C) revealed that production of three AHLs (3OHC4, 3OHC5, and 3OHC6) significantly increased at 30°C when compared to 24°C. 16S rRNA gene sequencing revealed that all of the AHL producing BBD isolates were vibrios. Metagenomic data of BBD communities showed the presence of AHL (and autoinducer-2) genes, many of which are known to be associated with vibrios. These findings suggest that quorum sensing may be involved in BBD pathobiology and community structure due to enhanced production of quorum sensing signal molecules (AHLs) above the temperature threshold of this globally distributed coral disease.

  9. Altered Energetics of Exercise Explain Risk of Rhabdomyolysis in Very Long-Chain Acyl-CoA Dehydrogenase Deficiency

    PubMed Central

    Diekman, E. F.; Visser, G.; Schmitz, J. P. J.; Nievelstein, R. A. J.; de Sain-van der Velden, M.; Wardrop, M.; Van der Pol, W. L.; Houten, S. M.; van Riel, N. A. W.; Takken, T.; Jeneson, J. A. L.

    2016-01-01

    Rhabdomyolysis is common in very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) and other metabolic myopathies, but its pathogenic basis is poorly understood. Here, we show that prolonged bicycling exercise against a standardized moderate workload in VLCADD patients is associated with threefold bigger changes in phosphocreatine (PCr) and inorganic phosphate (Pi) concentrations in quadriceps muscle and twofold lower changes in plasma acetyl-carnitine levels than in healthy subjects. This result is consistent with the hypothesis that muscle ATP homeostasis during exercise is compromised in VLCADD. However, the measured rates of PCr and Pi recovery post-exercise showed that the mitochondrial capacity for ATP synthesis in VLCADD muscle was normal. Mathematical modeling of oxidative ATP metabolism in muscle composed of three different fiber types indicated that the observed altered energy balance during submaximal exercise in VLCADD patients may be explained by a slow-to-fast shift in quadriceps fiber-type composition corresponding to 30% of the slow-twitch fiber-type pool in healthy quadriceps muscle. This study demonstrates for the first time that quadriceps energy balance during exercise in VLCADD patients is altered but not because of failing mitochondrial function. Our findings provide new clues to understanding the risk of rhabdomyolysis following exercise in human VLCADD. PMID:26881790

  10. Altered Energetics of Exercise Explain Risk of Rhabdomyolysis in Very Long-Chain Acyl-CoA Dehydrogenase Deficiency.

    PubMed

    Diekman, E F; Visser, G; Schmitz, J P J; Nievelstein, R A J; de Sain-van der Velden, M; Wardrop, M; Van der Pol, W L; Houten, S M; van Riel, N A W; Takken, T; Jeneson, J A L

    2016-01-01

    Rhabdomyolysis is common in very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) and other metabolic myopathies, but its pathogenic basis is poorly understood. Here, we show that prolonged bicycling exercise against a standardized moderate workload in VLCADD patients is associated with threefold bigger changes in phosphocreatine (PCr) and inorganic phosphate (Pi) concentrations in quadriceps muscle and twofold lower changes in plasma acetyl-carnitine levels than in healthy subjects. This result is consistent with the hypothesis that muscle ATP homeostasis during exercise is compromised in VLCADD. However, the measured rates of PCr and Pi recovery post-exercise showed that the mitochondrial capacity for ATP synthesis in VLCADD muscle was normal. Mathematical modeling of oxidative ATP metabolism in muscle composed of three different fiber types indicated that the observed altered energy balance during submaximal exercise in VLCADD patients may be explained by a slow-to-fast shift in quadriceps fiber-type composition corresponding to 30% of the slow-twitch fiber-type pool in healthy quadriceps muscle. This study demonstrates for the first time that quadriceps energy balance during exercise in VLCADD patients is altered but not because of failing mitochondrial function. Our findings provide new clues to understanding the risk of rhabdomyolysis following exercise in human VLCADD.

  11. Functional effects of different medium-chain acyl-CoA dehydrogenase genotypes and identification of asymptomatic variants.

    PubMed

    Sturm, Marga; Herebian, Diran; Mueller, Martina; Laryea, Maurice D; Spiekerkoetter, Ute

    2012-01-01

    Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency (OMIM 201450) is the most common inherited disorder of fatty acid metabolism presenting with hypoglycaemia, hepatopathy and Reye-like symptoms during catabolism. In the past, the majority of patients carried the prevalent c.985A>G mutation in the ACADM gene. Since the introduction of newborn screening many other mutations with unknown clinical relevance have been identified in asymptomatic newborns. In order to identify functional effects of these mutant genotypes we correlated residual MCAD (OMIM 607008) activities as measured by octanoyl-CoA oxidation in lymphocytes with both genotype and relevant medical reports in 65 newborns harbouring mutant alleles. We identified true disease-causing mutations with residual activities of 0 to 20%. In individuals carrying the c.199T>C or c.127G>A mutation on one allele, residual activities were much higher and in the range of heterozygotes (31%-60%). Therefore, both mutations cannot clearly be associated with a clinical phenotype. This demonstrates a correlation between the octanoyl-CoA oxidation rate in lymphocytes and the clinical outcome. With newborn screening, the natural course of disease is difficult to assess. The octanoyl-CoA oxidation rate, therefore, allows a risk assessment at birth and the identification of new ACADM genotypes associated with asymptomatic disease variants.

  12. Separation of isomeric short-chain acyl-CoAs in plant matrices using ultra-performance liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Purves, Randy W; Ambrose, Stephen J; Clark, Shawn M; Stout, Jake M; Page, Jonathan E

    2015-02-01

    Acyl coenzyme A (acyl-CoA) thioesters are important intermediates in cellular metabolism and being able to distinguish among them is critical to fully understanding metabolic pathways in plants. Although significant advances have been made in the identification and quantification of acyl-CoAs using liquid chromatography tandem mass spectrometry (LC-MS/MS), separation of isomeric species such as isobutyryl- and n-butyrl-CoA has remained elusive. Here we report an ultra-performance liquid chromatography (UPLC)-MS/MS method for quantifying short-chain acyl-CoAs including isomeric species n-butyryl-CoA and isobutyryl-CoA as well as n-valeryl-CoA and isovaleryl-CoA. The method was applied to the analysis of extracts of hop (Humulus lupulus) and provided strong evidence for the existence of an additional structural isomer of valeryl-CoA, 2-methylbutyryl-CoA, as well as an unexpected isomer of hexanoyl-CoA. The results showed differences in the acyl-CoA composition among varieties of Humulus lupulus, both in glandular trichomes and cone tissues. When compared with the analysis of hemp (Cannabis sativa) extracts, the contribution of isobutyryl-CoAs in hop was greater as would be expected based on the downstream polyketide products. Surprisingly, branched chain valeryl-CoAs (isovaleryl-CoA and 2-methylbutyryl-CoA) were the dominant form of valeryl-CoAs in both hop and hemp. The capability to separate these isomeric forms will help to understand biochemical pathways leading to specialized metabolites in plants.

  13. Sexual dimorphism of lipid metabolism in very long-chain acyl-CoA dehydrogenase deficient (VLCAD-/-) mice in response to medium-chain triglycerides (MCT).

    PubMed

    Tucci, Sara; Flögel, Ulrich; Spiekerkoetter, Ute

    2015-07-01

    Medium-chain triglycerides (MCT) are widely applied in the treatment of long-chain fatty acid oxidation disorders. Previously it was shown that long-term MCT supplementation strongly affects lipid metabolism in mice. We here investigate sex-specific effects in mice with very-long-chain-acyl-CoA dehydrogenase (VLCAD) deficiency in response to a long-term MCT modified diet. We quantified blood lipids, acylcarnitines, glucose, insulin and free fatty acids, as well as tissue triglycerides in the liver and skeletal muscle under a control and an MCT diet over 1 year. In addition, visceral and hepatic fat content and muscular intramyocellular lipids (IMCL) were assessed by in vivo(1)H magnetic resonance spectroscopy (MRS) techniques. The long-term application of an MCT diet induced a marked alteration of glucose homeostasis. However, only VLCAD-/- female mice developed a severe metabolic syndrome characterized by marked insulin resistance, dyslipidemia, severe hepatic and visceral steatosis, whereas VLCAD-/- males seemed to be protected and only presented with milder insulin resistance. Moreover, the highly saturated MCT diet is associated with a decreased hepatic stearoyl-CoA desaturase 1 (SCD1) activity in females aggravating the harmful effects of a saturated MCT diet. Long-term MCT supplementation deeply affects lipid metabolism in a sexual dimorphic manner resulting in a severe metabolic syndrome only in female mice. These findings are striking since the first signs of insulin resistance already occur in female VLCAD-/- mice during their reproductive period. How these metabolic adaptations are finally regulated needs to be determined. More important, the relevance of these findings for humans under these dietary modifications needs to be investigated.

  14. Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis[S

    PubMed Central

    Manichaikul, Ani; Wang, Xin-Qun; Zhao, Wei; Wojczynski, Mary K.; Siebenthall, Kyle; Stamatoyannopoulos, John A.; Saleheen, Danish; Borecki, Ingrid B.; Reilly, Muredach P.; Rich, Stephen S.; Bornfeldt, Karin E.

    2016-01-01

    Long-chain acyl-CoA synthetase 1 (ACSL1) converts free fatty acids into acyl-CoAs. Mouse studies have revealed that ACSL1 channels acyl-CoAs to β-oxidation, thereby reducing glucose utilization, and is required for diabetes-accelerated atherosclerosis. The role of ACSL1 in humans is unknown. We therefore examined common variants in the human ACSL1 locus by genetic association studies for fasting glucose, diabetes status, and preclinical atherosclerosis by using the MAGIC and DIAGRAM consortia; followed by analyses in participants from the Multi-Ethnic Study of Atherosclerosis, the Penn-T2D consortium, and a meta-analysis of subclinical atherosclerosis in African Americans; and finally, expression quantitative trait locus analysis and identification of DNase I hypersensitive sites (DHS). The results show that three SNPs in ACSL1 (rs7681334, rs735949, and rs4862423) are associated with fasting glucose or diabetes status in these large (>200,000 subjects) data sets. Furthermore, rs4862423 is associated with subclinical atherosclerosis and coincides with a DHS highly accessible in human heart. SNP rs735949 is in strong linkage disequilibrium with rs745805, significantly associated with ACSL1 levels in skin, suggesting tissue-specific regulatory mechanisms. This study provides evidence in humans of ACSL1 SNPs associated with fasting glucose, diabetes, and subclinical atherosclerosis and suggests links among these traits and acyl-CoA synthesis. PMID:26711138

  15. Multiple erythroid isoforms of human long-chain acyl-CoA synthetases are produced by switch of the fatty acid gate domains

    PubMed Central

    Soupene, Eric; Kuypers, Frans A

    2006-01-01

    Background The formation of acyl-CoA by the action of acyl-CoA synthetases plays a crucial role in membrane lipid turnover, including the plasma membrane of erythrocytes. In human, five Acyl-CoA Synthetase Long-chain (ACSL) genes have been identified with as many as 3 different transcript variants for each. Results Acyl-CoA Synthetase Long-chain member 6 (ACSL6) is responsible for activation of long-chain fatty acids in erythrocytes. Two additional transcript variants were also isolated from brain and testis. We report the expression in reticulocytes of two new variants and of the one isolated from brain. All three represented different spliced variants of a mutually exclusive exon pair. They encode a slightly different short motif which contains a conserved structural domain, the fatty acid Gate domain. The motifs differ in the presence of either the aromatic residue phenylalanine (Phe) or tyrosine (Tyr). Based on homology, two new isoforms for the closely related ACSL1 were predicted and characterized. One represented a switch of the Phe- to the Tyr-Gate domain motif, the other resulted from the exclusion of both. Swapping of this motif also appears to be common in all mammalian ACSL member 1 and 6 homologs. Conclusion We propose that a Phe to Tyr substitution or deletion of the Gate domain, is the structural reason for the conserved alternative splicing that affects these motifs. Our findings support our hypothesis that this region is structurally important to define the activity of these enzymes. PMID:16834775

  16. Successful Treatment of Cardiomyopathy due to Very Long-Chain Acyl-CoA Dehydrogenase Deficiency: First Case Report from Oman with Literature Review

    PubMed Central

    Sharef, Sharef Waadallah; Al-Senaidi, Khalfan; Joshi, Surendra Nath

    2013-01-01

    Very long-chain acyl-CoA dehydrogenase deficiency (MIM 201475) is a severe defect of mitochondrial energy production from oxidation of very long-chain fatty acids. This inherited metabolic disorder often presents in early neonatal period with episodes of symptomatic hypoglycemia usually responding well to intravenous glucose infusion. These babies are often discharged without establishment of diagnosis but return by 2-5 months of age with severe and progressive cardiac failure due to hypertrophic cardiomyopathy with or without hepatic failure and steatosis. An early diagnosis and treatment with high concentration medium chain triglycerides based feeding formula can be life saving in such patients. Here, we report the first diagnosed and treated case of Very long-chain acyl-CoA dehydrogenase deficiency in Oman. This infant developed heart failure with left ventricular dilation, hypertrophy and pericardial effusion at the age of 7 weeks. Prompt diagnosis and subsequent intervention with medium chain triglycerides-based formula resulted in a reversal of severe clinical symptoms with significant improvement of cardiac status. This treatment also ensured normal growth and neurodevelopment. It is stressed that the disease must be recognized by the pediatricians and cardiologists since the disease can be identified by Tandem Mass Spectrometry; therefore, it should be considered to be included in expanded newborn screening program, allowing early diagnosis and intervention in order to ensure better outcome and prevent complications. PMID:24044064

  17. Suppression of long chain acyl-CoA synthetase 3 decreases hepatic de novo fatty acid synthesis through decreased transcriptional activity.

    PubMed

    Bu, So Young; Mashek, Mara T; Mashek, Douglas G

    2009-10-30

    Long chain acyl-CoA synthetases (ACSL) and fatty acid transport proteins (FATP) activate fatty acids to acyl-CoAs in the initial step of fatty acid metabolism. Numerous isoforms of ACSL and FATP exist with different tissue distribution patterns, intracellular locations, and substrate preferences, suggesting that each isoform has distinct functions in channeling fatty acids into different metabolic pathways. Because fatty acids, acyl-CoAs, and downstream lipid metabolites regulate various transcription factors that control hepatic energy metabolism, we hypothesized that ACSL or FATP isoforms differentially regulate hepatic gene expression. Using small interference RNA (siRNA), we knocked down each liver-specific ACSL and FATP isoform in rat primary hepatocyte cultures and subsequently analyzed reporter gene activity of numerous transcription factors and performed quantitative mRNA analysis of their target genes. Compared with control cells, which were transfected with control siRNA, knockdown of acyl-CoA synthetase 3 (ACSL3) significantly decreased reporter gene activity of several lipogenic transcription factors such as peroxisome proliferator activation receptor-gamma, carbohydrate-responsive element-binding protein, sterol regulatory element-binding protein-1c, and liver X receptor-alpha and the expression of their target genes. These findings were further supported by metabolic labeling studies that showed [1-(14)C]acetate incorporation into lipid extracts was decreased in cells treated with ACSL3 siRNAs and that ACSL3 expression is up-regulated in ob/ob mice and mice fed a high sucrose diet. ACSL3 knockdown decreased total acyl-CoA synthetase activity without substantially altering the expression of other ACSL isoforms. In summary, these results identify a novel role for ACSL3 in mediating transcriptional control of hepatic lipogenesis.

  18. PPARδ activation induces hepatic long-chain acyl-CoA synthetase 4 expression in vivo and in vitro

    PubMed Central

    Kan, Chin Fung Kelvin; Singh, Amar Bahadur; Dong, Bin; Shende, Vikram Ravindra; Liu, Jingwen

    2017-01-01

    The arachidonic acid preferred long-chain acyl-CoA synthetase 4 (ACSL4) is a key enzyme for fatty acid metabolism in various metabolic tissues. In this study, we utilized hamsters fed a normal chow diet, a high-fat diet or a high cholesterol and high fat diet (HCHFD) as animal models to explore novel transcriptional regulatory mechanisms for ACSL4 expression under hyperlipidemic conditions. Through cloning hamster ACSL4 homolog and tissue profiling ACSL4 mRNA and protein expressions we observed a selective upregulation of ACSL4 in testis and liver of HCHFD fed animals. Examination of transcriptional activators of the ACSL family revealed an increased hepatic expression of PPARδ but not PPARα in HCHFD fed hamsters. To explore a role of PPARδ in dietary cholesterol-mediated upregulation of ACSL4, we administered a PPARδ specific agonist L165041 to normolipidemic and dyslipidemic hamsters. We observed significant increases of hepatic ACSL4 mRNA and protein levels in all L165041-treated hamsters as compared to control animals. The induction of ACSL4 expression by L165041 in liver tissue in vivo was recapitulated in human primary hepatocytes and hepatocytes isolated from hamster and mouse. Moreover, employing the approach of adenovirus-mediated gene knockdown, we showed that depletion of PPARδ in hamster hepatocytes specifically reduced ACSL4 expression. Finally, utilizing HepG2 as a model system, we demonstrate that PPARδ activation leads to increased ACSL4 promoter activity, mRNA and protein expression, and consequently higher arachidonoyl-CoA synthetase activity. Taken together, we have discovered a novel PPARδ-mediated regulatory mechanism for ACSL4 expression in liver tissue and cultured hepatic cells. PMID:25645621

  19. PPARδ activation induces hepatic long-chain acyl-CoA synthetase 4 expression in vivo and in vitro.

    PubMed

    Kan, Chin Fung Kelvin; Singh, Amar Bahadur; Dong, Bin; Shende, Vikram Ravindra; Liu, Jingwen

    2015-05-01

    The arachidonic acid preferred long-chain acyl-CoA synthetase 4 (ACSL4) is a key enzyme for fatty acid metabolism in various metabolic tissues. In this study, we utilized hamsters fed a normal chow diet, a high-fat diet or a high cholesterol and high fat diet (HCHFD) as animal models to explore novel transcriptional regulatory mechanisms for ACSL4 expression under hyperlipidemic conditions. Through cloning hamster ACSL4 homolog and tissue profiling ACSL4 mRNA and protein expressions we observed a selective upregulation of ACSL4 in testis and liver of HCHFD fed animals. Examination of transcriptional activators of the ACSL family revealed an increased hepatic expression of PPARδ but not PPARα in HCHFD fed hamsters. To explore a role of PPARδ in dietary cholesterol-mediated upregulation of ACSL4, we administered a PPARδ specific agonist L165041 to normolipidemic and dyslipidemic hamsters. We observed significant increases of hepatic ACSL4 mRNA and protein levels in all L165041-treated hamsters as compared to control animals. The induction of ACSL4 expression by L165041 in liver tissue in vivo was recapitulated in human primary hepatocytes and hepatocytes isolated from hamster and mouse. Moreover, employing the approach of adenovirus-mediated gene knockdown, we showed that depletion of PPARδ in hamster hepatocytes specifically reduced ACSL4 expression. Finally, utilizing HepG2 as a model system, we demonstrate that PPARδ activation leads to increased ACSL4 promoter activity, mRNA and protein expression, and consequently higher arachidonoyl-CoA synthetase activity. Taken together, we have discovered a novel PPARδ-mediated regulatory mechanism for ACSL4 expression in liver tissue and cultured hepatic cells.

  20. Effects of hypo- and hyperthyroidism on rat liver microsomal long-chain fatty acyl-CoA synthetase and hydrolase

    SciTech Connect

    Dang, A.Q.; Faas, F.H.; Carter, W.J.

    1986-05-01

    The effects of hyperthyroidism (hyperT/sub 3/), (tri-iodothryonine (T/sub 3/) injected rats), and hypothyroidism (hypoT/sub 3/) (thyroidectomized rats) on the activation of fatty acids by a microsomal long-chain fatty acyl-CoA (LCA-CoA) synthetase and the degradation of LCA-CoA by a microsomal LCA-CoA hydrolase was determined. MAS was assayed by measuring the (1-/sup 14/C)-palmitate or -1-/sup 14/C) oleate incorporated into its water soluble CoA ester. MAH was assayed spectrophotomerically by following the reduction of 5',5'-dithiobis-(2-nitrobenzoic acid) by the CoA released from palmitoyl-CoA or oleoyl-CoA. Enzyme activities are given as mean (nmoles/mg/min) +/- SEM. MAS activities were decreased 36-44% (p < 0.01) in both hypoT/sub 3/ and hyperT/sub 3/ (controls = 101 +/- 4 (n = 11, (1-/sup 14/C)-palmitate) of 72 +/- 2 (n = 5,(1-/sup 14/C)oleate)). These decreases may contribute to the decreased triacelyglycerol (TG) and phospholipid contents in the hyperT/sub 3/ liver and the decreased clearance rate of plasma TG in the hypoT/sub 3/. MAH was decreased 27-42% (p<0.01) only in hypoT/sub 3/ (controls = 77 +/- 3 (n = 11, palmitoyl-CoA) or 45 +/- 1 (n = 5, oleoyl-CoA)). This decrease was corrected by T/sub 3/ treatment. Since the decreased MAH would increase the availability of LCA-CoA, it may contribute to the increased TG synthesis in hypoT/sub 3/.

  1. Insertion of apoLp-III into a lipid monolayer is more favorable for saturated, more ordered, acyl-chains

    SciTech Connect

    Rathnayake, Sewwandi S.; Mirheydari, Mona; Schulte, Adam; Gillahan, James E.; Gentit, Taylor; Phillips, Ashley N.; Okonkwo, Rose K.; Burger, Koert N.J.; Mann, Elizabeth K.; Vaknin, David; Bu, Wei; Agra-Kooijman, Dena Mae; Kooijman, Edgar E.

    2013-10-04

    Neutral lipid transport in mammals is complicated involving many types of apolipoprotein. The exchangeable apolipoproteins mediate the transfer of hydrophobic lipids between tissues and particles, and bind to cell surface receptors. Amphipathic a-helices form a common structural motif that facilitates their lipid binding and exchangeability. ApoLp-III, the only exchangeable apolipoprotein found in insects, is a model amphipathic a:helix bundle protein and its three dimensional structure and function mimics that of the mammalian proteins apoE and apoAI. Even the intracellular exchangeable lipid droplet protein TIP47/perilipin 3 contains an a-helix bundle domain with high structural similarity to that of apoE and apoLp-III. Here, we investigated the interaction of apoLp-III from Locusta migratoria with lipid monolayers. Consistent with earlier work we find that insertion of apoLp-III into fluid lipid monolayers is highest for diacylglycerol. We observe a preference for saturated and more highly ordered lipids, suggesting a new mode of interaction for amphipathic a-helix bundles. X-ray reflectivity shows that apoLp-III unfolds at a hydrophobic interface and flexible loops connecting the amphipathic cc-helices stay in solution. X-ray diffraction indicates that apoLp-III insertion into diacylglycerol monolayers induces additional ordering of saturated acyl-chains. These results thus shed important new insight into the protein-lipid interactions of a model exchangeable apolipoprotein with significant implications for its mammalian counterparts. (C) 2013 Elsevier B.V. All rights reserved.

  2. Isolation of a Saccharomyces cerevisiae long chain fatty acyl:CoA synthetase gene (FAA1) and assessment of its role in protein N- myristoylation

    PubMed Central

    1992-01-01

    Regulation of myristoylCoA pools in Saccharomyces cerevisiae plays an important role in modulating the activity of myristoylCoA:protein N- myristoyltransferase (NMT), an essential enzyme with an ordered Bi Bi reaction that catalyzes the transfer of myristate from myristoylCoA to greater than or equal to 12 cellular proteins. At least two pathways are available for generating myristoylCoA: de novo synthesis by the multifunctional, multisubunit fatty acid synthetase complex (FAS) and activation of exogenous myristate by acylCoA synthetase. The FAA1 (fatty acid activation) gene has been isolated by genetic complementation of a faal mutant. This single copy gene, which maps to the right arm of chromosome XV, specifies a long chain acylCoA synthetase of 700 amino acids. Analyses of strains containing NMT1 and a faal null mutation indicated that FAA1 is not essential for vegetative growth when an active de novo pathway for fatty acid synthesis is present. The role of FAA1 in cellular lipid metabolism and protein N-myristoylation was therefore assessed in strains subjected to biochemical or genetic blockade of FAS. At 36 degrees C, FAA1 is required for the utilization of exogenous myristate by NMT and for the synthesis of several phospholipid species. This requirement is not apparent at 24 or 30 degrees C, suggesting that S. cerevisiae contains another acylCoA synthetase activity whose chain length and/or temperature optima may differ from Faalp. PMID:1572893

  3. Chain Dynamics in a Dilute Magnetorheological Fluid

    NASA Technical Reports Server (NTRS)

    Liu, Jing; Hagenbuchle, Martin

    1996-01-01

    The structure, formation, and dynamics of dilute, mono-dispersive ferrofluid emulsions in an external magnetic field have been investigated using dynamic light scattering techniques. In the absence of the magnetic field, the emulsion particles are randomly distributed and behave like hard spheres in Brownian motion. An applied magnetic field induces a magnetic dipole moment in each particle. Dipolar interactions between particles align them into chains where correlation functions show two decay processes. The short-time decay shows the motion of straight chains as a whole where the apparent chain length increases with the applied magnetic field and the particle volume fraction. Good scaling results are obtained showing that the apparent chain length grows with time following a power law with exponent of 0.6 and depends on the applied field, particle volume fraction, and diffusion constant of the particles. The long-time decay in the correlation function shows oscillation when the chains reach a certain length with time and stiffness with threshold field This result shows that chains not only fluctuate, but move in a periodic motion with a frequency of 364 Hz at lambda = 15. It may suggest the existence of phonons. This work is the first step in the understanding of the structure formation, especially chain coarsening mechanism, of magnetorheological (MR) fluids at higher volume fractions.

  4. Long-chain acyl-CoA synthetase 2 knockdown leads to decreased fatty acid oxidation in fat body and reduced reproductive capacity in the insect Rhodnius prolixus.

    PubMed

    Alves-Bezerra, Michele; Klett, Eric L; De Paula, Iron F; Ramos, Isabela B; Coleman, Rosalind A; Gondim, Katia C

    2016-07-01

    Long-chain acyl-CoA esters are important intermediates in lipid metabolism and are synthesized from fatty acids by long-chain acyl-CoA synthetases (ACSL). The hematophagous insect Rhodnius prolixus, a vector of Chagas' disease, produces glycerolipids in the midgut after a blood meal, which are stored as triacylglycerol in the fat body and eggs. We identified twenty acyl-CoA synthetase genes in R. prolixus, two encoding ACSL isoforms (RhoprAcsl1 and RhoprAcsl2). RhoprAcsl1 transcripts increased in posterior midgut on the second day after feeding, and RhoprAcsl2 was highly transcribed on the tenth day. Both enzymes were expressed in Escherichia coli. Recombinant RhoprACSL1 and RhoprACSL2 had broad pH optima (7.5-9.5 and 6.5-9.5, respectively), were inhibited by triacsin C, and were rosiglitazone-insensitive. Both showed similar apparent Km for palmitic and oleic acid (2-6 μM), but different Km for arachidonic acid (0.5 and 6 μM for RhoprACSL1-Flag and RhoprACSL2-Flag, respectively). The knockdown of RhoprAcsl1 did not result in noticeable phenotypes. However, RhoprACSL2 deficient insects exhibited a 2.5-fold increase in triacylglycerol content in the fat body, and 90% decrease in fatty acid β-oxidation. RhoprAcsl2 knockdown also resulted in 20% increase in lifespan, delayed digestion, 30% reduced oviposition, and 50% reduction in egg hatching. Laid eggs and hatched nymphs showed remarkable alterations in morphology. In summary, R. prolixus ACSL isoforms have distinct roles on lipid metabolism. Although RhoprACSL1 functions remain unclear, we propose that RhoprACSL2 is the main contributor for the formation of the intracellular acyl-CoA pool channeled for β-oxidation in the fat body, and is also required for normal reproduction.

  5. Long-term Correction of Very Long-chain Acyl-CoA Dehydrogenase Deficiency in Mice Using AAV9 Gene Therapy

    PubMed Central

    Keeler, Allison M; Conlon, Thomas; Walter, Glenn; Zeng, Huadong; Shaffer, Scott A; Dungtao, Fu; Erger, Kirsten; Cossette, Travis; Tang, Qiushi; Mueller, Christian; Flotte, Terence R

    2012-01-01

    Very long-chain acyl-coA dehydrogenase (VLCAD) is the rate-limiting step in mitochondrial fatty acid oxidation. VLCAD-deficient mice and patients clinical symptoms stem from not only an energy deficiency but also long-chain metabolite accumulations. VLCAD-deficient mice were treated systemically with 1 × 1012 vector genomes of recombinant adeno-associated virus 9 (rAAV9)-VLCAD. Biochemical correction was observed in vector-treated mice beginning 2 weeks postinjection, as characterized by a significant drop in long-chain fatty acyl accumulates in whole blood after an overnight fast. Changes persisted through the termination point around 20 weeks postinjection. Magnetic resonance spectroscopy (MRS) and tandem mass spectrometry (MS/MS) revealed normalization of intramuscular lipids in treated animals. Correction was not observed in liver tissue extracts, but cardiac muscle extracts showed significant reduction of long-chain metabolites. Disease-specific phenotypes were characterized, including thermoregulation and maintenance of euglycemia after a fasting cold challenge. Internal body temperatures of untreated VLCAD−/− mice dropped below 20 °C and the mice became lethargic, requiring euthanasia. In contrast, all rAAV9-treated VLCAD−/− mice and the wild-type controls maintained body temperatures. rAAV9-treated VLCAD−/− mice maintained euglycemia, whereas untreated VLCAD−/− mice suffered hypoglycemia following a fasting cold challenge. These promising results suggest rAAV9 gene therapy as a potential treatment for VLCAD deficiency in humans. PMID:22395529

  6. Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

    PubMed Central

    Sandoz, Patrick A.; Savoglidis, Georgios; Hatzimanikatis, Vassily; van der Goot, F. Gisou

    2016-01-01

    Cellular functions are largely regulated by reversible post-translational modifications of proteins which act as switches. Amongst these, S-palmitoylation is unique in that it confers hydrophobicity. Due to technical difficulties, the understanding of this modification has lagged behind. To investigate principles underlying dynamics and regulation of palmitoylation, we have here studied a key cellular protein, the ER chaperone calnexin, which requires dual palmitoylation for function. Apprehending the complex inter-conversion between single-, double- and non- palmitoylated species required combining experimental determination of kinetic parameters with extensive mathematical modelling. We found that calnexin, due to the presence of two cooperative sites, becomes stably acylated, which not only confers function but also a remarkable increase in stability. Unexpectedly, stochastic simulations revealed that palmitoylation does not occur soon after synthesis, but many hours later. This prediction guided us to find that phosphorylation actively delays calnexin palmitoylation in resting cells. Altogether this study reveals that cells synthesize 5 times more calnexin than needed under resting condition, most of which is degraded. This unused pool can be mobilized by preventing phosphorylation or increasing the activity of the palmitoyltransferase DHHC6. PMID:26900856

  7. Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin.

    PubMed

    Dallavilla, Tiziano; Abrami, Laurence; Sandoz, Patrick A; Savoglidis, Georgios; Hatzimanikatis, Vassily; van der Goot, F Gisou

    2016-02-01

    Cellular functions are largely regulated by reversible post-translational modifications of proteins which act as switches. Amongst these, S-palmitoylation is unique in that it confers hydrophobicity. Due to technical difficulties, the understanding of this modification has lagged behind. To investigate principles underlying dynamics and regulation of palmitoylation, we have here studied a key cellular protein, the ER chaperone calnexin, which requires dual palmitoylation for function. Apprehending the complex inter-conversion between single-, double- and non-palmitoylated species required combining experimental determination of kinetic parameters with extensive mathematical modelling. We found that calnexin, due to the presence of two cooperative sites, becomes stably acylated, which not only confers function but also a remarkable increase in stability. Unexpectedly, stochastic simulations revealed that palmitoylation does not occur soon after synthesis, but many hours later. This prediction guided us to find that phosphorylation actively delays calnexin palmitoylation in resting cells. Altogether this study reveals that cells synthesize 5 times more calnexin than needed under resting condition, most of which is degraded. This unused pool can be mobilized by preventing phosphorylation or increasing the activity of the palmitoyltransferase DHHC6.

  8. Identification of Middle Chain Fatty Acyl-CoA Ligase Responsible for the Biosynthesis of 2-Alkylmalonyl-CoAs for Polyketide Extender Unit*

    PubMed Central

    Miyazawa, Takeshi; Takahashi, Shunji; Kawata, Akihiro; Panthee, Suresh; Hayashi, Teruo; Shimizu, Takeshi; Nogawa, Toshihiko; Osada, Hiroyuki

    2015-01-01

    Understanding the biosynthetic mechanism of the atypical polyketide extender unit is important for the development of bioactive natural products. Reveromycin (RM) derivatives produced by Streptomyces sp. SN-593 possess several aliphatic extender units. Here, we studied the molecular basis of 2-alkylmalonyl-CoA formation by analyzing the revR and revS genes, which form a transcriptional unit with the revT gene, a crotonyl-CoA carboxylase/reductase homolog. We mainly focused on the uncharacterized adenylate-forming enzyme (RevS). revS gene disruption resulted in the reduction of all RM derivatives, whereas reintroduction of the gene restored the yield of RMs. Although RevS was classified in the fatty acyl-AMP ligase clade based on phylogenetic analysis, biochemical characterization revealed that the enzyme catalyzed the middle chain fatty acyl-CoA ligase (FACL) but not the fatty acyl-AMP ligase activity, suggesting the molecular evolution for acyl-CoA biosynthesis. Moreover, we examined the in vitro conversion of fatty acid into 2-alkylmalonyl-CoA using purified RevS and RevT. The coupling reaction showed efficient conversion of hexenoic acid into butylmalonyl-CoA. RevS efficiently catalyzed C8–C10 middle chain FACL activity; therefore, we speculated that the acyl-CoA precursor was truncated via β-oxidation and converted into (E)-2-enoyl-CoA, a RevT substrate. To determine whether the β-oxidation process is involved between the RevS and RevT reaction, we performed the feeding experiment using [1,2,3,4-13C]octanoic acid. 13C NMR analysis clearly demonstrated incorporation of the [3,4-13C]octanoic acid moiety into the structure of RM-A. Our results provide insight into the role of uncharacterized RevS homologs that may catalyze middle chain FACL to produce a unique polyketide extender unit. PMID:26378232

  9. [A two-year-old infant with a myopathic form of very-long-chain Acyl-CoA dehydrogenase deficiency].

    PubMed

    Ito, Yasushi; Nakano, Kazutoshi; Shishikura, Keiko; Suzuki, Haruko; Iida, Norihisa; Sasaki, Nobutaka; Kimura, Masahiko; Hasegawa, Yuki; Yamaguchi, Seiji; Osawa, Makiko

    2003-11-01

    A two-year-three-month old girl was hospitalized for detailed examination following repeated hyper-creatine kinasemia and cervical muscle cramps induced by pyrexia and persistent hypertonicity of the cervical muscles. Physical examination showed mild hypotonia but no muscle weakness. Induction of symptoms by continuous cervical muscular exercise and the appearance of dicarboxylic aciduria during the fasting test indicated a disorder of fatty acid oxidation. Free fatty acid and acyl carnitine analyses using dried blood spots, and acyl-CoA dehydrogenase activity assays using cultured skin fibroblasts established a diagnosis of very-long-chain acyl-CoA dehydrogenase (VLCAD) deficiency. Currently VLCAD deficiency has been divided into three phenotypes; a severe childhood form, a milder childhood form, and an adult form. However, we suggest that the severe and milder childhood forms would be better described as a systemic form, and the adult form and our infant case as a myopathic form. An early onset of the myopathic form within the first year of life, as well as its diagnosis in early infancy, has never been described in the literature.

  10. Newborn screening for medium-chain acyl-CoA dehydrogenase deficiency: regional experience and high incidence of carnitine deficiency

    PubMed Central

    2013-01-01

    Background Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the most common inherited defect in the mitochondrial fatty acid oxidation pathway, resulting in significant morbidity and mortality in undiagnosed patients. Newborn screening (NBS) has considerably improved MCADD outcome, but the risk of complication remains in some patients. The aim of this study was to evaluate the relationship between genotype, biochemical parameters and clinical data at diagnosis and during follow-up, in order to optimize monitoring of these patients. Methods We carried out a multicenter study in southwest Europe, of MCADD patients detected by NBS. Evaluated NBS data included free carnitine (C0) and the acylcarnitines C8, C10, C10:1 together with C8/C2 and C8/C10 ratios, clinical presentation parameters and genotype, in 45 patients. Follow-up data included C0 levels, duration of carnitine supplementation and occurrence of metabolic crises. Results C8/C2 ratio and C8 were the most accurate biomarkers of MCADD in NBS. We found a high number of patients homozygous for the prevalent c.985A > G mutation (75%). Moreover, in these patients C8, C8/C10 and C8/C2 were higher than in patients with other genotypes, while median value of C0 was significantly lower (23 μmol/L vs 36 μmol/L). The average follow-up period was 43 months. To keep carnitine levels within the normal range, carnitine supplementation was required in 82% of patients, and for a longer period in patients homozygotes for the c.985A>G mutation than in patients with other genotypes (average 31 vs 18 months). Even with treatment, median C0 levels remained lower in homozygous patients than in those with other genotypes (14 μmol/L vs 22 μmol/L). Two patients died and another three suffered a metabolic crisis, all of whom were homozygous for the c.985 A>G mutation. Conclusions Our data show a direct association between homozygosity for c.985A>G and lower carnitine values at diagnosis, and a higher dose of carnitine

  11. Loss of long-chain acyl-CoA synthetase isoform 1 impairs cardiac autophagy and mitochondrial structure through mechanistic target of rapamycin complex 1 activation

    PubMed Central

    Grevengoed, Trisha J.; Cooper, Daniel E.; Young, Pamela A.; Ellis, Jessica M.; Coleman, Rosalind A.

    2015-01-01

    Because hearts with a temporally induced knockout of acyl-CoA synthetase 1 (Acsl1T−/−) are virtually unable to oxidize fatty acids, glucose use increases 8-fold to compensate. This metabolic switch activates mechanistic target of rapamycin complex 1 (mTORC1), which initiates growth by increasing protein and RNA synthesis and fatty acid metabolism, while decreasing autophagy. Compared with controls, Acsl1T−/− hearts contained 3 times more mitochondria with abnormal structure and displayed a 35–43% lower respiratory function. To study the effects of mTORC1 activation on mitochondrial structure and function, mTORC1 was inhibited by treating Acsl1T−/− and littermate control mice with rapamycin or vehicle alone for 2 wk. Rapamycin treatment normalized mitochondrial structure, number, and the maximal respiration rate in Acsl1T−/− hearts, but did not improve ADP-stimulated oxygen consumption, which was likely caused by the 33–51% lower ATP synthase activity present in both vehicle- and rapamycin-treated Acsl1T−/− hearts. The turnover of microtubule associated protein light chain 3b in Acsl1T−/− hearts was 88% lower than controls, indicating a diminished rate of autophagy. Rapamycin treatment increased autophagy to a rate that was 3.1-fold higher than in controls, allowing the formation of autophagolysosomes and the clearance of damaged mitochondria. Thus, long-chain acyl-CoA synthetase isoform 1 (ACSL1) deficiency in the heart activated mTORC1, thereby inhibiting autophagy and increasing the number of damaged mitochondria.—Grevengoed, T. J., Cooper, D. E., Young, P. A., Ellis, J. M., Coleman, R. A. Loss of long-chain acyl-CoA synthetase isoform 1 impairs cardiac autophagy and mitochondrial structure through mechanistic target of rapamycin complex 1 activation. PMID:26220174

  12. Mouse Siglec-1 Mediates trans-Infection of Surface-bound Murine Leukemia Virus in a Sialic Acid N-Acyl Side Chain-dependent Manner.

    PubMed

    Erikson, Elina; Wratil, Paul R; Frank, Martin; Ambiel, Ina; Pahnke, Katharina; Pino, Maria; Azadi, Parastoo; Izquierdo-Useros, Nuria; Martinez-Picado, Javier; Meier, Chris; Schnaar, Ronald L; Crocker, Paul R; Reutter, Werner; Keppler, Oliver T

    2015-11-06

    Siglec-1 (sialoadhesin, CD169) is a surface receptor on human cells that mediates trans-enhancement of HIV-1 infection through recognition of sialic acid moieties in virus membrane gangliosides. Here, we demonstrate that mouse Siglec-1, expressed on the surface of primary macrophages in an interferon-α-responsive manner, captures murine leukemia virus (MLV) particles and mediates their transfer to proliferating lymphocytes. The MLV infection of primary B-cells was markedly more efficient than that of primary T-cells. The major structural protein of MLV particles, Gag, frequently co-localized with Siglec-1, and trans-infection, primarily of surface-bound MLV particles, efficiently occurred. To explore the role of sialic acid for MLV trans-infection at a submolecular level, we analyzed the potential of six sialic acid precursor analogs to modulate the sialylated ganglioside-dependent interaction of MLV particles with Siglec-1. Biosynthetically engineered sialic acids were detected in both the glycolipid and glycoprotein fractions of MLV producer cells. MLV released from cells carrying N-acyl-modified sialic acids displayed strikingly different capacities for Siglec-1-mediated capture and trans-infection; N-butanoyl, N-isobutanoyl, N-glycolyl, or N-pentanoyl side chain modifications resulted in up to 92 and 80% reduction of virus particle capture and trans-infection, respectively, whereas N-propanoyl or N-cyclopropylcarbamyl side chains had no effect. In agreement with these functional analyses, molecular modeling indicated reduced binding affinities for non-functional N-acyl modifications. Thus, Siglec-1 is a key receptor for macrophage/lymphocyte trans-infection of surface-bound virions, and the N-acyl side chain of sialic acid is a critical determinant for the Siglec-1/MLV interaction.

  13. Mouse Siglec-1 Mediates trans-Infection of Surface-bound Murine Leukemia Virus in a Sialic Acid N-Acyl Side Chain-dependent Manner*

    PubMed Central

    Erikson, Elina; Wratil, Paul R.; Frank, Martin; Ambiel, Ina; Pahnke, Katharina; Pino, Maria; Azadi, Parastoo; Izquierdo-Useros, Nuria; Martinez-Picado, Javier; Meier, Chris; Schnaar, Ronald L.; Crocker, Paul R.; Reutter, Werner; Keppler, Oliver T.

    2015-01-01

    Siglec-1 (sialoadhesin, CD169) is a surface receptor on human cells that mediates trans-enhancement of HIV-1 infection through recognition of sialic acid moieties in virus membrane gangliosides. Here, we demonstrate that mouse Siglec-1, expressed on the surface of primary macrophages in an interferon-α-responsive manner, captures murine leukemia virus (MLV) particles and mediates their transfer to proliferating lymphocytes. The MLV infection of primary B-cells was markedly more efficient than that of primary T-cells. The major structural protein of MLV particles, Gag, frequently co-localized with Siglec-1, and trans-infection, primarily of surface-bound MLV particles, efficiently occurred. To explore the role of sialic acid for MLV trans-infection at a submolecular level, we analyzed the potential of six sialic acid precursor analogs to modulate the sialylated ganglioside-dependent interaction of MLV particles with Siglec-1. Biosynthetically engineered sialic acids were detected in both the glycolipid and glycoprotein fractions of MLV producer cells. MLV released from cells carrying N-acyl-modified sialic acids displayed strikingly different capacities for Siglec-1-mediated capture and trans-infection; N-butanoyl, N-isobutanoyl, N-glycolyl, or N-pentanoyl side chain modifications resulted in up to 92 and 80% reduction of virus particle capture and trans-infection, respectively, whereas N-propanoyl or N-cyclopropylcarbamyl side chains had no effect. In agreement with these functional analyses, molecular modeling indicated reduced binding affinities for non-functional N-acyl modifications. Thus, Siglec-1 is a key receptor for macrophage/lymphocyte trans-infection of surface-bound virions, and the N-acyl side chain of sialic acid is a critical determinant for the Siglec-1/MLV interaction. PMID:26370074

  14. Cardiac failure in very long chain acyl-CoA dehydrogenase deficiency requiring extracorporeal membrane oxygenation (ECMO) treatment: A case report and review of the literature.

    PubMed

    Katz, Sharon; Landau, Yuval; Pode-Shakked, Ben; Pessach, Itai M; Rubinshtein, Marina; Anikster, Yair; Salem, Yishay; Paret, Gideon

    2017-03-01

    Fatty acid oxidation (FAO) defects often present with multi-system involvement, including several life-threatening cardiac manifestations, such as cardiomyopathy, pericardial effusion and arrhythmias. We report herein a fatal case of cardiac dysfunction and rapid-onset tamponade following an acute illness in a neonate with molecularly proven very long chain acyl-CoA dehydrogenase (VLCAD) deficiency (harboring the known del799_802 mutation), requiring 15 days of extracorporeal membrane oxygenation (ECMO) treatment. As data regarding the use of ECMO in FAO defects in general, and VLCAD in particular, are scarce, we review the literature and discuss insights from in vitro models and several successful reported cases.

  15. Spin Chains with Dynamical Lattice Supersymmetry

    NASA Astrophysics Data System (ADS)

    Hagendorf, Christian

    2013-02-01

    Spin chains with exact supersymmetry on finite one-dimensional lattices are considered. The supercharges are nilpotent operators on the lattice of dynamical nature: they change the number of sites. A local criterion for the nilpotency on periodic lattices is formulated. Any of its solutions leads to a supersymmetric spin chain. It is shown that a class of special solutions at arbitrary spin gives the lattice equivalents of the {N}=(2,2) superconformal minimal models. The case of spin one is investigated in detail: in particular, it is shown that the Fateev-Zamolodchikov chain and its off-critical extension possess a lattice supersymmetry for all its coupling constants. Its supersymmetry singlets are thoroughly analysed, and a relation between their components and the weighted enumeration of alternating sign matrices is conjectured.

  16. Familial very long chain acyl-CoA dehydrogenase deficiency as a cause of neonatal sudden infant death: improved survival by prompt diagnosis.

    PubMed

    Scalais, Emmanuel; Bottu, Jean; Wanders, Ronald J A; Ferdinandusse, Sacha; Waterham, Hans R; De Meirleir, Linda

    2015-01-01

    In neonates, very long chain acyl-CoA dehydrogenase (VLCAD) deficiency is often characterized by cardiomyopathy, hepatic encephalopathy, or severe hypoketotic hypoglycemia, or a combination thereof. The purpose of this study was to further elucidate a familial VLCAD deficiency in three patients, two of whom died in the neonatal period. We report on a family with VLCAD deficiency. Acyl-carnitine profiles were obtained from dried blood spot and/or from oxidation of (13) C-palmitate by cultured skin fibroblasts. In the index patient, VLCAD deficiency was ascertained by enzyme activity measurement in fibroblasts and by molecular analysis of ACADVL. At 30 hr of life, the proband was diagnosed with hypoglycemia (1.77 mmol/L), rhabdomyolysis (CK: 12966 IU/L) and hyperlactacidemia (10.6 mmol/L). Acylcarnitine profile performed at 31 hr of life was consistent with VLCAD deficiency and confirmed by cultured skin fibroblast enzyme activity measurement. Molecular analysis of ACADVL revealed a homozygous splice-site mutation (1077 + 2T>C). The acyl-carnitine profile obtained from the sibling's original newborn screening cards demonstrated a similar, but less pronounced abnormal profile. In the proband, the initial metabolic crisis was controlled with 10% dextrose solution and oral riboflavin followed by specific diet (Basic-F and medium chain triglyceride (MCT). This clinical report demonstrates a familial history of repeated neonatal deaths explained by VLCAD deficiency, and the clinical evolution of the latest affected, surviving sibling. It shows that very early metabolic screening is an effective approach to avoid sudden unexpected death.

  17. Slow dynamics in proteins and polymer chains

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun

    2013-02-01

    How a biological system can maintain in a non-equilibrium state for a very long time and why proteins aggregate are still not well understood. In this paper, we first review critical slow down of the Ising model and slow relaxation of a spin-glass model at low temperatures. The data indicate that relaxation of the spin glass model at low temperatures can be slower than the critical slowing down of the Ising model. We then review recent molecular dynamics results for the slow relaxation of polymer chains and experimental data for the glassy behavior of collagen fibrils. The slow dynamics in polymer chains and collagen fibrils can provide clues for understanding why a biological system can maintain in a non-equilibrium state for a very long time, and how to slow down protein aggregation related to neurodegenerative diseases.

  18. Effect of fatty acyl chain length and structure on the lamellar gel to liquid-crystalline and lamellar to reversed hexagonal phase transitions of aqueous phosphatidylethanolamine dispersions

    SciTech Connect

    Lewis, R.N.A.H.; Mannock, D.A.; McElhaney, R.N.; Turner, D.C.; Gruner, S.M. )

    1989-01-24

    The lamellar gel/liquid-crystalline and the lamellar liquid-crystalline/reversed hexagonal phase transitions of aqueous dispersions of a number of synthetic phosphatidylethanolamines containing linear saturated, branched chain, and alicyclic fatty acyl chains of varying length were studied by differential scanning calorimetry, {sup 31}P nuclear magnetic resonance spectroscopy, and X-ray diffraction. For any given homologous series of phosphatidylethanolamines containing a single chemical class of fatty acids, the lamellar gel/liquid-crystalline phase transition temperature increases and the lamellar liquid-crystalline/reversed hexagonal phase transition temperature decreases with increases in hydrocarbon chain length. For a series of phosphatidylethanolamines of the same hydrocarbon chain length but with different chemical structures, both the lamellar gel/liquid-crystalline and the lamellar liquid-crystalline/reversed hexagonal phase transition temperatures vary markedly and in the same direction. These results suggest that for any given hydrocarbon chain length, there may be a critical thickness at which the liquid-crystalline phosphatidylethanolamine bilayer becomes unstable with respect to inverted nonbilayer phases such as the H{sub II} phase and that the temperature at which this critical thickness is reached is dependent upon that bilayers proximity to the hydrocarbon chain-melting phase transition temperature.

  19. Molecular cloning and nutrient regulation analysis of long chain acyl-CoA synthetase 1 gene in grass carp, Ctenopharyngodon idella L.

    PubMed

    Cheng, Han-Liang; Chen, Shuai; Xu, Jian-He; Yi, Le-Fei; Peng, Yong-Xing; Pan, Qian; Shen, Xin; Dong, Zhi-Guo; Zhang, Xia-Qing; Wang, Wen-Xiang

    2017-02-01

    Long chain acyl-CoA synthetase 1 (ACSL1), a key regulatory enzyme of fatty acid metabolism, catalyzes the conversion of long-chain fatty acids to acyl-coenzyme A. The full-length cDNAs of ACSL1a and ACSL1b were cloned from the liver of a grass carp. Both cDNAs contained a 2094bp open reading frame encoding 697 amino acids. Amino acid sequence alignment showed that ACSL1a shared 73.5% sequence identity with ACSL1b. Each of the two ACSL1s proteins had a transmembrane domain, a P-loop domain, and L-, A-, and G-motifs, which were relatively conserved in comparison to other vertebrates. Relative expression profile of ACSL1 mRNAs in different tissues indicated that ACSL1a is highly expressed in heart, mesenteric adipose, and brain tissues, whereas ACSL1b is highly expressed in heart, white muscle, foregut, and liver tissues. Nutrient regulation research showed that the expression levels of ACSL1a and ACSL1b were significantly down-regulated when 3, 6, and 9% fish oil were added in diet of grass carp as compared to the control group. However, no significant difference in the levels of ACSL1 mRNA was observed between the experimental groups. This study demonstrated the relationship between ACSL1a and ACSL1b genes in grass carp and laid a foundation for further research on ACSL family members in other species.

  20. Isolated 2-methylbutyrylglycinuria caused by short/branched-chain acyl-CoA dehydrogenase deficiency: identification of a new enzyme defect, resolution of its molecular basis, and evidence for distinct acyl-CoA dehydrogenases in isoleucine and valine metabolism.

    PubMed

    Andresen, B S; Christensen, E; Corydon, T J; Bross, P; Pilgaard, B; Wanders, R J; Ruiter, J P; Simonsen, H; Winter, V; Knudsen, I; Schroeder, L D; Gregersen, N; Skovby, F

    2000-11-01

    Acyl-CoA dehydrogenase (ACAD) defects in isoleucine and valine catabolism have been proposed in clinically diverse patients with an abnormal pattern of metabolites in their urine, but they have not been proved enzymatically or genetically, and it is unknown whether one or two ACADs are involved. We investigated a patient with isolated 2-methylbutyrylglycinuria, suggestive of a defect in isoleucine catabolism. Enzyme assay of the patient's fibroblasts, using 2-methylbutyryl-CoA as substrate, confirmed the defect. Sequence analysis of candidate ACADs revealed heterozygosity for the common short-chain ACAD A625 variant allele and no mutations in ACAD-8 but a 100-bp deletion in short/branched-chain ACAD (SBCAD) cDNA from the patient. Our identification of the SBCAD gene structure (11 exons; >20 kb) enabled analysis of genomic DNA. This showed that the deletion was caused by skipping of exon 10, because of homozygosity for a 1228G-->A mutation in the patient. This mutation was not present in 118 control chromosomes. In vitro transcription/translation experiments and overexpression in COS cells confirmed the disease-causing nature of the mutant SBCAD protein and showed that ACAD-8 is an isobutyryl-CoA dehydrogenase and that both wild-type proteins are imported into mitochondria and form tetramers. In conclusion, we report the first mutation in the SBCAD gene, show that it results in an isolated defect in isoleucine catabolism, and indicate that ACAD-8 is a mitochondrial enzyme that functions in valine catabolism.

  1. Characterization of trans-monounsaturated alkenyl chains in total plasmalogens (1-O-alk-1'-enyl-2-acyl glycerophospholipids) from sheep heart.

    PubMed

    Wolff, Robert L

    2002-08-01

    In the present study, we investigated the alkenyl chains from sheep heart plasmalogens (1-O-alk-1'-enyl-2-acyl glycerophospholipids) after their conversion into trimethylene dioxyalkanyl (TMDOA) derivatives. Particular attention was given to monounsaturated alkenyl chains (C18 mainly). For this purpose, a combination of silver ion TLC and GLC on highly polar, very long capillary columns was applied to TMDOA derivatives. Approximately 30 different alkenyl chains could be separated, and the main observation was that the component previously reported as a cis-9 18:1 alkenyl chain in plasmalogens embraces in fact a wide range of trans and cis isomers, in amounts equal to 7.9 and 5.6%, respectively, of total alkenyl chains. Concerning the trans-monoenoate fraction, isomers with their ethylenic bond spanning from delta6-delta8 to delta16 were tentatively identified on the basis of their distribution profile, which was similar to that of trans-18:1 acids prepared and isolated from sheep adipose tissue. The main trans-monoenoic C18 alkenyl chain in sheep heart plasmalogens would thus have its double bond in position 11, which seems logical, as alkenyl chains are derived from the corresponding alcohols, themselves issued from the corresponding FA, and in this particular case, vaccenic (trans-11 18:1) acid. cis-Monoenoic C18 alkenyl chains also appear more complex than realized earlier, showing in particular isomers with their ethylenic bond farther than the delta9 position, in addition to the main isomer derived from oleic acid. Several trans-16:1 alkenyl chains could be observed (totaling ca. 1%), but cis-16:1 isomers were present in trace amounts only.

  2. Chemical Reporters for Exploring Protein Acylation

    PubMed Central

    Thinon, Emmanuelle; Hang, Howard C.

    2015-01-01

    Proteins are acylated by a variety of metabolites that regulates many important cellular pathways in all kingdoms of life. Acyl groups in cells can vary in structure from the smallest unit, acetate, to modified long chain fatty acids, all of which can be activated and covalently attached to diverse amino acid side chains and consequently modulate protein function. For example, acetylation of Lys residues can alter the charge state of proteins and generate new recognition elements for protein–protein interactions. Alternatively, long chain fatty-acylation targets proteins to membranes and enables spatial control of cell signalling. To facilitate the analysis of protein acylation in biology, acyl analogues bearing alkyne or azide tags have been developed that enable fluorescent imaging and proteomic profiling of modified proteins using bioorthogonal ligation methods. Herein, we summarize the currently available acylation chemical reporters and highlight their utility to discover and quantify the roles of protein acylation in biology. PMID:25849926

  3. Dynamic self-assembly of 'living' polymeric chains

    NASA Astrophysics Data System (ADS)

    Deng, Binghui; Shi, Yunfeng

    2017-01-01

    We report a dynamic self-assembly system of 'living' polymeric chains sustained by chemistry using reactive molecular dynamics simulations. The linear polymeric chains consist of self-assembled nanoparticles connected by metastable linker molecules. As such, the polymeric chains, once assembled, undergo spontaneous dissociation driven by thermodynamics. However, with a continuous supply of linker molecules and the stored chemical energy therein, the polymeric chains can survive and maintain a steady state averaged chain length. These dynamically self-assembled polymeric chains are analogous to biological systems that both are thermodynamically metastable, yet dynamically stable upon continuous influx of matter and energy.

  4. Increased long chain acyl-Coa synthetase activity and fatty acid import is linked to membrane synthesis for development of picornavirus replication organelles.

    PubMed

    Nchoutmboube, Jules A; Viktorova, Ekaterina G; Scott, Alison J; Ford, Lauren A; Pei, Zhengtong; Watkins, Paul A; Ernst, Robert K; Belov, George A

    2013-01-01

    All positive strand (+RNA) viruses of eukaryotes replicate their genomes in association with membranes. The mechanisms of membrane remodeling in infected cells represent attractive targets for designing future therapeutics, but our understanding of this process is very limited. Elements of autophagy and/or the secretory pathway were proposed to be hijacked for building of picornavirus replication organelles. However, even closely related viruses differ significantly in their requirements for components of these pathways. We demonstrate here that infection with diverse picornaviruses rapidly activates import of long chain fatty acids. While in non-infected cells the imported fatty acids are channeled to lipid droplets, in infected cells the synthesis of neutral lipids is shut down and the fatty acids are utilized in highly up-regulated phosphatidylcholine synthesis. Thus the replication organelles are likely built from de novo synthesized membrane material, rather than from the remodeled pre-existing membranes. We show that activation of fatty acid import is linked to the up-regulation of cellular long chain acyl-CoA synthetase activity and identify the long chain acyl-CoA syntheatse3 (Acsl3) as a novel host factor required for polio replication. Poliovirus protein 2A is required to trigger the activation of import of fatty acids independent of its protease activity. Shift in fatty acid import preferences by infected cells results in synthesis of phosphatidylcholines different from those in uninfected cells, arguing that the viral replication organelles possess unique properties compared to the pre-existing membranes. Our data show how poliovirus can change the overall cellular membrane homeostasis by targeting one critical process. They explain earlier observations of increased phospholipid synthesis in infected cells and suggest a simple model of the structural development of the membranous scaffold of replication complexes of picorna-like viruses, that may be

  5. The vertical location of α-tocopherol in phosphatidylcholine membranes is not altered as a function of the degree of unsaturation of the fatty acyl chains.

    PubMed

    Ausili, Alessio; de Godos, Ana M; Torrecillas, Alejandro; Aranda, Francisco J; Corbalán-García, Senena; Gómez-Fernández, Juan C

    2017-03-01

    α-Tocopherol is a natural preservative that prevents free radical chain oxidations in biomembranes. We have studied the location of α-tocopherol in model membranes formed by different unsaturated phosphatidylcholines, namely 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (PLPC), 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC) and 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC). Small angle X-ray diffraction revealed that α-tocopherol was well mixed with all the phospholipids. In all the cases only one lamellar phase was detected. Very modest changes occasioned by α-tocopherol were observed in the electron density profiles. The results obtained from quenching of α-tocopherol intrinsic fluorescence by acrylamide showed that this vitamin was inefficiently quenched in the four types of membranes, indicating that the fluorescent chromanol ring was poorly accessible for this hydrophilic quencher. Compatible with that, quenching by doxyl derivatives of phosphatidylcholines indicated that the chromanol ring was close in the four membranes to the nitroxide probe located at position 5. Quenching by doxyl-phosphatidylcholines also indicated that the efficiency of quenching was higher in POPC than in the other unsaturated phospholipids. (1)H-MAS-NMR showed that α-tocopherol induced chemical shifts of protons from the phospholipids, especially of those bonded to carbons 2 and 3 of the acyl chains of the four phospholipids studied. The (1)H-MAS-NMR NOESY results suggested that the lower part of the chromanol ring was located between the C3 of the fatty acyl chains and the centre of the hydrophobic monolayer for the four phospholipid membranes studied. Taken together, these results suggest that α-tocopherol is located, in all the membranes studied, with the chromanol ring within the hydrophobic palisade but not far away from the lipid-water interface.

  6. Compound heterozygous mutations of ACADS gene in newborn with short chain acyl-CoA dehydrogenase deficiency: case report and literatures review

    PubMed Central

    An, Se Jin; Kim, Sook Za; Kim, Gu Hwan; Yoo, Han Wook

    2016-01-01

    Short-chain acyl-CoA dehydrogenase deficiency (SCADD) is a rare autosomal recessive mitochondrial disorder of fatty acid β-oxidation, and is associated with mutations in the acyl-CoA dehydrogenase (ACADS) gene. Recent advances in spectrometric screening for inborn errors of metabolism have helped detect several metabolic disorders, including SCADD, without symptoms in the neonate period. This allows immediate initiation of treatment and monitoring, so they remain largely symptomless metabolic disease. Here, we report a 15-month-old asymptomatic male, who was diagnosed with SCADD by newborn screening. Spectrometric screening for inborn errors of metabolism 72 hours after birth revealed an elevated butyrylcarnitine (C4) concentration of 2.25 µmol/L (normal, <0.99 µmol/L). Urinary excretion of ethylmalonic acid was also elevated, as detected by urine organic acid analysis. To confirm the diagnosis of SCADD, direct sequencing analysis of 10 coding exons and the exon-intron boundaries of the ACADS gene were performed. Subsequent sequence analysis revealed compound heterozygous missense mutations c.164C>T (p.Pro55Leu) and c.1031A>G (p.Glu344Gly) on exons 2 and 9, respectively. The patient is now growing up, unretarded by symptoms such as seizure and developmental delay. PMID:28018444

  7. Efficient dynamic simulation for multiple chain robotic mechanisms

    NASA Technical Reports Server (NTRS)

    Lilly, Kathryn W.; Orin, David E.

    1989-01-01

    An efficient O(mN) algorithm for dynamic simulation of simple closed-chain robotic mechanisms is presented, where m is the number of chains, and N is the number of degrees of freedom for each chain. It is based on computation of the operational space inertia matrix (6 x 6) for each chain as seen by the body, load, or object. Also, computation of the chain dynamics, when opened at one end, is required, and the most efficient algorithm is used for this purpose. Parallel implementation of the dynamics for each chain results in an O(N) + O(log sub 2 m+1) algorithm.

  8. Recognition of medium-chain acyl-CoA dehydrogenase deficiency in asymptomatic siblings of children dying of sudden infant death or Reye-like syndromes.

    PubMed

    Roe, C R; Millington, D S; Maltby, D A; Kinnebrew, P

    1986-01-01

    The medium-chain acyl-CoA dehydrogenase (MCAD) deficiency of mitochondrial beta oxidation has been identified in two asymptomatic siblings in a family in which two previous deaths had been recorded, one attributed to sudden infant death syndrome and the other to Reye syndrome. Recognition of this disorder in one of the deceased and in the surviving siblings was accomplished by detection of a diagnostic metabolite, octanoylcarnitine, using a new mass spectrometric technique. This resulted in early treatment with L-carnitine supplement in the survivors, which should prevent metabolic deterioration. Further studies suggest that breast-feeding may be protective for infants with MCAD deficiency. Families with children who have had Reye syndrome or in which sudden infant death has occurred are at risk for MCAD deficiency. We suggest that survivors and asymptomatic siblings should be tested for this treatable disorder.

  9. Biochemical engineering of the N-acyl side chain of sialic acids alters the kinetics of a glycosylated potassium channel Kv3.1.

    PubMed

    Hall, M Kristen; Reutter, Werner; Lindhorst, Thisbe; Schwalbe, Ruth A

    2011-10-20

    The sialic acid of complex N-glycans can be biochemically engineered by substituting the physiological precursor N-acetylmannosamine with non-natural N-acylmannosamines. The Kv3.1 glycoprotein, a neuronal voltage-gated potassium channel, contains sialic acid. Western blots of the Kv3.1 glycoprotein isolated from transfected B35 neuroblastoma cells incubated with N-acylmannosamines verified sialylated N-glycans attached to the Kv3.1 glycoprotein. Outward ionic currents of Kv3.1 transfected B35 cells treated with N-pentanoylmannosamine or N-propanoylmannosamine had slower activation and inactivation rates than those of untreated cells. Therefore, the N-acyl side chain of sialic acid is intimately connected with the activation and inactivation rates of this glycosylated potassium channel.

  10. Long chain acyl-CoA synthetase 3-mediated phosphatidylcholine synthesis is required for assembly of very low density lipoproteins in human hepatoma Huh7 cells.

    PubMed

    Yao, Hongbing; Ye, Jin

    2008-01-11

    Hepatocytes play a crucial role in regulating lipid metabolism by exporting cholesterol and triglyceride into plasma through secretion of very low density lipoproteins (VLDL). VLDL production is also required for release of hepatitis C virus (HCV) from infected hepatocytes. Here, we show that long chain acyl-CoA synthetase 3 (ACSL3) plays a crucial role in secretion of VLDL and HCV from hepatocytes. In cultured human hepatoma Huh7 cells, ACSL3 is specifically required for incorporation of fatty acids into phosphatidylcholine. In cells receiving small interfering RNA targeting ACSL3, secretion of apolipoprotein B, the major protein component of VLDL, was inhibited and the lipoprotein was rapidly degraded. This inhibition in secretion was completely eliminated when these cells were treated with phosphatidylcholine. Treatment of cells with small interfering RNA targeting ACSL3 also inhibited secretion of HCV from Huh7-derived cells. These results identify ACSL3 as a new enzymatic target to limit VLDL secretion and HCV infection.

  11. Commentary on a Delphi clinical practice protocol for the diagnosis and management of very long chain acyl-CoA dehydrogenase deficiency by Arnold et al.

    PubMed

    Marsden, Deborah Louise

    2009-03-01

    Very long chain acyl-CoA dehydrogenase deficiency (VLCAD) can now be detected by newborn screening by tandem mass spectrometry. The incidence is higher than previously estimated because of the identification of potentially milder later onset variants by screening. Although there is little information in the literature on the optimal management of rare inborn errors, there is a need for management guidelines, especially for non-specialist providers in the community. In the accompanying article, Arnold et al. present a diagnostic and management guideline for VLCAD, developed by the Delphi method for gaining consensus from a panel of 14 metabolic specialists. While consensus was gained for some issues, there was no clear consensus for several important management issues, particularly for the later onset variants. Clearly, there is an urgent need for multinational collaborative protocol driven outcomes studies that will provide the data necessary to establish robust guidelines for inborn errors of metabolism.

  12. Imaging Mass Spectrometry Reveals Acyl-Chain- and Region-Specific Sphingolipid Metabolism in the Kidneys of Sphingomyelin Synthase 2-Deficient Mice

    PubMed Central

    Sugimoto, Masayuki; Wakabayashi, Masato; Shimizu, Yoichi; Yoshioka, Takeshi; Higashino, Kenichi; Numata, Yoshito; Okuda, Tomohiko; Zhao, Songji; Sakai, Shota; Igarashi, Yasuyuki; Kuge, Yuji

    2016-01-01

    Obesity was reported to cause kidney injury by excessive accumulation of sphingolipids such as sphingomyelin and ceramide. Sphingomyelin synthase 2 (SMS2) is an important enzyme for hepatic sphingolipid homeostasis and its dysfunction is considered to result in fatty liver disease. The expression of SMS2 is also high in the kidneys. However, the contribution of SMS2 on renal sphingolipid metabolism remains unclear. Imaging mass spectrometry is a powerful tool to visualize the distribution and provide quantitative data on lipids in tissue sections. Thus, in this study, we analyzed the effects of SMS2 deficiency on the distribution and concentration of sphingomyelins in the liver and kidneys of mice fed with a normal-diet or a high-fat-diet using imaging mass spectrometry and liquid chromatography/electrospray ionization-tandem mass spectrometry. Our study revealed that high-fat-diet increased C18–C22 sphingomyelins, but decreased C24-sphingomyelins, in the liver and kidneys of wild-type mice. By contrast, SMS2 deficiency decreased C18–C24 sphingomyelins in the liver. Although a similar trend was observed in the whole-kidneys, the effects were minor. Interestingly, imaging mass spectrometry revealed that sphingomyelin localization was specific to each acyl-chain length in the kidneys. Further, SMS2 deficiency mainly decreased C22-sphingomyelin in the renal medulla and C24-sphingomyelins in the renal cortex. Thus, imaging mass spectrometry can provide visual assessment of the contribution of SMS2 on acyl-chain- and region-specific sphingomyelin metabolism in the kidneys. PMID:27010944

  13. Modulation of cellulase activity by charged lipid bilayers with different acyl chain properties for efficient hydrolysis of ionic liquid-pretreated cellulose.

    PubMed

    Mihono, Kai; Ohtsu, Takeshi; Ohtani, Mai; Yoshimoto, Makoto; Kamimura, Akio

    2016-10-01

    The stability of cellulase activity in the presence of ionic liquids (ILs) is critical for the enzymatic hydrolysis of insoluble cellulose pretreated with ILs. In this work, cellulase was incorporated in the liposomes composed of negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) and zwitterionic phosphatidylcholines (PCs) with different length and degree of unsaturation of the acyl chains. The liposomal cellulase-catalyzed reaction was performed at 45°C in the acetate buffer solution (pH 4.8) with 2.0g/L CC31 as cellulosic substrate. The crystallinity of CC31 was reduced by treating with 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) at 120°C for 30min. The liposomal cellulase continuously catalyzed hydrolysis of the pretreated CC31 for 48h producing glucose in the presence of 15wt% [Bmim]Cl. The charged lipid membranes were interactive with [Bmim](+), as elucidated by the [Bmim]Cl-induced alterations in fluorescence polarization of the membrane-embedded 1,6-diphenyl-1,3,5-hexatriene (DPH) molecules. The charged membranes offered the microenvironment where inhibitory effects of [Bmim]Cl on the cellulase activity was relieved. The maximum glucose productivity GP of 10.8 mmol-glucose/(hmol-lipid) was obtained at the reaction time of 48h with the cellulase incorporated in the liposomes ([lipid]=5.0mM) composed of 50mol% POPG and 1,2-dilauroyl-sn-glycero-3-phosohocholine (DLPC) with relatively short and saturated acyl chains.

  14. Imaging Mass Spectrometry Reveals Acyl-Chain- and Region-Specific Sphingolipid Metabolism in the Kidneys of Sphingomyelin Synthase 2-Deficient Mice.

    PubMed

    Sugimoto, Masayuki; Wakabayashi, Masato; Shimizu, Yoichi; Yoshioka, Takeshi; Higashino, Kenichi; Numata, Yoshito; Okuda, Tomohiko; Zhao, Songji; Sakai, Shota; Igarashi, Yasuyuki; Kuge, Yuji

    2016-01-01

    Obesity was reported to cause kidney injury by excessive accumulation of sphingolipids such as sphingomyelin and ceramide. Sphingomyelin synthase 2 (SMS2) is an important enzyme for hepatic sphingolipid homeostasis and its dysfunction is considered to result in fatty liver disease. The expression of SMS2 is also high in the kidneys. However, the contribution of SMS2 on renal sphingolipid metabolism remains unclear. Imaging mass spectrometry is a powerful tool to visualize the distribution and provide quantitative data on lipids in tissue sections. Thus, in this study, we analyzed the effects of SMS2 deficiency on the distribution and concentration of sphingomyelins in the liver and kidneys of mice fed with a normal-diet or a high-fat-diet using imaging mass spectrometry and liquid chromatography/electrospray ionization-tandem mass spectrometry. Our study revealed that high-fat-diet increased C18-C22 sphingomyelins, but decreased C24-sphingomyelins, in the liver and kidneys of wild-type mice. By contrast, SMS2 deficiency decreased C18-C24 sphingomyelins in the liver. Although a similar trend was observed in the whole-kidneys, the effects were minor. Interestingly, imaging mass spectrometry revealed that sphingomyelin localization was specific to each acyl-chain length in the kidneys. Further, SMS2 deficiency mainly decreased C22-sphingomyelin in the renal medulla and C24-sphingomyelins in the renal cortex. Thus, imaging mass spectrometry can provide visual assessment of the contribution of SMS2 on acyl-chain- and region-specific sphingomyelin metabolism in the kidneys.

  15. Arabidopsis acyl-CoA-binding protein ACBP3 participates in plant response to hypoxia by modulating very-long-chain fatty acid metabolism.

    PubMed

    Xie, Li-Juan; Yu, Lu-Jun; Chen, Qin-Fang; Wang, Feng-Zhu; Huang, Li; Xia, Fan-Nv; Zhu, Tian-Ren; Wu, Jian-Xin; Yin, Jian; Liao, Bin; Yao, Nan; Shu, Wensheng; Xiao, Shi

    2015-01-01

    In Arabidopsis thaliana, acyl-CoA-binding proteins (ACBPs) are encoded by a family of six genes (ACBP1 to ACBP6), and are essential for diverse cellular activities. Recent investigations suggest that the membrane-anchored ACBPs are involved in oxygen sensing by sequestration of group VII ethylene-responsive factors under normoxia. Here, we demonstrate the involvement of Arabidopsis ACBP3 in hypoxic tolerance. ACBP3 transcription was remarkably induced following submergence under both dark (DS) and light (LS) conditions. ACBP3-overexpressors (ACBP3-OEs) showed hypersensitivity to DS, LS and ethanolic stresses, with reduced transcription of hypoxia-responsive genes as well as accumulation of hydrogen peroxide in the rosettes. In contrast, suppression of ACBP3 in ACBP3-KOs enhanced plant tolerance to DS, LS and ethanol treatments. By analyses of double combinations of OE-1 with npr1-5, coi1-2, ein3-1 as well as ctr1-1 mutants, we observed that the attenuated hypoxic tolerance in ACBP3-OEs was dependent on NPR1- and CTR1-mediated signaling pathways. Lipid profiling revealed that both the total amounts and very-long-chain species of phosphatidylserine (C42:2- and C42:3-PS) and glucosylinositolphosphorylceramides (C22:0-, C22:1-, C24:0-, C24:1-, and C26:1-GIPC) were significantly lower in ACBP3-OEs but increased in ACBP3-KOs upon LS exposure. By microscale thermophoresis analysis, the recombinant ACBP3 protein bound VLC acyl-CoA esters with high affinities in vitro. Further, a knockout mutant of MYB30, a master regulator of very-long-chain fatty acid (VLCFA) biosynthesis, exhibited enhanced sensitivities to LS and ethanolic stresses, phenotypes that were ameliorated by ACBP3-RNAi. Taken together, these findings suggest that Arabidopsis ACBP3 participates in plant response to hypoxia by modulating VLCFA metabolism.

  16. Picosecond fluorescence dynamics of auramine with a long aliphatic chain

    NASA Astrophysics Data System (ADS)

    Pereira, Robson Valentim; Gehlen, Marcelo Henrique

    2006-01-01

    The acyl derivative of auramine with dodecyl carbon chain has solvent dependent absorption and emission spectra. The Lippert-Mataga plot shows two trends, a small slope in alcohols and a significant one in polar aprotic solvents. The change of dipole moment between ground and excited-state in aprotic solvent is 12 D, indicating an intramolecular charge-transfer process. Decay components of 5 and 600 ps appear in aprotic polar solvents. In protic polar solvents, the fast component, ranging from 9 ps in ethanol up to 53 ps in n-octanol, is correlated with the Debye dielectric relaxation time of the n-alcohols.

  17. Effect of Acylglycerol Composition and Fatty Acyl Chain Length on Lipid Digestion in pH-Stat Digestion Model and Simulated In Vitro Digestion Model.

    PubMed

    Qi, Jin F; Jia, Cai H; Shin, Jung A; Woo, Jeong M; Wang, Xiang Y; Park, Jong T; Hong, Soon T; Lee, K-T

    2016-02-01

    In this study, a pH-stat digestion model and a simulated in vitro digestion model were employed to evaluate the digestion degree of lipids depending on different acylglycerols and acyl chain length (that is, diacylglycerol [DAG] compared with soybean oil representing long-chain triacylglycerol compared with medium-chain triacylglycerol [MCT]). In the pH-stat digestion model, differences were observed among the digestion degrees of 3 oils using digestion rate (k), digestion half-time (t1/2 ), and digestion extent (Φmax). The results showed the digestion rate order was MCT > soybean oil > DAG. Accordingly, the order of digestion half-times was MCT < soybean oil < DAG. In simulated in vitro digestion model, digestion rates (k') and digestion half-times (t'1/2 ) were also obtained and the results showed a digestion rate order of MCT (k' = 0.068 min(-1) ) > soybean oil (k' = 0.037 min(-1) ) > DAG (k' = 0.024 min(-1) ). Consequently, the order of digestion half-times was MCT (t'1/2 = 10.20 min) < soybean oil (t'1/2 = 18.74 min) < DAG (t'1/2 = 29.08 min). The parameters obtained using the 2 models showed MCT was digested faster than soybean oil, and that soybean oil was digested faster than DAG.

  18. Transcriptional Regulation by the Short-Chain Fatty Acyl Coenzyme A Regulator (ScfR) PccR Controls Propionyl Coenzyme A Assimilation by Rhodobacter sphaeroides

    PubMed Central

    Carter, Michael S.

    2015-01-01

    ABSTRACT Propionyl coenzyme A (propionyl-CoA) assimilation by Rhodobacter sphaeroides proceeds via the methylmalonyl-CoA pathway. The activity of the key enzyme of the pathway, propionyl-CoA carboxylase (PCC), was upregulated 20-fold during growth with propionate compared to growth with succinate. Because propionyl-CoA is an intermediate in acetyl-CoA assimilation via the ethylmalonyl-CoA pathway, acetate growth also requires the methylmalonyl-CoA pathway. PCC activities were upregulated 8-fold in extracts of acetate-grown cells compared to extracts of succinate-grown cells. The upregulation of PCC activities during growth with propionate or acetate corresponded to increased expression of the pccB gene, which encodes a subunit of PCC. PccR (RSP_2186) was identified to be a transcriptional regulator required for the upregulation of pccB transcript levels and, consequently, PCC activity: growth substrate-dependent regulation was lost when pccR was inactivated by an in-frame deletion. In the pccR mutant, lacZ expression from a 215-bp plasmid-borne pccB upstream fragment including 27 bp of the pccB coding region was also deregulated. A loss of regulation as a result of mutations in the conserved motifs TTTGCAAA-X4-TTTGCAAA in the presence of PccR allowed the prediction of a possible operator site. PccR, together with homologs from other organisms, formed a distinct clade within the family of short-chain fatty acyl coenzyme A regulators (ScfRs) defined here. Some members from other clades within the ScfR family have previously been shown to be involved in regulating acetyl-CoA assimilation by the glyoxylate bypass (RamB) or propionyl-CoA assimilation by the methylcitrate cycle (MccR). IMPORTANCE Short-chain acyl-CoAs are intermediates in essential biosynthetic and degradative pathways. The regulation of their accumulation is crucial for appropriate cellular function. This work identifies a regulator (PccR) that prevents the accumulation of propionyl-CoA by controlling

  19. Distinct transcriptional regulation of long-chain acyl-CoA synthetase isoforms and cytosolic thioesterase 1 in the rodent heart by fatty acids and insulin.

    PubMed

    Durgan, David J; Smith, Justin K; Hotze, Margaret A; Egbejimi, Oluwaseun; Cuthbert, Karalyn D; Zaha, Vlad G; Dyck, Jason R B; Abel, E Dale; Young, Martin E

    2006-06-01

    The molecular mechanism(s) responsible for channeling long-chain fatty acids (LCFAs) into oxidative versus nonoxidative pathways is (are) poorly understood in the heart. Intracellular LCFAs are converted to long-chain fatty acyl-CoAs (LCFA-CoAs) by a family of long-chain acyl-CoA synthetases (ACSLs). Cytosolic thioesterase 1 (CTE1) hydrolyzes cytosolic LCFA-CoAs to LCFAs, generating a potential futile cycle at the expense of ATP utilization. We hypothesized that ACSL isoforms and CTE1 are differentially regulated in the heart during physiological and pathophysiological conditions. Using quantitative RT-PCR, we report that the five known acsl isoforms (acsl1, acsl3, acsl4, acsl5, and acsl6) and cte1 are expressed in whole rat and mouse hearts, as well as adult rat cardiomyocytes (ARCs). Streptozotocin-induced insulin-dependent diabetes (4 wk) and fasting (

  20. Effect of small chain N acyl homoserine lactone quorum sensing signals on biofilms of food-borne pathogens.

    PubMed

    A, Jamuna Bai; V, Ravishankar Rai

    2016-09-01

    Quorum sensing or cell to cell communication which includes inter- and intra-cellular communication has been implicated in the production of virulence factor and formation of biofilm in food-borne pathogens. In the present study, the effect of quorum sensing signals on the biofilms of food-borne pathogens has been elucidated. N-butryl homoserine lactone and N-hexanoyl homoserine lactone belonging to acyl homoserine lactone (AHL) family of signaling molecules were investigated for their effect on the biofilm formation (attachment and exopolymeric substance production) in the food-borne pathogens Escherichia coli, Salmonella enterica serovar Typhimurium and Vibrio parahemolyticus. The signaling molecules at a concentration of 1 µM were capable of increasing biofilm formation in all the tested pathogens. There was an increase in the attachment of the bacterial cells and biomass as observed by microtiter plate assay and exopolymeric substances production in the biofilms in presence of the AHLs. Further, it needs to be elucidated if the effect of AHLS on the biofilms of E. coli and S. enterica serovar Typhimurium is SdiA dependent.

  1. Ontogeny of mRNA expression and activity of long-chain acyl-CoA synthetase (ACSL) isoforms in Mus musculus heart.

    PubMed

    de Jong, Hendrik; Neal, Andrea C; Coleman, Rosalind A; Lewin, Tal M

    2007-01-01

    Long-chain acyl-CoA synthetases (ACSL) activate fatty acids (FA) and provide substrates for virtually every metabolic pathway that catabolizes FA or synthesizes complex lipids. We have hypothesized that each of the five cloned ACSL isoforms partitions FA towards specific downstream pathways. Adult heart expresses all five cloned ACSL isoforms, but their independent functional roles have not been elucidated. Studies implicate ACSL1 in both oxidative and lipid synthetic pathways. To clarify the functional role of ACSL1 and the other ACSL isoforms (3-6), we examined ACS specific activity and Acsl mRNA expression in the developing mouse heart which increases FA oxidative pathways for energy production after birth. Compared to the embryonic heart, ACS specific activity was 14-fold higher on post-natal day 1 (P1). On P1, as compared to the fetus, only Acsl1 mRNA increased, whereas transcripts for the other Acsl isoforms remained the same, suggesting that ACSL1 is the major isoform responsible for activating long-chain FA for myocardial oxidation after birth. In contrast, the mRNA abundance of Acsl3 was highest on E16, and decreased dramatically by P7, suggesting that ACSL3 may play a critical role during the development of the fetal heart. Our data support the hypothesis that each ACSL has a specific role in the channeling of FA towards distinct metabolic fates.

  2. Evidence that the major metabolites accumulating in medium-chain acyl-CoA dehydrogenase deficiency disturb mitochondrial energy homeostasis in rat brain.

    PubMed

    Schuck, Patrícia Fernanda; Ferreira, Gustavo da Costa; Tonin, Anelise Miotti; Viegas, Carolina Maso; Busanello, Estela Natacha Brandt; Moura, Alana Pimentel; Zanatta, Angela; Klamt, Fábio; Wajner, Moacir

    2009-11-03

    Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is an inherited metabolic disorder of fatty acid oxidation in which the affected patients predominantly present high levels of octanoic (OA) and decanoic (DA) acids and their glycine and carnitine by-products in tissues and body fluids. It is clinically characterized by episodic encephalopathic crises with coma and seizures, as well as by progressive neurological involvement, whose pathophysiology is poorly known. In the present work, we investigated the in vitro effects of OA and DA on various parameters of energy homeostasis in mitochondrial preparations from brain of young rats. We found that OA and DA markedly increased state 4 respiration and diminished state 3 respiration as well as the respiratory control ratio, the mitochondrial membrane potential and the matrix NAD(P)H levels. In addition, DA-elicited increase in oxygen consumption in state 4 respiration was partially prevented by atractyloside, indicating the involvement of the adenine nucleotide translocator. OA and DA also reduced ADP/O ratio, CCCP-stimulated respiration and the activities of respiratory chain complexes. The data indicate that the major accumulating fatty acids in MCADD act as uncouplers of oxidative phosphorylation and as metabolic inhibitors. Furthermore, DA, but not OA, provoked a marked mitochondrial swelling and cytochrome c release from mitochondria, reflecting a permeabilization of the inner mitochondrial membrane. Taken together, these data suggest that OA and DA impair brain mitochondrial energy homeostasis that could underlie at least in part the neuropathology of MCADD.

  3. Acyl-Lipid Metabolism

    PubMed Central

    Li-Beisson, Yonghua; Shorrosh, Basil; Beisson, Fred; Andersson, Mats X.; Arondel, Vincent; Bates, Philip D.; Baud, Sébastien; Bird, David; DeBono, Allan; Durrett, Timothy P.; Franke, Rochus B.; Graham, Ian A.; Katayama, Kenta; Kelly, Amélie A.; Larson, Tony; Markham, Jonathan E.; Miquel, Martine; Molina, Isabel; Nishida, Ikuo; Rowland, Owen; Samuels, Lacey; Schmid, Katherine M.; Wada, Hajime; Welti, Ruth; Xu, Changcheng; Zallot, Rémi; Ohlrogge, John

    2010-01-01

    Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables. PMID:22303259

  4. Acyl-Lipid Metabolism

    PubMed Central

    Li-Beisson, Yonghua; Shorrosh, Basil; Beisson, Fred; Andersson, Mats X.; Arondel, Vincent; Bates, Philip D.; Baud, Sébastien; Bird, David; DeBono, Allan; Durrett, Timothy P.; Franke, Rochus B.; Graham, Ian A.; Katayama, Kenta; Kelly, Amélie A.; Larson, Tony; Markham, Jonathan E.; Miquel, Martine; Molina, Isabel; Nishida, Ikuo; Rowland, Owen; Samuels, Lacey; Schmid, Katherine M.; Wada, Hajime; Welti, Ruth; Xu, Changcheng; Zallot, Rémi; Ohlrogge, John

    2013-01-01

    Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables. PMID:23505340

  5. De novo fatty acid biosynthesis and elongation in very long-chain acyl-CoA dehydrogenase-deficient mice supplemented with odd or even medium-chain fatty acids.

    PubMed

    Tucci, Sara; Behringer, Sidney; Spiekerkoetter, Ute

    2015-11-01

    An even medium-chain triglyceride (MCT)-based diet is the mainstay of treatment in very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD). Previous studies with magnetic resonance spectroscopy have shown an impact of MCT on the average fatty acid chain length in abdominal fat. We therefore assume that medium-chain fatty acids (MCFAs) are elongated and accumulate in tissue as long-chain fatty acids. In this study, we explored the hepatic effects of long-term supplementation with MCT or triheptanoin, an odd-chain C7-based triglyceride, in wild-type and VLCAD-deficient (VLCAD(-/-) ) mice after 1 year of supplementation as compared with a control diet. The de novo biosynthesis and elongation of fatty acids, and peroxisomal β-oxidation, were quantified by RT-PCR. This was followed by a comprehensive analysis of hepatic and cardiac fatty acid profiles by GC-MS. Long-term application of even and odd MCFAs strongly induced de novo biosynthesis and elongation of fatty acids in both wild-type and VLCAD(-/-) mice, leading to an alteration of the hepatic fatty acid profiles. We detected de novo-synthesized and elongated fatty acids, such as heptadecenoic acid (C17:1n9), eicosanoic acid (C20:1n9), erucic acid (C22:1n9), and mead acid (C20:3n9), that were otherwise completely absent in mice under control conditions. In parallel, the content of monounsaturated fatty acids was massively increased. Furthermore, we observed strong upregulation of peroxisomal β-oxidation in VLCAD(-/-) mice, especially when they were fed an MCT diet. Our data raise the question of whether long-term MCFA supplementation represents the most efficient treatment in the long term. Studies on the hepatic toxicity of triheptanoin are still ongoing.

  6. Rat long-chain acyl-CoA synthetase mRNA, protein, and activity vary in tissue distribution and in response to diet.

    PubMed

    Mashek, Douglas G; Li, Lei O; Coleman, Rosalind A

    2006-09-01

    Distinct isoforms of long-chain acyl-CoA synthetases (ACSLs) may partition fatty acids toward specific metabolic cellular pathways. For each of the five members of the rat ACSL family, we analyzed tissue mRNA distributions, and we correlated the mRNA, protein, and activity of ACSL1 and ACSL4 after fasting and refeeding a 69% sucrose diet. Not only did quantitative real-time PCR analyses reveal unique tissue expression patterns for each ACSL isoform, but expression varied markedly in different adipose depots. Fasting increased ACSL4 mRNA abundance in liver, muscle, and gonadal and inguinal adipose tissues, and refeeding decreased ACSL4 mRNA. A similar pattern was observed for ACSL1, but both fasting and refeeding decreased ACSL1 mRNA in gonadal adipose. Fasting also decreased ACSL3 and ACSL5 mRNAs in liver and ACSL6 mRNA in muscle. Surprisingly, in nearly every tissue measured, the effects of fasting and refeeding on the mRNA abundance of ACSL1 and ACSL4 were discordant with changes in protein abundance. These data suggest that the individual ACSL isoforms are distinctly regulated across tissues and show that mRNA expression may not provide useful information about isoform function. They further suggest that translational or posttranslational modifications are likely to contribute to the regulation of ACSL isoforms.

  7. Sudden unexpected infant death (SUDI) in a newborn due to medium chain acyl CoA dehydrogenase (MCAD) deficiency with an unusual severe genotype

    PubMed Central

    2012-01-01

    Medium chain acyl CoA dehydrogenase deficiency (MCAD) is the most common inborn error of fatty acid oxidation. This condition may lead to cellular energy shortage and cause severe clinical events such as hypoketotic hypoglycemia, Reye syndrome and sudden death. MCAD deficiency usually presents around three to six months of life, following catabolic stress as intercurrent infections or prolonged fasting, whilst neonatal-onset of the disease is quite rare. We report the case of an apparently healthy newborn who suddenly died at the third day of life, in which the diagnosis of MCAD deficiency was possible through peri-mortem blood-spot acylcarnitine analysis that showed very high concentrations of octanoylcarnitine. Genetic analysis at the ACADM locus confirmed the biochemical findings by demonstrating the presence in homozygosity of the frame-shift c.244dup1 (p.Trp82LeufsX23) mutation, a severe genotype that may explain the unusual and very early fatal outcome in this newborn. This report confirms that inborn errors of fatty acid oxidation represent one of the genetic causes of sudden unexpected deaths in infancy (SUDI) and underlines the importance to include systematically specific metabolic screening in any neonatal unexpected death. PMID:23095120

  8. AHL signaling molecules with a large acyl chain enhance biofilm formation on sulfur and metal sulfides by the bioleaching bacterium Acidithiobacillus ferrooxidans.

    PubMed

    González, Alex; Bellenberg, Sören; Mamani, Sigde; Ruiz, Lina; Echeverría, Alex; Soulère, Laurent; Doutheau, Alain; Demergasso, Cecilia; Sand, Wolfgang; Queneau, Yves; Vera, Mario; Guiliani, Nicolas

    2013-04-01

    Biofilm formation plays a pivotal role in bioleaching activities of bacteria in both industrial and natural environments. Here, by visualizing attached bacterial cells on energetic substrates with different microscopy techniques, we obtained the first direct evidence that it is possible to positively modulate biofilm formation of the extremophilic bacterium Acidithiobacillus ferrooxidans on sulfur and pyrite surfaces by using Quorum Sensing molecules of the N-acylhomoserine lactone type (AHLs). Our results revealed that AHL-signaling molecules with a long acyl chain (12 or 14 carbons) increased the adhesion of A. ferrooxidans cells to these substrates. In addition, Card-Fish experiments demonstrated that C14-AHL improved the adhesion of indigenous A. ferrooxidans cells from a mixed bioleaching community to pyrite. Finally, we demonstrated that this improvement of cell adhesion is correlated with an increased production of extracellular polymeric substances. Our results open up a promising means to develop new strategies for the improvement of bioleaching efficiency and metal recovery, which could also be used to control environmental damage caused by acid mine/rock drainage.

  9. Genetic basis for correction of very-long-chain acyl-coenzyme A dehydrogenase deficiency by bezafibrate in patient fibroblasts: toward a genotype-based therapy.

    PubMed

    Gobin-Limballe, S; Djouadi, F; Aubey, F; Olpin, S; Andresen, B S; Yamaguchi, S; Mandel, H; Fukao, T; Ruiter, J P N; Wanders, R J A; McAndrew, R; Kim, J J; Bastin, J

    2007-12-01

    Very-long-chain acyl-coenzyme A dehydrogenase (VLCAD) deficiency is an inborn mitochondrial fatty-acid beta-oxidation (FAO) defect associated with a broad mutational spectrum, with phenotypes ranging from fatal cardiopathy in infancy to adolescent-onset myopathy, and for which there is no established treatment. Recent data suggest that bezafibrate could improve the FAO capacities in beta-oxidation-deficient cells, by enhancing the residual level of mutant enzyme activity via gene-expression stimulation. Since VLCAD-deficient patients frequently harbor missense mutations with unpredictable effects on enzyme activity, we investigated the response to bezafibrate as a function of genotype in 33 VLCAD-deficient fibroblasts representing 45 different mutations. Treatment with bezafibrate (400 microM for 48 h) resulted in a marked increase in FAO capacities, often leading to restoration of normal values, for 21 genotypes that mainly corresponded to patients with the myopathic phenotype. In contrast, bezafibrate induced no changes in FAO for 11 genotypes corresponding to severe neonatal or infantile phenotypes. This pattern of response was not due to differential inductions of VLCAD messenger RNA, as shown by quantitative real-time polymerase chain reaction, but reflected variable increases in measured VLCAD residual enzyme activity in response to bezafibrate. Genotype cross-analysis allowed the identification of alleles carrying missense mutations, which could account for these different pharmacological profiles and, on this basis, led to the characterization of 9 mild and 11 severe missense mutations. Altogether, the responses to bezafibrate reflected the severity of the metabolic blockage in various genotypes, which appeared to be correlated with the phenotype, thus providing a new approach for analysis of genetic heterogeneity. Finally, this study emphasizes the potential of bezafibrate, a widely prescribed hypolipidemic drug, for the correction of VLCAD deficiency and

  10. Regioselective self-acylating cyclodextrins in organic solvent

    PubMed Central

    Cho, Eunae; Yun, Deokgyu; Jeong, Daham; Im, Jieun; Kim, Hyunki; Dindulkar, Someshwar D.; Choi, Youngjin; Jung, Seunho

    2016-01-01

    Amphiphilic cyclodextrins have been synthesized with self-acylating reaction using vinyl esters in dimethylformamide. In the present study no base, catalyst, or enzyme was used, and the structural analyses using thin layer chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry show that the cyclodextrin is substituted preferentially by one acyl moiety at the C2 position of the glucose unit, suggesting that cyclodextrin functions as a regioselective catalytic carbohydrate in organic solvent. In the self-acylation, the most acidic OH group at the 2-position and the inclusion complexing ability of cyclodextrin were considered to be significant. The substrate preference was also observed in favor of the long-chain acyl group, which could be attributed to the inclusion ability of cyclodextrin cavity. Furthermore, using the model amphiphilic building block, 2-O-mono-lauryl β-cyclodextrin, the self-organized supramolecular architecture with nano-vesicular morphology in water was investigated by fluorescence spectroscopy, dynamic light scattering and transmission electron microscopy. The cavity-type nano-assembled vesicle and the novel synthetic methods for the preparation of mono-acylated cyclodextrin should be of great interest with regard to drug/gene delivery systems, functional surfactants, and carbohydrate derivatization methods. PMID:27020946

  11. Regioselective self-acylating cyclodextrins in organic solvent

    NASA Astrophysics Data System (ADS)

    Cho, Eunae; Yun, Deokgyu; Jeong, Daham; Im, Jieun; Kim, Hyunki; Dindulkar, Someshwar D.; Choi, Youngjin; Jung, Seunho

    2016-03-01

    Amphiphilic cyclodextrins have been synthesized with self-acylating reaction using vinyl esters in dimethylformamide. In the present study no base, catalyst, or enzyme was used, and the structural analyses using thin layer chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry show that the cyclodextrin is substituted preferentially by one acyl moiety at the C2 position of the glucose unit, suggesting that cyclodextrin functions as a regioselective catalytic carbohydrate in organic solvent. In the self-acylation, the most acidic OH group at the 2-position and the inclusion complexing ability of cyclodextrin were considered to be significant. The substrate preference was also observed in favor of the long-chain acyl group, which could be attributed to the inclusion ability of cyclodextrin cavity. Furthermore, using the model amphiphilic building block, 2-O-mono-lauryl β-cyclodextrin, the self-organized supramolecular architecture with nano-vesicular morphology in water was investigated by fluorescence spectroscopy, dynamic light scattering and transmission electron microscopy. The cavity-type nano-assembled vesicle and the novel synthetic methods for the preparation of mono-acylated cyclodextrin should be of great interest with regard to drug/gene delivery systems, functional surfactants, and carbohydrate derivatization methods.

  12. The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine carboxyl peptidase kumamolisin-As†

    PubMed Central

    Xu, Qin; Guo, Hao-Bo; Wlodawer, Alexander; Nakayama, Toru; Guo, Hong

    2008-01-01

    Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations are performed to study the acylation reaction catalyzed by kumamolisin-As, a serine-carboxyl peptidase, and to elucidate the catalytic mechanism and the origin of substrate specificity. It is demonstrated that the nucleophilic attack by the serine residue on the substrate may not be the rate limiting step for the acylation of the GPH*FF substrate. The present study also confirms the earlier suggestions that Asp 164 acts as a general acid during the catalysis and that the electrostatic oxyanion-hole interactions may not be sufficient to lead a stable tetrahedral intermediate along the reaction pathway. Moreover, Asp 164 is found to act as a general base during the formation of the acyl-enzyme from the tetrahedral intermediate. The role of dynamic substrate assisted catalysis (DSAC) involving His at the P1 site of the substrate is examined for the acylation reaction. It is demonstrated that the bond breaking and making events at each stage of the reaction trigger a change of the position for the His sidechain and lead to the formation of the alternative hydrogen bonds. The back and forth movements of the His sidechain between the C=O group of Pro at P2 and Oδ2 of Asp 164 in a P1ng-pong-like mechanism and the formation of the alternative hydrogen bonds effectively lower the free energy barriers for both the nucleophilic attack and the acyl-enzyme formation and may therefore contribute to the relatively high activity of kumamolisin-As towards to the substrates with His at P1 site. PMID:17326662

  13. Long Chain Fatty Acid Acylated Derivatives of Quercetin-3-O-Glucoside as Antioxidants to Prevent Lipid Oxidation

    PubMed Central

    Warnakulasuriya, Sumudu N.; Ziaullah; Rupasinghe, H.P. Vasantha

    2014-01-01

    Flavonoids have shown promise as natural plant-based antioxidants for protecting lipids from oxidation. It was hypothesized that their applications in lipophilic food systems can be further enhanced by esterification of flavonoids with fatty acids. Quercetin-3-O-glucoside (Q3G) was esterified individually with six selected long chain fatty acids: stearic acid (STA), oleic acid (OLA), linoleic acid (LNA), α-linolenic acid (ALA), eicosapentaenoic acid (EPA) and decosahexaenoic acid (DHA), using Candida antarctica B lipase as the biocatalyst. The antioxidant activity of esterified flavonoids was evaluated using lipid oxidation model systems of poly-unsaturated fatty acids-rich fish oil and human low density lipoprotein (LDL), in vitro. In the oil-in-water emulsion, Q3G esters exhibited 50% to 100% inhibition in primary oxidation and 30% to 75% inhibition in secondary oxidation. In bulk oil, Q3G esters did not provide considerable protection from lipid oxidation; however, Q3G demonstrated more than 50% inhibition in primary oxidation. EPA, DHA and ALA esters of Q3G showed significantly higher inhibition in Cu2+- and peroxyl radical-induced LDL oxidation in comparison to Q3G. PMID:25384198

  14. Measuring long-chain acyl-coenzyme A concentrations and enrichment using liquid chromatography/tandem mass spectrometry with selected reaction monitoring.

    PubMed

    Blachnio-Zabielska, Agnieszka U; Koutsari, Christina; Jensen, Michael D

    2011-08-15

    Long-chain acyl-coenzymes A (acyl-CoAs) (LCACoA) are the activated forms of long-chain fatty acids and serve as key lipid metabolites. Excess accumulation of intracellular LCACoA, diacylglycerols (DAGs) and ceramides may create insulin resistance with respect to glucose metabolism. We present a new method to measure LCACoA concentrations and isotopic enrichment of palmitoyl-CoA ([U-(13) C]16-CoA) and oleoyl-CoA ([U-(13) C]18:1-CoA) using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) to quantitate seven different LCACoA (C14-CoA, C16-CoA, C16:1-CoA, C18-CoA, C18:1-CoA, C18:2-CoA, C20-CoA). The molecules are separated on a reversed-phase UPLC column using a binary gradient with ammonium hydroxide (NH(4) OH) in water and NH(4) OH in acetonitrile (ACN). The LCACoA are quantified using selected reaction monitoring (SRM) on a triple quadrupole mass spectrometer in positive electrospray ionization (ESI) mode. All LCACoA ions except enriched palmitate enrichment of palmitoyl-CoA ([U(-13)C]16-CoA) and oleoyl-CoA ([U(-13)C]18:1-CoA) using ultra-performance liquid chromatography/mass spectrometry (UPLC/MS/MS) to quantitate seven different LCACoA (C14-CoA, C16-CoA, C16:1-CoA, C18-CoA, C18:1-CoA, C18:2-CoA, C20-CoA). The molecules are separated on a reversed-phase UPLC column using a binary gradient with ammonium hydroxide (NH(4) OH) in water and NH(4) OH in acetonitrile. The LCACoA are quantified using selected reaction monitoring (SRM) on a triple quadrupolemass spectrometer in positive electrospray ionization (ESI) mode. All LCACoA ions except enriched palmitate and oleate were monitored as [M+2+H](+) and [U(13)C]16-CoA and [U(13)C]18:1-CoA were monitored as [M+16+H](+) and [M+18+H](+), respectively. The method is simple, sensitive and efficient (run time as short as 5 min) and allowed us to measure the concentration and detect enrichment in intramyocellular [U(13) C]16-CoA and [U(13) C]18:1-CoA during a low dose intravenous infusion of [U(13

  15. Chain Dynamics in Single Chain Limit by Rheological and Diffusion Measurements

    NASA Astrophysics Data System (ADS)

    Wang, Shi-Qing; Wang, Shanfeng

    2004-03-01

    Our recent trace and self diffusion measurements , indicate (a) (b) that the molecular weight scaling of the self-diffusion coefficient is non-reptative for moderately entangled polymer melts as noted previously (c) but asymptotically approaches the reptative exponent of -2.0 for sufficiently entangled polymers, whereas the trace diffusion coefficient, measured by immersing a dilute amount of probe chains in a matrix of sufficiently entangled polymer of the same species, scales reptatively even for the probe chains of moderate entanglement. To further understand the behavior of probe chain dynamics in a matrix, we have measured the intrinsic viscosity and intrinsic storage and loss moduli of dilute solutions made of long chains (in dilution) and short chains, where both chain lengths can be much longer than the entanglement chain length. A rich variety of chain dynamics is observed including Stokes-Zimm behavior and Rouse like behavior as a function of the long and short chain lengths and concentration. (a) S.Q. Wang, Highlight Article, J. Polym. Sci. Polym. Phys., 41, 1589 (2003). (b) "Diffusion and Rheology of Binary Polymer Mixtures", S. Wang et al, Macromolecules, in press (2003). (c) T.P. Lodge, Phys. Rev. Lett. 83, 3218 (1999).

  16. A Rare Case of Short-Chain Acyl-COA Dehydrogenase Deficiency: The Apparent Rarity of the Disorder Results in Under Diagnosis.

    PubMed

    Reddy, G Shilpa; Sujatha, M

    2011-07-01

    Short-chain acyl-CoA dehydrogenase (ACAD) deficiency is an extremely rare inherited mitochondrial disorder of fat metabolism. This belongs to a group of diseases known as fatty acid oxidation disorders. Screening programmes have provided evidence that all the fatty acid oxidation disorders combined are among the most common inborn errors of metabolism. Mitochondrial beta oxidation of fatty acids is an essential energy producing pathway. It is a particularly important pathway during prolonged periods of starvation and during periods of reduced caloric intake due to gastrointestinal illness or increased energy expenditure during febrile illness. The most common presentation is an acute episode of life threatening coma and hypoglycemia induced by a period of fasting due to defective hepatic ketogenesis. Here, the case of a 4 month old female patient who had seizures since the third day of her birth and persistent hypoglycemia is described. She was born to parents of second degree consanguinity after 10 years of infertility treatment. There was history of delayed cry after birth. Metabolic screening for TSH, galactosemia, 17-OHP, G6PD, cystic fibrosis, biotinidase were normal. Tandem mass spectrometric (TMS) screening for blood amino acids, organic acids, fatty acids showed elevated butyryl carnitine (C4) as 3.40 μmol/L (normal <2.00 μmol/L), hexanoyl carnitine (C6) as 0.92 μmol/L (normal <0.72 μmol/L), C4/C3 as 2.93 μmol/L (normal <1.18 μmol/L). The child was started immediately on carnitor syrup (carnitine) 1/2 ml twice daily. Limitation of fasting stress and dietary fat was advised. Baby responded well by gaining weight and seizures were controlled. Until now, less than 25 patients have been reported worldwide. The limited number of patients diagnosed until now is due to the rarity of the disorder resulting in under diagnosis.

  17. Data mining methods for classification of Medium-Chain Acyl-CoA dehydrogenase deficiency (MCADD) using non-derivatized tandem MS neonatal screening data.

    PubMed

    Van den Bulcke, Tim; Vanden Broucke, Paul; Van Hoof, Viviane; Wouters, Kristien; Vanden Broucke, Seppe; Smits, Geert; Smits, Elke; Proesmans, Sam; Van Genechten, Toon; Eyskens, François

    2011-04-01

    Newborn screening programs for severe metabolic disorders using tandem mass spectrometry are widely used. Medium-Chain Acyl-CoA dehydrogenase deficiency (MCADD) is the most prevalent mitochondrial fatty acid oxidation defect (1:15,000 newborns) and it has been proven that early detection of this metabolic disease decreases mortality and improves the outcome. In previous studies, data mining methods on derivatized tandem MS datasets have shown high classification accuracies. However, no machine learning methods currently have been applied to datasets based on non-derivatized screening methods. A dataset with 44,159 blood samples was collected using a non-derivatized screening method as part of a systematic newborn screening by the PCMA screening center (Belgium). Twelve MCADD cases were present in this partially MCADD-enriched dataset. We extended three data mining methods, namely C4.5 decision trees, logistic regression and ridge logistic regression, with a parameter and threshold optimization method and evaluated their applicability as a diagnostic support tool. Within a stratified cross-validation setting, a grid search was performed for each model for a wide range of model parameters, included variables and classification thresholds. The best performing model used ridge logistic regression and achieved a sensitivity of 100%, a specificity of 99.987% and a positive predictive value of 32% (recalibrated for a real population), obtained in a stratified cross-validation setting. These results were further validated on an independent test set. Using a method that combines ridge logistic regression with variable selection and threshold optimization, a significantly improved performance was achieved compared to the current state-of-the-art for derivatized data, while retaining more interpretability and requiring less variables. The results indicate the potential value of data mining methods as a diagnostic support tool.

  18. FAT/CD36 is located on the outer mitochondrial membrane, upstream of long-chain acyl-CoA synthetase, and regulates palmitate oxidation.

    PubMed

    Smith, Brennan K; Jain, Swati S; Rimbaud, Stéphanie; Dam, Aaron; Quadrilatero, Joe; Ventura-Clapier, Renée; Bonen, Arend; Holloway, Graham P

    2011-07-01

    FAT/CD36 (fatty acid translocase/Cluster of Differentiation 36), a plasma membrane fatty-acid transport protein, has been found on mitochondrial membranes; however, it remains unclear where FAT/CD36 resides on this organelle or its functional role within mitochondria. In the present study, we demonstrate, using several different approaches, that in skeletal muscle FAT/CD36 resides on the OMM (outer mitochondrial membrane). To determine the functional role of mitochondrial FAT/CD36 in this tissue, we determined oxygen consumption rates in permeabilized muscle fibres in WT (wild-type) and FAT/CD36-KO (knockout) mice using a variety of substrates. Despite comparable muscle mitochondrial content, as assessed by unaltered mtDNA (mitochondrial DNA), citrate synthase, β-hydroxyacyl-CoA dehydrogenase, cytochrome c oxidase complex IV and respiratory capacities [maximal OXPHOS (oxidative phosphorylation) respiration] in WT and KO mice, palmitate-supported respiration was 34% lower in KO animals. In contrast, palmitoyl-CoA-supported respiration was unchanged. These results indicate that FAT/CD36 is key for palmitate-supported respiration. Therefore we propose a working model of mitochondrial fatty-acid transport, in which FAT/CD36 is positioned on the OMM, upstream of long-chain acyl-CoA synthetase, thereby contributing to the regulation of mitochondrial fatty-acid transport. We further support this model by providing evidence that FAT/CD36 is not located in mitochondrial contact sites, and therefore does not directly interact with carnitine palmitoyltransferase-I as original proposed.

  19. Long chain acyl-CoA synthetase-3 is a molecular target for peroxisome proliferator-activated receptor delta in HepG2 hepatoma cells.

    PubMed

    Cao, Aiqin; Li, Hai; Zhou, Yue; Wu, Minhao; Liu, Jingwen

    2010-05-28

    ACSL3 is a member of the long chain acyl-CoA synthetase (ACSL) family that plays key roles in fatty acid metabolism in various tissues in an isozyme-specific manner. Our previous studies showed that ACSL3 was transcriptionally up-regulated by the cytokine oncostatin M (OSM) in HepG2 cells, accompanied by reduced cellular triglyceride content and enhanced beta-oxidation. In this study, we investigated the molecular mechanism underlying the OSM-induced activation of ACSL3 gene transcription in HepG2 cells. We showed that OSM treatment resulted in a coordinated elevation of mRNA levels of ACSL3 and peroxisome proliferator-activated receptor delta (PPARdelta). The effect of OSM on ACSL3 mRNA expression was inhibited by cellular depletion of PPARdelta. By utilizing a PPARdelta agonist, L165041, we demonstrated that activation of PPARdelta led to increases in ACSL3 promoter activity, mRNA level, and protein level in HepG2 cells. Analysis of the ACSL3 promoter sequence identified two imperfect PPAR-responsive elements (PPRE) located in the ACSL3 promoter region -944 to -915, relative to the transcription start site. The up-regulation of ACSL3 promoter activity by PPARdelta was abolished by deletion of this PPRE-containing region or mutation to disrupt the binding sites. Direct interactions of PPARdelta with ACSL3-PPRE sequences were demonstrated by gel mobility shift and chromatin immunoprecipitation assays. Finally, we provided in vivo evidence showing that activation of PPARdelta by L165041 in hamsters increased ACSL3 mRNA and protein levels in the liver. These new findings define ACSL3 as a novel molecular target of PPARdelta in HepG2 cells and provide a regulatory mechanism for ACSL3 transcription in liver tissue.

  20. Reduction of serum free fatty acids and triglycerides by liver-targeted expression of long chain acyl-CoA synthetase 3.

    PubMed

    Wu, Minhao; Cao, Aiqin; Dong, Bin; Liu, Jingwen

    2011-05-01

    ACSL3 is a member of the long chain acyl-CoA synthetase (ACSL) family that consists of 5 isozymes responsible for cellular fatty acid metabolism in various tissues in an isozyme-specific manner. Our previous studies have demonstrated that expression of ACSL3 mRNA and protein in liver was specifically increased after feeding hamsters with a fat- and cholesterol-enriched diet, providing the first in vivo evidence for the regulated expression of ACSL3 in liver tissue. The aim of the current study was to further investigate the role of ACSL3 in regulating hepatic lipid metabolism in vitro and in vivo. We utilized an adenoviral-mediated gene delivery approach to exogenously express hamster ACSL3 in hamster liver as well as in HepG2 cells. Transduction of HepG2 cells with Ad-hamACSL3 adenovirus elevated total cellular ACSL enzyme activity, which was accompanied by a significant reduction of cellular contents of triglycerides and total phospholipids. Immunostaining and confocal microscopy studies revealed that ACSL3 was localized to endoplasmic reticulum and mitochondria. In vivo, infection of hamsters with Ad-hamACSL3 led to sustained expression of ACSL3 mRNA and protein in liver two weeks after infection. Importantly, compared with Ad-GFP control virus infected hamsters, we observed significantly lower free fatty acids and triglycerides plus modest reduction of phospholipids in the serum of Ad-hamACSL3 infected animals. Furthermore, triglyceride levels were significantly reduced in Ad-hamACSL3 infected hamster liver. Altogether, these results provide important and physiologically relevant evidence that strengthens the link between ACSL3 expression and hepatic reduction of triglycerides and fatty acids.

  1. High-fructose diet downregulates long-chain acyl-CoA synthetase 3 expression in liver of hamsters via impairing LXR/RXR signaling pathway.

    PubMed

    Dong, Bin; Kan, Chin Fung Kelvin; Singh, Amar B; Liu, Jingwen

    2013-05-01

    Long-chain acyl-CoA synthetases (ACSL) play key roles in fatty acid metabolism in liver and other metabolic tissues in an isozyme-specific manner. In this study, we examined the effects of a fructose-enriched diet on expressions of ACSL isoforms in the liver of hamsters. We showed that the fructose diet markedly reduced the mRNA and protein expressions of ACSL3 in hamster liver without significant effects on other ACSLs. The decrease in ACSL3 abundance was accompanied by a reduction in ACSL-catalyzed synthesis of arachidonyl-CoA and oleoyl-CoA in liver homogenates of hamsters fed the fructose diet as opposed to normal diet. We further showed that fructose diet specifically reduced expressions of three key components of the LXR signaling pathway, namely, liver X receptor (LXR)α, LXRβ, and retinoid X receptor (RXR)β. Exogenous expression and activation of LXRα/β increased hamster ACSL3 promoter activities in a LXR-responsive element (LXRE)-dependent fashion. Finally, we showed that treating hamsters with LXR agonist GW3965 increased hepatic ACSL3 expression without affecting other ACSL isoforms. Furthermore, the ligand-induced increases of ACSL3 expression were accompanied with the reduction of hepatic triglyceride levels in GW3965-treated hamster liver. Altogether, our studies demonstrate that fructose diet has a negative impact on LXR signaling pathway in liver tissue and reduction of ACSL3 expression/activity could be a causal factor for fructose-induced hepatic steatosis.

  2. Acylcarnitine profiles during carnitine loading and fasting tests in a Japanese patient with medium-chain acyl-CoA dehydrogenase deficiency.

    PubMed

    Yokoi, Kyoko; Ito, Tetsuya; Maeda, Yasuhiro; Nakajima, Yoko; Ueta, Akihito; Nomura, Takayasu; Koyama, Norihisa; Kato, Ineko; Suzuki, Satoshi; Kurono, Yukihisa; Sugiyama, Naruji; Togari, Hajime

    2007-12-01

    Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is rare among Asian individuals, and the clinical course and biochemical findings remain unclear. We report herein a 3-year-old Japanese girl with MCADD. The diagnosis was suggested by acylcarnitine profiles and confirmed by enzyme activity and genetic analysis after clinical presentation. Our described method with high-performance liquid chromatography/tandem mass spectrometry allows quantification of levels of n-octanoylcarnitine (C8-N) and other isomers (e.g. valproylcarnitine). We examined the patient's acylcarnitine profiles in serum and urine samples during carnitine loading and 14-hr fasting tests with/without carnitine supplementation. Under hypocarnitinemia, serum level of C8-N was 0.16 micromol/l and C8-N/decanoylcarnitine (C10) ratio was 1.8, which did not correspond to the diagnostic criteria for MCADD. However, intravenous carnitine loading test (100 mg/kg/day for 3 days and 50 mg/kg/day for 1 day) led to increased serum C8-N levels and urinary excretion was obvious, strongly suggesting MCADD. In the fasting test with carnitine supplementation, marked production of acylcarnitines (C8-N > C2 > C6 > C10) was found, compared to the fasting test without carnitine supplementation. These results indicate that carnitine supplementation may be useful for detoxification of accumulated acylcarnitines even in an asymptomatic state. Moreover, the one-point examination for serum C8-N level and/or C8-N/C10 ratio may make the diagnosis of MCADD difficult, particularly in the presence of significant hypocarnitinemia. To avoid this pitfall, attention should be given to serum levels of free carnitine, and carnitine loading may be demanded in hypocarnitinemia.

  3. Prolonged QT interval and lipid alterations beyond β-oxidation in very long-chain acyl-CoA dehydrogenase null mouse hearts

    PubMed Central

    Gélinas, Roselle; Thompson-Legault, Julie; Bouchard, Bertrand; Daneault, Caroline; Mansour, Asmaa; Gillis, Marc-Antoine; Charron, Guy; Gavino, Victor; Labarthe, François

    2011-01-01

    Patients with very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency frequently present cardiomyopathy and heartbeat disorders. However, the underlying factors, which may be of cardiac or extra cardiac origins, remain to be elucidated. In this study, we tested for metabolic and functional alterations in the heart from 3- and 7-mo-old VLCAD null mice and their littermate counterparts, using validated experimental paradigms, namely, 1) ex vivo perfusion in working mode, with concomitant evaluation of myocardial contractility and metabolic fluxes using 13C-labeled substrates under various conditions; as well as 2) in vivo targeted lipidomics, gene expression analysis as well as electrocardiogram monitoring by telemetry in mice fed various diets. Unexpectedly, when perfused ex vivo, working VLCAD null mouse hearts maintained values similar to those of the controls for functional parameters and for the contribution of exogenous palmitate to β-oxidation (energy production), even at high palmitate concentration (1 mM) and increased energy demand (with 1 μM epinephrine) or after fasting. However, in vivo, these hearts displayed a prolonged rate-corrected QT (QTc) interval under all conditions examined, as well as the following lipid alterations: 1) age- and condition-dependent accumulation of triglycerides, and 2) 20% lower docosahexaenoic acid (an omega-3 polyunsaturated fatty acid) in membrane phospholipids. The latter was independent of liver but affected by feeding a diet enriched in saturated fat (exacerbated) or fish oil (attenuated). Our finding of a longer QTc interval in VLCAD null mice appears to be most relevant given that such condition increases the risk of sudden cardiac death. PMID:21685264

  4. Probing the role of the ceramide acyl chain length and sphingosine unsaturation in model skin barrier lipid mixtures by (2)H solid-state NMR spectroscopy.

    PubMed

    Stahlberg, Sören; Školová, Barbora; Madhu, Perunthiruthy K; Vogel, Alexander; Vávrová, Kateřina; Huster, Daniel

    2015-05-05

    We investigated equimolar mixtures of ceramides with lignoceric acid and cholesterol as models for the human stratum corneum by differential scanning calorimetry and (2)H solid-state NMR spectroscopy. Our reference system consisted of lignoceroyl sphingosine (Cer[NS24]), which represents one of the ceramides in the human stratum corneum. Furthermore, the effect of ceramide acyl chain truncation to 16 carbons as in Cer[NS16] and the loss of the C4 trans double bond as in dihydroceramide Cer[NDS24] were studied. Fully relaxed (2)H NMR spectra were acquired for each deuterated component of each mixture separately, allowing the quantitative determination of the individual lipid phases. At skin temperature, the reference system containing Cer[NS24] is characterized by large portions of each component of the mixture in a crystalline phase, which largely restricts the permeability of the skin lipid barrier. The loss of the C4 trans double bond in Cer[NDS24] leads to the replacement of more than 25% of the crystalline phase by an isotropic phase of the dihydroceramide that shows the importance of dihydroceramide desaturation in the formation of the skin lipid barrier. The truncated Cer[NS16] is mostly found in the gel phase at skin temperature, which may explain its negative effect on the transepidermal water loss in atopic dermatitis patients. These significant alterations in the phase behavior of all lipids are further reflected at elevated temperatures. The molecular insights of our study may help us to understand the importance of the structural parameters of ceramides in healthy and compromised skin barriers.

  5. Dynamics of Polymer Chains Confined in Slit-Like Pores

    NASA Astrophysics Data System (ADS)

    Milchev, Andrey; Binder, Kurt

    1996-01-01

    Monte Carlo simulations of an off-lattice bead sping model of polymer chains are presented, confining the chains between two repulsive parallel planes a distance D apart. Varying the chain length N from N=16 to N=128, we show that under good solvent conditions the chains behave like two-dimensional self-avoiding walks, their mean square gyration radius scales as <~ngle R_g^2ranglepropto N^{2ν} with ν =3/4. The density profile across the slit is independent of N and maximal in the center of the slit. The dynamical properties of the chains are found to be in full agreement with the Rouse model with excluded volume in d=2 dimensions, the relaxation times vary like taupropto N^z with z=2ν+1=5/2, the diffusion constant still being given by D_Npropto 1/N. The dynamical behavior of various mean square displacements is analyzed in detail.

  6. Nanoparticle effect on polymer chain dynamics and entanglement network

    NASA Astrophysics Data System (ADS)

    Li, Ying; Kroger, Martin

    We investigated structure and dynamics of polymer nanocomposites through molecular modeling, by considering different molecular weights of polymers chains, and volume fractions of fillers. The dynamics of unentangled chains can be separated into two phases, a bulk polymer phase and a confined polymer phase between fillers. The dynamics of a confined polymer is slower than that of a bulk polymer, while still exhibiting high mobility. The amount of the bulk polymer phase is found to exponentially decay with increasing volume fraction of fillers. When highly entangled polymer chains are confined between fillers, their conformation and entanglement network are dramatically changed, in district with their unentangled counterparts. The entangled polymer chains are found to be significantly disentangled and flattened during increment of the volume fractions of spherical nonattractive fillers. A critical volume fraction is found to control the crossover from polymer chain entanglements to `nanoparticle entanglements', below which the polymer chain relaxation accelerates upon filling. These results provide a microscopic understanding of the dynamics of entangled polymer chains inside their composites, and offer an explanation for the unusual rheological properties of polymer composites. Supported by Department of Mechanical Engineering, University of Connecticut.

  7. Characterization of recombinant long-chain rat acyl-CoA synthetase isoforms 3 and 6: identification of a novel variant of isoform 6.

    PubMed

    Van Horn, Cynthia G; Caviglia, Jorge M; Li, Lei O; Wang, Shuli; Granger, Deborah A; Coleman, Rosalind A

    2005-02-08

    The metabolism of long-chain fatty acids in brain and their incorporation into signaling molecules such as diacylglycerol and LPA and into structural components of membranes, including myelin, requires activation by long-chain acyl-CoA synthetase (ACSL). Because ACSL3 and ACSL6 are the predominant ACSL isoforms in brain, we cloned and characterized these isoforms from rat brain and identified a novel ACSL6 clone (ACSL6_v2). ACSL6_v2 and the previously reported ACSL6_v1 represent splice variants that include exon 13 or 14, respectively. Homologue sequences of both of these variants are present in the human and mouse databases. ACSL3, ACSL6_v1, and ACSL6_v2 with Flag-epitopes at the C-termini were expressed in Escherichia coli and purified on Flag-affinity columns. The three recombinant proteins were characterized. Compared to ACSL4, another brain isoform, ACSL3, ACSL6_v1, and ACSL6_v2 showed similarities in kinetic values for CoA, palmitate, and arachidonate, but their apparent Km values for oleate were 4- to 6-fold lower than for ACSL4. In a direct competition assay with palmitate, all the polyunsaturated fatty acids tested were strong competitors only for ACSL4 with IC50 values of 0.5 to 5 microM. DHA was also strongly preferred by ACSL6_v2. The apparent Km value for ATP of ACSL6_v1 was 8-fold higher than that of ACSL6_v2. ACSL3 and the two variants of ACSL6 were more resistant than ACSL4 to heat inactivation. Despite the high amino acid identity between ACSL3 and ACSL4, rosiglitazone inhibited only ACSL4. Triacsin C, an inhibitor of ACSL1 and ACSL4, also inhibited ACSL3, but did not inhibit the ACSL6 variants. These data further document important differences in the closely related ACSL isoforms and show that amino acid changes near the consensus nucleotide binding site alter function in the two splice variants of ACSL6.

  8. Microscopic Chain Motion in Polymer Nanocomposites with Dynamically Asymmetric Interphases

    PubMed Central

    Senses, Erkan; Faraone, Antonio; Akcora, Pinar

    2016-01-01

    Dynamics of the interphase region between matrix and bound polymers on nanoparticles is important to understand the macroscopic rheological properties of nanocomposites. Here, we present neutron scattering investigations on nanocomposites with dynamically asymmetric interphases formed by a high-glass transition temperature polymer, poly(methyl methacrylate), adsorbed on nanoparticles and a low-glass transition temperature miscible matrix, poly(ethylene oxide). By taking advantage of selective isotope labeling of the chains, we studied the role of interfacial polymer on segmental and collective dynamics of the matrix chains from subnanoseconds to 100 nanoseconds. Our results show that the Rouse relaxation remains unchanged in a weakly attractive composite system while the dynamics significantly slows down in a strongly attractive composite. More importantly, the chains disentangle with a remarkable increase of the reptation tube size when the bound polymer is vitreous. The glassy and rubbery states of the bound polymer as temperature changes underpin the macroscopic stiffening of nanocomposites. PMID:27457056

  9. Microscopic Chain Motion in Polymer Nanocomposites with Dynamically Asymmetric Interphases

    NASA Astrophysics Data System (ADS)

    Senses, Erkan; Faraone, Antonio; Akcora, Pinar

    2016-07-01

    Dynamics of the interphase region between matrix and bound polymers on nanoparticles is important to understand the macroscopic rheological properties of nanocomposites. Here, we present neutron scattering investigations on nanocomposites with dynamically asymmetric interphases formed by a high-glass transition temperature polymer, poly(methyl methacrylate), adsorbed on nanoparticles and a low-glass transition temperature miscible matrix, poly(ethylene oxide). By taking advantage of selective isotope labeling of the chains, we studied the role of interfacial polymer on segmental and collective dynamics of the matrix chains from subnanoseconds to 100 nanoseconds. Our results show that the Rouse relaxation remains unchanged in a weakly attractive composite system while the dynamics significantly slows down in a strongly attractive composite. More importantly, the chains disentangle with a remarkable increase of the reptation tube size when the bound polymer is vitreous. The glassy and rubbery states of the bound polymer as temperature changes underpin the macroscopic stiffening of nanocomposites.

  10. Confinement dynamics of a semiflexible chain inside nano-spheres.

    PubMed

    Fathizadeh, A; Heidari, Maziar; Eslami-Mossallam, B; Ejtehadi, M R

    2013-07-28

    We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.

  11. The Physiology of Protein S-acylation

    PubMed Central

    Chamberlain, Luke H.; Shipston, Michael J.

    2015-01-01

    Protein S-acylation, the only fully reversible posttranslational lipid modification of proteins, is emerging as a ubiquitous mechanism to control the properties and function of a diverse array of proteins and consequently physiological processes. S-acylation results from the enzymatic addition of long-chain lipids, most typically palmitate, onto intracellular cysteine residues of soluble and transmembrane proteins via a labile thioester linkage. Addition of lipid results in increases in protein hydrophobicity that can impact on protein structure, assembly, maturation, trafficking, and function. The recent explosion in global S-acylation (palmitoyl) proteomic profiling as a result of improved biochemical tools to assay S-acylation, in conjunction with the recent identification of enzymes that control protein S-acylation and de-acylation, has opened a new vista into the physiological function of S-acylation. This review introduces key features of S-acylation and tools to interrogate this process, and highlights the eclectic array of proteins regulated including membrane receptors, ion channels and transporters, enzymes and kinases, signaling adapters and chaperones, cell adhesion, and structural proteins. We highlight recent findings correlating disruption of S-acylation to pathophysiology and disease and discuss some of the major challenges and opportunities in this rapidly expanding field. PMID:25834228

  12. Unveiling the Pathogenic Molecular Mechanisms of the Most Common Variant (p.K329E) in Medium-Chain Acyl-CoA Dehydrogenase Deficiency by in Vitro and in Silico Approaches.

    PubMed

    Bonito, Cátia A; Nunes, Joana; Leandro, João; Louro, Filipa; Leandro, Paula; Ventura, Fátima V; Guedes, Rita C

    2016-12-27

    Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the most common genetic disorder affecting the mitochondrial fatty acid β-oxidation pathway. The mature and functional form of human MCAD (hMCAD) is a homotetramer assembled as a dimer of dimers (monomers A/B and C/D). Each monomer binds a FAD cofactor, necessary for the enzyme's activity. The most frequent mutation in MCADD results from the substitution of a lysine with a glutamate in position 304 of mature hMCAD (p.K329E in the precursor protein). Here, we combined in vitro and in silico approaches to assess the impact of the p.K329E mutation on the protein's structure and function. Our in silico results demonstrated for the first time that the p.K329E mutation, despite lying at the dimer-dimer interface and being deeply buried inside the tetrameric core, seems to affect the tetramer surface, especially the β-domain that forms part of the catalytic pocket wall. Additionally, the molecular dynamics data indicate a stronger impact of the mutation on the protein's motions in dimer A/B, while dimer C/D remains similar to the wild type. For dimer A/B, severe disruptions in the architecture of the pockets and in the FAD and octanoyl-CoA binding affinities were also observed. The presence of unaffected pockets (C/D) in the in silico studies may explain the decreased enzymatic activity determined for the variant protein (46% residual activity). Moreover, the in silico structural changes observed for the p.K329E variant protein provide an explanation for the structural instability observed experimentally, namely, the disturbed oligomeric profile, thermal stability, and conformational flexibility, with respect to the wild-type.

  13. Stochastic Dynamics through Hierarchically Embedded Markov Chains

    NASA Astrophysics Data System (ADS)

    Vasconcelos, Vítor V.; Santos, Fernando P.; Santos, Francisco C.; Pacheco, Jorge M.

    2017-02-01

    Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects—such as mutations in evolutionary dynamics and a random exploration of choices in social systems—including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

  14. Stochastic Dynamics through Hierarchically Embedded Markov Chains.

    PubMed

    Vasconcelos, Vítor V; Santos, Fernando P; Santos, Francisco C; Pacheco, Jorge M

    2017-02-03

    Studying dynamical phenomena in finite populations often involves Markov processes of significant mathematical and/or computational complexity, which rapidly becomes prohibitive with increasing population size or an increasing number of individual configuration states. Here, we develop a framework that allows us to define a hierarchy of approximations to the stationary distribution of general systems that can be described as discrete Markov processes with time invariant transition probabilities and (possibly) a large number of states. This results in an efficient method for studying social and biological communities in the presence of stochastic effects-such as mutations in evolutionary dynamics and a random exploration of choices in social systems-including situations where the dynamics encompasses the existence of stable polymorphic configurations, thus overcoming the limitations of existing methods. The present formalism is shown to be general in scope, widely applicable, and of relevance to a variety of interdisciplinary problems.

  15. Acyl hydrolases from trans-AT polyketide synthases target acetyl units on acyl carrier proteins.

    PubMed

    Jenner, Matthew; Afonso, Jose P; Kohlhaas, Christoph; Karbaum, Petra; Frank, Sarah; Piel, Jörn; Oldham, Neil J

    2016-04-18

    Acyl hydrolase (AH) domains are a common feature of trans-AT PKSs. They have been hypothesised to perform a proofreading function by removing acyl chains from stalled sites. This study determines the substrate tolerance of the AH PedC for a range of acyl-ACPs. Clear preference towards short, linear acyl-ACPs is shown, with acetyl-ACP the best substrate. These results imply a more targeted housekeeping role for PedC: namely the removal of unwanted acetyl groups from ACP domains caused by erroneous transfer of acetyl-CoA, or possibly by decarboxylation of malonyl-ACP.

  16. Molecular Dynamics Approach to Relaxation and Aggregationof Polymer Chains

    NASA Astrophysics Data System (ADS)

    Hu, C.; Ma, W.

    We have used molecular dynamics to simulate various systems ofpolymer chains and Lennard-Jones molecules; the neighboring monomers along a polymer chain are connected by rigid bonds or spring of strength k_{spring}. We find that the velocity distributions of monomers in a wide range of simulation time can be well described by Tsallis q-statistics [C. Tsallis, J. Stat. Phys. 52 (1988), 479] (q ≥ 1) and a single scaling function; the value of q is related to the conformation constraining potential, the interactions with background fluid, the destruction of chain homogeneity or the value of k_{spring}; when q -> 1, the velocity distribution of monomers becomes Maxwell-Boltzmann distribution. We also find that the polymer chains tend to aggregate as neighboring monomers of a polymer chain have small or zero bending-angle and torsion-angle dependent potentials. The implication of our results for the aggregation of proteins is discussed.

  17. The Penicillium chrysogenum aclA gene encodes a broad-substrate-specificity acyl-coenzyme A ligase involved in activation of adipic acid, a side-chain precursor for cephem antibiotics.

    PubMed

    Koetsier, Martijn J; Gombert, Andreas K; Fekken, Susan; Bovenberg, Roel A L; van den Berg, Marco A; Kiel, Jan A K W; Jekel, Peter A; Janssen, Dick B; Pronk, Jack T; van der Klei, Ida J; Daran, Jean-Marc

    2010-01-01

    Activation of the cephalosporin side-chain precursor to the corresponding CoA-thioester is an essential step for its incorporation into the beta-lactam backbone. To identify an acyl-CoA ligase involved in activation of adipate, we searched in the genome database of Penicillium chrysogenum for putative structural genes encoding acyl-CoA ligases. Chemostat-based transcriptome analysis was used to identify the one presenting the highest expression level when cells were grown in the presence of adipate. Deletion of the gene renamed aclA, led to a 32% decreased specific rate of adipate consumption and a threefold reduction of adipoyl-6-aminopenicillanic acid levels, but did not affect penicillin V production. After overexpression in Escherichia coli, the purified protein was shown to have a broad substrate range including adipate. Finally, protein-fusion with cyan-fluorescent protein showed co-localization with microbody-borne acyl-transferase. Identification and functional characterization of aclA may aid in developing future metabolic engineering strategies for improving the production of different cephalosporins.

  18. Systematic Analysis of Gene Expression Alterations and Clinical Outcomes for Long-Chain Acyl-Coenzyme A Synthetase Family in Cancer

    PubMed Central

    Chen, Wei-Ching; Wang, Chih-Yang; Hung, Yu-Hsuan; Weng, Tzu-Yang; Yen, Meng-Chi; Lai, Ming-Derg

    2016-01-01

    Dysregulated lipid metabolism contributes to cancer progression. Our previous study indicates that long-chain fatty acyl-Co A synthetase (ACSL) 3 is essential for lipid upregulation induced by endoplasmic reticulum stress. In this report, we aimed to identify the role of ACSL family in cancer with systematic analysis and in vitro experiment. We explored the ACSL expression using Oncomine database to determine the gene alteration during carcinogenesis and identified the association between ACSL expression and the survival of cancer patient using PrognoScan database. ACSL1 may play a potential oncogenic role in colorectal and breast cancer and play a potential tumor suppressor role in lung cancer. Co-expression analysis revealed that ACSL1 was coexpressed with MYBPH, PTPRE, PFKFB3, SOCS3 in colon cancer and with LRRFIP1, TSC22D1 in lung cancer. In accordance with PrognoScan analysis, downregulation of ACSL1 in colon and breast cancer cell line inhibited proliferation, migration, and anchorage-independent growth. In contrast, increase of oncogenic property was observed in lung cancer cell line by attenuating ACSL1. High ACSL3 expression predicted a better prognosis in ovarian cancer; in contrast, high ACSL3 predicted a worse prognosis in melanoma. ACSL3 was coexpressed with SNUPN, TRIP13, and SEMA5A in melanoma. High expression of ACSL4 predicted a worse prognosis in colorectal cancer, but predicted better prognosis in breast, brain and lung cancer. ACSL4 was coexpressed with SERPIN2, HNRNPCL1, ITIH2, PROCR, LRRFIP1. High expression of ACSL5 predicted good prognosis in breast, ovarian, and lung cancers. ACSL5 was coexpressed with TMEM140, TAPBPL, BIRC3, PTPRE, and SERPINB1. Low ACSL6 predicted a worse prognosis in acute myeloid leukemia. ACSL6 was coexpressed with SOX6 and DARC. Altogether, different members of ACSLs are implicated in diverse types of cancer development. ACSL-coexpressed molecules may be used to further investigate the role of ACSL family in

  19. Systematic Analysis of Gene Expression Alterations and Clinical Outcomes for Long-Chain Acyl-Coenzyme A Synthetase Family in Cancer.

    PubMed

    Chen, Wei-Ching; Wang, Chih-Yang; Hung, Yu-Hsuan; Weng, Tzu-Yang; Yen, Meng-Chi; Lai, Ming-Derg

    2016-01-01

    Dysregulated lipid metabolism contributes to cancer progression. Our previous study indicates that long-chain fatty acyl-Co A synthetase (ACSL) 3 is essential for lipid upregulation induced by endoplasmic reticulum stress. In this report, we aimed to identify the role of ACSL family in cancer with systematic analysis and in vitro experiment. We explored the ACSL expression using Oncomine database to determine the gene alteration during carcinogenesis and identified the association between ACSL expression and the survival of cancer patient using PrognoScan database. ACSL1 may play a potential oncogenic role in colorectal and breast cancer and play a potential tumor suppressor role in lung cancer. Co-expression analysis revealed that ACSL1 was coexpressed with MYBPH, PTPRE, PFKFB3, SOCS3 in colon cancer and with LRRFIP1, TSC22D1 in lung cancer. In accordance with PrognoScan analysis, downregulation of ACSL1 in colon and breast cancer cell line inhibited proliferation, migration, and anchorage-independent growth. In contrast, increase of oncogenic property was observed in lung cancer cell line by attenuating ACSL1. High ACSL3 expression predicted a better prognosis in ovarian cancer; in contrast, high ACSL3 predicted a worse prognosis in melanoma. ACSL3 was coexpressed with SNUPN, TRIP13, and SEMA5A in melanoma. High expression of ACSL4 predicted a worse prognosis in colorectal cancer, but predicted better prognosis in breast, brain and lung cancer. ACSL4 was coexpressed with SERPIN2, HNRNPCL1, ITIH2, PROCR, LRRFIP1. High expression of ACSL5 predicted good prognosis in breast, ovarian, and lung cancers. ACSL5 was coexpressed with TMEM140, TAPBPL, BIRC3, PTPRE, and SERPINB1. Low ACSL6 predicted a worse prognosis in acute myeloid leukemia. ACSL6 was coexpressed with SOX6 and DARC. Altogether, different members of ACSLs are implicated in diverse types of cancer development. ACSL-coexpressed molecules may be used to further investigate the role of ACSL family in

  20. The tissue-specific expression and developmental regulation of two nuclear genes encoding rat mitochondrial proteins. Medium chain acyl-CoA dehydrogenase and mitochondrial malate dehydrogenase.

    PubMed

    Kelly, D P; Gordon, J I; Alpers, R; Strauss, A W

    1989-11-15

    To study the regulation of nuclear genes which encode mitochondrial enzymes involved in oxidative metabolism, absolute levels of mRNA encoding rat medium chain acyl-CoA dehydrogenase (MCAD) and rat mitochondrial malate dehydrogenase (mMDH) were determined in developing and adult male rat tissues. MCAD mRNA is expressed in a variety of adult male tissues with highest steady state levels in heart, adrenal, and skeletal muscle and lowest levels in brain, lung, and testes. In comparison, steady state levels of mMDH mRNA in adult male rat tissues were similar to those of MCAD mRNA in heart, small intestine, adrenal, and skeletal muscle but markedly different in brain, stomach, and testes. Thus, the steady-state levels of MCAD and mMDH mRNA are highest in adult tissues with high energy requirements. Dot blot analysis of RNA prepared from late fetal, suckling, and weaning rat heart, liver, and brain demonstrated the presence of MCAD and mMDH mRNA during the fetal period in all three tissues. Both MCAD and mMDH mRNA levels increased 2-2.5-fold at birth followed by a decline during the first postnatal week in heart and liver. The patterns of accumulation of these mRNAs in heart and liver during the weaning and early adult periods were also similar, although the absolute levels were significantly different. Brain MCAD mRNA levels were consistently low (less than 0.1 pg/micrograms total cellular RNA) throughout the developmental stages. However, brain mMDH mRNA levels exhibited a marked increase during the weaning period, reaching a peak concentration which is higher than the level of mMDH mRNA in heart and liver at any point during development. These results indicate that the level of expression of the nuclear genes encoding MCAD and mMDH is tissue-specific and developmentally regulated. The patterns of MCAD and mMDH mRNA accumulation parallel the changes in energy metabolism which occur during development and among adult tissues.

  1. Electrospray Ionization Tandem Mass Spectrometry (Esi-Ms/Ms) Analysis of the Lipid Molecular Species Composition of Yeast Subcellular Membranes Reveals Acyl Chain-Based Sorting/Remodeling of Distinct Molecular Species En Route to the Plasma Membrane

    PubMed Central

    Schneiter, Roger; Brügger, Britta; Sandhoff, Roger; Zellnig, Günther; Leber, Andrea; Lampl, Manfred; Athenstaedt, Karin; Hrastnik, Claudia; Eder, Sandra; Daum, Günther; Paltauf, Fritz; Wieland, Felix T.; Kohlwein, Sepp D.

    1999-01-01

    Nano-electrospray ionization tandem mass spectrometry (nano-ESI-MS/MS) was employed to determine qualitative differences in the lipid molecular species composition of a comprehensive set of organellar membranes, isolated from a single culture of Saccharomyces cerevisiae cells. Remarkable differences in the acyl chain composition of biosynthetically related phospholipid classes were observed. Acyl chain saturation was lowest in phosphatidylcholine (15.4%) and phosphatidylethanolamine (PE; 16.2%), followed by phosphatidylserine (PS; 29.4%), and highest in phosphatidylinositol (53.1%). The lipid molecular species profiles of the various membranes were generally similar, with a deviation from a calculated average profile of ∼± 20%. Nevertheless, clear distinctions between the molecular species profiles of different membranes were observed, suggesting that lipid sorting mechanisms are operating at the level of individual molecular species to maintain the specific lipid composition of a given membrane. Most notably, the plasma membrane is enriched in saturated species of PS and PE. The nature of the sorting mechanism that determines the lipid composition of the plasma membrane was investigated further. The accumulation of monounsaturated species of PS at the expense of diunsaturated species in the plasma membrane of wild-type cells was reversed in elo3Δ mutant cells, which synthesize C24 fatty acid-substituted sphingolipids instead of the normal C26 fatty acid-substituted species. This observation suggests that acyl chain-based sorting and/or remodeling mechanisms are operating to maintain the specific lipid molecular species composition of the yeast plasma membrane. PMID:10459010

  2. The mitochondrial precursor protein apocytochrome c strongly influences the order of the headgroup and acyl chains of phosphatidylserine dispersions. A sup 2 H and sup 31 P NMR study

    SciTech Connect

    Jordi, W.; de Kroon, A.I.P.M.; Killian, A.; de Kruijff, B. )

    1990-03-06

    Deuterium and phosphorus nuclear magnetic resonance techniques were used to study the interaction of the mitochondrial precursor protein apocytochrome c with headgroup-deuterated (dioleoylphosphatidyl-L-(2-{sup 2}H{sub 1})serine) and acyl chain deuterated (1,2-(11,11-{sup 2}H{sub 2})dioleoylphosphatidylserine) dispersions. Binding of the protein to dioleoylphosphatidylserine liposomes results in phosphorus nuclear magnetic resonance spectra typical of phospholipids undergoing fast axial rotation in extended liquid-crystalline bilayers with a reduced residual chemical shift anisotropy and an increased line width. {sup 2}H NMR spectra on headgroup-deuterated dioleoylphosphatidylserine dispersions showed a decrease in quadrupolar splitting and a broadening of the signal on interaction with apocytochrome c. Addition of increasing amounts of apocytochrome c to the acyl chain deuterated dioleoylphosphatidylserine dispersions results in the gradual appearance of a second component in the spectra with a 44% reduced quadrupolar splitting. Such large reduction of the quadrupolar splitting has never been observed for any protein studied yet. The induction of a new spectral component with a well-defined reduced quadrupolar splitting seems to be confined to the N-terminus since addition of a small hydrophilic amino-terminal peptide (residues 1-38) also induces a second component with a strongly reduced quadrupolar splitting. A chemically synthesized peptide corresponding to amino acid residues 2-17 of the presequence of the mitochondrial protein cytochrome oxidase subunit IV also has a large perturbing effect on the order of the acyl chains, indicating that the observed effects may be a property shared by many mitochondrial precursor proteins. Implications of these data for the import of apocytochrome c into mitochondria will be discussed.

  3. Markov Chain Monte Carlo from Lagrangian Dynamics

    PubMed Central

    Lan, Shiwei; Stathopoulos, Vasileios; Shahbaba, Babak; Girolami, Mark

    2014-01-01

    Hamiltonian Monte Carlo (HMC) improves the computational e ciency of the Metropolis-Hastings algorithm by reducing its random walk behavior. Riemannian HMC (RHMC) further improves the performance of HMC by exploiting the geometric properties of the parameter space. However, the geometric integrator used for RHMC involves implicit equations that require fixed-point iterations. In some cases, the computational overhead for solving implicit equations undermines RHMC's benefits. In an attempt to circumvent this problem, we propose an explicit integrator that replaces the momentum variable in RHMC by velocity. We show that the resulting transformation is equivalent to transforming Riemannian Hamiltonian dynamics to Lagrangian dynamics. Experimental results suggests that our method improves RHMC's overall computational e ciency in the cases considered. All computer programs and data sets are available online (http://www.ics.uci.edu/~babaks/Site/Codes.html) in order to allow replication of the results reported in this paper. PMID:26240515

  4. Relaxation dynamics of internal segments of DNA chains in nanochannels

    NASA Astrophysics Data System (ADS)

    Jain, Aashish; Muralidhar, Abhiram; Dorfman, Kevin; Dorfman Group Team

    We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called ``DNA barcode'') are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size.

  5. Dynamics of two topologically entangled chains

    SciTech Connect

    Ferrari, F.; Paturej, J.; Piatek, M.; Vilgis, T. A.

    2011-04-15

    Starting from a given topological invariant, we argue that it is possible to construct a topological field theory with a finite number of Feynman diagrams and an amplitude of gauge invariant objects that is a function of that invariant. This is, for example, the case of the Gauss linking number and of the abelian BF models which have been already successfully applied in the statistical mechanics of polymers. In this work it is shown that a suitable generalization of the BF model can be applied also to polymer dynamics, where the polymer trajectories are not static, but change their shape during time.

  6. Ghrelin acylation and metabolic control.

    PubMed

    Al Massadi, O; Tschöp, M H; Tong, J

    2011-11-01

    Since its discovery, many physiologic functions have been ascribed to ghrelin, a gut derived hormone. The presence of a median fatty acid side chain on the ghrelin peptide is required for the binding and activation of the classical ghrelin receptor, the growth hormone secretagogue receptor (GHSR)-1a. Ghrelin O-acyl transferase (GOAT) was recently discovered as the enzyme responsible for this acylation process. GOAT is expressed in all tissues that have been found to express ghrelin and has demonstrated actions on several complex endocrine organ systems such as the hypothalamus-pituitary-gonadal, insular and adrenal axis as well as the gastrointestinal (GI) tract, bone and gustatory system. Ghrelin acylation is dependent on the function of GOAT and the availability of substrates such as proghrelin and short- to medium-chain fatty acids (MCFAs). This process is governed by GOAT activity and has been shown to be modified by dietary lipids. In this review, we provided evidence that support an important role of GOAT in the regulation of energy homeostasis and glucose metabolism by modulating acyl ghrelin (AG) production. The relevance of GOAT and AG during periods of starvation remains to be defined. In addition, we summarized the recent literature on the metabolic effects of GOAT specific inhibitors and shared our view on the potential of targeting GOAT for the treatment of metabolic disorders such as obesity and type 2 diabetes.

  7. Constraints on food chain length arising from regional metacommunity dynamics.

    PubMed

    Calcagno, Vincent; Massol, François; Mouquet, Nicolas; Jarne, Philippe; David, Patrice

    2011-10-22

    Classical ecological theory has proposed several determinants of food chain length, but the role of metacommunity dynamics has not yet been fully considered. By modelling patchy predator-prey metacommunities with extinction-colonization dynamics, we identify two distinct constraints on food chain length. First, finite colonization rates limit predator occupancy to a subset of prey-occupied sites. Second, intrinsic extinction rates accumulate along trophic chains. We show how both processes concur to decrease maximal and average food chain length in metacommunities. This decrease is mitigated if predators track their prey during colonization (habitat selection) and can be reinforced by top-down control of prey vital rates (especially extinction). Moreover, top-down control of colonization and habitat selection can interact to produce a counterintuitive positive relationship between perturbation rate and food chain length. Our results show how novel limits to food chain length emerge in spatially structured communities. We discuss the connections between these constraints and the ones commonly discussed, and suggest ways to test for metacommunity effects in food webs.

  8. Confinement and viscoelastic effects on chain closure dynamics

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Pinaki; Sharma, Rati; Cherayil, Binny J.

    2012-06-01

    Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time tc of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, tc ˜ Nd2, and that in case (b), tc ˜ N2/(2 - 2H), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), tc ˜ N3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium.

  9. Quantum dynamics of a semi-infinite homogeneous harmonic chain

    NASA Astrophysics Data System (ADS)

    Prato, Domingo; Lamberti, Pedro W.

    1993-07-01

    The quantum dynamics of a semi-infinite homogeneous harmonic chain is studied. Assuming the system to be in its ground state, a harmonic motion, A sin(ω t), is imposed on the mass at the beginning of the chain. The quantum state of the system for t>0 is calculated by means of the evolution operator. Two different regimes occur: one for angular frequencies ω outside the allowed band ω>ω 0 and the other one for ω inside the band. After a transient the time derivative of the total energy of the chain vanishes for the first regime and tends to a constant for the second one. The mean values of the displacements from their equilibrium position are also calculated for masses along the chain. These averaged displacements and the time derivative of the total energy are shown to give exactly the same expression as in the classical case.

  10. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxgenase with a bacterial type-I fatty acid synthase in E. coli

    DOE PAGES

    Coursolle, Dan; Shanklin, John; Lian, Jiazhang; ...

    2015-06-23

    Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products inmore » BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg/L long chain alcohol/alkane products including a 57 mg/L titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.« less

  11. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxygenase with a bacterial type-I fatty acid synthase in E. coli.

    PubMed

    Coursolle, Dan; Lian, Jiazhang; Shanklin, John; Zhao, Huimin

    2015-09-01

    Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products in BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg L(-1) long chain alcohol/alkane products including a 57 mg L(-1) titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.

  12. Production of long chain alcohols and alkanes upon coexpression of an acyl-ACP reductase and aldehyde-deformylating oxgenase with a bacterial type-I fatty acid synthase in E. coli

    SciTech Connect

    Coursolle, Dan; Shanklin, John; Lian, Jiazhang; Zhao, Huimin

    2015-06-23

    Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with the highest activity in this strain. Next, we used catalase coexpression to remove toxic byproducts and increase the overall titer. Finally, by introducing the type-I fatty acid synthase from Corynebacterium ammoniagenes, we were able to bypass host regulatory mechanisms of fatty acid synthesis that have thus far hampered efforts to optimize the yield of acyl-ACP-derived products in BL21(DE3). When all these engineering strategies were combined with subsequent optimization of fermentation conditions, we were able to achieve a final titer around 100 mg/L long chain alcohol/alkane products including a 57 mg/L titer of pentadecane, the highest titer reported in E. coli BL21(DE3) to date. The expression of prokaryotic type-I fatty acid synthases offer a unique strategy to produce fatty acid-derived products in E. coli that does not rely exclusively on the endogenous type-II fatty acid synthase system.

  13. Dynamics of the Kitaev chain model under parametric pumping

    NASA Astrophysics Data System (ADS)

    Zvyagin, A. A.

    2014-07-01

    Dynamics of the Kitaev chain model under the effect of parametric pumping is studied. Two contributions to dynamical characteristics are considered: from the extended eigenstates and from the edge bound state (zero Majorana modes). It is shown that in the dynamical regime the frequencies of Rabi oscillations for zero Majorana modes are much larger than those related to gapped extended states. In the steady-state regime, the Rabi oscillations are blurred due to relaxation processes, and only oscillations of the characteristics of the model with the pumping frequency exist, producing absorption of the pumping power by extended states. Experimental realizations of the considered effect are discussed.

  14. Momentum-Based Dynamics for Spacecraft with Chained Revolute Appendages

    NASA Technical Reports Server (NTRS)

    Queen, Steven; London, Ken; Gonzalez, Marcelo

    2005-01-01

    An efficient formulation is presented for a sub-class of multi-body dynamics problems that involve a six degree-of-freedom base body and a chain of N rigid linkages connected in series by single degree-of-freedom revolute joints. This general method is particularly well suited for simulations of spacecraft dynamics and control that include the modeling of an orbiting platform with or without internal degrees of freedom such as reaction wheels, dampers, and/or booms. In the present work, particular emphasis is placed on dynamic simulation of multi-linkage robotic manipulators. The differential equations of motion are explicitly given in terms of linear and angular momentum states, which can be evaluated recursively along a serial chain of linkages for an efficient real-time solution on par with the best of the O(N3) methods.

  15. Influence of credit scoring on the dynamics of Markov chain

    NASA Astrophysics Data System (ADS)

    Galina, Timofeeva

    2015-11-01

    Markov processes are widely used to model the dynamics of a credit portfolio and forecast the portfolio risk and profitability. In the Markov chain model the loan portfolio is divided into several groups with different quality, which determined by presence of indebtedness and its terms. It is proposed that dynamics of portfolio shares is described by a multistage controlled system. The article outlines mathematical formalization of controls which reflect the actions of the bank's management in order to improve the loan portfolio quality. The most important control is the organization of approval procedure of loan applications. The credit scoring is studied as a control affecting to the dynamic system. Different formalizations of "good" and "bad" consumers are proposed in connection with the Markov chain model.

  16. Dynamics of Single Chains of Suspended Ferrofluid Particles

    NASA Technical Reports Server (NTRS)

    Cutillas, S.; Liu, J.

    1999-01-01

    We present an experimental study of the dynamics of isolated chains made of super-paramagnetic particles under the influence of a magnetic field. The motivation of this work is to understand if the chain fluctuations exist and, if it does, how does the fluctuation affect chain aggregation. We find that single chains strongly fluctuate and that the characteristic frequency of their fluctuations is inversely proportional to the magnetic field strength. The higher the field the lower the characteristic frequency of the chain fluctuations. In the high magnetic field limit, chains behave like rigid rods without any internal motions. In this work, we used ferrofluid particles suspended in water. These particles do not have any intrinsic magnetization. Once a magnetic field is applied, a dipole moment is induced in each particle, proportional to the magnetic field. A dipolar magnetic interaction then occurs between particles. If dipole-dipole magnetic energy is higher than the thermal energy, the result is a structure change inside the dipolar fluid. The ratio of these two energies is expressed by a coupling constant lambda as: lambda = (pi(a(exp 3))(chi(exp 2))(mu(sub 0))(H(sub 0))(exp 2))/18kT Where a is the particle radius, mu(sub 0) is the vacuum magnetic permeability, H(sub 0) the applied magnetic field, k the Boltzmann constant and T the absolute temperature. If lambda > 1, magnetic particles form chains along the field direction. The lateral coalescence of several chains may form bigger aggregates especially if the particle volume fraction is high. While many studies and applications deal with the rheological properties and the structural changes of these dipolar fluids, this work focuses on the understanding of the chain dynamics. In order to probe the chain dynamics, we used dynamic light scattering (DLS) in self-beating mode as our experimental technique. The experimental geometry is such that the scattering plane is perpendicular to the magnetic field

  17. Acyl-CoA binding proteins: multiplicity and function.

    PubMed

    Gossett, R E; Frolov, A A; Roths, J B; Behnke, W D; Kier, A B; Schroeder, F

    1996-09-01

    The physiological role of long-chain fatty acyl-CoA is thought to be primarily in intermediary metabolism of fatty acids. However, recent data show that nM to microM levels of these lipophilic molecules are potent regulators of cell functions in vitro. Although long-chain fatty acyl-CoA are present at several hundred microM concentration in the cell, very little long-chain fatty acyl-CoA actually exists as free or unbound molecules, but rather is bound with high affinity to membrane lipids and/or proteins. Recently, there is growing awareness that cytosol contains nonenzymatic proteins also capable of binding long-chain fatty acyl-CoA with high affinity. Although the identity of the cytosolic long-chain fatty acyl-CoA binding protein(s) has been the subject of some controversy, there is growing evidence that several diverse nonenzymatic cytosolic proteins will bind long-chain fatty acyl-CoA. Not only does acyl-CoA binding protein specifically bind medium and long-chain fatty acyl-CoA (LCFA-CoA), but ubiquitous proteins with multiple ligand specificities such as the fatty acid binding proteins and sterol carrier protein-2 also bind LCFA-CoA with high affinity. The potential of these acyl-CoA binding proteins to influence the level of free LCFA-CoA and thereby the amount of LCFA-CoA bound to regulatory sites in proteins and enzymes is only now being examined in detail. The purpose of this article is to explore the identity, nature, function, and pathobiology of these fascinating newly discovered long-chain fatty acyl-CoA binding proteins. The relative contributions of these three different protein families to LCFA-CoA utilization and/or regulation of cellular activities are the focus of new directions in this field.

  18. SREBP2 Activation Induces Hepatic Long-chain Acyl-CoA Synthetase 1 (ACSL1) Expression in Vivo and in Vitro through a Sterol Regulatory Element (SRE) Motif of the ACSL1 C-promoter.

    PubMed

    Singh, Amar Bahadur; Kan, Chin Fung Kelvin; Dong, Bin; Liu, Jingwen

    2016-03-04

    Long-chain acyl-CoA synthetase 1 (ACSL1) plays a key role in fatty acid metabolism. To identify novel transcriptional modulators of ACSL1, we examined ACSL1 expression in liver tissues of hamsters fed a normal diet, a high fat diet, or a high cholesterol and high fat diet (HCHFD). Feeding hamsters HCHFD markedly reduced hepatic Acsl1 mRNA and protein levels as well as acyl-CoA synthetase activity. Decreases in Acsl1 expression strongly correlated with reductions in hepatic Srebp2 mRNA level and mature Srebp2 protein abundance. Conversely, administration of rosuvastatin (RSV) to hamsters increased hepatic Acsl1 expression. These new findings were reproduced in mice treated with RSV or fed the HCHFD. Furthermore, the RSV induction of acyl-CoA activity in mouse liver resulted in increases in plasma and hepatic cholesterol ester concentrations and reductions in free cholesterol amounts. Investigations on different ACSL1 transcript variants in HepG2 cells revealed that the mRNA expression of C-ACSL1 was specifically regulated by the sterol regulatory element (SRE)-binding protein (SREBP) pathway, and RSV treatment increased the C-ACSL1 abundance from a minor mRNA species to an abundant transcript. We analyzed 5'-flanking sequence of exon 1C of the human ACSL1 gene and identified one putative SRE site. By performing a promoter activity assay and DNA binding assays, we firmly demonstrated the key role of this SRE motif in SREBP2-mediated activation of C-ACSL1 gene transcription. Finally, we demonstrated that knockdown of endogenous SREBP2 in HepG2 cells lowered ACSL1 mRNA and protein levels. Altogether, this work discovered an unprecedented link between ACSL1 and SREBP2 via the specific regulation of the C-ACSL1 transcript.

  19. SREBP2 Activation Induces Hepatic Long-chain Acyl-CoA Synthetase 1 (ACSL1) Expression in Vivo and in Vitro through a Sterol Regulatory Element (SRE) Motif of the ACSL1 C-promoter*

    PubMed Central

    Singh, Amar Bahadur; Kan, Chin Fung Kelvin; Dong, Bin; Liu, Jingwen

    2016-01-01

    Long-chain acyl-CoA synthetase 1 (ACSL1) plays a key role in fatty acid metabolism. To identify novel transcriptional modulators of ACSL1, we examined ACSL1 expression in liver tissues of hamsters fed a normal diet, a high fat diet, or a high cholesterol and high fat diet (HCHFD). Feeding hamsters HCHFD markedly reduced hepatic Acsl1 mRNA and protein levels as well as acyl-CoA synthetase activity. Decreases in Acsl1 expression strongly correlated with reductions in hepatic Srebp2 mRNA level and mature Srebp2 protein abundance. Conversely, administration of rosuvastatin (RSV) to hamsters increased hepatic Acsl1 expression. These new findings were reproduced in mice treated with RSV or fed the HCHFD. Furthermore, the RSV induction of acyl-CoA activity in mouse liver resulted in increases in plasma and hepatic cholesterol ester concentrations and reductions in free cholesterol amounts. Investigations on different ACSL1 transcript variants in HepG2 cells revealed that the mRNA expression of C-ACSL1 was specifically regulated by the sterol regulatory element (SRE)-binding protein (SREBP) pathway, and RSV treatment increased the C-ACSL1 abundance from a minor mRNA species to an abundant transcript. We analyzed 5′-flanking sequence of exon 1C of the human ACSL1 gene and identified one putative SRE site. By performing a promoter activity assay and DNA binding assays, we firmly demonstrated the key role of this SRE motif in SREBP2-mediated activation of C-ACSL1 gene transcription. Finally, we demonstrated that knockdown of endogenous SREBP2 in HepG2 cells lowered ACSL1 mRNA and protein levels. Altogether, this work discovered an unprecedented link between ACSL1 and SREBP2 via the specific regulation of the C-ACSL1 transcript. PMID:26728456

  20. Dynamical entanglement purification using chains of atoms and optical cavities

    SciTech Connect

    Gonta, Denis; Loock, Peter van

    2011-10-15

    In the framework of cavity QED, we propose a practical scheme to purify dynamically a bipartite entangled state using short chains of atoms coupled to high-finesse optical cavities. In contrast to conventional entanglement purification protocols, we avoid controlled-not gates, thus reducing complicated pulse sequences and superfluous qubit operations. Our interaction scheme works in a deterministic way and, together with entanglement distribution and swapping, opens a route toward efficient quantum repeaters for long-distance quantum communication.

  1. Metabolic engineering of omega-3 long-chain polyunsaturated fatty acids in plants using an acyl-CoA Delta6-desaturase with omega3-preference from the marine microalga Micromonas pusilla.

    PubMed

    Petrie, James R; Shrestha, Pushkar; Mansour, Maged P; Nichols, Peter D; Liu, Qing; Singh, Surinder P

    2010-05-01

    Long-chain (> or = C20) polyunsaturated fatty acids (LC-PUFA) EPA and DHA (20:5(Delta5,8,11,14,17) and 22:6(Delta4,7,10,13,16,19)) have well-documented health benefits against coronary heart disease, rheumatoid arthritis and other disorders. Currently, the predominant sources of these fatty acids are marine fish and algal oils, but research is being conducted to ensure that a sustainable, land-based production system can be developed. We here describe the metabolic engineering of an artificial pathway that produces 26% EPA in leaf triacylglycerol using a newly-identified Delta6-desaturase from the marine microalga Micromonas pusilla. We also demonstrate that this enzyme appears to function as an acyl-CoA desaturase that has preference for omega3 substrates both in planta and in yeast. Phylogenetic analysis indicates that this desaturase shares highly conserved motifs with previously described acyl-CoA Delta6-desaturases.

  2. Overexpression of human fatty acid transport protein 2/very long chain acyl-CoA synthetase 1 (FATP2/Acsvl1) reveals distinct patterns of trafficking of exogenous fatty acids.

    PubMed

    Melton, Elaina M; Cerny, Ronald L; DiRusso, Concetta C; Black, Paul N

    2013-11-01

    In mammals, the fatty acid transport proteins (FATP1 through FATP6) are members of a highly conserved family of proteins, which function in fatty acid transport proceeding through vectorial acylation and in the activation of very long chain fatty acids, branched chain fatty acids and secondary bile acids. FATP1, 2 and 4, for example directly function in fatty acid transport and very long chain fatty acids activation while FATP5 does not function in fatty acid transport but activates secondary bile acids. In the present work, we have used stable isotopically labeled fatty acids differing in carbon length and saturation in cells expressing FATP2 to gain further insights into how this protein functions in fatty acid transport and intracellular fatty acid trafficking. Our previous studies showed the expression of FATP2 modestly increased C16:0-CoA and C20:4-CoA and significantly increased C18:3-CoA and C22:6-CoA after 4h. The increases in C16:0-CoA and C18:3-CoA suggest FATP2 must necessarily partner with a long chain acyl CoA synthetase (Acsl) to generate C16:0-CoA and C18:3-CoA through vectorial acylation. The very long chain acyl CoA synthetase activity of FATP2 is consistent in the generation of C20:4-CoA and C22:6-CoA coincident with transport from their respective exogenous fatty acids. The trafficking of exogenous fatty acids into phosphatidic acid (PA) and into the major classes of phospholipids (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidyserine (PS)) resulted in distinctive profiles, which changed with the expression of FATP2. The trafficking of exogenous C16:0 and C22:6 into PA was significant where there was 6.9- and 5.3-fold increased incorporation, respectively, over the control; C18:3 and C20:4 also trended to increase in the PA pool while there were no changes for C18:1 and C18:2. The trafficking of C18:3 into PC and PI trended higher and approached significance. In the case of C20:4, expression of

  3. Overexpression of Human Fatty Acid Transport Protein 2/Very Long Chain Acyl-CoA Synthetase 1 (FATP2/Acsvl1) Reveals Distinct Patterns of Trafficking of Exogenous Fatty Acids

    PubMed Central

    Melton, Elaina M.; Cerny, Ronald L.; DiRusso, Concetta C.; Black, Paul N.

    2014-01-01

    In mammals, the fatty acid transport proteins (FATP1 through FATP6) are members of a highly conserved family of proteins, which function in fatty acid transport proceeding through vectorial acylation and in the activation of very long chain fatty acids, branched chain fatty acids and secondary bile acids. FATP1, 2 and 4, for example directly function in fatty acid transport and very long chain fatty acids activation while FATP5 does not function in fatty acid transport but activates secondary bile acids. In the present work, we have used stable isotopically labeled fatty acids differing in carbon length and saturation in cells expressing FATP2 to gain further insights into how this protein functions in fatty acid transport and intracellular fatty acid trafficking. Our previous studies showed the expression of FATP2 modestly increased C16:0-CoA and C20:4-CoA and significantly increased C18:3-CoA and C22:6-CoA after 4hr. The increases in C16:0-CoA and C18:3-CoA suggest FATP2 must necessarily partner with a long chain acyl CoA synthetase (Acsl) to generate C16:0-CoA and C18:3-CoA through vectorial acylation. The very long chain acyl CoA synthetase activity of FATP2 is consistent in the generation of C20:4-CoA and C22:6-CoA coincident with transport from their respective exogenous fatty acids. The trafficking of exogenous fatty acids into phosphatidic acid (PA) and into the major classes of phospholipids (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidyserine (PS)) resulted in distinctive profiles, which changed with the expression of FATP2. The trafficking of exogenous C16:0 and C22:6 into PA was significant where there was 6.9- and 5.3-fold increased incorporation, respectively, over the control; C18:3 and C20:4 also trended to increase in the PA pool while there were no changes for C18:1 and C18:2. The trafficking of C18:3 into PC and PI trended higher and approached significance. In the case of C20:4, expression of

  4. Overexpression of human fatty acid transport protein 2/very long chain acyl-CoA synthetase 1 (FATP2/Acsvl1) reveals distinct patterns of trafficking of exogenous fatty acids

    SciTech Connect

    Melton, Elaina M.; Cerny, Ronald L.; DiRusso, Concetta C.; Black, Paul N.

    2013-11-01

    Highlights: •Roles of FATP2 in fatty acid transport/activation contribute to lipid homeostasis. •Use of 13C- and D-labeled fatty acids provide novel insights into FATP2 function. •FATP2-dependent trafficking of FA into phospholipids results in distinctive profiles. •FATP2 functions in the transport and activation pathways for exogenous fatty acids. -- Abstract: In mammals, the fatty acid transport proteins (FATP1 through FATP6) are members of a highly conserved family of proteins, which function in fatty acid transport proceeding through vectorial acylation and in the activation of very long chain fatty acids, branched chain fatty acids and secondary bile acids. FATP1, 2 and 4, for example directly function in fatty acid transport and very long chain fatty acids activation while FATP5 does not function in fatty acid transport but activates secondary bile acids. In the present work, we have used stable isotopically labeled fatty acids differing in carbon length and saturation in cells expressing FATP2 to gain further insights into how this protein functions in fatty acid transport and intracellular fatty acid trafficking. Our previous studies showed the expression of FATP2 modestly increased C16:0-CoA and C20:4-CoA and significantly increased C18:3-CoA and C22:6-CoA after 4 h. The increases in C16:0-CoA and C18:3-CoA suggest FATP2 must necessarily partner with a long chain acyl CoA synthetase (Acsl) to generate C16:0-CoA and C18:3-CoA through vectorial acylation. The very long chain acyl CoA synthetase activity of FATP2 is consistent in the generation of C20:4-CoA and C22:6-CoA coincident with transport from their respective exogenous fatty acids. The trafficking of exogenous fatty acids into phosphatidic acid (PA) and into the major classes of phospholipids (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), and phosphatidyserine (PS)) resulted in distinctive profiles, which changed with the expression of FATP2. The

  5. Scaling of the dynamics of flexible Lennard-Jones chains.

    PubMed

    Veldhorst, Arno A; Dyre, Jeppe C; Schrøder, Thomas B

    2014-08-07

    The isomorph theory provides an explanation for the so-called power law density scaling which has been observed in many molecular and polymeric glass formers, both experimentally and in simulations. Power law density scaling (relaxation times and transport coefficients being functions of ρ(γ(S)), where ρ is density, T is temperature, and γ(S) is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We confirm the existence of isomorphs, which are curves in the phase diagram along which the dynamics is invariant in the appropriate reduced units. This holds not only for the relaxation times but also for the full time dependence of the dynamics, including chain specific dynamics such as the end-to-end vector autocorrelation function and the relaxation of the Rouse modes. As predicted by the isomorph theory, jumps between different state points on the same isomorph happen instantaneously without any slow relaxation. Since the LJC is a simple coarse-grained model for alkanes and polymers, our results provide a possible explanation for why power-law density scaling is observed experimentally in alkanes and many polymeric systems. The theory provides an independent method of determining the scaling exponent, which is usually treated as an empirical scaling parameter.

  6. dAcsl, the Drosophila ortholog of acyl-CoA synthetase long-chain family member 3 and 4, inhibits synapse growth by attenuating bone morphogenetic protein signaling via endocytic recycling.

    PubMed

    Liu, Zhihua; Huang, Yan; Hu, Wen; Huang, Sheng; Wang, Qifu; Han, Junhai; Zhang, Yong Q

    2014-02-19

    Fatty acid metabolism plays an important role in brain development and function. Mutations in acyl-CoA synthetase long-chain family member 4 (ACSL4), which converts long-chain fatty acids to acyl-CoAs, result in nonsyndromic X-linked mental retardation. ACSL4 is highly expressed in the hippocampus, a structure critical for learning and memory. However, the underlying mechanism by which mutations of ACSL4 lead to mental retardation remains poorly understood. We report here that dAcsl, the Drosophila ortholog of ACSL4 and ACSL3, inhibits synaptic growth by attenuating BMP signaling, a major growth-promoting pathway at neuromuscular junction (NMJ) synapses. Specifically, dAcsl mutants exhibited NMJ overgrowth that was suppressed by reducing the doses of the BMP pathway components, accompanied by increased levels of activated BMP receptor Thickveins (Tkv) and phosphorylated mothers against decapentaplegic (Mad), the effector of the BMP signaling at NMJ terminals. In addition, Rab11, a small GTPase involved in endosomal recycling, was mislocalized in dAcsl mutant NMJs, and the membrane association of Rab11 was reduced in dAcsl mutant brains. Consistently, the BMP receptor Tkv accumulated in early endosomes but reduced in recycling endosomes in dAcsl mutant NMJs. dAcsl was also required for the recycling of photoreceptor rhodopsin in the eyes, implying a general role for dAcsl in regulating endocytic recycling of membrane receptors. Importantly, expression of human ACSL4 rescued the endocytic trafficking and NMJ phenotypes of dAcsl mutants. Together, our results reveal a novel mechanism whereby dAcsl facilitates Rab11-dependent receptor recycling and provide insights into the pathogenesis of ACSL4-related mental retardation.

  7. Thermotropic phase behavior of model membranes composed of phosphatidylcholines containing cis-monounsaturated acyl chain homologues of oleic acid: differential scanning calorimetric and /sup 31/P NMR spectroscopic studies

    SciTech Connect

    Lewis, R.N.A.H.; Sykes, B.D.; McElhaney, R.N.

    1988-02-09

    The thermotropic phase behavior of dioleoylphosphatidylcholine and six of its longer chain homologues was studied by differential scanning calorimetry and /sup 31/P nuclear magnetic resonance (NMR) spectroscopy. Aqueous dispersions of these compounds all exhibit a single endotherm upon heating but upon cooling exhibit at least two exotherms, both of which occur at temperatures lower than those of their heating endotherm. The single transition observed upon heating was shown by /sup 31/P NMR spectroscopy to be a net conversion from a condensed, subgel-like phase (L/sub c/ phase) to the liquid-crystalline state. Aqueous ethylene glycol dispersions of these compounds also exhibit single endotherms upon heating and cooling exotherms centered at temperatures lower than those of their corresponding heating endotherm. However, the behavior of the aqueous ethylene glycol dispersions differs with respect to their transition temperatures and enthalpies as well as the extent of undercooling observed, and there is some evidence of discontinuities in the cooling behavior of the odd- and even-numbered members of the homologous series. Like the aqueous dispersions, /sup 31/P NMR spectroscopy also shows that the calorimetric events observed in aqueous ethylene glycol involve net interconversions between an L/sub c/-like phase and the liquid-crystalline state. These results demonstrate that although the presence of a cis double bond can perturb the solid-state packing of the acyl chains, its presence does not preclude the formation of highly ordered subgel-like phases in lipid bilayers. In the particular case of these unsaturated phosphatidylcholines, the formation of the subgel phases is more kinetically favorable than is the case with their saturated n-acyl counterparts.

  8. Dynamics of exciton transfer in coupled polymer chains

    NASA Astrophysics Data System (ADS)

    Zhang, Y. L.; Liu, X. J.; Sun, Z.; An, Z.

    2013-05-01

    The dynamics of singlet and triplet exciton transfer in coupled polymer chains are investigated within the Su-Schrieffer-Heeger+Pariser-Parr-Pople model including both electron-phonon (e-p) coupling and electron-electron (e-e) interactions, using a multi-configurational time-dependent Hartree-Fock dynamic method. In order to explain the processes involved, the effects of on-site and long-range e-e interactions on the locality of the singlet and triplet excitons are first investigated on an isolated chain. It is found that the locality of the singlet exciton decreases, while the locality of the triplet exciton increases with an increase in the on-site e-e interactions. On the other hand, an increase in the long-range e-e interaction results in a more localized singlet exciton and triplet exciton. In coupled polymer chains, we then quantitatively show the yields of singlet and triplet exciton transfer products under the same interchain coupling. It is found that the yield of singlet interchain excitons is much higher than that of triplet interchain excitons, that is to say, singlet exciton transfer is significantly easier than that for triplet excitons. This results from the fact that the singlet exciton is more delocalized than the triplet exciton. In addition, hopping of electrons with opposite spins between the coupled chains can facilitate the transfer of singlet excitons. The results are of great significance for understanding the photoelectric conversion process and developing high-power organic optoelectronic applications.

  9. Metabolism of ricinoleic acid into gamma-decalactone: beta-oxidation and long chain acyl intermediates of ricinoleic acid in the genus Sporidiobolus sp.

    PubMed

    Blin-Perrin, C; Molle, D; Dufosse, L; Le-Quere, J L; Viel, C; Mauvais, G; Feron, G

    2000-07-01

    In order to study differences in gamma-decalactone production in yeast, four species of Sporidiobolus were cultivated with 5% of methyl ricinoleate as the lactone substrate. In vivo studies showed different time courses of intermediates of ricinoleic acid breakdown between the four species. In vitro studies of the beta-oxidation system were conducted with crude cell extracts of Sporidiobolus spp. and with ricinoleyl-CoA (RCoA) as substrate. The beta-oxidation was detected by measuring acyl-CoA oxidase, 3-hydroxyacyl-CoA dehydrogenase activities, and acetyl-CoA production. The time courses of the CoA esters resulting from RCoA breakdown by crude extract of Sporidiobolus spp. permit the proposal of different metabolic models in the yeast. These models explained the differences observed during in vivo studies.

  10. Photoactivation Reduces Side-Chain Dynamics of a LOV Photoreceptor

    PubMed Central

    Stadler, Andreas M.; Knieps-Grünhagen, Esther; Bocola, Marco; Lohstroh, Wiebke; Zamponi, Michaela; Krauss, Ulrich

    2016-01-01

    We used neutron-scattering experiments to probe the conformational dynamics of the light, oxygen, voltage (LOV) photoreceptor PpSB1-LOV from Pseudomonas putida in both the dark and light states. Global protein diffusion and internal macromolecular dynamics were measured using incoherent neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond timescales. Global protein diffusion of PpSB1-LOV is not influenced by photoactivation. Observation-time-dependent global diffusion coefficients were found, which converge on the nanosecond timescale toward diffusion coefficients determined by dynamic light scattering. Mean-square displacements of localized internal motions and effective force constants, , describing the resilience of the proteins were determined on the respective timescales. Photoactivation significantly modifies the flexibility and the resilience of PpSB1-LOV. On the fast, picosecond timescale, small changes in the mean-square displacement and are observed, which are enhanced on the slower, nanosecond timescale. Photoactivation results in a slightly larger resilience of the photoreceptor on the fast, picosecond timescale, whereas in the nanosecond range, a significantly less resilient structure of the light-state protein is observed. For a residue-resolved interpretation of the experimental neutron-scattering data, we analyzed molecular dynamics simulations of the PpSB1-LOV X-ray structure. Based on these data, it is tempting to speculate that light-induced changes in the protein result in altered side-chain mobility mostly for residues on the protruding Jα helix and on the LOV-LOV dimer interface. Our results provide strong experimental evidence that side-chain dynamics play a crucial role in photoactivation and signaling of PpSB1-LOV via modulation of conformational entropy. PMID:26958884

  11. Different effects of fibrates on the microsomal fatty acid chain elongation and the acyl composition of phospholipids in guinea-pigs.

    PubMed

    Vázquez, M; Alegret, M; López, M; Rodríguez, C; Adzet, T; Merlos, M; Laguna, J C

    1995-12-01

    1. The effects in vitro and in vivo of three fibric acid derivatives, clofibrate (CFB), bezafibrate (BFB) and gemfibrozil (GFB) on some enzyme activities related to fatty acid biosynthesis, namely palmitoyl-CoA synthetase and hydrolases (microsomal and cytosolic), NADH and NADPH cytochrome c reductases and acyl-CoA elongases were investigated in guinea-pigs. 2. The three fibrates inhibited acyl-CoA elongation in vitro, irrespective of the substrate of elongation used (saturated, monounsaturated, polyunsaturated) and with an order of potency GFB > BFB > CFB. In the case of GFB, inhibition occurred at concentrations that can be reached in vivo. 3. Microsomal palmitoyl-CoA hydrolase and synthetase were also inhibited in vitro (GFB > or = BFB > CFB), whereas NADH cytochrome c reductase activity was increased by GFB. Nevertheless, the magnitude of changes were lower than those observed in elongation activities. 4. Treatment with fibrates did not produce peroxisomal proliferation in guinea-pigs, as measured by peroxisomal beta-oxidation activity and liver weight/body weight ratio. Nevertheless, fibrates provoked a reduction in plasma cholesterol and triglycerides, at least in GFB- and BFB-treated animals. 5. Fatty acid elongation was significantly modified by GFB treatment in vivo. The remaining enzyme activities studied were only slightly changed by fibrate treatment. 6. Treatment with BFB and to a lesser extent with CFB, increased the relative proportion of MUFA (palmitoleic and oleic acids) in microsomal phospholipids, whereas PUFA (mainly linoleic acid) decreased. GFB behaved differently, increasing palmitic and linoleic acids and decreasing stearic and oleic acids. The latter changes are attributable to an inhibition of elongation activity by GFB. 7. The changes observed after fibrate treatment in both rats and guinea-pigs, as they are not directly related to peroxisome proliferation, could be more reliably extrapolated to man than those observed only in rats.

  12. Different effects of fibrates on the microsomal fatty acid chain elongation and the acyl composition of phospholipids in guinea-pigs.

    PubMed Central

    Vázquez, M.; Alegret, M.; López, M.; Rodríguez, C.; Adzet, T.; Merlos, M.; Laguna, J. C.

    1995-01-01

    1. The effects in vitro and in vivo of three fibric acid derivatives, clofibrate (CFB), bezafibrate (BFB) and gemfibrozil (GFB) on some enzyme activities related to fatty acid biosynthesis, namely palmitoyl-CoA synthetase and hydrolases (microsomal and cytosolic), NADH and NADPH cytochrome c reductases and acyl-CoA elongases were investigated in guinea-pigs. 2. The three fibrates inhibited acyl-CoA elongation in vitro, irrespective of the substrate of elongation used (saturated, monounsaturated, polyunsaturated) and with an order of potency GFB > BFB > CFB. In the case of GFB, inhibition occurred at concentrations that can be reached in vivo. 3. Microsomal palmitoyl-CoA hydrolase and synthetase were also inhibited in vitro (GFB > or = BFB > CFB), whereas NADH cytochrome c reductase activity was increased by GFB. Nevertheless, the magnitude of changes were lower than those observed in elongation activities. 4. Treatment with fibrates did not produce peroxisomal proliferation in guinea-pigs, as measured by peroxisomal beta-oxidation activity and liver weight/body weight ratio. Nevertheless, fibrates provoked a reduction in plasma cholesterol and triglycerides, at least in GFB- and BFB-treated animals. 5. Fatty acid elongation was significantly modified by GFB treatment in vivo. The remaining enzyme activities studied were only slightly changed by fibrate treatment. 6. Treatment with BFB and to a lesser extent with CFB, increased the relative proportion of MUFA (palmitoleic and oleic acids) in microsomal phospholipids, whereas PUFA (mainly linoleic acid) decreased. GFB behaved differently, increasing palmitic and linoleic acids and decreasing stearic and oleic acids. The latter changes are attributable to an inhibition of elongation activity by GFB. 7. The changes observed after fibrate treatment in both rats and guinea-pigs, as they are not directly related to peroxisome proliferation, could be more reliably extrapolated to man than those observed only in rats. PMID

  13. Polymer Chain Dynamics in a Random Environment: Heterogeneous Mobilities

    SciTech Connect

    Niedzwiedz, K.; Wischnewski, A.; Monkenbusch, M.; Richter, D.; Strauch, M.; Straube, E.; Genix, A.-C.; Arbe, A.

    2007-04-20

    We present a neutron scattering investigation on a miscible blend of two polymers with greatly different glass-transition temperatures T{sub g}. Under such conditions, the nearly frozen high-T{sub g} component imposes a random environment on the mobile chain. The results demand the consideration of a distribution of heterogeneous mobilities in the material and demonstrate that the larger scale dynamics of the fast component is not determined by the average local environment alone. This distribution of mobilities can be mapped quantitatively on the spectrum of local relaxation rates measured at high momentum transfers.

  14. Physiological Consequences of Compartmentalized Acyl-CoA Metabolism*

    PubMed Central

    Cooper, Daniel E.; Young, Pamela A.; Klett, Eric L.; Coleman, Rosalind A.

    2015-01-01

    Meeting the complex physiological demands of mammalian life requires strict control of the metabolism of long-chain fatty acyl-CoAs because of the multiplicity of their cellular functions. Acyl-CoAs are substrates for energy production; stored within lipid droplets as triacylglycerol, cholesterol esters, and retinol esters; esterified to form membrane phospholipids; or used to activate transcriptional and signaling pathways. Indirect evidence suggests that acyl-CoAs do not wander freely within cells, but instead, are channeled into specific pathways. In this review, we will discuss the evidence for acyl-CoA compartmentalization, highlight the key modes of acyl-CoA regulation, and diagram potential mechanisms for controlling acyl-CoA partitioning. PMID:26124277

  15. Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity

    PubMed Central

    2011-01-01

    Background Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. This reaction terminates acyl chain elongation of fatty acid biosynthesis, and in plant seeds it is the biochemical determinant of the fatty acid compositions of storage lipids. Results To explore acyl-ACP TE diversity and to identify novel acyl ACP-TEs, 31 acyl-ACP TEs from wide-ranging phylogenetic sources were characterized to ascertain their in vivo activities and substrate specificities. These acyl-ACP TEs were chosen by two different approaches: 1) 24 TEs were selected from public databases on the basis of phylogenetic analysis and fatty acid profile knowledge of their source organisms; and 2) seven TEs were molecularly cloned from oil palm (Elaeis guineensis), coconut (Cocos nucifera) and Cuphea viscosissima, organisms that produce medium-chain and short-chain fatty acids in their seeds. The in vivo substrate specificities of the acyl-ACP TEs were determined in E. coli. Based on their specificities, these enzymes were clustered into three classes: 1) Class I acyl-ACP TEs act primarily on 14- and 16-carbon acyl-ACP substrates; 2) Class II acyl-ACP TEs have broad substrate specificities, with major activities toward 8- and 14-carbon acyl-ACP substrates; and 3) Class III acyl-ACP TEs act predominantly on 8-carbon acyl-ACPs. Several novel acyl-ACP TEs act on short-chain and unsaturated acyl-ACP or 3-ketoacyl-ACP substrates, indicating the diversity of enzymatic specificity in this enzyme family. Conclusion These acyl-ACP TEs can potentially be used to diversify the fatty acid biosynthesis pathway to produce novel fatty acids. PMID:21831316

  16. Synthesis of fluorescent C24-ceramide: evidence for acyl chain length dependent differences in penetration of exogenous NBD-ceramides into human skin.

    PubMed

    Novotný, Jakub; Pospechová, Katerina; Hrabálek, Alexandr; Cáp, Robert; Vávrová, Katerina

    2009-12-15

    Topical skin lipid supplementation may provide opportunities for controlling ceramide (Cer) deficiency in skin diseases such as atopic dermatitis or psoriasis. Here we describe the synthesis of a long-chain 7-nitrobenzo[c][1,2,5]oxadiazol-4-yl (NBD)-labeled Cer and its different penetration through human skin compared to widely used short-chain fluorescent Cer tools.

  17. Modified acyl-ACP desaturase

    DOEpatents

    Cahoon, E.B.; Shanklin, J.; Lindgvist, Y.; Schneider, G.

    1998-01-06

    Disclosed is a method for modifying the chain length and double bond positional specificities of a soluble plant fatty acid desaturase. More specifically, the method involves modifying amino acid contact residues in the substrate binding channel of the soluble fatty acid desaturase which contact the fatty acid. Specifically disclosed is the modification of an acyl-ACP desaturase. Amino acid contact residues which lie within the substrate binding channel are identified, and subsequently replaced with different residues to effect the modification of activity. 1 fig.

  18. Oxidative acylation using thioacids

    NASA Technical Reports Server (NTRS)

    Liu, R.; Orgel, L. E.

    1997-01-01

    Several important prebiotic reactions, including the coupling of amino acids into polypeptides by the formation of amide linkages, involve acylation. Theae reactions present a challenge to the understanding of prebiotic synthesis. Condensation reactions relying on dehydrating agents are either inefficient in aqueous solution or require strongly acidic conditions and high temperatures. Activated amino acids such as thioester derivatives have therefore been suggested as likely substrates for prebiotic peptide synthesis. Here we propose a closely related route to amide bond formation involving oxidative acylation by thioacids. We find that phenylalanine, leucine and phenylphosphate are acylated efficiently in aqueous solution by thioacetic acid and an oxidizing agent. From a prebiotic point of view, oxidative acylation has the advantage of proceeding efficiently in solution and under mild conditions. We anticipate that oxidative acylation should prove to be a general method for activating carboxylic acids, including amino acids.

  19. Acyl-coenzyme A:cholesterol acyltransferases

    PubMed Central

    Chang, Ta-Yuan; Li, Bo-Liang; Chang, Catherine C. Y.; Urano, Yasuomi

    2009-01-01

    The enzymes acyl-coenzyme A (CoA):cholesterol acyltransferases (ACATs) are membrane-bound proteins that utilize long-chain fatty acyl-CoA and cholesterol as substrates to form cholesteryl esters. In mammals, two isoenzymes, ACAT1 and ACAT2, encoded by two different genes, exist. ACATs play important roles in cellular cholesterol homeostasis in various tissues. This chapter summarizes the current knowledge on ACAT-related research in two areas: 1) ACAT genes and proteins and 2) ACAT enzymes as drug targets for atherosclerosis and for Alzheimer's disease. PMID:19141679

  20. A Genetically Amenable Platensimycin- and Platencin- Overproducer as a Platform for Biosynthetic Explorations: a Showcase of PtmO4, a Long-Chain Acyl-CoA Dehydrogenase

    PubMed Central

    Rudolf, Jeffrey D.; Dong, Liao-Bin; Huang, Tingting; Shen, Ben

    2015-01-01

    Platensimycin (PTM) and platencin (PTN) are members of a new class of promising drug leads that target bacterial and mammalian fatty acid synthases. We previously cloned and sequenced the PTM and PTN gene clusters, discovered six additional PTM-PTN dual producing strains, and demonstrated the dramatic overproduction of PTM and PTN by inactivating the pathway-specific regulators ptmR1 or ptnR1 in four different strains. Our ability to utilize these PTM-PTN dual overproducing strains was limited by their lack of genetic amenability. Here we report the construction of Streptomyces platensis SB12029, a genetically amenable, in-frame ΔptmR1 dual PTM-PTN overproducing strain. To highlight the potential of this strain for future PTM and PTN biosynthetic studies, we created the ΔptmR1 ΔptmO4 double mutant S. platensis SB12030. Fourteen PTM and PTN congeners, ten of which were new, were isolated from SB12030, shedding new insights into PTM and PTN biosynthesis. PtmO4, a long-chain acyl-CoA dehydrogenase, is strongly implicated to catalyze β-oxidation of the diterpenoid intermediates in to the PTM and PTN scaffolds. SB12029 sets the stage for future biosynthetic and bioengineering studies of the PTM and PTN family of natural products. PMID:26055255

  1. Fluorescently labelled bovine acyl-CoA-binding protein acting as an acyl-CoA sensor: interaction with CoA and acyl-CoA esters and its use in measuring free acyl-CoA esters and non-esterified fatty acids.

    PubMed Central

    Wadum, Majken C T; Villadsen, Jens K; Feddersen, Søren; Møller, Rikke S; Neergaard, Thomas B F; Kragelund, Birthe B; Højrup, Peter; Faergeman, Nils J; Knudsen, Jens

    2002-01-01

    Long-chain acyl-CoA esters are key metabolites in lipid synthesis and beta-oxidation but, at the same time, are important regulators of intermediate metabolism, insulin secretion, vesicular trafficking and gene expression. Key tools in studying the regulatory functions of acyl-CoA esters are reliable methods for the determination of free acyl-CoA concentrations. No such method is presently available. In the present study, we describe the synthesis of two acyl-CoA sensors for measuring free acyl-CoA concentrations using acyl-CoA-binding protein as a scaffold. Met24 and Ala53 of bovine acyl-CoA-binding protein were replaced by cysteine residues, which were covalently modified with 6-bromoacetyl-2-dimethylaminonaphthalene to make the two fluorescent acyl-CoA indicators (FACIs) FACI-24 and FACI-53. FACI-24 and FACI-53 showed fluorescence emission maximum at 510 and 525 nm respectively, in the absence of ligand (excitation 387 nm). Titration of FACI-24 and FACI-53 with hexadecanoyl-CoA and dodecanoyl-CoA increased the fluorescence yield 5.5-and 4.7-fold at 460 and 495 nm respectively. FACI-24 exhibited a high, and similar increase in, fluorescence yield at 460 nm upon binding of C14-C20 saturated and unsaturated acyl-CoA esters. Both indicators bind long-chain (>C14) acyl-CoA esters with high specificity and affinity (K(d)=0.6-1.7 nM). FACI-53 showed a high fluorescence yield for C8-C12 acyl chains. It is shown that FACI-24 acts as a sensitive acyl-CoA sensor for measuring the concentration of free acyl-CoA, acyl-CoA synthetase activity and the concentrations of free fatty acids after conversion of the fatty acid into their respective acyl-CoA esters. PMID:12071849

  2. Changes in conformational dynamics of basic side chains upon protein–DNA association

    PubMed Central

    Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B. Montgometry; Iwahara, Junji

    2016-01-01

    Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. PMID:27288446

  3. Unusual long-chain N-acyl homoserine lactone production by and presence of quorum quenching activity in bacterial isolates from diseased tilapia fish.

    PubMed

    Chang, Chien-Yi; Koh, Chong-Lek; Sam, Choon-Kook; Chan, Xin-Yue; Yin, Wai Fong; Chan, Kok Gan

    2012-01-01

    Growth-dependent cell-cell communication termed quorum sensing is a key regulatory system in bacteria for controlling gene expression including virulence factors. In this study five potential bacterial pathogens including Bacillus sp. W2.2, Klebsiella sp. W4.2, Pseudomonas sp. W3 and W3.1 and Serratia sp. W2.3 were isolated from diseased Tilapia fish in Malaysia, supplied by the leading global fish supplier. Proteolytic activity assays confirmed that with the exception of Klebsiella sp. W4.2, all isolates showed distinct proteolytic activity. Furthermore Bacillus sp. W2.2 and Pseudomonas sp. strains W3 and W3.1 also displayed haemolytic activity. By using high resolution liquid chromatography mass spectrometry, we revealed the presence of unusually long-chain N-(3-oxohexadecanoyl)-homoserine lactone (3-oxo-C16-HSL) from Pseudomonas sp. W3.1 and N-dodecanoyl-homoserine lactone (C12-HSL) from Serratia sp. W2.3, respectively. Interestingly, Pseudomonas sp. W3.1 also produced a wide range of Pseudomonas quinolone signalling (PQS) molecules. Pseudomonas sp. W3 did not show any quorum sensing properties but possessed quorum quenching activity that inactivated AHLs. This study is the first documentation that shows unusual long-chain AHLs production in Serratia sp. and Pseudomonas sp. isolated from diseased fish and the latter also produce a wide range of PQS molecules.

  4. Unusual Long-Chain N-Acyl Homoserine Lactone Production by and Presence of Quorum Quenching Activity in Bacterial Isolates from Diseased Tilapia Fish

    PubMed Central

    Chang, Chien-Yi; Koh, Chong-Lek; Sam, Choon-Kook; Chan, Xin-Yue; Yin, Wai Fong; Chan, Kok Gan

    2012-01-01

    Growth-dependent cell-cell communication termed quorum sensing is a key regulatory system in bacteria for controlling gene expression including virulence factors. In this study five potential bacterial pathogens including Bacillus sp. W2.2, Klebsiella sp. W4.2, Pseudomonas sp. W3 and W3.1 and Serratia sp. W2.3 were isolated from diseased Tilapia fish in Malaysia, supplied by the leading global fish supplier. Proteolytic activity assays confirmed that with the exception of Klebsiella sp. W4.2, all isolates showed distinct proteolytic activity. Furthermore Bacillus sp. W2.2 and Pseudomonas sp. strains W3 and W3.1 also displayed haemolytic activity. By using high resolution liquid chromatography mass spectrometry, we revealed the presence of unusually long-chain N-(3-oxohexadecanoyl)-homoserine lactone (3-oxo-C16-HSL) from Pseudomonas sp. W3.1 and N-dodecanoyl-homoserine lactone (C12-HSL) from Serratia sp. W2.3, respectively. Interestingly, Pseudomonas sp. W3.1 also produced a wide range of Pseudomonas quinolone signalling (PQS) molecules. Pseudomonas sp. W3 did not show any quorum sensing properties but possessed quorum quenching activity that inactivated AHLs. This study is the first documentation that shows unusual long-chain AHLs production in Serratia sp. and Pseudomonas sp. isolated from diseased fish and the latter also produce a wide range of PQS molecules. PMID:22952864

  5. Cole-Davidson dynamics of simple chain models.

    SciTech Connect

    Dotson, Taylor C.; McCoy, John Dwane; Adolf, Douglas Brian; Budzien, Joanne Louise

    2008-10-01

    Rotational relaxation functions of the end-to-end vector of short, freely jointed and freely rotating chains were determined from molecular dynamics simulations. The associated response functions were obtained from the one-sided Fourier transform of the relaxation functions. The Cole-Davidson function was used to fit the response functions with extensive use being made of Cole-Cole plots in the fitting procedure. For the systems studied, the Cole-Davidson function provided remarkably accurate fits [as compared to the transform of the Kohlrausch-Williams-Watts (KWW) function]. The only appreciable deviations from the simulation results were in the high frequency limit and were due to ballistic or free rotation effects. The accuracy of the Cole-Davidson function appears to be the result of the transition in the time domain from stretched exponential behavior at intermediate time to single exponential behavior at long time. Such a transition can be explained in terms of a distribution of relaxation times with a well-defined longest relaxation time. Since the Cole-Davidson distribution has a sharp cutoff in relaxation time (while the KWW function does not), it makes sense that the Cole-Davidson would provide a better frequency-domain description of the associated response function than the KWW function does.

  6. Progress toward Understanding Protein S-acylation: Prospective in Plants.

    PubMed

    Li, Yaxiao; Qi, Baoxiu

    2017-01-01

    S-acylation, also known as S-palmitoylation or palmitoylation, is a reversible post-translational lipid modification in which long chain fatty acid, usually the 16-carbon palmitate, covalently attaches to a cysteine residue(s) throughout the protein via a thioester bond. It is involved in an array of important biological processes during growth and development, reproduction and stress responses in plant. S-acylation is a ubiquitous mechanism in eukaryotes catalyzed by a family of enzymes called Protein S-Acyl Transferases (PATs). Since the discovery of the first PAT in yeast in 2002 research in S-acylation has accelerated in the mammalian system and followed by in plant. However, it is still a difficult field to study due to the large number of PATs and even larger number of putative S-acylated substrate proteins they modify in each genome. This is coupled with drawbacks in the techniques used to study S-acylation, leading to the slower progress in this field compared to protein phosphorylation, for example. In this review we will summarize the discoveries made so far based on knowledge learnt from the characterization of protein S-acyltransferases and the S-acylated proteins, the interaction mechanisms between PAT and its specific substrate protein(s) in yeast and mammals. Research in protein S-acylation and PATs in plants will also be covered although this area is currently less well studied in yeast and mammalian systems.

  7. Progress toward Understanding Protein S-acylation: Prospective in Plants

    PubMed Central

    Li, Yaxiao; Qi, Baoxiu

    2017-01-01

    S-acylation, also known as S-palmitoylation or palmitoylation, is a reversible post-translational lipid modification in which long chain fatty acid, usually the 16-carbon palmitate, covalently attaches to a cysteine residue(s) throughout the protein via a thioester bond. It is involved in an array of important biological processes during growth and development, reproduction and stress responses in plant. S-acylation is a ubiquitous mechanism in eukaryotes catalyzed by a family of enzymes called Protein S-Acyl Transferases (PATs). Since the discovery of the first PAT in yeast in 2002 research in S-acylation has accelerated in the mammalian system and followed by in plant. However, it is still a difficult field to study due to the large number of PATs and even larger number of putative S-acylated substrate proteins they modify in each genome. This is coupled with drawbacks in the techniques used to study S-acylation, leading to the slower progress in this field compared to protein phosphorylation, for example. In this review we will summarize the discoveries made so far based on knowledge learnt from the characterization of protein S-acyltransferases and the S-acylated proteins, the interaction mechanisms between PAT and its specific substrate protein(s) in yeast and mammals. Research in protein S-acylation and PATs in plants will also be covered although this area is currently less well studied in yeast and mammalian systems. PMID:28392791

  8. Biological relevance of fatty acyl heterogeneity to the neural membrane dynamics of Rhesus macaques during normative aging

    PubMed Central

    Lam, Sin Man; Chua, Gek Huey; Li, Xiao-Jiang; Su, Bing; Shui, Guanghou

    2016-01-01

    Lipidomic analyses of the frontal cortex of Rhesus macaques across three selected age groups (young, sexually-mature, old) revealed that docosahexaenoic acids (DHAs) displayed notable and unique accretions in sexually-mature macaques for all phospholipid classes examined, which were not observable in all remaining polyunsaturated fatty acids (PUFAs) investigated. On the other hand, arachidonic acid (ARA) exhibited sharp attritions in the membrane lipidomes of sexually-mature macaques, a decline which was attenuated only for cardiolipins (CLs). DHA enrichment in phospholipids was lost in old macaques, with accompanying augmentations in very-long-chain sphingomyelins (VLC-SMs). Age-dependent alterations in membrane lipidomes point to a possibly complex temporal interplay between DHA-enriched membrane microdomains and SM-/cholesterol-rich rafts in neural membranes during normative aging. Lipid co-regulation data revealed an increasingly intense degree of co-regulation between membrane lipid classes with age, and suggest that reduction in CLs during normative brain aging may prompt alternative membrane lipid synthetic pathways driven by a compromised energy availability in the aging brain. PMID:27517158

  9. Dynamic Bandwidth Provisioning Using Markov Chain Based on RSVP

    DTIC Science & Technology

    2013-09-01

    Cambridge University Press,2008. [20] P. Bremaud, Markov Chains : Gibbs Fields, Monte Carlo Simulation and Queues, New York, NY, Springer Science...is successful.  Qualnet, a simulation platform for the wireless environment is used to simulate the algorithm (integration of Markov chain ...in Qualnet, the simulation platform used. 16 THIS PAGE INTENTIONALLY LEFT BLANK 17 III. GENERAL DISCUSSION OF MARKOV CHAIN ALGORITHM AND RSVP

  10. Phase behavior and nanoscale structure of phospholipid membranes incorporated with acylated C14-peptides.

    PubMed

    Pedersen, Tina B; Kaasgaard, Thomas; Jensen, Morten Ø; Frokjaer, Sven; Mouritsen, Ole G; Jørgensen, Kent

    2005-10-01

    The thermotropic phase behavior and lateral structure of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers containing an acylated peptide has been characterized by differential scanning calorimetry (DSC) on vesicles and atomic force microscopy (AFM) on mica-supported bilayers. The acylated peptide, which is a synthetic decapeptide N-terminally linked to a C14 acyl chain (C14-peptide), is incorporated into DPPC bilayers in amounts ranging from 0-20 mol %. The calorimetric scans of the two-component system demonstrate a distinct influence of the C14-peptide on the lipid bilayer thermodynamics. This is manifested as a concentration-dependent downshift of both the main phase transition and the pretransition. In addition, the main phase transition peak is significantly broadened, indicating phase coexistence. In the AFM imaging scans we found that the C14-peptide, when added to supported gel phase DPPC bilayers, inserts preferentially into preexisting defect regions and has a noticeable influence on the organization of the surrounding lipids. The presence of the C14-peptide gives rise to a laterally heterogeneous bilayer structure with coexisting lipid domains characterized by a 10 A height difference. The AFM images also show that the appearance of the ripple phase of the DPPC lipid bilayers is unaffected by the C14-peptide. The experimental results are supported by molecular dynamics simulations, which show that the C14-peptide has a disordering effect on the lipid acyl chains and causes a lateral expansion of the lipid bilayer. These effects are most pronounced for gel-like bilayer structures and support the observed downshift in the phase-transition temperature. Moreover, the molecular dynamics data indicate a tendency of a tryptophan residue in the peptide sequence to position itself in the bilayer headgroup region.

  11. Engineering a disulfide bond in the lid hinge region of Rhizopus chinensis lipase: increased thermostability and altered acyl chain length specificity.

    PubMed

    Yu, Xiao-Wei; Tan, Nian-Jiang; Xiao, Rong; Xu, Yan

    2012-01-01

    The key to enzyme function is the maintenance of an appropriate balance between molecular stability and structural flexibility. The lid domain which is very important for "interfacial activation" is the most flexible part in the lipase structure. In this work, rational design was applied to explore the relationship between lid rigidity and lipase activity by introducing a disulfide bond in the hinge region of the lid, in the hope of improving the thermostability of R. chinensis lipase through stabilization of the lid domain without interfering with its catalytic performance. A disulfide bridge between F95C and F214C was introduced into the lipase from R. chinensis in the hinge region of the lid according to the prediction of the "Disulfide by Design" algorithm. The disulfide variant showed substantially improved thermostability with an eleven-fold increase in the t(1/2) value at 60°C and a 7°C increase of T(m) compared with the parent enzyme, probably contributed by the stabilization of the geometric structure of the lid region. The additional disulfide bond did not interfere with the catalytic rate (k(cat)) and the catalytic efficiency towards the short-chain fatty acid substrate, however, the catalytic efficiency of the disulfide variant towards pNPP decreased by 1.5-fold probably due to the block of the hydrophobic substrate channel by the disulfide bond. Furthermore, in the synthesis of fatty acid methyl esters, the maximum conversion rate by RCLCYS reached 95% which was 9% higher than that by RCL. This is the first report on improving the thermostability of the lipase from R. chinensis by introduction of a disulfide bond in the lid hinge region without compromising the catalytic rate.

  12. Nonideal mixing and phase separation in phosphatidylcholine-phosphatidic acid mixtures as a function of acyl chain length and pH.

    PubMed Central

    Garidel, P; Johann, C; Blume, A

    1997-01-01

    The miscibilities of phosphatidic acids (PAs) and phosphatidylcholines (PCs) with different chain lengths (n = 14, 16) at pH 4, pH 7, and pH 12 were examined by differential scanning calorimetry. Simulation of heat capacity curves was performed using a new approach that incorporates changes of cooperativity of the transition in addition to nonideal mixing in the gel and the liquid-crystalline phase as a function of composition. From the simulations of the heat capacity curves, first estimates for the nonideality parameters for nonideal mixing as a function of composition were obtained, and phase diagrams were constructed using temperatures for onset and end of melting, which were corrected for the broadening effect caused by a decrease in cooperativity. In all cases the composition dependence of the nonideality parameters indicated nonsymmetrical mixing behavior. The phase diagrams were therefore further refined by simulations of the coexistence curves using a four-parameter approximation to account for nonideal and nonsymmetrical mixing in the gel and the liquid-crystalline phase. The mixing behavior was studied at three different pH values to investigate how changes in headgroup charge of the PA influences the miscibility. The experiments showed that at pH 7, where the PA component is negatively charged, the nonideality parameters are in most cases negative, indicating that electrostatic effects favor a mixing of the two components. Partial protonation of the PA component at pH 4 leads to strong changes in miscibility; the nonideality parameters for the liquid-crystalline phase are now in most cases positive, indicating clustering of like molecules. The phase diagram for 1,2-dimyristoyl-sn-glycero-3-phosphatidic acid:1,2-dipalmitoyl-sn-glycero-3-phosphorylcholine mixtures at pH 4 indicates that a fluid-fluid immiscibility is likely. The results show that a decrease in ionization of PAs can induce large changes in mixing behavior. This occurs because of a

  13. Differential turnover of phospholipid acyl groups in mouse peritoneal macrophages

    SciTech Connect

    Kuwae, T.; Schmid, P.C.; Johnson, S.B.; Schmid, H.H. )

    1990-03-25

    Phospholipid acyl turnover was assessed in mouse peritoneal exudate cells which consisted primarily of macrophages. The cells were incubated for up to 5 h in media containing 40% H218O, and uptake of 18O into ester carbonyls of phospholipids was determined by gas chromatography-mass spectrometry of hydrogenated methyl esters. The uptake was highest in choline phospholipids and phosphatidylinositol, less in ethanolamine phospholipids, and much less in phosphatidylserine. Acyl groups at the sn-1 and sn-2 positions of diacyl glycerophospholipids, including arachidonic and other long-chain polyunsaturated fatty acids, acquired 18O at about the same rate. Acyl groups of alkylacyl glycerophosphocholine exhibited lower rates of 18O uptake, and acyl groups of ethanolamine plasmalogens (alkenylacyl glycerophosphoethanolamines) acquired only minimal amounts of 18O within 5 h, indicating a low average acyl turnover via free fatty acids. Pulse experiments with exogenous 3H-labeled arachidonic acid supported the concept that acylation of alkenyl glycerophosphoethanolamine occurs by acyl transfer from other phospholipids rather than via free fatty acids and acyl-CoA. The 18O content of intracellular free fatty acids increased gradually over a 5-h period, whereas in extracellular free fatty acids it reached maximal 18O levels within the first hour. Arachidonate and other long-chain polyunsaturated fatty acids were found to participate readily in deacylation-reacylation reactions but were present only in trace amounts in the free fatty acid pools inside and outside the cells. We conclude that acyl turnover of macrophage phospholipids through hydrolysis and reacylation is rapid but tightly controlled so that appreciable concentrations of free arachidonic acid do not occur.

  14. The Level of Circulating Octanoate Does Not Predict Ghrelin O-Acyl Transferase (GOAT)-Mediated Acylation of Ghrelin During Fasting

    PubMed Central

    Nikolayev, Alexander; Liu, Jianhua; Pezzoli, Suzan S.; Farhy, Leon S.; Patrie, James; Gaylinn, Bruce D.; Heiman, Mark; Thorner, Michael O.

    2015-01-01

    Background: Acyl-ghrelin is a 28-amino acid peptide released from the stomach. Ghrelin O-acyl transferase (GOAT) attaches an 8-carbon medium-chain fatty acid (MCFA) (octanoate) to serine 3 of ghrelin. This acylation is necessary for the activity of ghrelin. Animal data suggest that MCFAs provide substrate for GOAT and an increase in nutritional octanoate increases acyl-ghrelin. Objectives: To address the question of the source of substrate for acylation, we studied whether the decline in ghrelin acylation during fasting is associated with a decline in circulating MCFAs. Methods: Eight healthy young men (aged 18–28 years, body mass index range, 20.6–26.2 kg/m2) had blood drawn every 10 minutes for acyl- and desacyl-ghrelin and every hour for free fatty acids (FFAs) during the last 24 hours of a 61.5-hour fast and during a fed day. FFAs were measured by a highly sensitive liquid chromatography-mass spectroscopy method. Acyl- and desacyl-ghrelin were measured in an in-house assay; the results were published previously. Ghrelin acylation was assessed by the ratio of acyl-ghrelin to total ghrelin. Results: With the exception of MCFAs C8 and C10, all other FFAs, the MCFAs (C6 and C12), and the long-chain fatty acids (C14–C18) significantly increased with fasting (P < .05). There was no significant association between the fold change in ghrelin acylation and circulating FFAs. Conclusions: These results suggest that changes in circulating MCFAs are not linked to the decline in ghrelin acylation during fasting and support the hypothesis that acylation of ghrelin depends at least partially on the availability of gastroluminal MCFAs or the regulation of GOAT activity. PMID:25337923

  15. Modeling compositionality by dynamic binding of synfire chains.

    PubMed

    Abeles, Moshe; Hayon, Gaby; Lehmann, Daniel

    2004-01-01

    This paper examines the feasibility of manifesting compositionality by a system of synfire chains. Compositionality is the ability to construct mental representations, hierarchically, in terms of parts and their relations. We show that synfire chains may synchronize their waves when a few orderly cross links are available. We propose that synchronization among synfire chains can be used for binding component into a whole. Such synchronization is shown both for detailed simulations, and by numerical analysis of the propagation of a wave along a synfire chain. We show that global inhibition may prevent spurious synchronization among synfire chains. We further show that selecting which synfire chains may synchronize to which others may be improved by including inhibitory neurons in the synfire pools. Finally we show that in a hierarchical system of synfire chains, a part-binding problem may be resolved, and that such a system readily demonstrates the property of priming. We compare the properties of our system with the general requirements for neural networks that demonstrate compositionality.

  16. Acylation of salmon calcitonin modulates in vitro intestinal peptide flux through membrane permeability enhancement.

    PubMed

    Trier, Sofie; Linderoth, Lars; Bjerregaard, Simon; Strauss, Holger M; Rahbek, Ulrik L; Andresen, Thomas L

    2015-10-01

    Acylation of peptide drugs with fatty acid chains has proven beneficial for prolonging systemic circulation, as well as increasing enzymatic stability and interactions with lipid cell membranes. Thus, acylation offers several potential benefits for oral delivery of therapeutic peptides, and we hypothesize that tailoring the acylation may be used to optimize intestinal translocation. This work aims to characterize acylated analogues of the therapeutic peptide salmon calcitonin (sCT), which lowers blood calcium, by systematically increasing acyl chain length at two positions, in order to elucidate its influence on intestinal cell translocation and membrane interaction. We find that acylation drastically increases in vitro intestinal peptide flux and confers a transient permeability enhancing effect on the cell layer. The analogues permeabilize model lipid membranes, indicating that the effect is due to a solubilization of the cell membrane, similar to transcellular oral permeation enhancers. The effect is dependent on pH, with larger effect at lower pH, and is impacted by acylation chain length and position. Compared to the unacylated peptide backbone, N-terminal acylation with a short chain provides 6- or 9-fold increase in peptide translocation at pH 7.4 and 5.5, respectively. Prolonging the chain length appears to hamper translocation, possibly due to self-association or aggregation, although the long chain acylated analogues remain superior to the unacylated peptide. For K(18)-acylation a short chain provides a moderate improvement, whereas medium and long chain analogues are highly efficient, with a 12-fold increase in permeability compared to the unacylated peptide backbone, on par with currently employed oral permeation enhancers. For K(18)-acylation the medium chain acylation appears to be optimal, as elongating the chain causes greater binding to the cell membrane but similar permeability, and we speculate that increasing the chain length further may

  17. A Framework of Multi Objectives Negotiation for Dynamic Supply Chain Model

    NASA Astrophysics Data System (ADS)

    Chai, Jia Yee; Sakaguchi, Tatsuhiko; Shirase, Keiichi

    Trends of globalization and advances in Information Technology (IT) have created opportunity in collaborative manufacturing across national borders. A dynamic supply chain utilizes these advances to enable more flexibility in business cooperation. This research proposes a concurrent decision making framework for a three echelons dynamic supply chain model. The dynamic supply chain is formed by autonomous negotiation among agents based on multi agents approach. Instead of generating negotiation aspects (such as amount, price and due date) arbitrary, this framework proposes to utilize the information available at operational level of an organization in order to generate realistic negotiation aspect. The effectiveness of the proposed model is demonstrated by various case studies.

  18. Enthalpic Effects of Chain Length and Unsaturation on Water Permeability across Droplet Bilayers of Homologous Monoglycerides.

    PubMed

    Lopez, Maria; Evangelista, Sue Ellen; Morales, Melissa; Lee, Sunghee

    2017-01-31

    A deeper understanding of unassisted passive transport processes can better delineate basic lipid dynamics in biological membranes. A droplet interface bilayer (DIB) is made by contacting two aqueous droplets covered with a lipid monolayer, and has increasingly been employed as a model artificial biological membrane. In this study, we have investigated the effect of acyl chain structure of amphiphilic monoglycerides on the osmotic permeability of water across DIB membranes composed of these monoglycerides, where the acyl chain length (C14-C24), number of double bonds (1-4), and the position of double bond are varied systematically along the acyl chains. Both permeability values and activation energies have been extracted for water transport across a lipid bilayer formed of a homologous series of lipids, allowing us to make ready comparisons between the different lipids and potentially better elucidate the contributions that molecular motifs make to the permeation process.

  19. Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails.

    PubMed

    Paloncýová, Markéta; Vávrová, Kateřina; Sovová, Žofie; DeVane, Russell; Otyepka, Michal; Berka, Karel

    2015-07-30

    Ceramides are indispensable constituents of the stratum corneum (SC), the uppermost impermeable layer of human skin. Ceramides with shorter (four- to eight-carbon acyl chains) fatty acid chains increase skin and model membrane permeability, while further shortening of the chain leads to increased resistance to penetration almost as good as that of ceramides from healthy skin (24 carbons long on average). Here we address the extent to which the atomistic CHARMM36 and coarse-grain MARTINI molecular dynamics (MD) simulations reflect the skin permeability data. As a result, we observed the same bell-shaped permeability trend for water that was observed in the skin and multilayer membrane experiments for model compounds. We showed that the enhanced permeability of the short ceramides is mainly caused by the disturbance of their headgroup conformation because of their inability to accommodate the shorter lipid acyl chain into a typical hairpin conformation, which further led to their destabilization and phase separation. As MD simulations described well delicate structural features of SC membranes, they seem to be suitable for further studies of the SC superstructure, including the development of skin penetration enhancers for transdermal drug delivery and skin toxicity risk assessment studies.

  20. Dynamics of Polyelectrolyte Chains within Layer-by-Layer Assemblies

    NASA Astrophysics Data System (ADS)

    Sukhishvili, Svetlana

    2015-03-01

    Layer-by-layer (LbL) assembly of charged polymers/nanoparticles finds diverse industrial applications ranging from NIR reflective heat-reduction to multi-stage drug delivery. Internal layering of film components lies at the heart of their performance. I will discuss experiments aimed to unravel relationships between center-of-mass diffusion of polyelectrolyte (PE) chains within LbL films, PE molecular characteristics, environmental conditions (salt concentration), and film structure. Upon film annealing in salt solutions, chain diffusion is highly anisotropic (as probed by fluorescence recovery after photobleaching and neutron reflectometry), and is strongly coupled with film structure. For layered LbL films, PE diffusion in the direction parallel to the substrate reveals quasi-Rouse scaling with molecular weight (D ~ M-1) , even for long chains, suggesting that chains disentangle upon adsorption. Finally, I will discuss quantitative aspects of salt-induced PE chain diffusion in directions parallel and perpendicular to the substrate, and their consequences for persistent layering within LbL films. This work was supported by the National Science Foundation under Award DMR-0906474.

  1. Dynamical Systems Based Non Equilibrium Statistical Mechanics for Markov Chains

    NASA Astrophysics Data System (ADS)

    Prevost, Mireille

    We introduce an abstract framework concerning non-equilibrium statistical mechanics in the specific context of Markov chains. This framework encompasses both the Evans-Searles and the Gallavotti-Cohen fluctuation theorems. To support and expand on these concepts, several results are proven, among which a central limit theorem and a large deviation principle. The interest for Markov chains is twofold. First, they model a great variety of physical systems. Secondly, their simplicity allows for an easy introduction to an otherwise complicated field encompassing the statistical mechanics of Anosov and Axiom A diffeomorphisms. We give two examples relating the present framework to physical cases modelled by Markov chains. One of these concerns chemical reactions and links key concepts from the framework to their well known physical counterpart.

  2. Dynamics of Cancer Cell near Collagen Fiber Chain

    NASA Astrophysics Data System (ADS)

    Kim, Jihan; Sun, Bo

    Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. When cell migrates through connective extracellular matrix (ECM), it applies cellular traction force to ECM and senses the rigidity of their local environment. We used human breast cancer cell (MDA-MB-231) which is highly invasive and applies strong traction force to ECM. As cancer cell applies traction force to type I collage-based ECM, it deforms collagen fibers near the surface. Patterns of deforming collagen fibers are significantly different with pairs of cancer cells compared to a single cancer cell. While a pair of cancer cells within 60 um creates aligned collagen fiber chains between them permanently, a single cancer cell does not form any fiber chains. In this experiment we measured a cellular response and an interaction between a pair of cells through the chain. Finally, we analyzed correlation of directions between cancer cell migration and the collagen chain alignment.

  3. Event-chain algorithm for the Heisenberg model: Evidence for z ≃1 dynamic scaling

    NASA Astrophysics Data System (ADS)

    Nishikawa, Yoshihiko; Michel, Manon; Krauth, Werner; Hukushima, Koji

    2015-12-01

    We apply the event-chain Monte Carlo algorithm to the three-dimensional ferromagnetic Heisenberg model. The algorithm is rejection-free and also realizes an irreversible Markov chain that satisfies global balance. The autocorrelation functions of the magnetic susceptibility and the energy indicate a dynamical critical exponent z ≈1 at the critical temperature, while that of the magnetization does not measure the performance of the algorithm. We show that the event-chain Monte Carlo algorithm substantially reduces the dynamical critical exponent from the conventional value of z ≃2 .

  4. Event-chain algorithm for the Heisenberg model: Evidence for z≃1 dynamic scaling.

    PubMed

    Nishikawa, Yoshihiko; Michel, Manon; Krauth, Werner; Hukushima, Koji

    2015-12-01

    We apply the event-chain Monte Carlo algorithm to the three-dimensional ferromagnetic Heisenberg model. The algorithm is rejection-free and also realizes an irreversible Markov chain that satisfies global balance. The autocorrelation functions of the magnetic susceptibility and the energy indicate a dynamical critical exponent z≈1 at the critical temperature, while that of the magnetization does not measure the performance of the algorithm. We show that the event-chain Monte Carlo algorithm substantially reduces the dynamical critical exponent from the conventional value of z≃2.

  5. On the dynamics of chain systems. [applications in manipulator and human body models

    NASA Technical Reports Server (NTRS)

    Huston, R. L.; Passerello, C. E.

    1974-01-01

    A computer-oriented method for obtaining dynamical equations of motion for chain systems is presented. A chain system is defined as an arbitrarily assembled set of rigid bodies such that adjoining bodies have at least one common point and such that closed loops are not formed. The equations of motion are developed through the use of Lagrange's form of d'Alembert's principle. The method and procedure is illustrated with an elementary study of a tripod space manipulator. The method is designed for application with systems such as human body models, chains and cables, and dynamic finite-segment models.

  6. "Light-cone" dynamics after quantum quenches in spin chains.

    PubMed

    Bonnes, Lars; Essler, Fabian H L; Läuchli, Andreas M

    2014-10-31

    Signal propagation in the nonequilibrium evolution after quantum quenches has recently attracted much experimental and theoretical interest. A key question arising in this context is what principles, and which of the properties of the quench, determine the characteristic propagation velocity. Here we investigate such issues for a class of quench protocols in one of the central paradigms of interacting many-particle quantum systems, the spin-1/2 Heisenberg XXZ chain. We consider quenches from a variety of initial thermal density matrices to the same final Hamiltonian using matrix product state methods. The spreading velocities are observed to vary substantially with the initial density matrix. However, we achieve a striking data collapse when the spreading velocity is considered to be a function of the excess energy. Using the fact that the XXZ chain is integrable, we present an explanation of the observed velocities in terms of "excitations" in an appropriately defined generalized Gibbs ensemble.

  7. The Role of the β5-α11 Loop in the Active-Site Dynamics of Acylated Penicillin-Binding Protein A from Mycobacterium tuberculosis

    SciTech Connect

    Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher

    2013-04-22

    Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constants for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.

  8. Simulating the dynamic behavior of chain drive systems by advanced CAE programs

    SciTech Connect

    Ross, J.; Meyer, J.

    1996-09-01

    Due to the increased requirements for chain drive systems of 4-stroke internal combustion engines CAE-tools are necessary to design the optimum dynamic system. In comparison to models used din the past the advantage of the new model CDD (Chain Drive Dynamics) is the capability of simulating the trajectory of each chain link around the drive system. Each chain link is represented by a mass with two degrees of freedom and is coupled to the next by a spring-damper element. The drive sprocket can be moved with a constant or non-constant speed. As in reality the other sprockets are driven by the running chain and can be excited by torques. Due to these unique model features it is possible to calculate all vibration types of the chain, polygon effects and radial or angular vibrations of the sprockets very accurately. The model includes the detailed simulation of a mechanical or a hydraulic tensioner as well. The method is ready to be coupled to other detailed calculation models (e.g. valve train systems, crankshaft, etc.). The high efficiency of the tool predicting the dynamic and acoustic behavior of a chain drive system will be demonstrated in comparison to measurements.

  9. Kinematic and dynamic modeling and approximate analysis of a roller chain drive

    NASA Astrophysics Data System (ADS)

    Fuglede, Niels; Thomsen, Jon Juel

    2016-03-01

    A simple roller chain drive consisting of two sprockets connected by tight chain spans is investigated. First, a kinematic model is presented which include both spans and sprockets. An approach for calculating the chain wrapping length is presented, which also allows for the exact calculation of sprocket center positions for a given chain length. The kinematic analysis demonstrates that the total length of the chain wrapped around the sprockets generally varies during one tooth period. Analytical predictions for the wrapping length are compared to multibody simulation results and show very good agreement. It is thereby demonstrated that chain drives with tight chain spans must include compliant components to function. Second, a dynamic model is presented which includes the two spans and the driven sprocket. Assuming the presence of a stationary operating state, the presented dynamic model allows for analytical studies of the coupled motion of the chain spans and driven sprocket. Parametric excitation of the spans come from sprocket angular displacements, and the driven sprocket acts as a boundary which can be compliant in the axial direction. External transverse excitation of the spans comes from polygonal action, and is treated through kinematic forcing at the moving string boundaries. Perturbation analysis of the model is carried out using the method of multiple scales. Results show a multitude of internal and external resonance conditions, and some examples are presented of both decoupled and coupled motion. Together, the kinematic and dynamic model are aimed toward providing a framework for conducting and understanding both numerical, and experimental investigations of roller chain drive dynamics.

  10. Plant Microsomal Phospholipid Acyl Hydrolases Have Selectivities for Uncommon Fatty Acids.

    PubMed Central

    Stahl, U.; Banas, A.; Stymne, S.

    1995-01-01

    Developing endosperms and embryos accumulating triacylglycerols rich in caproyl (decanoyl) groups (i.e. developing embryos of Cuphea procumbens and Ulmus glabra) had microsomal acyl hydrolases with high selectivities toward phosphatidylcholine with this acyl group. Similarly, membranes from Euphorbia lagascae and Ricinus communis endosperms, which accumulate triacylglycerols with vernoleate (12-epoxy-octadeca-9-enoate) and ricinoleate (12-hydroxy-octadeca-9-enoate), respectively, had acyl hydrolases that selectively removed their respective oxygenated acyl group from the phospholipids. The activities toward phospholipid substrates with epoxy, hydroxy, and medium-chain acyl groups varied greatly between microsomal preparations from different plant species. Epoxidated and hydroxylated acyl groups in sn-1 and sn-2 positions of phosphatidylcholine and in sn-1-lysophosphatidylcholine were hydrolyzed to a similar extent, whereas the hydrolysis of caproyl groups was highly dependent on the positional localization. PMID:12228415

  11. Dynamic model for tritium transfer in an aquatic food chain.

    PubMed

    Melintescu, A; Galeriu, D

    2011-08-01

    Tritium ((3)H) is released from some nuclear facilities in relatively large quantities. It is a ubiquitous isotope because it enters straight into organisms, behaving essentially identically to its stable analogue (hydrogen). Tritium is a key radionuclide in the aquatic environment, in some cases, contributing significantly to the doses received by aquatic, non-human biota and by humans. The updated model presented here is based on more standardized, comprehensive assessments than previously used for the aquatic food chain, including the benthic flora and fauna, with an explicit application to the Danube ecosystem, as well as an extension to the special case of dissolved organic tritium (DOT). The model predicts the organically bound tritium (OBT) in the primary producers (the autotrophs, such as phytoplankton and algae) and in the consumers (the heterotrophs) using their bioenergetics, which involves the investigation of energy expenditure, losses, gains and efficiencies of transformations in the body. The model described in the present study intends to be more specific than a screening-level model, by including a metabolic approach and a description of the direct uptake of DOT in marine phytoplankton and invertebrates. For a better control of tritium transfer into the environment, not only tritiated water must be monitored, but also the other chemical forms and most importantly OBT, in the food chain.

  12. Acyl-acyl carrier protein as a source of fatty acids for bacterial bioluminescence

    SciTech Connect

    Byers, D.M.; Meighen, E.A.

    1985-09-01

    Pulse-chase experiments with (/sup 3/H)tetradecanoic acid and ATP showed that the bioluminescence-related 32-kDa acyltransferase from Vibrio harveyi can specifically catalyze the deacylation of a /sup 3/H-labeled 18-kDa protein observed in extracts of this bacterium. The 18-kDa protein has been partially purified and its physical and chemical properties strongly indicate that it is fatty acyl-acyl carrier protein (acyl-ACP). Both this V. harveyi (/sup 3/H)acylprotein and (/sup 3/H)palmitoyl-ACP from Escherichia coli were substrates in vitro for either the V. harveyi 32-kDa acyltransferase or the analogous enzyme (34K) from Photobacterium phosphoreum. TLC analysis indicated that the hexane-soluble product of the reaction is fatty acid. No significant cleavage of either E. coli or V. harveyi tetradecanoyl-ACP was observed in extracts of these bacteria unless the 32-kDa or 34K acyltransferase was present. Since these enzymes are believed to be responsible for the supply of fatty acids for reduction to form the aldehyde substrate of luciferase, the above results suggest that long-chain acyl-ACP is the source of fatty acids for bioluminescence.

  13. Time-Resolved Conformational Dynamics in Hydrocarbon Chains

    SciTech Connect

    Minitti, Michael P.; Weber, Peter M.

    2007-06-22

    Internal rotation about carbon-carbon bonds allows N,N-dimethyl-2-butanamine (DM2BA) and N,N-dimethyl-3-hexanamine (DM3HA) to assume multiple conformeric structures. We explore the equilibrium composition and dynamics between such conformeric structures using Rydberg fingerprint spectroscopy. Time constants for conformeric interconversion of DM2BA (at 1.79 eV of internal energy) are 19 and 66 ps, and for DM3HA (1.78 eV) 23 and 41 ps. For the first time, a time-resolved and quantitative view of conformational dynamics of flexible hydrocarbon molecules at high temperatures is revealed.

  14. The surprising dynamics of a chain on a pulley: lift off and snapping.

    PubMed

    Brun, P-T; Audoly, Basile; Goriely, Alain; Vella, Dominic

    2016-06-01

    The motion of weights attached to a chain or string moving on a frictionless pulley is a classic problem of introductory physics used to understand the relationship between force and acceleration. Here, we consider the dynamics of the chain when one of the weights is removed and, thus, one end is pulled with constant acceleration. This simple change has dramatic consequences for the ensuing motion: at a finite time, the chain 'lifts off' from the pulley, and the free end subsequently accelerates faster than the end that is pulled. Eventually, the chain undergoes a dramatic reversal of curvature reminiscent of the crack or snap, of a whip. We combine experiments, numerical simulations and theoretical arguments to explain key aspects of this dynamical problem.

  15. Plasmon-induced dynamics of H{sub 2} splitting on a silver atomic chain

    SciTech Connect

    Yan, Lei; Ding, Zijing; Song, Peng; Wang, Fangwei; Meng, Sheng

    2015-08-24

    Localized surface plasmon resonances (LSPR) supported in metal nanostructures can be efficiently harnessed to drive photocatalytic reactions, whose atomic scale mechanism remains a challenge. Here, real-time dynamics of H{sub 2} photosplitting on a linear silver atomic chain, upon exposure to femtosecond laser pulses, has been investigated using time-dependent density functional theory. The wavelength dependent H{sub 2} splitting process is strongly coupled to LSPR excitation in silver chain. We identify that hot electrons produced in the silver chain by plasmon excitation are transferred to the antibonding state of the adsorbed H{sub 2} and trigger H{sub 2} dissociation, consistent with experimental observations. Increasing illumination intensity and the length of atomic chain promote H{sub 2} splitting, thanks to stronger LSPR. Dynamic electronic response can be quantitatively described within the present approach, providing insights towards a complete fundamental understanding on plasmon-induced chemical reactions at the microscopic scale.

  16. Functionalized chitosan derivatives as nonviral vectors: physicochemical properties of acylated N,N,N-trimethyl chitosan/oligonucleotide nanopolyplexes.

    PubMed

    Santos, Joyce C C; Moreno, Pedro M D; Mansur, Alexandra A P; Leiro, Victoria; Mansur, Herman S; Pêgo, Ana Paula

    2015-11-07

    Cationic polymers have recently attracted attention due to their proven potential for nonviral gene delivery. In this study, we report novel biocompatible nanocomplexes produced using chemically functionalized N,N,N-trimethyl chitosan (TMC) with different N-acyl chain lengths (C5-C18) associated with single-stranded oligonucleotides. The TMC derivatives were synthesized by covalent coupling reactions of quaternized chitosan with n-pentanoic (C5), n-decanoic (C10), and n-octadecanoic (C18) fatty acids, which were extensively characterized by Fourier transform-infrared spectroscopy (FT-IR) and proton nuclear magnetic resonance ((1)H NMR). These N-acylated TMC derivatives (TMCn) were used as cationic polymeric matrices for encapsulating anionic 18-base single-stranded thiophosphorylated oligonucleotides (ssONs), leading to the formation of polyplexes further characterized by zeta potential (ZP), dynamic light scattering (DLS), binding affinity, transfection efficiency and in vitro cytotoxicity assays. The results demonstrated that the length of the grafted hydrophobic N-acyl chain and the relative amino:phosphate groups ratio (N/P ratio) between the TMC derivatives and ssON played crucial roles in determining the physicochemical properties of the obtained nanocomplexes. While none of the tested derivatives showed appreciable cytotoxicity, the type of acyl chain had a remarkable influence on the cell transfection capacity of TMC-ssON nanocomplexes with the derivatives based on stearic acid showing the best performance based on the results of in vitro assays using a model cell line expressing luciferase (HeLa/Luc705).

  17. Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

    DOE PAGES

    Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

    2015-06-11

    Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[ni(t,z)•ni(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

  18. Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

    SciTech Connect

    Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; Goswami, Monojoy; Sokolov, Alexei P; Sumpter, Bobby G.

    2015-06-11

    Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z), mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[ni(t,z)•ni(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.

  19. Conformations, transverse fluctuations, and crossover dynamics of a semi-flexible chain in two dimensions

    NASA Astrophysics Data System (ADS)

    Huang, Aiqun; Bhattacharya, Aniket; Binder, Kurt

    2014-06-01

    We present a unified scaling description for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length L is comparable to the persistence length ℓp and the case L ≫ ℓp. Our theory captures the early time monomer dynamics of a stiff chain characterized by t3/4 dependence for the mean square displacement of the monomers, but predicts a first crossover to the Rouse regime of t2ν/1 + 2ν for τ _1 ˜ ℓ _p^3, and a second crossover to the purely diffusive dynamics for the entire chain at τ2 ˜ L5/2. We confirm the predictions of this scaling description by studying monomer dynamics of dilute solution of semi-flexible chains under good solvent conditions obtained from our Brownian dynamics (BD) simulation studies for a large choice of chain lengths with number of monomers per chain N = 16-2048 and persistence length ℓp = 1-500 Lennard-Jones units. These BD simulation results further confirm the absence of Gaussian regime for a two-dimensional (2D) swollen chain from the slope of the plot of < R_N^2 > /2L ℓ _p ˜ L/ℓ _p which around L/ℓp ˜ 1 changes suddenly from (L/ℓp) → (L/ℓp)0.5, also manifested in the power law decay for the bond autocorrelation function disproving the validity of the worm-like-chain in 2D. We further observe that the normalized transverse fluctuations of the semiflexible chains for different stiffness √{< l_{bot }^2> }/L as a function of renormalized contour length L/ℓp collapse on the same master plot and exhibits power law scaling √{< l_{bot }^2> }/L ˜ (L/ℓ _p)^η at extreme limits, where η = 0.5 for extremely stiff chains (L/ℓp ≫ 1), and η = -0.25 for fully flexible chains. Finally, we compare the radial distribution functions obtained from our simulation studies with those obtained analytically.

  20. Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

    NASA Astrophysics Data System (ADS)

    Asadinezhad, Ahmad; Kelich, Payam

    2017-01-01

    The effects of nanofiller chemistry and geometry on static and dynamic properties of an aromatic polyester, poly (trimethylene terephthalate), were addressed thanks to long-run classical molecular dynamics simulation. Two carbon nanofillers, graphene and carbon nanotube, were employed, where graphene was used in pristine and functionalized forms and carbon nanotube was used in two different diameters. The nanofiller geometry and chemistry were found to exert significant effects on conformation and dynamic behavior of PTT chain at the interface within the time scale the simulation was performed. It was found that PTT chain underwent interaction of van der Waals type with nanofiller via two subsequent phases, adsorption and orientation. The former stage, with definite characteristic time, involved translation of polymer chain toward interface while the latter was controlled by vibrational motions of chain atoms. The consequence of interaction was an increase in conformational order of polymer chain by transition to folded shape being favorable for any subsequent structural ordering (crystallization). The interaction of polymer with nanofiller gave rise to a reduction in overall mobility of polymer chain characterized by crossover from normal diffusive motion to subdiffusive mode.

  1. Acyl migration kinetics of vegetable oil 1,2-diacylglycerols

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The acyl migration kinetics of long-chain 1,2-diacylglycerol (1,2-DAG) to form 1,3-diacylglycerol (1,3-DAG) over the temperature range of 25 to 80 degrees Celsius were examined using proton NMR spectroscopy. The 1,2-DAG mole fraction of 0.32 at equilibrium was found to be insensitive to temperature...

  2. The chain sucker: Translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow

    NASA Astrophysics Data System (ADS)

    Luo, Kaifu; Metzler, Ralf

    2011-04-01

    Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width R embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/microfluidics. During the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling τ ˜ N/F of the translocation time τ with the driving force F per bead and the number N of monomers per chain. With smaller channel width R, steady state motion cannot be achieved, effecting a nonuniversal dependence of τ on N and F. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate s feature a maximum located at identical smax, while with increasing the driving force or the channel width the value of smax decreases.

  3. Long-Chain Fatty Acid Oxidation Disorders (LC-FAOD) Extension Study for Subjects Previously Enrolled in Triheptanoin Studies.

    ClinicalTrials.gov

    2016-09-15

    Carnitine Palmitoyltransferase (CPT I or CPT II) Deficiency; Very Long Chain Acyl-CoA Dehydrogenase (VLCAD) Deficiency; Long-chain 3-hydroxy-acyl-CoA Dehydrogenase (LCHAD) Deficiency; Trifunctional Protein (TFP) Deficiency; Carnitine-acylcarnitine Translocase (CACT) Deficiency

  4. Heterogeneous chain dynamics and aggregate lifetimes in precise acid-containing polyethylenes: Experiments and simulations

    DOE PAGES

    Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; ...

    2016-11-10

    Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less

  5. Heterogeneous chain dynamics and aggregate lifetimes in precise acid-containing polyethylenes: Experiments and simulations

    SciTech Connect

    Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; Tyagi, Madhusudan; Soles, Christopher L.; Frischknecht, Amalie L.; Winey, Karen I.

    2016-11-10

    Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation of the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.

  6. Brownian Dynamics Simulations of Flow Induced Conformation of Single Polymer Chains

    NASA Astrophysics Data System (ADS)

    Oztekin, Alparslan; Webb, Edward; Zhang, Frank; Cheng, Xuanhong

    2012-11-01

    Coarse-grained molecular dynamics simulation of single polymer chains is conducted to examine flow induced conformational changes of single polymer chains in shear and extensional flows. Dynamic properties of polymeric molecules are described using bead-spring models; these models put coarse grain groups of atoms into single particles, connected to adjacent particles via spring like interactions. A common representation of the bonded interaction, or spring, is given by the Finitely Extensible Non-linear Elastic model. The constants used in the model are determined form single-molecule force spectroscopic experiments. Simulations and experiments will help to achieve a clear picture of how von Willebrand Factor, a blood clotting protein, model system for flow-induced activation, achieves flow sensing at the single protein/polymer level. The model includes bead-bead interactions, hydrodynamic interaction, the volume of the beads and spring-spring interaction for finitely extensible dumbbell and other spring models. The effects of walls on the dynamics of polymer chains are also presented. The results are presented for various chain lengths and flow conditions. Hydrodynamic interaction and the presence of wall have strong influences on the dynamics of the polymer chain.

  7. Collective Chain Dynamics in Lipid Bilayers by Inelastic X-Ray Scattering

    SciTech Connect

    Weiss, Thomas M.; Chen, Poe-Jou; Sinn, Harald; Alp, Ercan E.; Chen, Sow-Hsin; Huang, Huey W.

    2003-06-01

    We investigated the application of inelastic x-ray scattering (IXS) to lipid bilayers. This technique directly measures the dynamic structure factor S(q,{omega}) which is the space-time Fourier transform of the electron density correlation function of the measured system. For a multiatomic system, the analysis of S(q,{omega}) is usually complicated. But for multiple bilayers of lipid, S(q,{omega}) is dominated by chain-chain correlations within individual bilayers. Thus IXS provides a unique probe for the collective dynamics of lipid chains in a bilayer that cannot be obtained by any other method. IXS of dimyristoyl phosphatidylcholine and dimyristoyl phosphatidylcholine + cholesterol at two different concentrations were measured. S(q,{omega}) was analyzed by three-mode hydrodynamic equations, including a thermal diffusive mode and two propagating acoustic modes. We obtained the dispersion curves for the phonons that represent the collective in-plane excitations of lipid chains. The effect of cholesterol on chain dynamics was detected. Our analysis shows the importance of having a high instrument resolution as well as the requirement of sufficient signal-to-noise ratio to obtain meaningful results from such an IXS experiment. The requirement on signal-to-noise also applies to molecular dynamics simulations.

  8. Synthesis of acyl arbutin by an immobilized lipase and its suppressive ability against lipid oxidation in a bulk system and O/W emulsion.

    PubMed

    Nagai, Mizuka; Watanabe, Yoshiyuki; Nomura, Masato

    2009-11-01

    Acyl arbutin was synthesized through the condensation of arbutin with a saturated fatty acid (C6-18) by the immobilized lipase in a batch reaction. The conversion at 10 and 20 g/l-solvent of immobilized lipase reached 45% over 2 d, but the initial reaction rate per amount of immobilized lipase decreased at 20 g/l-solvent. The radical scavenging activity of acyl arbutin in an ethanol solution was independent of the acyl chain length, although the rate constant, k, estimated for the oxidation of methyl linoleate in a bulk system with acyl arbutin by using the Weibull equation, decreased as the acyl chain length increased. This indicates the antioxidative ability of acyl arbutin with a long acyl chain to be due to its lipophilicity. Furthermore, it is suggested that dodecanoyl arbutin mainly acted on the interface between the oil and water phases in an O/W emulsion, and effectively suppressed the oxidation induced at the interface.

  9. Degenerated ground-states in a spin chain with pair interactions: a characterization by symbolic dynamics

    NASA Astrophysics Data System (ADS)

    Corona, L. A.; Salgado-García, R.

    2016-12-01

    In this paper we study a class of one-dimensional spin chain having a highly degenerated set of ground-state configurations. The model consists of spin chain having infinite-range pair interactions with a given structure. We show that the set of ground-state configurations of such a model can be fully characterized by means of symbolic dynamics. Particularly we found that the set ground-state configurations define what in symbolic dynamics is called sofic shift space. Finally we prove that this system has a non-vanishing residual entropy (the topological entropy of the shift space), which can be exactly calculated.

  10. A Two-Layered Model for Dynamic Supply Chain Management Considering Transportation Constraint

    NASA Astrophysics Data System (ADS)

    Tanimizu, Yoshitaka; Harada, Kana; Ozawa, Chisato; Iwamura, Koji; Sugimura, Nobuhiro

    This research proposes a two-layered model for dynamic supply chain management considering transportation constraint. The model provides a method for suppliers to estimate suitable prices and delivery times of products based on not only production schedules but also transportation plans in consideration of constraints about shipping times and loading capacities for transportation. A prototype of dynamic supply chain simulation system was developed and some computational experiments were carried out in order to verify the effectiveness of the model. The prototype system is available to determine suitable shipping times and loading capacities of transportation vehicles.

  11. Dynamic Patterns and Self-Knotting of a Driven Hanging Chain

    NASA Astrophysics Data System (ADS)

    Belmonte, Andrew; Shelley, Michael J.; Eldakar, Shaden T.; Wiggins, Chris H.

    2001-09-01

    When shaken vertically, a hanging chain displays a startling variety of distinct behaviors. We find experimentally that instabilities occur in tonguelike bands of parameter space, to swinging or rotating pendular motion, or to chaotic states. Mathematically, the dynamics are described by a nonlinear wave equation. A linear stability analysis predicts instabilities within the well-known resonance tongues; their boundaries agree very well with experiment. Full simulations of the 3D dynamics reproduce and elucidate many aspects of the experiment. The chain is also observed to tie knots in itself, some quite complex. This is beyond the reach of the current analysis and simulations.

  12. Dynamics and thermal stability of surface-confined metal-organic chains

    NASA Astrophysics Data System (ADS)

    Ecija, D.; Marschall, M.; Reichert, J.; Kasperski, A.; Nieckarz, D.; Szabelski, P.; Auwärter, W.; Barth, J. V.

    2016-01-01

    Understanding the dynamics and thermal stability of metallosupramolecular chains on surfaces is of relevance for the development of molecular connectors in nanoelectronics or other fields. Here we present a combined study using temperature-controlled STM and Monte Carlo simulations to explore the behavior of metal-organic porphyrin chains on Cu(111) based on two-fold pyridyl-Cu-pyridyl coordination motifs. We monitor their behavior in the 180-360 K range, revealing three thermal regimes: i) flexibility up to 240 K, ii) diffusion of chain fragments and partial dissociation into a fluid phase for T > 240 K, and iii) full dissolution with temperatures exceeding ~ 320 K. The experimentally estimated reaction enthalpy of the metal-organic bonding is ~ 0.6 eV. Monte Carlo simulations reproduce qualitatively our STM observations and reveal the preference for linear and extended supramolecular chains with reduced substrate temperatures.

  13. System dynamics research of remanufacturing closed-loop supply chain dominated by the third party.

    PubMed

    Miao, Shidi; Wang, Tengfei; Chen, Deyun

    2017-01-01

    With the rapid development of the electronic information industry in recent years, electronic products are being updated faster and faster, and e-waste recycling has become a common problem around the world. Firstly, this article contrasts recycling at home and abroad using the predicament of Midea Corp. Based on a closed-loop supply chain with the system dynamics method, a model is constructed and simulated. In this model, the collection point coverage rate is introduced to adjust the e-waste recycling rate dynamically. Aiming at a recycling mode dominated by the third party of the closed-loop supply chain, the article mainly discusses the impact on the sales rate and market share of the recycling model by third-party enterprises and compares the total revenue of all supply chains. Simulation results show that the model is more effective and optimal than the traditional recycling model.

  14. Response of a single grafted polyethylene chain to simple shear flow: A Brownian dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Haliloglu, Turkan; Bahar, Ivet; Erman, Burak

    1996-08-01

    The behavior of a single polyethylene chain grafted to an impenetrable surface, under shear flow, is investigated using Brownian dynamics simulations. Both short-range conformational energies and excluded volume effects are included in the model. Simulations are performed in good and poor solvent conditions in order to explore the effect of solvent quality. The shear flow is represented by the superposition of a force profile increasing linearly with the distance from the surface. Distribution of rotational angles, chain dimensions, components of the radius of gyration, segment density distribution, average layer thickness, and average orientation of bond vectors with respect to flow direction are determined and compared with other studies. Above a certain value of the shear rate, a significant increase in chain dimensions is observed for both good and poor solvents, the transition from coiled to stretched state being sharper in poor solvent. In good solvent, chain dimensions along the two perpendicular directions to the flow direction diminish with increasing shear rate. On the other hand, in poor solvent, there is an overall expansion in chain dimensions in all directions at low shear rates, which is subsequently followed by the orientation and alignment of the chain along the direction of flow. The experimentally observed increase in chain dimensions normal to the flow field at low shear rates is evidenced for the first time by simulations.

  15. Studying the lateral chain packing in a ceramide bilayer with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Papadimitriou, N. I.; Karozis, S. N.; Kainourgiakis, M. E.; Charalambopoulou, G. Ch

    2015-01-01

    In this work, we present a novel technique, based on molecular dynamics simulations, that allows the study of the lateral chain packing in a lipid bilayer. It utilizes the radial distribution function of the alkyl chains to determine the arrangement of the chains along the bilayer plane. The positions of the mass centres of the chains are projected onto the bilayer plane and a 2D radial distribution function is calculated for these projections. The proposed technique can be particularly useful for lipid bilayers in the gel (solid) phase where the chains present a limited degree of mobility. As a case study, we have examined a bilayer that consists of ceramide NS 24:0. Ceramide bilayers can be found in the lipid domain of the skin where they have a significant role in its barrier function. The specific bilayer was found (at 300 K) to adopt a strictly hexagonal chain packing with a separation distance between the chains of 0.466 nm, in good agreement with the available experimental data.

  16. Molecular dynamics simulations of end-grafted centipede-like polymers with stiff charged side chains.

    PubMed

    Cao, Q Q; Zuo, C C; Li, L J

    2010-05-01

    We use molecular dynamics simulations to investigate centipede-like polymers with stiff charged side chains, end-grafted to a planar wall. The effect of the grafting density and the Bjerrum length on the conformational behaviour of the brush is examined in detail. In addition, we make a comparison of centipede-like polyelectrolyte (CPE) brushes with neutral centipede-like polymer (NCP) and linear polyelectrolyte (LPE) brushes. At weak electrostatic interaction, the main chains of the CPE chains adopt a strongly stretched conformation, and the monomer density profiles of side chains exhibit a clear oscillatory behaviour. With increasing Bjerrum length, the CPE brush undergoes a collapse transition. Compared to the CPE brushes, the counterion condensation effect is stronger for the LPE brushes, regardless of whether the electrostatic interaction is weak or strong and of whether the grafting density is low or high. Additionally, it is shown that the architecture of the grafted chains makes a weak contribution to the counterion condensation at strong electrostatic interaction. We also find that the electrostatic repulsion between charged side chains can enhance the stiffness of the main chains and thus limit the range of movement of the free-end monomers.

  17. A novel plasmid for detection of N-acyl homoserine lactones.

    PubMed

    Ling, Elizabeth A; Ellison, Matthew L; Pesci, Everett C

    2009-07-01

    Many bacteria utilize acyl-homoserine lactones as cell to cell signals that can regulate the expression of numerous genes. Structural differences in acyl-homoserine lactones produced by different bacteria, such as acyl side chain length and the presence or absence of an oxy group, make many of the commonly used detection bioassays impractical for broad range detection. Here we present a simple, broad range acyl-homoserine lactone detection bioassay that can be used to detect a wide range of these chemical signals. A plasmid (pEAL01) was constructed and transformed into Pseudomonas aeruginosa strain QSC105 to allow for detection of a broad range of acyl-homoserine lactones through induction of a lasB'-lacZ transcriptional fusion. Monitoring beta-galactosidase activity from this bioassay showed that P. aeruginosa strain QSC105 (pEAL01) could detect the presence of eight acyl-homoserine lactones tested at physiological concentrations. This novel strain could also detect acyl-homoserine lactones from the extracts of four different bacteria that produce different acyl-homoserine lactones signals. These data indicate that strain QSC105 (pEAL01) can be used to detect a wide variety of acyl-homoserine lactones by a simple beta-galactosidase assay and this bioassay could be a useful and inexpensive tool to quickly identify the presence of these signal molecules.

  18. Fatty acid acylation of rat brain myelin proteolipid protein in vitro: identification of the lipid donor.

    PubMed

    Bizzozero, O A; Lees, M B

    1986-02-01

    The immediate acyl chain donor for fatty acid esterification of proteolipid protein (PLP) was identified in an in vitro system. Rat brain total membranes, after removal of crude nuclear and mitochondrial fractions, were incubated with radioactive acyl donors, extracted with chloroform/methanol, and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In the presence of [3H]palmitic acid, CoA, ATP, and Mg2+, acylation of endogenous PLP occurred at a linear rate for at least 2 h. The radioactivity was associated with the protein via an ester linkage, mainly as palmitic acid. Omission of ATP, CoA, Mg2+, or all three reduced fatty acid incorporation into PLP to 44, 27, 8, and 4%, respectively, of the values in the complete system. Incubation of the membrane fraction with [3H]palmitoyl-CoA in the absence of CoA and ATP led to highly labeled PLP. These data demonstrate that activation of free fatty acid is required for acylation. Phospholipids and glycolipids were not able to acylate the PLP directly. Finally, when isolated myelin was incubated with [3H]palmitoyl-CoA in the absence of cofactors, only PLP was labeled, thus confirming the identity of palmitoyl-CoA as the direct acyl chain donor and suggesting that the acylating activity and the PLP pool available for acylation are both in the myelin.

  19. Selective acylation of plasma membrane proteins of Mycoplasma agalactiae: the causal agent of agalactia.

    PubMed

    Le Hénaff, M; Guéguen, M M; Fontenelle, C

    2000-01-01

    Revealed by in vivo labeling with (14)C-palmitic acid, about 15 acylated proteins were identified in the plasma membrane of Mycoplasma agalactiae (type strain PG2), including the major component p40. Triton X-114 phase partitioning and Western blotting demonstrated the amphiphilic properties of the acyl proteins and showed that they were also antigenic components. Chemical analyses of fatty acids bound to proteins revealed the following selectivity order within acylation: stearic acid (18:0) > linoleic acid (18:2c) approximately palmitic acid (16:0) > oleic acid (18:1c) > myristic acid (14:0), with 16:0 and 18:1c preferred for the O-acylation and 18:0 for the N-acylation. The ratio [O-ester- + amide-bound acyl chains]/O-ester-linked chains being close to 1.4 as well as the presence of S-glycerylcysteine suggest that acyl proteins in M. agalactiae are true lipoproteins containing N-acyl diacyl glycerylcysteine, probably processed by a mechanism analogous to that described for Gram-negative eubacteria.

  20. Acylation of Ferrocene: A Greener Approach

    ERIC Educational Resources Information Center

    Birdwhistell, Kurt R.; Nguyen, Andy; Ramos, Eric J.; Kobelja, Robert

    2008-01-01

    The acylation of ferrocene is a common reaction used in organic laboratories to demonstrate Friedel-Crafts acylation and the purification of compounds using column chromatography. This article describes an acylation of ferrocene experiment that is more eco-friendly than the conventional acylation experiment. The traditional experiment was modified…

  1. Probing the Phosphopantetheine Arm Conformations of Acyl Carrier Proteins Using Vibrational Spectroscopy

    PubMed Central

    2015-01-01

    Acyl carrier proteins (ACPs) are universal and highly conserved domains central to both fatty acid and polyketide biosynthesis. These proteins tether reactive acyl intermediates with a swinging 4′-phosphopantetheine (Ppant) arm and interact with a suite of catalytic partners during chain transport and elongation while stabilizing the growing chain throughout the biosynthetic pathway. The flexible nature of the Ppant arm and the transient nature of ACP–enzyme interactions impose a major obstacle to obtaining structural information relevant to understanding polyketide and fatty acid biosynthesis. To overcome this challenge, we installed a thiocyanate vibrational spectroscopic probe on the terminal thiol of the ACP Ppant arm. This site-specific probe successfully reported on the local environment of the Ppant arm of two ACPs previously characterized by solution NMR, and was used to determine the solution exposure of the Ppant arm of an ACP from 6-deoxyerythronolide B synthase (DEBS). Given the sensitivity of the probe’s CN stretching band to conformational distributions resolved on the picosecond time scale, this work lays a foundation for observing the dynamic action-related structural changes of ACPs using vibrational spectroscopy. PMID:25080832

  2. Effect of chain stiffness and temperature on the dynamics and microstructure of crystallizable bead-spring polymer melts

    NASA Astrophysics Data System (ADS)

    Nguyen, Hong T.; Hoy, Robert S.

    2016-11-01

    We contrast the dynamics in model unentangled polymer melts of chains of three different stiffnesses: flexible, intermediate, and rodlike. Flexible and rodlike chains, which readily solidify into close-packed crystals (respectively, with randomly oriented and nematically aligned chains), display simple melt dynamics with Arrhenius temperature dependence and a discontinuous change upon solidification. Intermediate-stiffness chains, however, are fragile glass-formers displaying Vogel-Fulcher dynamical arrest, despite the fact that they also possess a nematic-close-packed crystalline ground state. To connect this difference in dynamics to the differing microstructure of the melts, we examine how various measures of structure, including cluster-level metrics recently introduced in studies of colloidal systems, vary with chain stiffness and temperature. No clear static-structural cause of the dynamical arrest is found. However, we find that the intermediate-stiffness chains display qualitatively different dynamical heterogeneity. Specifically, their stringlike motion (cooperative rearrangement) is correlated along chain backbones in a way not found for either flexible or rodlike chains. This activated "crawling" motion is clearly associated with the dynamical arrest observed in these systems, and illustrates one way in which factors controlling the crystallization versus glass formation competition in polymers can depend nonmonotonically on chain stiffness.

  3. Communication: Role of short chain branching in polymer structure and dynamics.

    PubMed

    Kim, Jun Mo; Baig, Chunggi

    2016-02-28

    A comprehensive understanding of chain-branching effects, essential for establishing general knowledge of the structure-property-phenomenon relationship in polymer science, has not yet been found, due to a critical lack of knowledge on the role of short-chain branches, the effects of which have mostly been neglected in favor of the standard entropic-based concepts of long polymers. Here, we show a significant effect of short-chain branching on the structural and dynamical properties of polymeric materials, and reveal the molecular origins behind the fundamental role of short branches, via atomistic nonequilibrium molecular dynamics and mesoscopic Brownian dynamics by systematically varying the strength of the mobility of short branches. We demonstrate that the fast random Brownian kinetics inherent to short branches plays a key role in governing the overall structure and dynamics of polymers, leading to a compact molecular structure and, under external fields, to a lesser degree of structural deformation of polymer, to a reduced shear-thinning behavior, and to a smaller elastic stress, compared with their linear analogues. Their fast dynamical nature being unaffected by practical flow fields owing to their very short characteristic time scale, short branches would substantially influence (i.e., facilitate) the overall relaxation behavior of polymeric materials under various flowing conditions.

  4. Synthesis and evaluation of novel acyl derivatives from jatropha oil as potential lubricant basestocks.

    PubMed

    Sammaiah, Arukali; Padmaja, Korlipara V; Prasad, Rachapudi B N

    2014-05-21

    A novel class of jatropha oil-based acylated derivatives from hydroxy alkyl esters of jatropha fatty acids (C1, C3, C4, and C8) and various anhydrides (C2, C3, C4, and C6) were synthesized and their physicochemical and lubricant properties reported. Jatropha fatty acid alkyl esters were dihydroxylated using the in situ performic acid method and further acylated with different anhydrides to produce acylated derivatives. Acylated derivatives of dihydroxy jatropha fatty acid alkyl esters were charaterized by NMR, FTIR, GC, and GC-MS analysis and were evaluated for their viscosity, viscosity index, pour and flash points, and oxidation stability. Most of the derivatives are either in ISO VG 22 or 32 viscosity grade with good viscosity index. It was observed that increase in acyl chain length and branching in the end-chain ester improved the pour point of the diacyl derivatives. All of the hexanoylated esters exhibited better oxidation stability compared to other acylated products, and their pour points are comparable to those of synthetic esters such as TMP trioleates. In general, isoalcohol esters with longer acyl chains showed promise as potential candidates for hydraulic fluids and metal-working fluids in ISO VG 22 and 32 viscosity range.

  5. N-Acylation During Glidobactin Biosynthesis by the Tridomain Nonribosomal Peptide Synthetase Module GlbF

    PubMed Central

    Imker, Heidi J.; Krahn, Daniel; Clerc, Jérôme; Kaiser, Markus; Walsh, Christopher T.

    2011-01-01

    Summary Glidobactins are hybrid NRPS-PKS natural products that function as irreversible proteasome inhibitors. A variety of medium chain 2(E),4(E)-diene fatty acids N-acylate the peptidolactam core and contribute significantly to the potency of proteasome inhibition. We have expressed the initiation NRPS module GlbF (C-A-T) in Escherichia coli and observe soluble active protein only on co-expression with the 8 kDa MbtH-like protein, GlbE. Following adenylation and installation of Thr as a T-domain thioester, the starter condensation domain utilizes fatty acyl-CoA donors to acylate the Thr1 amino group and generate the fatty acyl-Thr1-S-pantetheinyl-GlbF intermediate to be used in subsequent chain elongation. Previously proposed to be mediated via acyl carrier protein fatty acid donors, direct utilization of fatty acyl-CoA donors for N-acylation of T-domain tethered amino acids is likely a common strategy for chain initiation in NRPS-mediated lipopeptide biosynthesis. PMID:21035730

  6. Neutron reflectivity as a tool to study the interdigitation of grafted polymer chains and its dynamics

    NASA Astrophysics Data System (ADS)

    Leger, Liliane; Restagno, Frédéric; Cousin, Fabrice; Boue, François; Chenneviere, Alexis

    Three series of experiments aimed at characterizing the interdigitation between a brush and a melt, and based on neutron reflectivity, are presented and discussed. The density profile of brush chains has been analysed for series of annealing times, on h-PS brushes in contact with d-PS melts, as a function of molecular weights and grafting densities. We show that the relaxation dynamics of the brush chains can be modelled taking into account the long relaxation time of end tethered chains along with the reptation of the melt chains which accelerates the arm retraction process. Using a non-grafted layer with a thickness smaller than the equilibrium size of the brush when immersed into a thick melt allows one to apply chosen degrees of confinement to the brush. We show that the interdigitation dynamics is affected by such confinements, in a way reminiscent of the change of the glass transition temperature in nanometric PS films. Finally, when the upper d-PS layer is sheared above Tg, flow with large slip at the wall has been observed and interpreted in terms of stretching and expulsion of the grafted chains from the melt. We show how neutron reflectivity directly evidence this expulsion.

  7. Identification of Unusual Phospholipid Fatty Acyl Compositions of Acanthamoeba castellanii

    PubMed Central

    Palusinska-Szysz, Marta; Kania, Magdalena; Turska-Szewczuk, Anna; Danikiewicz, Witold; Russa, Ryszard; Fuchs, Beate

    2014-01-01

    Acanthamoeba are opportunistic protozoan pathogens that may lead to sight-threatening keratitis and fatal granulomatous encephalitis. The successful prognosis requires early diagnosis and differentiation of pathogenic Acanthamoeba followed by aggressive treatment regimen. The plasma membrane of Acanthamoeba consists of 25% phospholipids (PL). The presence of C20 and, recently reported, 28- and 30-carbon fatty acyl residues is characteristic of amoeba PL. A detailed knowledge about this unusual PL composition could help to differentiate Acanthamoeba from other parasites, e.g. bacteria and develop more efficient treatment strategies. Therefore, the detailed PL composition of Acanthamoeba castellanii was investigated by 31P nuclear magnetic resonance spectroscopy, thin-layer chromatography, gas chromatography, high performance liquid chromatography and liquid chromatography-mass spectrometry. Normal and reversed phase liquid chromatography coupled with mass spectrometric detection was used for detailed characterization of the fatty acyl composition of each detected PL. The most abundant fatty acyl residues in each PL class were octadecanoyl (18∶0), octadecenoyl (18∶1 Δ9) and hexadecanoyl (16∶0). However, some selected PLs contained also very long fatty acyl chains: the presence of 28- and 30-carbon fatty acyl residues was confirmed in phosphatidylethanolamine (PE), phosphatidylserine, phosphatidic acid and cardiolipin. The majority of these fatty acyl residues were also identified in PE that resulted in the following composition: 28∶1/20∶2, 30∶2/18∶1, 28∶0/20∶2, 30∶2/20∶4 and 30∶3/20∶3. The PL of amoebae are significantly different in comparison to other cells: we describe here for the first time unusual, very long chain fatty acids with Δ5-unsaturation (30∶35,21,24) and 30∶221,24 localized exclusively in specific phospholipid classes of A. castellanii protozoa that could serve as specific biomarkers for the presence of these

  8. Two fatty acyl reductases involved in moth pheromone biosynthesis

    PubMed Central

    Antony, Binu; Ding, Bao-Jian; Moto, Ken’Ichi; Aldosari, Saleh A.; Aldawood, Abdulrahman S.

    2016-01-01

    Fatty acyl reductases (FARs) constitute an evolutionarily conserved gene family found in all kingdoms of life. Members of the FAR gene family play diverse roles, including seed oil synthesis, insect pheromone biosynthesis, and mammalian wax biosynthesis. In insects, FAR genes dedicated to sex pheromone biosynthesis (pheromone-gland-specific fatty acyl reductase, pgFAR) form a unique clade that exhibits substantial modifications in gene structure and possesses unique specificity and selectivity for fatty acyl substrates. Highly selective and semi-selective ‘single pgFARs’ produce single and multicomponent pheromone signals in bombycid, pyralid, yponomeutid and noctuid moths. An intriguing question is how a ‘single reductase’ can direct the synthesis of several fatty alcohols of various chain lengths and isomeric forms. Here, we report two active pgFARs in the pheromone gland of Spodoptera, namely a semi-selective, C14:acyl-specific pgFAR and a highly selective, C16:acyl-specific pgFAR, and demonstrate that these pgFARs play a pivotal role in the formation of species-specific signals, a finding that is strongly supported by functional gene expression data. The study envisages a new area of research for disclosing evolutionary changes associated with C14- and C16-specific FARs in moth pheromone biosynthesis. PMID:27427355

  9. Quality of service management framework for dynamic chaining of geographic information services

    NASA Astrophysics Data System (ADS)

    Onchaga, Richard

    2006-06-01

    Dynamic chaining of geographic information services (geo-services) is gaining popularity as a new paradigm for evolving flexible geo-information systems and for providing on-demand access to geo-information. In dynamic chaining, disparate geo-services are discovered and composed at run time to yield more elaborate functionality and create value-added geo-information. Common approaches to service chaining discover and compose disparate geo-services based on the functional capability of individual geo-services. The primary concern of common approaches is thus the emergent behavior of the resulting composite geo-service. However, as geo-services become mundane and take on a greater and more strategic role in mission critical processes, deliverable quality of service (QoS) becomes an important concern. QoS concerns operational characteristics of a service that determine its utility in an application context. To address pertinent QoS requirements, a new approach to service chaining becomes necessary. In this paper we propose a QoS-aware chaining approach in which geo-services are discovered, composed and executed considering both functional and QoS requirements. We prescribe a QoS management framework that defines fundamental principles, concepts and mechanisms which can be applied to evolve an effective distributed computing platform for QoS-aware chaining of geo-services - the so-called geo-service infrastructure. The paper also defines an extensible QoS model for services delivered by dynamic compositions of geo-services. The process of orthophoto generation is used to demonstrate the applicability of the prescribed framework to service-oriented geographic information processing.

  10. Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

    NASA Astrophysics Data System (ADS)

    Huizhong, Dong; Hongli, Song

    An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.

  11. Charges and currents in quantum spin chains: late-time dynamics and spontaneous currents

    NASA Astrophysics Data System (ADS)

    Fagotti, Maurizio

    2017-01-01

    We review the structure of the conservation laws in noninteracting spin chains and unveil a formal expression for the corresponding currents. We briefly discuss how interactions affect the picture. In the second part, we explore the effects of a localized defect. We show that the emergence of spontaneous currents near the defect undermines any description of the late-time dynamics by means of a stationary state in a finite chain. In particular, the diagonal ensemble does not work. Finally, we provide numerical evidence that simple generic localized defects are not sufficient to induce thermalization.

  12. Dynamic phase transitions of a driven Ising chain in a dissipative cavity

    NASA Astrophysics Data System (ADS)

    Luo, Xi-Wang; Zhang, Yu-Na; Zhou, Xingxiang; Guo, Guang-Can; Zhou, Zheng-Wei

    2016-11-01

    We study the nonequilibrium quantum phase transition of an Ising chain in a dissipative cavity driven by an external transverse light field. When driving and dissipation are in balance, the system can reach a nonequilibrium steady state which undergoes a superradiant phase transition as the driving strength increases. Interestingly, the superradiant field changes the effective bias of the Ising chain in return and drives its own transition between the ferromagnetic and the paramagnetic phase. We study the rich physics in this system with sophisticated behavior and investigate important issues in its dynamics such as the stability of the system and criticality of the phase transition.

  13. Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions.

    PubMed

    Butler, Jason E; Shaqfeh, Eric S G

    2005-01-01

    Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

  14. Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions

    NASA Astrophysics Data System (ADS)

    Butler, Jason E.; Shaqfeh, Eric S. G.

    2005-01-01

    Using methods adapted from the simulation of suspension dynamics, we have developed a Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules. The polymer molecule is modeled as a chain composed of a series of inextensible, rigid rods with constraints at each joint to ensure continuity of the chain. The linear and rotational velocities of each segment of the polymer chain are described by the slender-body theory of Batchelor [J. Fluid Mech. 44, 419 (1970)]. To include hydrodynamic interactions between the segments of the chain, the line distribution of forces on each segment is approximated by making a Legendre polynomial expansion of the disturbance velocity on the segment, where the first two terms of the expansion are retained in the calculation. Thus, the resulting linear force distribution is specified by a center of mass force, couple, and stresslet on each segment. This method for calculating the hydrodynamic interactions has been successfully used to simulate the dynamics of noncolloidal suspensions of rigid fibers [O. G. Harlen, R. R. Sundararajakumar, and D. L. Koch, J. Fluid Mech. 388, 355 (1999); J. E. Butler and E. S. G. Shaqfeh, J. Fluid Mech. 468, 204 (2002)]. The longest relaxation time and center of mass diffusivity are among the quantities calculated with the simulation technique. Comparisons are made for different levels of approximation of the hydrodynamic interactions, including multibody interactions, two-body interactions, and the "freely draining" case with no interactions. For the short polymer chains studied in this paper, the results indicate a difference in the apparent scaling of diffusivity with polymer length for the multibody versus two-body level of approximation for the hydrodynamic interactions.

  15. An Open-label Phase 2 Study of UX007 (Triheptanoin) in Subjects With Long-Chain Fatty Acid Oxidation Disorders (LC-FAOD)

    ClinicalTrials.gov

    2016-11-23

    Long-chain Fatty Acid Oxidation Disorders (LC-FAOD); Carnitine Palmitoyltransferase (CPT II) Deficiency; Very Long Chain Acyl-CoA Dehydrogenase (VLCAD) Deficiency; Longchain 3-hydroxy-acyl-CoA Dehydrogenase (LCHAD) Deficiency; Trifunctional Protein (TFP) Deficiency

  16. Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

    PubMed Central

    Cote, Yoann; Senet, Patrick; Delarue, Patrice; Maisuradze, Gia G.; Scheraga, Harold A.

    2012-01-01

    Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) γn based on four successive Cα atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs δn formed by the virtual bond joining two consecutive Cα atoms (n, n + 1) and the bonds joining these Cα atoms to their respective Cβ atoms] was analyzed. The motions of SCs (δn) and MC (γn) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (δn) and those of the MC (γn) are generally poorly correlated on a ps time-scale with a correlation increasing with time to reach a maximum value at about 10 ns. This maximum value is close to the correlation between the δn(t) and γn(t) time-series extracted from the entire duration of the MD runs (400 ns) and varies significantly along the amino acid sequence. High correlations between the SC and MC motions [δ(t) and γ(t) time-series] were found only in flexible regions of the protein for a few residues which contribute the most to the slowest collective modes of the molecule. These results are a possible indication of the role of the flexible regions of proteins for the biological function and folding. PMID:22689963

  17. Instability dynamics and breather formation in a horizontally shaken pendulum chain.

    PubMed

    Xu, Y; Alexander, T J; Sidhu, H; Kevrekidis, P G

    2014-10-01

    Inspired by the experimental results of Cuevas et al. [Phys. Rev. Lett. 102, 224101 (2009)], we consider theoretically the behavior of a chain of planar rigid pendulums suspended in a uniform gravitational field and subjected to a horizontal periodic driving force applied to the pendulum pivots. We characterize the motion of a single pendulum, finding bistability near the fundamental resonance and near the period-3 subharmonic resonance. We examine the development of modulational instability in a driven pendulum chain and find both a critical chain length and a critical frequency for the appearance of the instability. We study the breather solutions and show their connection to the single-pendulum dynamics and extend our analysis to consider multifrequency breathers connected to the period-3 periodic solution, showing also the possibility of stability in these breather states. Finally we examine the problem of breather generation and demonstrate a robust scheme for generation of on-site and off-site breathers.

  18. Dynamic properties of spin-1/2 XY chains (in English)

    NASA Astrophysics Data System (ADS)

    Derzhko, O.; Krokhmalskii, T.

    We have considered a numerical scheme for the calculation of the equilibrium properties of spin-{1/2} XY chains. Within its frames it is necessary to solve in the last resort only the 2N× 2N eigenvalue and eigenvector problem but not the 2^N× 2^N one as for an arbitrary system consisting of N spins {1/2}. To illustrate the approach we have presented some new results. Namely, the xx dynamic structure factor for the Ising model in transverse field, the density of states for the isotropic chain with random intersite couplings and transverse fields that linearly depend on the surrounding couplings, and the zz dynamic structure factor for the Ising model in the random transverse field. The results obtained are hoped to be useful for an interpretation of observable data for one-dimensional spin-{1/2} XY substances.

  19. Stochastic dynamics and control of a driven nonlinear spin chain: the role of Arnold diffusion

    NASA Astrophysics Data System (ADS)

    Chotorlishvili, L.; Toklikishvili, Z.; Berakdar, J.

    2009-09-01

    We study a chain of nonlinear interacting spins driven by a static and a time-dependent magnetic field. The aim is to identify the conditions for the locally and temporally controlled spin switching. Analytical and full numerical calculations show the possibility of stochastic control if the underlying semiclassical dynamics is chaotic. This is achievable by tuning the external field parameters according to the method described in this paper. We show analytically for a finite spin chain that Arnold diffusion is the underlying mechanism for the present stochastic control. Quantum mechanically we consider the regime where the classical dynamics is regular or chaotic. For the latter we utilize the random matrix theory. The efficiency and the stability of the non-equilibrium quantum spin states are quantified by the time dependence of the Bargmann angle related to the geometric phases of the states.

  20. Acylation type determines ghrelin's effects on energy homeostasis in rodents.

    PubMed

    Heppner, Kristy M; Chaudhary, Nilika; Müller, Timo D; Kirchner, Henriette; Habegger, Kirk M; Ottaway, Nickki; Smiley, David L; Dimarchi, Richard; Hofmann, Susanna M; Woods, Stephen C; Sivertsen, Bjørn; Holst, Birgitte; Pfluger, Paul T; Perez-Tilve, Diego; Tschöp, Matthias H

    2012-10-01

    Ghrelin is a gastrointestinal polypeptide that acts through the ghrelin receptor (GHSR) to promote food intake and increase adiposity. Activation of GHSR requires the presence of a fatty-acid (FA) side chain on amino acid residue serine 3 of the ghrelin molecule. However, little is known about the role that the type of FA used for acylation plays in the biological action of ghrelin. We therefore evaluated a series of differentially acylated peptides to determine whether alterations in length or stability of the FA side chain have an impact on the ability of ghrelin to activate GHSR in vitro or to differentially alter food intake, body weight, and body composition in vivo. Fatty acids principally available in the diet (such as palmitate C16) and therefore representing potential substrates for the ghrelin-activating enzyme ghrelin O-acyltransferase (GOAT) were used for dose-, time-, and administration/route-dependent effects of ghrelin on food intake, body weight, and body composition in rats and mice. Our data demonstrate that altering the length of the FA side chain of ghrelin results in the differential activation of GHSR. Additionally, we found that acylation of ghrelin with a long-chain FA (C16) delays the acute central stimulation of food intake. Lastly, we found that, depending on acylation length, systemic and central chronic actions of ghrelin on adiposity can be enhanced or reduced. Together our data suggest that modification of the FA side-chain length can be a novel approach to modulate the efficacy of pharmacologically administered ghrelin.

  1. Monolignol acylation and lignin structure in some nonwoody plants: a 2D NMR study.

    PubMed

    Martínez, Angel T; Rencoret, Jorge; Marques, Gisela; Gutiérrez, Ana; Ibarra, David; Jiménez-Barbero, Jesús; del Río, José C

    2008-11-01

    Lignins from three nonwoody angiosperms were analyzed by 2D NMR revealing important differences in their molecular structures. The Musa textilis milled-wood-lignin (MWL), with a syringyl-to-guaiacyl (S/G) ratio of 9, was strongly acylated (near 85% of side-chains) at the gamma-carbon by both acetates and p-coumarates, as estimated from (1)H-(13)C correlations in C(gamma)-esterified and C(gamma)-OH units. The p-coumarate H(3,5)-C(3,5) correlation signal was completely displaced by acetylation, and disappeared after alkali treatment, indicating that p-coumaric acid was esterified maintaining its free phenolic group. By contrast, the Cannabis sativa MWL (S/G approximately 0.8) was free of acylating groups, and the Agave sisalana MWL (S/G approximately 4) showed high acylation degree (near 80%) but exclusively with acetates. Extensive C(gamma)-acylation results in the absence (in M. textilis lignin) or low abundance (4% in A. sisalana lignin) of beta-beta' resinol linkages, which require free C(gamma)-OH to form the double tetrahydrofuran ring. However, minor signals revealed unusual acylated beta-beta' structures confirming that acylation is produced at the monolignol level, in agreement with chromatographic identification of gamma-acetylated sinapyl alcohol among the plant extractives. In contrast, resinol substructures involved 22% side-chains in the C.sativa MWL. The ratio between beta-beta' and beta-O-4' side-chains in these and other MWL varied from 0.32 in C.sativa MWL to 0.02 in M. textilis MWL, and was inversely correlated with the degree of acylation. The opposite was observed for the S/G ratio that was directly correlated with the acylation degree. Monolignol acylation is discussed as a mechanism potentially involved in the control of lignin structure.

  2. Palmitoyl-acyl carrier protein (ACP) thioesterase and the evolutionary origin of plant acyl-ACP thioesterases.

    PubMed Central

    Jones, A; Davies, H M; Voelker, T A

    1995-01-01

    Acyl-acyl carrier protein (ACP) thioesterases play an essential role in chain termination during de novo fatty acid synthesis and in the channeling of carbon flux between the two lipid biosynthesis pathways in plants. We have discovered that there are two distinct but related thioesterase gene classes in higher plants, termed FatA and FatB, whose evolutionary divergence appears to be ancient. FatA encodes the already described 18:1-ACP thioesterase. In contrast, FatB representatives encode thioesterases preferring acyl-ACPs having saturated acyl groups. We unexpectedly obtained a 16:0-ACP thioesterase cDNA from Cuphea hookeriana seed, which accumulate predominantly 8:0 and 10:0. The 16:0 thioesterase transcripts were found in non-seed tissues, and expression in transgenic Brassica napus led to the production of a 16:0-rich oil. We present evidence that this type of FatB gene is ancient and ubiquitous in plants and that specialized plant medium-chain thioesterases have evolved independently from such enzymes several times during angiosperm evolution. Also, the ubiquitous 18:1-ACP thioesterase appears to be a derivative of a 16:0 thioesterase. PMID:7734968

  3. Consistent model reduction of polymer chains in solution in dissipative particle dynamics: Model description

    NASA Astrophysics Data System (ADS)

    Moreno, Nicolas; Nunes, Suzana P.; Calo, Victor M.

    2015-11-01

    We introduce a framework for model reduction of polymer chain models for dissipative particle dynamics (DPD) simulations, where the properties governing the phase equilibria such as the characteristic size of the chain, compressibility, density, and temperature are preserved. The proposed methodology reduces the number of degrees of freedom required in traditional DPD representations to model equilibrium properties of systems with complex molecules (e.g., linear polymers). Based on geometrical considerations we explicitly account for the correlation between beads in fine-grained DPD models and consistently represent the effect of these correlations in a reduced model, in a practical and simple fashion via power laws and the consistent scaling of the simulation parameters. In order to satisfy the geometrical constraints in the reduced model we introduce bond-angle potentials that account for the changes in the chain free energy after the model reduction. Following this coarse-graining process we represent high molecular weight DPD chains (i.e., ≥ 200 beads per chain) with a significant reduction in the number of particles required (i.e., ≥ 20 times the original system). We show that our methodology has potential applications modeling systems of high molecular weight molecules at large scales, such as diblock copolymer and DNA.

  4. Slow spin dynamics between ferromagnetic chains in a pure-inorganic framework.

    PubMed

    David, Rénald; Kabbour, Houria; Colis, Silviu; Mentré, Olivier

    2013-12-02

    The crystal structure of the new phase BaCo(II)2(As(III)3O6)2·2(H2O) is built from the stacking of infinite [BaCo2(As3O6)2·H2O] sheets containing ∞[Co(II)O4](6-) chains interconnected by perpendicular ∞[As(III)O2](-) chains. It shows a metamagnetic transition below ∼9 K at a critical field of ∼0.11 T, leading to a moment value of 70% of the expected saturation, related to the spin flip between individual robust canted ferromagnetic chains. We propose a field-dependent scenario with magnetic moments lying in the Co(II)O6 octahedral basal planes, fully compatible with our experimental results. Magnetic measurements under ac-field show slow spin dynamics with an intrinsic single-chain magnet (SCM)-like component slightly modified in the field-aligned regime. The characteristic relaxation time and energy barrier are about τo = 5.1 × 10(-10) s and Δτ = 35.3 K at H(dc) = 0, respectively, which falls close to values found for other (but organometallic) SCM Co(II) chains. This magnetic behavior is unique in the field of pure-inorganic compounds.

  5. Translocation of a Polymer Chain across a Nanopore: A Brownian Dynamics Simulation Study

    NASA Technical Reports Server (NTRS)

    Tian, Pu; Smith, Grant D.

    2003-01-01

    We carried out Brownian dynamics simulation studies of the translocation of single polymer chains across a nanosized pore under the driving of an applied field (chemical potential gradient). The translocation process can be either dominated by the entropic barrier resulted from restricted motion of flexible polymer chains or by applied forces (or chemical gradient across the wall), we focused on the latter case in our studies. Calculation of radius of gyrations at the two opposite sides of the wall shows that the polymer chains are not in equilibrium during the translocation process. Despite this fact, our results show that the one-dimensional diffusion and the nucleation model provide an excellent description of the dependence of average translocation time on the chemical potential gradients, the polymer chain length and the solvent viscosity. In good agreement with experimental results and theoretical predictions, the translocation time distribution of our simple model shows strong non-Gaussian characteristics. It is observed that even for this simple tubelike pore geometry, more than one peak of translocation time distribution can be generated for proper pore diameter and applied field strengths. Both repulsive Weeks-Chandler-Anderson and attractive Lennard-Jones polymer-nanopore interaction were studied, attraction facilitates the translocation process by shortening the total translocation time and dramatically improve the capturing of polymer chain. The width of the translocation time distribution was found to decrease with increasing temperature, increasing field strength, and decreasing pore diameter.

  6. Lattice Dynamics of the Binary Aperiodic Chains of Atoms I:. Fractal Dimension of Phonon Spectra

    NASA Astrophysics Data System (ADS)

    Salejda, Włodzimierz

    The microscopic harmonic model of lattice dynamics of the binary chains of atoms is formulated and studied numerically. The dependence of spring constants of the nearest-neighbor (NN) interactions on the average distance between atoms are taken into account. The covering fractal dimensions Df{( c ; )} of the Cantor-set-like phonon spec-tra (PS) of generalized Fibonacci and non-Fibonaccian aperiodic chains containing of 16384≤N≤33461 atoms are determined numerically. The dependence of Df{( c ; )} on the strength Q of NN interactions and on R=mH/mL, where mH and mL denotes the mass of heavy and light atoms, respectively, are calculated for a wide range of Q and R. In particular we found: (1) The fractal dimension Df{( c ; )} of the PS for the so-called goldenmean, silver-mean, bronze-mean, dodecagonal and Severin chain shows a local maximum at increasing magnitude of Q and R>1 (2) At sufficiently large Q we observe power-like diminishing of Df{( c ; )} , i.e. Df{( c ; )} ( {R > 1, Q} ; ) = a ḑot Qα , where α=-0.14±0.02 and α=-0.10±0.02 for the above specified chains and so-called octagonal, copper-mean, nickel-mean, Thue-Morse, Rudin-Shapiro chain, respectively.

  7. Dynamical view of the positions of key side chains in protein-protein recognition.

    PubMed Central

    Kimura, S R; Brower, R C; Vajda, S; Camacho, C J

    2001-01-01

    When a complex is constructed from the separately determined rigid structures of a receptor and its ligand, some key side chains are usually in wrong positions. These distortions of the interface yield an apparent loss in affinity and would unfavorably affect the kinetics of association. It is generally assumed that the interacting proteins should drive the appropriate conformational changes, leading to their complementarity, but this hypothesis does not explain their fast association rates. However, nanosecond explicit solvent molecular dynamics simulations of misfolded surface side chains from the independently solved structures of barstar, bovine pancreatic trypsin inhibitor, and lysozyme show that even before any receptor-ligand interaction, key side chains frequently visit the rotamer conformations seen in the complex. We show that these simple structural motifs can reconcile most of the binding affinity required for a rapid and highly specific association process. Side chains amenable to induced fit are also identified. These results corroborate that solvent-side chain interactions play a critical role in the recognition process. Our findings are also supported by crystallographic data. PMID:11159432

  8. Lean production in improving supply chain performance through hybrid model SCOR 11.0 - system dynamics

    NASA Astrophysics Data System (ADS)

    Saleh, Chairul; Fatcha Mubiena, Ghaida; Immawan, Taufiq; Hassan, Azmi

    2016-02-01

    Supply Chain Operation Reference (SCOR) is a method to measure supply chain serving the business process framework, performance indicators and unique technologies to support communication and collaboration among supply chain partners. The objective of this paper is to measure Supply Chain Management performance by using SCOR version 11.0 for production typology of MTS-MTO in Indonesian Batik Industry. This research combines SCOR's model and System Dynamics in order to predict the complex activities on batik industry. The hybrid SCOR-SD could identify the interaction among five attributes with the associated variables simultaneously. The results are obtained after the performance of lean production application is increased and the targets are achieved, even exceeding the target. For reliability attributes that associated with perfect order fulfilment started from 2015 to 2019 respectively are calculated as 80.06%, 103.53%, 105.58%, 93.76%, and 72.17%. Responsiveness attributes associated with the order fulfilment cycle time, respectively 122.45%, 149.10%, 159.26%, 131.53%, and 119.36%. Attributes associated with the total cost of service charge respectively 93.46%, 93.53%, 93.45%, 93.49, and 93.49%. Attributes associated with cash management assets to cash cycle time in a row were 160%, 153%, 146.3%, 150%, and 126.7%. The latter attribute is agility attributes associated with supply chain flexibility upside respectively 100%, 87.2%, 100%, 82%, and 82%.

  9. Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

    PubMed

    Mugler, Andrew; Tans, Sander J; Mashaghi, Alireza

    2014-11-07

    Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

  10. Molecular dynamics simulation of secondary sorption behavior of montmorillonite modified by single chain quaternary ammonium cations.

    PubMed

    Zhao, Qian; Burns, Susan E

    2012-04-03

    Organoclays synthesized from single chain quaternary ammonium cations (QAC) ((CH(3))(3)NR(+)) exhibit different mechanisms for the sorption of nonpolar organic compounds as the length of the carbon chain is increased. The interaction between a nonpolar sorbate and an organoclay intercalated with small QACs has been demonstrated to be surface adsorption, while partitioning is the dominant mechanism in clays intercalated with long chain surfactants. This study presents the results of a molecular dynamics (MD) simulation performed to examine the sorption mechanisms of benzene in the interlayer of three organoclays with chain lengths ranging from 1 to 16 carbons: tetramethylammonium (TMA) clay; decyltrimethylammonium (DTMA) clay; and hexadecyltrimethylammonium (HDTMA) clay. The basis of the overall simulation was a combined force field of ClayFF and CVFF. In the simulations, organic cations were intercalated and benzene molecules were introduced to the interlayer, followed by whole system NPT and NVT time integration. Trajectories of all the species were recorded after the system reached equilibrium and subsequently analyzed. Simulation results confirmed that the arrangement of the surfactants controlled the sorption mechanism of organoclays. Benzene molecules were observed to interact directly with the clay surface in the presence of TMA cations, but tended to interact with the aliphatic chain of the HDTMA cation in the interlayer. The simulation provided insight into the nature of the adsorption/partitioning mechanisms in organoclays, and explained experimental observations of decreased versus increased uptake capacities as a function of increasing total organic carbon (TOC) for TMA clay and HDTMA clay, respectively. The transition of sorption mechanisms was also quantified with simulation of DTMA clay, with a chain length between that of TMA and HDTMA. Furthermore, this study suggested that at the molecular level, the controlling factor for the ultimate sorption

  11. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid–vapor interface

    SciTech Connect

    Nagayama, Gyoko Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-07

    The structure and thermodynamic properties of the liquid–vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid–vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid–vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid–vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid–vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  12. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface

    NASA Astrophysics Data System (ADS)

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  13. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

    PubMed

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-07

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  14. Molecular dynamics simulation aiming at interfacial characteristics of polymer chains on nanotubes with different layers

    NASA Astrophysics Data System (ADS)

    Li, Kun; Gu, Boqin; Zhu, Wanfu

    2017-03-01

    A molecular dynamics (MD) simulations study is performed on multiwalled carbon nanotubes (MWNTs)/acrylonitrile-butadiene rubber (NBR) composites. The physisorption and interfacial characteristics between the various MWNTs and polymer macromolecular chains are identified. The effects of nanotube layers on the nanotubes/polymer interactions are examined. Each of the situation result and surface features is characterized by binding energy (Eb). It is shown that the binding energy (Eb) increase with the number of layers.

  15. Dispersion curves from short-time molecular dynamics simulation. 1. Diatomic chain results

    SciTech Connect

    Noid, D.W.; Broocks, B.T.; Gray, S.K.; Marple, S.L.

    1988-06-16

    The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, i.e., along a trajectory. The method is ideally suited for analyzing molecular dynamics simulations of large systems.

  16. Pressure dependence of structural and dynamical properties in melt sulfur: Evidence for two successive chain breakages

    NASA Astrophysics Data System (ADS)

    Zhao, G.; Mu, H. F.

    2014-11-01

    Using ab initio molecular dynamics simulations, the pressure dependence of structural and dynamical properties in melt sulfur along 1085 K isotherm was studied with pressure range from 4.18 to 15.8 GPa. It was found that the atomic chains in melt sulfur abruptly break twice with increasing pressure. The electric density of state near EF and the diffusion coefficient both show abrupt increase along with these two times of breakages. These changes would strongly influence the physical properties such as conductivity and viscosity. However, the density discontinuity along the isotherm, indication of a first-order phase transition, was not found.

  17. Observing the nonequilibrium dynamics of the quantum transverse-field Ising chain in circuit QED.

    PubMed

    Viehmann, Oliver; von Delft, Jan; Marquardt, Florian

    2013-01-18

    We show how a quantum Ising spin chain in a time-dependent transverse magnetic field can be simulated and experimentally probed in the framework of circuit QED with current technology. The proposed setup provides a new platform for observing the nonequilibrium dynamics of interacting many-body systems. We calculate its spectrum to offer a guideline for its initial experimental characterization. We demonstrate that quench dynamics and the propagation of localized excitations can be observed with the proposed setup and discuss further possible applications and modifications of this circuit QED quantum simulator.

  18. Scaling of the dynamics of flexible Lennard-Jones chains: Effects of harmonic bonds.

    PubMed

    Veldhorst, Arno A; Dyre, Jeppe C; Schrøder, Thomas B

    2015-11-21

    The previous paper [A. A. Veldhorst et al., J. Chem. Phys. 141, 054904 (2014)] demonstrated that the isomorph theory explains the scaling properties of a liquid of flexible chains consisting of ten Lennard-Jones particles connected by rigid bonds. We here investigate the same model with harmonic bonds. The introduction of harmonic bonds almost completely destroys the correlations in the equilibrium fluctuations of the potential energy and the virial. According to the isomorph theory, if these correlations are strong a system has isomorphs, curves in the phase diagram along which structure, dynamics, and the excess entropy are invariant. The Lennard-Jones chain liquid with harmonic bonds does have curves in the phase diagram along which the structure and dynamics are invariant. The excess entropy is not invariant on these curves, which we refer to as "pseudoisomorphs." In particular, this means that Rosenfeld's excess-entropy scaling (the dynamics being a function of excess entropy only) does not apply for the Lennard-Jones chain with harmonic bonds.

  19. Acyl tunichlorins: a new class of nickel chlorins isolated from the Caribbean tunicate Trididemnum solidum.

    PubMed Central

    Sings, H L; Bible, K C; Rinehart, K L

    1996-01-01

    A new class of nickel-containing chlorins (acyl tunichlorins) has been isolated from the Caribbean tunicate Trididemnum solidum. The structures of 28 of these nickel (II) hydroporphyrins were elucidated using mass spectrometry, one- and two-dimensional NMR spectroscopy, and chemical degradation/derivatization. Unique structural features of these compounds include the diversity of aliphatic side chains, which are derived from C14:0 to C22:6 fatty acids, and their location at an unprecedented position at C-2a on the hydroporphyrin nucleus. No chlorins with ester-linked acyl side chains at C-2a have been reported previously. Although the exact biological role that these compounds play in T. solidum remains unknown, acyl tunichlorins represent the only nickel-containing chlorins to be isolated from a living system and are the C-2a acyl derivatives of tunichlorin, a nickel chlorin reported by this laboratory in 1988. PMID:8855217

  20. Chain representations of Open Quantum Systems and Lieb-Robinson like bounds for the dynamics

    NASA Astrophysics Data System (ADS)

    Woods, Mischa

    2013-03-01

    This talk is concerned with the mapping of the Hamiltonian of open quantum systems onto chain representations, which forms the basis for a rigorous theory of the interaction of a system with its environment. This mapping progresses as an interaction which gives rise to a sequence of residual spectral densities of the system. The rigorous mathematical properties of this mapping have been unknown so far. Here we develop the theory of secondary measures to derive an analytic, expression for the sequence solely in terms of the initial measure and its associated orthogonal polynomials of the first and second kind. These mappings can be thought of as taking a highly nonlocal Hamiltonian to a local Hamiltonian. In the latter, a Lieb-Robinson like bound for the dynamics of the open quantum system makes sense. We develop analytical bounds on the error to observables of the system as a function of time when the semi-infinite chain in truncated at some finite length. The fact that this is possible shows that there is a finite ``Speed of sound'' in these chain representations. This has many implications of the simulatability of open quantum systems of this type and demonstrates that a truncated chain can faithfully reproduce the dynamics at shorter times. These results make a significant and mathematically rigorous contribution to the understanding of the theory of open quantum systems; and pave the way towards the efficient simulation of these systems, which within the standard methods, is often an intractable problem. EPSRC CDT in Controlled Quantum Dynamics, EU STREP project and Alexander von Humboldt Foundation

  1. Influence of Solute Charge and Pyrrolidinium Ionic Liquid Alkyl Chain Length on Probe Rotational Reorientation Dynamics

    SciTech Connect

    Guo, Jianchang; Mahurin, Shannon Mark; Baker, Gary A; Hillesheim, Patrick C; Dai, Sheng; Shaw, Robert W

    2014-01-01

    In recent years, the effect of molecular charge on the rotational dynamics of probe solutes in room temperature ionic liquids (RTILs) has been a subject of growing interest. For the purpose of extending our understanding of charged solute behavior within RTILs, we have studied the rotational dynamics of three illustrative xanthene fluorescent probes within a series of N-alkylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([Cnmpyr][Tf2N]) RTILs with different n-alkyl chain lengths (n = 3, 4, 6, 8, or 10) using time-resolved fluorescence anisotropy decay. The rotational dynamics of the neutral probe rhodamine B dye lies between the stick and slip boundary conditions due to the influence of specific hydrogen bonding interactions. The rotation of the negatively-charged sulforhodamine 640 is slower than that of its positively-charged counterpart rhodamine 6G. An analysis based upon Stokes-Einstein-Debye hydrodynamics indicates that SR640 adheres to stick boundary conditions due to specific interactions, whereas the faster rotation of R6G is attributed to weaker electrostatic interactions. No dependence of the rotational dynamics on the solvent alkyl chain length was observed for any of the three dyes, suggesting that the specific interactions between dyes and RTILs are independent of this solvent parameter.

  2. Non-Markovian dynamics in the extended cluster spin-1/2 XX chain

    NASA Astrophysics Data System (ADS)

    Mahmoudi, M.; Mahdavifar, S.; Zadeh, T. Mohammad Ali; Soltani, M. R.

    2017-01-01

    We study the dynamics of entanglement, mutual information, and quantum discord in the extended cluster spin-1/2 XX chain, equivalent to a one-dimensional spin-1/2 XX model with three-spin interaction (TSI). Selecting the nearest neighbor pair spins as an open quantum system, the rest of the chain plays the role of the environment. The two-point Heisenberg and the TSI are responsible for coupling between the system and the environment. Although the revival phenomenon of quantum correlations as an indication of non-Markovian dynamics is observed for TSI stronger than the Heisenberg interaction, the study of the trace distance has proven that the dynamical phase transition from the Markovian to the non-Markovian regime happens at a critical value where the TSI is equal to half of the Heisenberg interaction. By focusing on the nearest neighbor pair spins of the environment, we have also shown that the dynamics of quantum correlation in the environment is sensitive to Markovian and non-Markovian regions.

  3. Transportation and dynamic networks: Models, theory, and applications to supply chains, electric power, and financial networks

    NASA Astrophysics Data System (ADS)

    Liu, Zugang

    Network systems, including transportation and logistic systems, electric power generation and distribution networks as well as financial networks, provide the critical infrastructure for the functioning of our societies and economies. The understanding of the dynamic behavior of such systems is also crucial to national security and prosperity. The identification of new connections between distinct network systems is the inspiration for the research in this dissertation. In particular, I answer two questions raised by Beckmann, McGuire, and Winsten (1956) and Copeland (1952) over half a century ago, which are, respectively, how are electric power flows related to transportation flows and does money flow like water or electricity? In addition, in this dissertation, I achieve the following: (1) I establish the relationships between transportation networks and three other classes of complex network systems: supply chain networks, electric power generation and transmission networks, and financial networks with intermediation. The establishment of such connections provides novel theoretical insights as well as new pricing mechanisms, and efficient computational methods. (2) I develop new modeling frameworks based on evolutionary variational inequality theory that capture the dynamics of such network systems in terms of the time-varying flows and incurred costs, prices, and, where applicable, profits. This dissertation studies the dynamics of such network systems by addressing both internal competition and/or cooperation, and external changes, such as varying costs and demands. (3) I focus, in depth, on electric power supply chains. By exploiting the relationships between transportation networks and electric power supply chains, I develop a large-scale network model that integrates electric power supply chains and fuel supply markets. The model captures both the economic transactions as well as the physical transmission constraints. The model is then applied to the New

  4. Structural basis for acyl-group discrimination by human Gcn5L2

    PubMed Central

    Ringel, Alison E.; Wolberger, Cynthia

    2016-01-01

    Gcn5 is a conserved acetyltransferase that regulates transcription by acetylating the N-terminal tails of histones. Motivated by recent studies identifying a chemically diverse array of lysine acyl modifications in vivo, the acyl-chain specificity of the acetyltransferase human Gcn5 (Gcn5L2) was examined. Whereas Gcn5L2 robustly catalyzes lysine acetylation, the acyltransferase activity of Gcn5L2 becomes progressively weaker with increasing acyl-chain length. To understand how Gcn5 discriminates between different acyl-CoA molecules, structures of the catalytic domain of human Gcn5L2 bound to propionyl-CoA and butyryl-CoA were determined. Although the active site of Gcn5L2 can accommodate propionyl-CoA and butyryl-CoA without major structural rearrangements, butyryl-CoA adopts a conformation incompatible with catalysis that obstructs the path of the incoming lysine residue and acts as a competitive inhibitor of Gcn5L2 versus acetyl-CoA. These structures demonstrate how Gcn5L2 discriminates between acyl-chain donors and explain why Gcn5L2 has weak activity for acyl moieties that are larger than an acetyl group. PMID:27377381

  5. Video analysis of sliding chains: A dynamic model based on variable-mass systems

    NASA Astrophysics Data System (ADS)

    Moreno, R.; Page, A.; Riera, J.; Hueso, J. L.

    2015-06-01

    This paper presents an experimental study of the dynamics of a chain sliding off of a table, using video analysis to test a theoretical model. The model consists of two variable-mass subsystems, with friction between the chain and the table and assumes that all links move at the same speed. In order to check the model, the chain position x(t) is obtained using video analysis. The smoothed function x(t) and its derivatives v(t) and a(t) are numerically computed using a local regression algorithm. In this way, the differential equation governing the motion can be directly tested, instead of comparing the position with the solution of the differential equation. Our procedure is very sensitive to deviations between the model and reality, so we can detect the point at which the chain ceases to be in tension and the model is no longer valid. This experiment shows students the limitations of simplified models and offers an opportunity to assess a model's range of validity.

  6. Performance evaluation of Warshall algorithm and dynamic programming for Markov chain in local sequence alignment.

    PubMed

    Khan, Mohammad Ibrahim; Kamal, Md Sarwar

    2015-03-01

    Markov Chain is very effective in prediction basically in long data set. In DNA sequencing it is always very important to find the existence of certain nucleotides based on the previous history of the data set. We imposed the Chapman Kolmogorov equation to accomplish the task of Markov Chain. Chapman Kolmogorov equation is the key to help the address the proper places of the DNA chain and this is very powerful tools in mathematics as well as in any other prediction based research. It incorporates the score of DNA sequences calculated by various techniques. Our research utilize the fundamentals of Warshall Algorithm (WA) and Dynamic Programming (DP) to measures the score of DNA segments. The outcomes of the experiment are that Warshall Algorithm is good for small DNA sequences on the other hand Dynamic Programming are good for long DNA sequences. On the top of above findings, it is very important to measure the risk factors of local sequencing during the matching of local sequence alignments whatever the length.

  7. Conformation and translational diffusion of a xanthan polyelectrolyte chain: Brownian dynamics simulation and single molecule tracking

    NASA Astrophysics Data System (ADS)

    Chun, Myung-Suk; Kim, Chongyoup; Lee, Duck E.

    2009-05-01

    In our recent Brownian dynamics (BD) simulation study, the structure and dynamics of anionic polyelectrolyte xanthan in bulk solution as well as confined spaces of slitlike channel were examined by applying a coarse-grained model with nonlinear bead-spring discretization of a whole chain [J. Jeon and M.-S. Chun, J. Chem. Phys. 126, 154904 (2007)]. This model goes beyond other simulations as they did not consider both long-range electrostatic and hydrodynamic interactions between pairs of beads. Simulation parameters are obtained from the viscometric method of rheology data on the native and sonicated xanthan polysaccharides, which have a contour length less than 1μm . The size of the semiflexible polyelectrolyte can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at a long length scale. For experimental verifications, single molecule visualization was performed on fluorescein-labeled xanthan using an inverted fluorescence microscope, and the motion of an individual molecule was quantified. Experimental results on the conformational changes in xanthan chain in the electrolyte solution have a reasonable trend to agree with the prediction by BD simulations. In the translational diffusion induced by the Debye screening effect, the simulation prediction reveals slightly higher values compared to those of our measurements, although it agrees with the literature data. Considering the experimental restrictions, our BD simulations are verified to model the single polyelectrolyte well.

  8. Dynamical behavior of fractional-order Hastings-Powell food chain model and its discretization

    NASA Astrophysics Data System (ADS)

    Matouk, A. E.; Elsadany, A. A.; Ahmed, E.; Agiza, H. N.

    2015-10-01

    In this work, the dynamical behavior of fractional-order Hastings-Powell food chain model is investigated and a new discretization method of the fractional-order system is introduced. A sufficient condition for existence and uniqueness of the solution of the proposed system is obtained. Local stability of the equilibrium points of the fractional-order system is studied. Furthermore, the necessary and sufficient conditions of stability of the discretized system are also studied. It is shown that the system's fractional parameter has effect on the stability of the discretized system which shows rich variety of dynamical behaviors such as Hopf bifurcation, an attractor crisis and chaotic attractors. Numerical simulations show the tea-cup chaotic attractor of the fractional-order system and the richer dynamical behavior of the corresponding discretized system.

  9. Value-Chain Dynamics of the West Point Foundry, 1817-1911: A Historical Case Analysis in Marketing

    ERIC Educational Resources Information Center

    Petkus, Ed, Jr.

    2013-01-01

    This case provides the opportunity for students to explore marketing and value/supply-chain dynamics in a unique historical context. The West Point Foundry (WPF), located in Cold Spring, New York, was one of the most important manufacturing ventures in the United States from 1817 to 1911. The case outlines the supply-chain details of the WPF as…

  10. New Factorization Techniques and Parallel (log N) Algorithms for Forward Dynamics Solution of Single Closed-Chain Robot Manipulators

    NASA Technical Reports Server (NTRS)

    Fijany, Amir

    1993-01-01

    In this paper parallel 0(log N) algorithms for dynamic simulation of single closed-chain rigid multibody system as specialized to the case of a robot manipulatoar in contact with the environment are developed.

  11. Investigation of some characteristics of polyhydroxy milkweed triglycerides and their acylated derivatives in relation to lubricity.

    PubMed

    Harry-O'kuru, Rogers E; Biresaw, Girma; Cermak, Steven C; Gordon, Sherald H; Vermillion, Karl

    2011-05-11

    Most industrial lubricants are derived from nonrenewable petroleum-based sources. As useful as these lubricants are, their unintended consequences are the pollution of the Earth's environment as a result of the slow degradation of the spent materials. Native seed oils, on the other hand, are renewable and are also biodegradable in the environment, but these oils often suffer a drawback in having lower thermal stability and a shorter shelf life because of the intrinsic -C═C- unsaturation in their structures. This drawback can be overcome, yet the inherent biodegradative property retained, by appropriate derivatization of the oil. Pursuant to this, this study investigated derivatized polyhydroxy milkweed oil to assess its suitability as lubricant. The milkweed plant is a member of the Asclepiadaceae, a family with many genera including the common milkweeds, Asclepias syriaca L., Asclepias speciosa L., Asclepias tuberosa L., etc. The seeds of these species contain mainly C-18 triglycerides that are highly unsaturated, 92%. The olefinic character of this oil has been chemically modified by generating polyhydroxy triglycerides (HMWO) that show high viscosity and excellent moisturizing characteristics. In this work, HMWO have been chemically modified by esterifying their hydroxyl groups with acyl groups of various chain lengths (C2-C5). The results of investigation into the effect of the acyl derivatives' chemical structure on kinematic and dynamic viscosity, oxidation stability, cold-flow (pour point, cloud point) properties, coefficient of friction, wear, and elastohydrodynamic film thickness are discussed.

  12. The effect of chain rigidity on the interfacial layer thickness and dynamics of polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Cheng, Shiwang; Carrillo, Jan-Michael Y.; Carroll, Bobby; Sumpter, Bobby G.; Sokolov, Alexei P.

    There are growing experimental evidences showing the existence of an interfacial layer that has a finite thickness with slowing down dynamics in polymer nanocomposites (PNCs). Moreover, it is believed that the interfacial layer plays a significant role on various macroscopic properties of PNCs. A thicker interfacial layer is found to have more pronounced effect on the macroscopic properties such as the mechanical enhancement. However, it is not clear what molecular parameter controls the interfacial layer thickness. Inspired by our recent computer simulations that showed the chain rigidity correlated well with the interfacial layer thickness, we performed systematic experimental studies on different polymer nanocomposites by varying the chain stiffness. Combining small-angle X-ray scattering, broadband dielectric spectroscopy and temperature modulated differential scanning calorimetry, we find a good correlation between the polymer Kuhn length and the thickness of the interfacial layer, confirming the earlier computer simulations results. Our findings provide a direct guidance for the design of new PNCs with desired properties.

  13. Effect of Composition and Chain Length on χ Parameter of Polyolefin Blends: A Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Khare, Rajesh; Ravichandran, Ashwin; Chen, Chau-Chyun

    Polymer blends exhibit complex phase behavior which is governed by several factors including temperature, composition and molecular weight of components. The thermodynamics of polymer blends is commonly described using the χ parameter. While variety of experimental studies exist on identifying the factors affecting the χ parameter, a detailed molecular scale understanding of these is a topic of current research. We have studied the effect of blend composition and chain length on χ parameter values for two model polyolefin blends. The blends studied are: polyisobutylene (PIB)/polybutadiene (PBD) and polyethylene (PE)/atactic polypropylene (aPP). Molecular dynamics simulations in combination with the integral equation theory formalism proposed by Schweizer and Curro [Journal of Chemical Physics, 91, 5059 (1989)] are used to determine the χ parameter for these systems and thereby study the effect of blend composition and chain length. The resulting χ parameter values are explained in terms of the molecular structure of these polymeric systems.

  14. Inhomogeneous quasi-adiabatic driving of quantum critical dynamics in weakly disordered spin chains

    NASA Astrophysics Data System (ADS)

    Rams, Marek M.; Mohseni, Masoud; del Campo, Adolfo

    2016-12-01

    We introduce an inhomogeneous protocol to drive a weakly disordered quantum spin chain quasi-adiabatically across a quantum phase transition and minimize the residual energy of the final state. The number of spins that simultaneously reach the critical point is controlled by the length scale in which the magnetic field is modulated, introducing an effective size that favors adiabatic dynamics. The dependence of the residual energy on this length scale and the velocity at which the magnetic field sweeps out the chain is shown to be nonmonotonic. We determine the conditions for an optimal suppression of the residual energy of the final state and show that inhomogeneous driving can outperform conventional adiabatic schemes based on homogeneous control fields by several orders of magnitude.

  15. Activation of Exogenous Fatty Acids to Acyl-Acyl Carrier Protein Cannot Bypass FabI Inhibition in Neisseria*

    PubMed Central

    Yao, Jiangwei; Bruhn, David F.; Frank, Matthew W.; Lee, Richard E.; Rock, Charles O.

    2016-01-01

    Neisseria is a Gram-negative pathogen with phospholipids composed of straight chain saturated and monounsaturated fatty acids, the ability to incorporate exogenous fatty acids, and lipopolysaccharides that are not essential. The FabI inhibitor, AFN-1252, was deployed as a chemical biology tool to determine whether Neisseria can bypass the inhibition of fatty acid synthesis by incorporating exogenous fatty acids. Neisseria encodes a functional FabI that was potently inhibited by AFN-1252. AFN-1252 caused a dose-dependent inhibition of fatty acid synthesis in growing Neisseria, a delayed inhibition of growth phenotype, and minimal inhibition of DNA, RNA, and protein synthesis, showing that its mode of action is through inhibiting fatty acid synthesis. Isotopic fatty acid labeling experiments showed that Neisseria encodes the ability to incorporate exogenous fatty acids into its phospholipids by an acyl-acyl carrier protein-dependent pathway. However, AFN-1252 remained an effective antibacterial when Neisseria were supplemented with exogenous fatty acids. These results demonstrate that extracellular fatty acids are activated by an acyl-acyl carrier protein synthetase (AasN) and validate type II fatty acid synthesis (FabI) as a therapeutic target against Neisseria. PMID:26567338

  16. Finite-Temperature Entanglement Dynamics in an Anisotropic Two-Qubit Heisenberg Spin Chain

    NASA Astrophysics Data System (ADS)

    Chen, Tao; Shan, Chuanjia; Li, Jinxing; Liu, Tangkun; Huang, Yanxia; Li, Hong

    2010-07-01

    This paper investigates the entanglement dynamics of an anisotropic two-qubit Heisenberg spin chain in the presence of decoherence at finite temperature. The time evolution of the concurrence is studied for different initial Werner states. The influences of initial purity, finite temperature, spontaneous decay and Hamiltonian on the entanglement evolution are analyzed in detail. Our calculations show that the finite temperature restricts the evolution of the entanglement all the time when the Hamiltonian improves it and the spontaneous decay to the reservoirs can produce quantum entanglement with the anisotropy of spin-spin interaction. Finally, the steady-state concurrence which may remain non-zero for low temperature is also given.

  17. Dissipative soliton dynamics in a discrete magnetic nano-dot chain

    SciTech Connect

    Lee, Kyeong-Dong; You, Chun-Yeol; Song, Hyon-Seok; Shin, Sung-Chul; Park, Byong-Guk

    2014-02-03

    Soliton dynamics is studied in a discrete magnetic nano-dot chain by means of micromagnetic simulations together with an analytic model equation. A soliton under a dissipative system is driven by an applied field. The field-driven dissipative soliton enhances its mobility nonlinearly, as the characteristic frequency and the intrinsic Gilbert damping decrease. During the propagation, the soliton emits spin waves which act as an extrinsic damping channel. The characteristic frequency, the maximum velocity, and the localization length of the soliton are found to be proportional to the threshold field, the threshold velocity, and the initial mobility, respectively.

  18. Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

    Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

  19. Dynamics of hot random quantum spin chains: from anyons to Heisenberg spins

    NASA Astrophysics Data System (ADS)

    Parameswaran, Siddharth; Potter, Andrew; Vasseur, Romain

    2015-03-01

    We argue that the dynamics of the random-bond Heisenberg spin chain are ergodic at infinite temperature, in contrast to the many-body localized behavior seen in its random-field counterpart. First, we show that excited-state real-space renormalization group (RSRG-X) techniques suffer from a fatal breakdown of perturbation theory due to the proliferation of large effective spins that grow without bound. We repair this problem by deforming the SU (2) symmetry of the Heisenberg chain to its `anyonic' version, SU(2)k , where the growth of effective spins is truncated at spin S = k / 2 . This enables us to construct a self-consistent RSRG-X scheme that is particularly simple at infinite temperature. Solving the flow equations, we compute the excited-state entanglement and show that it crosses over from volume-law to logarithmic scaling at a length scale ξk ~eαk3 . This reveals that (a) anyon chains have random-singlet-like excited states for any finite k; and (b) ergodicity is restored in the Heisenberg limit k --> ∞ . We acknowledge support from the Quantum Materials program of LBNL (RV), the Gordon and Betty Moore Foundation (ACP), and UC Irvine startup funds (SAP).

  20. Dynamic effective connectivity in cortically embedded systems of recurrently coupled synfire chains.

    PubMed

    Trengove, Chris; Diesmann, Markus; van Leeuwen, Cees

    2016-02-01

    As a candidate mechanism of neural representation, large numbers of synfire chains can efficiently be embedded in a balanced recurrent cortical network model. Here we study a model in which multiple synfire chains of variable strength are randomly coupled together to form a recurrent system. The system can be implemented both as a large-scale network of integrate-and-fire neurons and as a reduced model. The latter has binary-state pools as basic units but is otherwise isomorphic to the large-scale model, and provides an efficient tool for studying its behavior. Both the large-scale system and its reduced counterpart are able to sustain ongoing endogenous activity in the form of synfire waves, the proliferation of which is regulated by negative feedback caused by collateral noise. Within this equilibrium, diverse repertoires of ongoing activity are observed, including meta-stability and multiple steady states. These states arise in concert with an effective connectivity structure (ECS). The ECS admits a family of effective connectivity graphs (ECGs), parametrized by the mean global activity level. Of these graphs, the strongly connected components and their associated out-components account to a large extent for the observed steady states of the system. These results imply a notion of dynamic effective connectivity as governing neural computation with synfire chains, and related forms of cortical circuitry with complex topologies.

  1. Food chain dynamics and potential ecological risks of mercury at the Carson River site

    SciTech Connect

    Peterson, S.C.

    1995-12-31

    The USEPA is conducting a remedial investigation of mercury contamination in the Carson River watershed, located near Carson City in central west Nevada. As a component of this investigation, water, sediment, and tissue samples were collected for mercury speciation and other analyses. Tissues analyses from the seven site-investigation areas and four background areas include: whole-body and fillet analyses of five species of fish, composite and individual analyses of three species of benthic macroinvertebrates, blood, feather and liver analyses of two bird species, composite analyses of zooplankton, and whole-body analyses of lizards. The data are used to develop site-specific estimates of mercury bioaccumulation in aquatic food chains of riverine/riparian, open-water, and mudflat habitats at the Carson River site. Because the behavior and food chain dynamics of mercury in semi-arid ecosystems of the southwestern US is poorly understood, these data can be compared and contrasted with bioaccumulation estimates derived from well-studied ecosystems such as northern temperate lakes. Potential ecological risks of mercury exposure through the food chain and through ingestion of and contact with contaminated media are evaluated for important wildlife receptors occurring at the Carson River site.

  2. Calculations of critical micelle concentration by dissipative particle dynamics simulations: the role of chain rigidity.

    PubMed

    Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V

    2013-09-05

    Micelle formation in surfactant solutions is a self-assembly process governed by complex interplay of solvent-mediated interactions between hydrophilic and hydrophobic groups, which are commonly called heads and tails. However, the head-tail repulsion is not the only factor affecting the micelle formation. For the first time, we present a systematic study of the effect of chain rigidity on critical micelle concentration and micelle size, which is performed with the dissipative particle dynamics simulation method. Rigidity of the coarse-grained surfactant molecule was controlled by the harmonic bonds set between the second-neighbor beads. Compared to flexible molecules with the nearest-neighbor bonds being the only type of bonded interactions, rigid molecules exhibited a lower critical micelle concentration and formed larger and better-defined micelles. By varying the strength of head-tail repulsion and the chain rigidity, we constructed two-dimensional diagrams presenting how the critical micelle concentration and aggregation number depend on these parameters. We found that the solutions of flexible and rigid molecules that exhibited approximately the same critical micelle concentration could differ substantially in the micelle size and shape depending on the chain rigidity. With the increase of surfactant concentration, primary micelles of more rigid molecules were found less keen to agglomeration and formation of nonspherical aggregates characteristic of flexible molecules.

  3. Examining fundamental movement competency and closed chain upper extremity dynamic balance in swimmers.

    PubMed

    Bullock Spt, Garrett S; Brookerson, Nate; Knab, Amy M; Butler, Robert J

    2016-09-16

    Abnormal fundamental movement patterns and upper quarter dynamic balance are proposed mechanisms affecting athletic performance and injury risk. There are few studies investigating functional movement and closed chain upper extremity dynamic stability in swimmers. The purpose of this study was to determine differences in fundamental movement competency and closed chain upper extremity dynamic balance, utilizing the Functional Movement Screen (FMS) and Upper Quarter Y-Balance Test (YBT-UQ), of high school (HS; n=70) and collegiate (COL; n=70) swimmers. Variables included the individual movement tests on the FMS, and the average normalized reach (%LL) for each direction, with the YBT-UQ. Statistical analysis was completed utilizing a chi-square for the independent test scores on the FMS while independent samples t-test to examine performance on the YBT-UQ (p<0.05). HS swimmers exhibited a statistically significant greater percentage of below average performance (score of 0 or 1) on the following FMS tests: lunge (HS:22.9%, COL:4.3%), hurdle step (HS:31.4%, COL:7.1%) and push up (HS:61.4 %, COL:31.4%). Furthermore, COL males performed worse in the lunge (Male 9%, Female 0%), while COL females had poorer efficiency in the pushup (Male: 17.6%, Female 44%). Significant effects of competition level and sex were observed in YBT-UQ medial reach (HS: Female 92.06, Male 101.63, COL: Female 101.3, Male 101.5 %LL). Individual fundamental movement patterns that involved lumbopelvic neuromuscular control differed between HS and COL swimmers. General upper extremity dynamic balance differed between competition levels. These data may be helpful in understanding injury and performance based normative data for participation and return to swimming.

  4. Plant fatty acyl reductases: enzymes generating fatty alcohols for protective layers with potential for industrial applications.

    PubMed

    Rowland, Owen; Domergue, Frédéric

    2012-09-01

    Primary fatty alcohols are found throughout the biological world, either in free form or in a combined state. They are common components of plant surface lipids (i.e. cutin, suberin, sporopollenin, and associated waxes) and their absence can significantly perturb these essential barriers. Fatty alcohols and/or derived compounds are also likely to have direct functions in plant biotic and abiotic interactions. An evolutionarily related set of alcohol-forming fatty acyl reductases (FARs) is present in all kingdoms of life. Plant microsomal and plastid-associated FAR enzymes have been characterized, acting on acyl-coenzymeA (acyl-CoA) or acyl-acyl carrier protein (acyl-ACP) substrates, respectively. FARs have distinct substrate specificities both with regard to chain length and chain saturation. Fatty alcohols and wax esters, which are a combination of fatty alcohol and fatty acid, have a variety of commercial applications. The expression of FARs with desired specificities in transgenic microbes or oilseed crops would provide a novel means of obtaining these valuable compounds. In the present review, we report on recent progress in characterizing plant FAR enzymes and in understanding the biological roles of primary fatty alcohols, as well as describe the biotechnological production and industrial uses of fatty alcohols.

  5. High temperature spin dynamics in linear magnetic chains, molecular rings, and segments by nuclear magnetic resonance

    SciTech Connect

    Adelnia, Fatemeh; Lascialfari, Alessandro; Mariani, Manuel; Ammannato, Luca; Caneschi, Andrea; Rovai, Donella; Winpenny, Richard; Timco, Grigore; Corti, Maurizio Borsa, Ferdinando

    2015-05-07

    We present the room temperature proton nuclear magnetic resonance (NMR) nuclear spin-lattice relaxation rate (NSLR) results in two 1D spin chains: the Heisenberg antiferromagnetic (AFM) Eu(hfac){sub 3}NITEt and the magnetically frustrated Gd(hfac){sub 3}NITEt. The NSLR as a function of external magnetic field can be interpreted very well in terms of high temperature spin dynamics dominated by a long time persistence of the decay of the two-spin correlation function due to the conservation of the total spin value for isotropic Heisenberg chains. The high temperature spin dynamics are also investigated in Heisenberg AFM molecular rings. In both Cr{sub 8} closed ring and in Cr{sub 7}Cd and Cr{sub 8}Zn open rings, i.e., model systems for a finite spin segment, an enhancement of the low frequency spectral density is found consistent with spin diffusion but the high cut-off frequency due to intermolecular anisotropic interactions prevents a detailed analysis of the spin diffusion regime.

  6. Dynamics of a discrete chain of bi-stable elements: A biomimetic shock absorbing mechanism

    NASA Astrophysics Data System (ADS)

    Cohen, T.; Givli, S.

    2014-03-01

    A biomimetic shock absorbing mechanism, inspired by the bi-stable elongation behavior of the giant protein titin, is examined. A bi-stable element, composed of three mass particles with monotonous interaction forces, is suggested to facilitate an internal degree of freedom of finite mass which contributes significantly to dissipation upon unlocking of an internal link. An essential feature of the suggested element is that it undergoes reversible rapture and therefore retrieves its initial configuration once unloaded. The quasistatic and dynamic behaviors are investigated showing similarity to the common tri-linear bi-stable response, with two steady phases separated by a spinodal region. The dynamic behavior of a chain of elements is also examined, for several loading scenarios, showing that the suggested mechanism serves as an efficient shock absorber in a sub-critical dampening environment, as compared with a simple mass on spring system. Propagation of shock waves and refraction waves in an element chain is observed and the effect of natural imperfections is considered.

  7. Bubble dynamics and bubble-induced turbulence of a single-bubble chain

    NASA Astrophysics Data System (ADS)

    Lee, Joohyoung; Park, Hyungmin

    2016-11-01

    In the present study, the bubble dynamics and liquid-phase turbulence induced by a chain of bubbles injected from a single nozzle have been experimentally investigated. Using a high-speed two-phase particle image velociemtry, measurements on the bubbles and liquid-phase velocity field are conducted in a transparent tank filled with water, while varying the bubble release frequency from 0.1 to 35 Hz. The tested bubble size ranges between 2.0-3.2 mm, and the corresponding bubble Reynolds number is 590-1100, indicating that it belongs to the regime of path instability. As the release frequency increases, it is found that the global shape of bubble dispersion can be classified into two regimes: from asymmetric (regular) to axisymmetric (irregular). In particular, at higher frequency, the wake vortices of leading bubbles cause an irregular behaviour of the following bubble. For the liquid phase, it is found that a specific trend on the bubble-induced turbulence appears in a strong relation to the above bubble dynamics. Considering this, we try to provide a theoretical model to estimate the liquid-phase turbulence induced by a chain of bubbles. Supported by a Grant funded by Samsung Electronics, Korea.

  8. Nonlinear dynamics of a friction-limited drive: Application to a chain continuously variable transmission (CVT) system

    NASA Astrophysics Data System (ADS)

    Srivastava, Nilabh; Haque, Imtiaz

    2009-03-01

    Over the past two decades, extensive research has been conducted on developing vehicle transmissions that meet the goals of reduced exhaust emissions and increased vehicle efficiency. A continuously variable transmission is an emerging automotive transmission technology that offers a continuum of gear ratios between desired limits. A chain CVT is a friction-limited drive whose dynamic performance and torque capacity rely significantly on the friction characteristic of the contact patch between the chain and the pulley. Although a CVT helps to maximize the vehicle fuel economy, its complete potential has not been accomplished in a mass-production vehicle. The present research focuses on developing models to analyze friction-induced nonlinear dynamics of a chain CVT drive and identify possible mechanisms that cause degradation of the overall dynamic performance by inducing chaos and self-sustained vibrations in the system. Two different mathematical models of friction, which characterize different operating or loading conditions, are embedded into a detailed planar multibody model of chain CVT in order to capture the various friction-induced effects in the system. Tools such as stick-slip oscillator dynamics, Lyapunov exponents, phase-space reconstruction, and recurrence plotting are incorporated to characterize the nonlinear dynamics of such a friction-limited system. The mathematical models, the computational scheme, and the results corresponding to different loading scenarios are discussed. The results discuss the influence of friction characteristics on the nonlinear dynamics and torque transmitting capacity of a chain CVT drive.

  9. Defect Dynamics of the Dipole Ordered Water Chain in a Polar Nanochannel

    NASA Astrophysics Data System (ADS)

    Matsui, Hiroshi; Suzuki, Yuta; Fukumochi, Hiroyuki; Tadokoro, Makoto

    2014-05-01

    Using large single molecular porous crystals of ({[CoIII(H2bim)3](TATC)•7H2O}n), we have studied the dynamics of hydrated protons and configurational defects via the water chain by measuring the Raman and infrared spectra, and microwave conductivity. The highly one-dimensional water chain is affected by the periodic arrangement of charged groups, which yield short- and long-range interfacial interactions. Below a critical temperature (Tc) of about 270 K, the electric dipole of water molecules forming the water chain exhibits antiferroelectric ordering through weak long-range interpore correlation with spatial anisotropy. Above Tc, the small dielectric constant indicates that the antiferroelectric correlation remains, and the configuration of the oxygen atoms in the water molecules is restricted by the short-range interfacial interactions. The anisotropic microwave response with respect to the water chain originates from the Eigen-type hydrated proton (protonic hole) accompanying local distortions, which mutually couples to the mobile configurational D (L) defect. The proton and protonic hole are introduced by self-dissociation of water molecules hydrogen bonded to the carboxylate, and the configurational defect is caused by the rotation of water molecules violating an ice rule. The effective mass of the hydrated proton (protonic hole) is enhanced, in combination with the configurational defect that behaves as the rate-determining step, and consequently the mobility is suppressed by two orders of magnitude compared with the water nanotube in the TMA salt. Owing to the integration of periodic charge-modulation effect during the transfer, we have experimentally clarified the dramatic suppression of one-dimensional proton conductivity and mobility for the first time.

  10. Detachment of semiflexible polymer chains from a substrate: A molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Paturej, J.; Erbas, A.; Milchev, A.; Rostiashvili, V. G.

    2014-12-01

    Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force ⟨f⟩ vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the ⟨f⟩-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the ⟨f⟩-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ɛ _s^B / ɛ _s^A of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the ⟨f⟩-D profile whereby the B-spikes vanish when ɛ _s^B / ɛ _s^A < 0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

  11. Detachment of semiflexible polymer chains from a substrate: A molecular dynamics investigation

    SciTech Connect

    Paturej, J.; Erbas, A.; Milchev, A.; Rostiashvili, V. G.

    2014-12-07

    Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force 〈f〉 vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the 〈f〉-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the 〈f〉-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ε{sub s}{sup B}/ε{sub s}{sup A} of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the 〈f〉-D profile whereby the B-spikes vanish when ε{sub s}{sup B}/ε{sub s}{sup A}<0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

  12. Peptide chain dynamics in light and heavy water: zooming in on internal friction.

    PubMed

    Schulz, Julius C F; Schmidt, Lennart; Best, Robert B; Dzubiella, Joachim; Netz, Roland R

    2012-04-11

    Frictional effects due to the chain itself, rather than the solvent, may have a significant effect on protein dynamics. Experimentally, such "internal friction" has been investigated by studying folding or binding kinetics at varying solvent viscosity; however, the molecular origin of these effects is hard to pinpoint. We consider the kinetics of disordered glycine-serine and α-helix forming alanine peptides and a coarse-grained protein folding model in explicit-solvent molecular dynamics simulations. By varying the solvent mass over more than two orders of magnitude, we alter only the solvent viscosity and not the folding free energy. Folding dynamics at the near-vanishing solvent viscosities accessible by this approach suggests that solvent and internal friction effects are intrinsically entangled. This finding is rationalized by calculation of the polymer end-to-end distance dynamics from a Rouse model that includes internal friction. An analysis of the friction profile along different reaction coordinates, extracted from the simulation data, demonstrates that internal as well as solvent friction varies substantially along the folding pathways and furthermore suggests a connection between friction and the formation of hydrogen bonds upon folding.

  13. Modular and dynamic approaches to the formation of single-chain polymer nanoparticles

    NASA Astrophysics Data System (ADS)

    Tuten, Bryan Tyler

    The methodology towards the creation of nanoscale polymeric objects by way of the folding of single polymer chains has been enjoying success in the field of polymer chemistry and materials science. By synthesizing polymer chains with built in functionality either through functional side groups, or direct incorporation into the polymer backbone, polymer chemists are able to fold single polymer chains onto themselves through a broad range of covalent and non-covalent interactions in dilute solution. These compact, nano-sized objects can now be used in a wide arrange of functions and applications. The aim of this dissertation is to provide first, a comprehensive overview of the recent advances and success enjoyed by this field and second, to showcase some of the various routes towards the dynamic and modular creation of these single-chain polymer nanoparticles (SCNPs). Chapter 2 of this work discusses the use of dynamic covalent cross-linking chemistry via reversible disulfide bridges in the folding and unfolding of SCNPs. Through the use of triple detection size-exclusion chromatography (SEC) it was shown through changes in retention time, a phenomena indicative of hydrodynamic volume, a polymer was being folded into compact SCNPs and then unfolded and refolded via redox chemistry. Chapter 3 explores the design of polymers that had various different cross-linkable moieties incorporated into the monomer side units. By having cross-linkable moieties that can undergo different chemical cross-linking reactions (i.e thiol-yne click reactions, epoxide ring-opening reactions, activated esters), a modular approach towards the folding and subsequent functionalization of SCNPs is created. Looking to design a system with a greater degree of control over the modular functionality, chapter 4 investigates the use of norbornene imide monomers containing pentafluorophenyl activated esters with varying methylene spacer unites between the polymerizable olefin and the activated ester

  14. Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

    PubMed Central

    Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

    2017-01-01

    Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

  15. Linear ion-trap MSn with high resolution mass spectrometry reveals structural diversity of epidermal 1-O-acyl ceramide family in mouse epidermis.

    PubMed

    Lin, Meei-Hua; Miner, Jeffery; Turk, John; Hsu, Fong-Fu

    2017-02-02

    1-O-acylceramide is a new class of epidermal ceramide found in humans and mice. Here, we report ESI linear ion-trap (LIT) multiple stage mass spectrometric (MSn) approach with high resolution towards structural characterization of this lipid family isolated from mice. Molecular species desorbed as the [M + H]+ ions was subjected to LIT MS2 to yield predominately the [M + H - H2O]+ ions, followed by MS3 to cleave the 1-O-acyl residue to yield the [M + H - H2O - (1-O-fatty acid)]+ ions. The structures of the N-acyl chain and long-chain base (LCB) of the molecule were determined by MS4 on ([M + H - H2O - (1-O-fatty acid)]+) ions that yielded multiple sets of specific ions. Using this approach, isomers varied in the 1-O-acyl (from 14:0- to 26:0-O-acyl) and N-acyl chains (from 20:0- to 26:0-N-acyl) with 18:1-sphingosine as the major LCB were found for the entire family. Minor isomers consisting of 16:1- 17:1-, 18:2-, and 19:1-sphingosine LCB, with odd fatty acyl chain, or with monounsaturated N- or O- fatty acyl substituents were also identified. An estimation of more than 700 1-O-acylceramide species, largely isobaric isomers are present, underscoring the complexity of this ceramide family.

  16. Acyl CoA synthetase 5 (ACSL5) ablation in mice increases energy expenditure and insulin sensitivity and delays fat absorption

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: The family of acyl-CoA synthetase enzymes (ACSL) activates fatty acids within cells to generate long chain fatty acyl CoA (FACoA). The differing metabolic fates of FACoAs such as incorporation into neutral lipids, phospholipids, and oxidation pathways are differentially regulated by the ...

  17. An extended patch-dynamic framework for food chains in fragmented landscapes

    PubMed Central

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

    2016-01-01

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

  18. Coarsening dynamics in condensing zero-range processes and size-biased birth death chains

    NASA Astrophysics Data System (ADS)

    Jatuviriyapornchai, Watthanan; Grosskinsky, Stefan

    2016-05-01

    Zero-range processes with decreasing jump rates are well known to exhibit a condensation transition under certain conditions on the jump rates, and the dynamics of this transition continues to be a subject of current research interest. Starting from homogeneous initial conditions, the time evolution of the condensed phase exhibits an interesting coarsening phenomenon of mass transport between cluster sites characterized by a power law. We revisit the approach in Godrèche (2003 J. Phys. A: Math. Gen. 36 6313) to derive effective single site dynamics which form a nonlinear birth death chain describing the coarsening behavior. We extend these results to a larger class of parameter values, and introduce a size-biased version of the single site process, which provides an effective tool to analyze the dynamics of the condensed phase without finite size effects and is the main novelty of this paper. Our results are based on a few heuristic assumptions and exact computations, and are corroborated by detailed simulation data.

  19. Computer simulation of the static and dynamic properties of a polymer chain

    SciTech Connect

    Ceperley, David; Kalos, M. H.; Lebowitz, Joel L.

    1981-09-01

    We have carried out computer simulations of the statics and dynamics of an isolated model polymer chain with excluded volume in a solvent acting as a heat bath. We find that the disbribution function for the separation of a pair of beads scales as the number of beads N to the power {nu} and that edge effects are small. The dynamical correlation functions, such as that of the end-to-end vector, scale as N{sup 2{nu}+1} with {nu} ~ 0.6. The results of a dynamical lattice polymer model are shown to be consistent with the present results if one adjusts the time scales in such a way that the center of mass diffuses at the same rate in the two models. The relaxation of the stress tensor, is shown to be quite similar to that of the Rouse model. Finally, it is shown that edge effects are much more pronounced in the diffusive motion of the individual beads, there being a skin comprising about 30% of the total polymer, where bead motion is relatively quicker.

  20. Mechanisms of compensatory dynamics in zooplankton and maintenance of food chain efficiency under toxicant stress.

    PubMed

    Mano, Hiroyuki; Tanaka, Yoshinari

    2016-03-01

    Communities with species that are tolerant to environmental stresses may be able to maintain the ecosystem functions under the stress, because the tolerant species can compensate for the loss of sensitive species. In this study, we focused on the food chain efficiency (FCE), the trophic transfer across three trophic levels, as an important process for ecosystem function, and examined the conditions under which such compensation could occur with aquarium experiments using an insecticide (methomyl) as the stressor. Our aquariums included one of two pairs of insecticide-tolerant and insecticide-sensitive cladoceran species, and a fish as the predator. The response of FCE to the insecticide stress, as indicated by the fish biomass production, depended on the zooplankton species combinations. FCE and total zooplankton biomass were maintained in the pair in which the compensatory changes of species abundances were clear, whereas they decreased in the pair in which the compensatory changes were not clear. This indicated the compensatory dynamics in the zooplankton community responsible for the observed resistance to the stress. We inferred the driving factors for the compensatory dynamics and the community resistance with respect to species traits of ecological importance, and concluded that a dissimilarity between species as regards the tolerance trait and a clear trade-off between the tolerance and the competitive ability was required to drive the compensatory dynamics, and a similarity or a superiority of the tolerant species as regards the functional effect trait (the predator avoidance and the reproductive potential) were required to maintain FCE.

  1. Dynamics of helical worm-like chains. VIII. Higher-order subspace approximations to dielectric and magnetic relaxation and fluorescence depolarization for flexible chains

    NASA Astrophysics Data System (ADS)

    Yamakawa, Hiromi; Yoshizaki, Takenao; Fujii, Motoharu

    1986-04-01

    Following the general scheme developed in the preceding paper (paper VII), dielectric and magnetic relaxation and fluorescence depolarization for flexible chain polymers in dilute solution are reinvestigated on the basis of the discrete helical worm-like chain in the higher-order subspace approximation. A comparison of theory with experiment is made with respect to the dielectric correlation time τD, the spin-lattice relaxation time T1, the spin-spin relaxation time T2, the nuclear Overhauser enhancement (NOE), the fluorescence emission anisotropy r(t), the average fluorescence anisotropy r¯, and the fluorescence correlation time τF. It is found that there is agreement between the diameters of the chains determined from these dynamic properties and those from chemical structures, better than in the previous crude subspace approximation, indicating that the theory is remarkably improved in the present approximation. The magnetic correlation time τM is in general not an observable, and therefore an empirical equation to be used for its determination from the observed T1 is constructed. It is then found that there is good correlation between the dynamic chain stiffness τX/τ0X and the static chain stiffness λ-1, where τ0X is the correlation time of the isolated subbody (monomer unit) with X=D, M, and F; τX/τ0X is a monotonically increasing function of λ-1 nearly independent of X as far as perpendicular dipoles are concerned. An explanation of this result is given. However, the dependence of τX on temperature cannot be explained very satisfactorily.

  2. An insight on acyl migration in solvent-free ethanolysis of model triglycerides using Novozym 435.

    PubMed

    Sánchez, Daniel Alberto; Tonetto, Gabriela Marta; Ferreira, María Luján

    2016-02-20

    In this work, the ethanolysis of triglycerides catalyzed by immobilized lipase was studied, focusing on the secondary reaction of acyl migration. The catalytic tests were performed in a solvent-free reaction medium using Novozym 435 as biocatalyst. The selected experimental variables were biocatalyst loading (5-20mg), reaction time (30-90min), and chain length of the fatty acids in triglycerides with and without unsaturation (short (triacetin), medium (tricaprylin) and long (tripalmitin/triolein)). The formation of 2-monoglyceride by ethanolysis of triglycerides was favored by long reaction times and large biocatalyst loading with saturated short- to medium-chain triglycerides. In the case of long-chain triglycerides, the formation of this monoglyceride was widely limited by acyl migration. In turn, acyl migration increased the yield of ethyl esters and minimized the content of monoglycerides and diglycerides. Thus, the enzymatic synthesis of biodiesel was favored by long-chain triglycerides (which favor the acyl migration), long reaction times and large biocatalyst loading. The conversion of acylglycerides made from long-chain fatty acids with unsaturation was relatively low due to limitations in their access to the active site of the lipase.

  3. Effect of cholesterol on molecular order and dynamics in highly polyunsaturated phospholipid bilayers.

    PubMed Central

    Mitchell, D C; Litman, B J

    1998-01-01

    The effect of cholesterol on phospholipid acyl chain packing in bilayers consisting of highly unsaturated acyl chains in the liquid crystalline phase was examined for a series of symmetrically and asymmetrically substituted phosphatidylcholines (PCs). The time-resolved fluorescence emission and decay of fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene (DPH) was used to characterize equilibrium and dynamic structural properties of bilayers containing 30 mol % cholesterol. The bilayers were composed of symmetrically substituted PCs with acyl chains of 14:0, 18:1n9, 20:4n6, or 22:6n3, containing 0, 1, 4, or 6 double bonds, respectively, and mixed-chain PCs with a saturated 16:0 sn-1 chain and 1, 4, or 6 double bonds in the sn-2 chain. DPH excited-state lifetime was fit to a Lorentzian lifetime distribution, the center of which was increased 1-2 ns by 30 mol % cholesterol relative to the cholesterol-free bilayers. Lifetime distributions were dramatically narrowed by the addition of cholesterol in all bilayers except the two consisting of dipolyunsaturated PCs. DPH anisotropy decay was interpreted in terms of the Brownian rotational diffusion model. The effect of cholesterol on both the perpendicular diffusion coefficient D perpendicular and the orientational distribution function f(theta) varied with acyl chain unsaturation. In all bilayers, except the two dipolyunsaturated PCs, 30 mol % cholesterol dramatically slowed DPH rotational motion and restricted DPH orientational freedom. The effect of cholesterol was especially diminished in di-22:6n3 PC, suggesting that this phospholipid may be particularly effective at promoting lateral domains, which are cholesterol-rich and unsaturation-rich, respectively. The results are discussed in terms of a model for lipid packing in membranes containing cholesterol and PCs with highly unsaturated acyl chains. PMID:9675190

  4. Test of a dynamical downscaling chain for assessing climate at regional scale.

    NASA Astrophysics Data System (ADS)

    Vargiu, A.; Peneva, E.; Marrocu, M.

    2009-04-01

    During last years reanalysis datasets (ECMWF ERA40 or NCEP Reanalysis Project) have been widely used to investigate climate and detect some signals of global climate changes. Heavy limitations of those datasets are found when investigating the variables with intrinsic small coherence: precipitation, local winds, fogs, etc. Our aim was to perform a dynamical downscaling of ERA40 dataset using a local model (BOLAM, developed at the ISAC-CNR, Bologna, Italy). We focused our study mainly on precipitation verification. More specifically we verified the downscaling chain with CRU daily precipitation over Europe at 0.25 degrees. A test period, covering about a year, was studied adding up runs of 36 hours forecast. Some common verification indexes for precipitation, (ETS, POD, FAR, HK, etc.) were computed at different thresholds. The verification results have shown the benefits of the downscaling chain particularly for events of deep convective precipitation and precipitation forced by orography. Comparison of the results obtained using the BOLAM model and a specific regional climate model (REGCM3, developed at the ICTP, Trieste, Italy) will be also discussed.

  5. Ricin A-chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis.

    PubMed

    Olson, M A

    1997-01-01

    Ricin A-chain is a cytotoxic protein that attacks ribosomes by hydrolyzing a specific adenine base from a highly conserved, single-stranded rRNA hairpin containing the tetraloop sequence GAGA. Molecular-dynamics simulation methods are used to analyze the structural determinant for three substrate analogues bound to the ricin A-chain molecule. Simulations were applied to the binding of the dinucleotide adenyl-3',5'-guanosine employing the x-ray crystal structure of the ricin complex and a modeled CGAGAG hexanucleotide loop taken from the NMR solution structure of a 29-mer oligonucleotide hairpin. A third simulation model is also presented describing a conformational search of the docked 29-mer structure by using a simulated-annealing method. Analysis of the structural interaction energies for each model shows the overall binding dominated by nonspecific interactions, which are mediated by specific arginine contracts from the highly basic region on the protein surface. The tetraloop conformation of the 29-mer was found to make specific interactions with conserved protein residues, in a manner that favored the GAGA sequence. A comparison of the two docked loop conformations with the NMR structure revealed significant positional deviations, suggesting that ricin may use an induced fit mechanism to recognize and bind the rRNA substrate. The conserved Tyr-80 may play an important conformational entropic role in the binding and release of the target adenine in the active site.

  6. Myosin light chain kinase and Src control membrane dynamics in volume recovery from cell swelling

    PubMed Central

    Barfod, Elisabeth T.; Moore, Ann L.; Van de Graaf, Benjamin G.; Lidofsky, Steven D.

    2011-01-01

     The expansion of the plasma membrane, which occurs during osmotic swelling of epithelia, must be retrieved for volume recovery, but the mechanisms are unknown. Here we have identified myosin light chain kinase (MLCK) as a regulator of membrane internalization in response to osmotic swelling in a model liver cell line. On hypotonic exposure, we found that there was time-dependent phosphorylation of the MLCK substrate myosin II regulatory light chain. At the sides of the cell, MLCK and myosin II localized to swelling-induced membrane blebs with actin just before retraction, and MLCK inhibition led to persistent blebbing and attenuated cell volume recovery. At the base of the cell, MLCK also localized to dynamic actin-coated rings and patches upon swelling, which were associated with uptake of the membrane marker FM4-64X, consistent with sites of membrane internalization. Hypotonic exposure evoked increased biochemical association of the cell volume regulator Src with MLCK and with the endocytosis regulators cortactin and dynamin, which colocalized within these structures. Inhibition of either Src or MLCK led to altered patch and ring lifetimes, consistent with the concept that Src and MLCK form a swelling-induced protein complex that regulates volume recovery through membrane turnover and compensatory endocytosis under osmotic stress. PMID:21209319

  7. Comparative study of polymer chain dynamics in aqueous solutions by FPR and DLS

    NASA Astrophysics Data System (ADS)

    Streletzky, Kiril; McDonough, Ryan; Cueto, Rafael; Russo, Paul

    2012-02-01

    Self diffusion of tagged polymer chains in aqueous solutions of hydroxypropylcellulose (HPC) was measured by Fluorescence Photo-bleaching Recovery (FPR) and compared to mutual diffusion of scattering species in the same solutions measured by Dynamic Light Scattering (DLS). The effect of the dye presence on thermodynamic concentration fluctuations observed by DLS was also studied. The observed multimodal spectra in DLS and FPR were analyzed with CONTIN and stretched exponential fits. A set of consistent dissimilarities in the modal distributions of FPR and DLS spectra was found. This indicates a comparative limitation or sensitivity in range of detectable diffusive processes between FPR and DLS in this complex system. In addition, it was found that the fluorescent tag and/or tagging process seem to alter the mutual diffusion processes seen by DLS. In particular, a slower mode which is apparent in the non-tagged sample does not appear in the tagged sample. It seems likely that the dye chemically affects the polymer chains keeping them from clustering with each other, altering the solvent environment preventing formation of polymer clusters responsible for the slow mode usually seen in HPC.

  8. Nonequilibrium dynamics of the Ising chain in a fluctuating transverse field

    NASA Astrophysics Data System (ADS)

    Roósz, Gergő; Juhász, Róbert; Iglói, Ferenc

    2016-04-01

    We study nonequilibrium dynamics of the quantum Ising chain at zero temperature when the transverse field is varied stochastically. In the equivalent fermion representation, the equation of motion of Majorana operators is derived in the form of a one-dimensional, continuous-time quantum random walk with stochastic, time-dependent transition amplitudes. This type of external noise gives rise to decoherence in the associated quantum walk and the semiclassical wave packet generally has a diffusive behavior. As a consequence, in the quantum Ising chain, the average entanglement entropy grows in time as t1 /2 and the logarithmic average magnetization decays in the same form. In the case of a dichotomous noise, when the transverse field is changed in discrete time steps, τ , there can be excitation modes, for which coherence is maintained, provided their energy satisfies ɛkτ ≈n π with a positive integer n . If the dispersion of ɛk is quadratic, the long-time behavior of the entanglement entropy and the logarithmic magnetization is dominated by these ballistically traveling coherent modes and both will have a t3 /4 time dependence.

  9. Designing a mathematical model for integrating dynamic cellular manufacturing into supply chain system

    NASA Astrophysics Data System (ADS)

    Aalaei, Amin; Davoudpour, Hamid

    2012-11-01

    This article presents designing a new mathematical model for integrating dynamic cellular manufacturing into supply chain system with an extensive coverage of important manufacturing features consideration of multiple plants location, multi-markets allocation, multi-period planning horizons with demand and part mix variation, machine capacity, and the main constraints are demand of markets satisfaction in each period, machine availability, machine time-capacity, worker assignment, available time of worker, production volume for each plant and the amounts allocated to each market. The aim of the proposed model is to minimize holding and outsourcing costs, inter-cell material handling cost, external transportation cost, procurement & maintenance and overhead cost of machines, setup cost, reconfiguration cost of machines installation and removal, hiring, firing and salary worker costs. Aimed to prove the potential benefits of such a design, presented an example is shown using a proposed model.

  10. Real-time visualization of excited-state dynamics in molecular chains

    NASA Astrophysics Data System (ADS)

    Li, Yonghui; Ullrich, Carsten

    2011-03-01

    Time-dependent density-functional theory allows one to calculate excitation energies and the associated transition densities in principle exactly. The transition density matrix (TDM) provides additional information on electron-hole localization and coherence of a specific excitation. We have extended the TDM concept into the real-time domain in order to visualize the excited-state dynamics in conjugated molecules. Our computational scheme is based on solving the time-dependent Kohn-Sham equations with the OCTOPUS code and then calculating the time-dependent Kohn-Sham TDM using a spatial partitioning scheme. The method is applied to show in real time how locally created electron-hole pairs spread out over neighboring conjugated molecular chains. The coupling mechanism, electron-hole coherence, and the possibility of charge separation are discussed. This work is supported by NSF Grants DMR-0553485 and DMR-1005651.

  11. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    SciTech Connect

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak contact

  12. The mitochondrial acyl carrier protein (ACP) coordinates mitochondrial fatty acid synthesis with iron sulfur cluster biogenesis

    PubMed Central

    Van Vranken, Jonathan G; Jeong, Mi-Young; Wei, Peng; Chen, Yu-Chan; Gygi, Steven P; Winge, Dennis R; Rutter, Jared

    2016-01-01

    Mitochondrial fatty acid synthesis (FASII) and iron sulfur cluster (FeS) biogenesis are both vital biosynthetic processes within mitochondria. In this study, we demonstrate that the mitochondrial acyl carrier protein (ACP), which has a well-known role in FASII, plays an unexpected and evolutionarily conserved role in FeS biogenesis. ACP is a stable and essential subunit of the eukaryotic FeS biogenesis complex. In the absence of ACP, the complex is destabilized resulting in a profound depletion of FeS throughout the cell. This role of ACP depends upon its covalently bound 4’-phosphopantetheine (4-PP)-conjugated acyl chain to support maximal cysteine desulfurase activity. Thus, it is likely that ACP is not simply an obligate subunit but also exploits the 4-PP-conjugated acyl chain to coordinate mitochondrial fatty acid and FeS biogenesis. DOI: http://dx.doi.org/10.7554/eLife.17828.001 PMID:27540631

  13. Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

    NASA Astrophysics Data System (ADS)

    Jiang, Yang-Wei; Ran, Shi-Yong; He, Lin-Li; Wang, Xiang-Hong; Zhang, Lin-Xi

    2015-11-01

    Using molecular dynamics simulations and atomic force microscopy (AFM), we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transitions of DNA are also experimentally observed in mixing spermidine with λ-phage DNA at different concentrations of NaCl/MgCl2 solutions. Project supported by the National Natural Science Foundation of China (Grant No. 31340026), the Natural Science Foundation of Zhejiang Province, China (Grant Nos. Z13F20019 and LQ12E01003), and the Science and Technology Project of Zhejiang Science and Technology Department, China (Grant No. 2014C31147).

  14. Thermal conductivity and dynamics of a chain of free and bound particles

    NASA Astrophysics Data System (ADS)

    Mimnagh, Dominic James Redmond

    The proportionality of heat current, J, to temperature gradient, nabla T, is an accepted tenet of thermal physics, Fourier's law, and can be written as J = {-}kappanabla T, where kappa represents the thermal conductivity. This behaviour has been shown empirically, but is difficult to derive from first principles. In the past, the thermal conductivity has been calculated for many different dynamical models to help shed light on the foundations of Fourier's law. Systems that have a finite kappa that is also an intensive property of the lattice are considered to have normal thermal conductivity. Surprisingly, this property has been demonstrated for only two dynamical systems. One is the well known Toda model (a lattice of exponentially bound particles) the other is the ding-a-ling model (a lattice of alternately free and harmonically bound particles) (G. Casati, J. Ford, F. Vivaldi, and W. M. Visscher, Physical Review Letters 52, 1861 (1984)). The initial aim of the research was to measure dynamic quantities of the ding-a-ling model and to look for correlations with a possible transition to normal thermal conductivity. This work was delayed initially when we were unable to confirm Casati, Ford, Vivaldi, and Visscher's (CFVV) assertion that the thermal conductivity of the ding-a-ling model was independent of chain length. We have shown that what CFVV quote as an asymptotic value of kappa is only a transitory plateau, and kappa actually increases for longer chains. Ultimately, however, a saturation value can be established and CFVV's conclusion that the ding-a-ling model displays normal thermal conductivity is correct. In fact, the model appears to possess normal thermal conductivity for all parameter values explored, though it does demonstrate a transition in the length of chain needed to observe this Fourier law behaviour. We were able to demonstrate that this transition in scale coincides with transitions in a number of dynamical measures of the system, such as, the

  15. Natural variability in acyl moieties of sugar esters produced by certain tobacco and other Solanaceae species.

    PubMed

    Kroumova, Antoaneta B M; Zaitlin, Dave; Wagner, George J

    2016-10-01

    A unique feature of glandular trichomes of plants in the botanical family Solanaceae is that they produce sugar esters (SE), chemicals that have been shown to possess insecticidal, antifungal, and antibacterial properties. Sugar esters of tobacco (Nicotiana tabacum) provide pest resistance, and are important flavor precursors in oriental tobacco cultivars. Acyl moieties of SEs in Nicotiana spp., petunia, and tomato are shown to vary with respect to carbon length and isomer structure (2-12 carbon chain length; anteiso-, iso-, and straight-chain). Sugar esters and their acyl groups could serve as a model to explore the basis of phenotypic diversity and adaptation to natural and agricultural environments. However, information on the diversity of acyl composition among species, cultivars, and accessions is lacking. Herein, described is the analysis of SE acyl groups found in 21 accessions of Nicotiana obtusifolia (desert tobacco), six of Nicotiana occidentalis subsp. hesperis, three of Nicotiana alata, two of N. occidentalis, four modern tobacco cultivars, five petunia hybrids, and one accession each of a primitive potato (Solanum berthaultii) and tomato (Solanum pennellii). A total of 20 different acyl groups was observed that were represented differently among cultivars, species, and accessions. In Nicotiana species, acetate and iso- and anteiso-branched acids prevailed. Straight-chain groups (2-8 carbons) were prominent in petunias, while octanoic acid was prominent in N. alata and N. × sanderae. Two unexpected acyl groups, 8-methyl nonanoate and decanoate were found in N. occidentalis subsp. hesperis. Longer chain groups were found in the petunia, tomato, and potato species studied.

  16. A chiroptical switch based on supramolecular chirality transfer through alkyl chain entanglement and dynamic covalent bonding.

    PubMed

    Lv, Kai; Qin, Long; Wang, Xiufeng; Zhang, Li; Liu, Minghua

    2013-12-14

    Chirality transfer is an interesting phenomenon in Nature, which represents an important step to understand the evolution of chiral bias and the amplification of the chirality. In this paper, we report the chirality transfer via the entanglement of the alkyl chains between chiral gelator molecules and achiral amphiphilic Schiff base. We have found that although an achiral Schiff base amphiphile could not form organogels in any kind of organic solvents, it formed co-organogels when mixed with a chiral gelator molecule. Interestingly, the chirality of the gelator molecules was transferred to the Schiff base chromophore in the mixed co-gels and there was a maximum mixing ratio for the chirality transfer. Furthermore, the supramolecular chirality was also produced based on a dynamic covalent chemistry of an imine formed by the reaction between an aldehyde and an amine. Such a covalent bond of imine was formed reversibly depending on the pH variation. When the covalent bond was formed the chirality transfer occurred, when it was destroyed, the transfer stopped. Thus, a supramolecular chiroptical switch is obtained based on supramolecular chirality transfer and dynamic covalent chemistry.

  17. Towards dynamic coating of glass microchip chambers for amplifying DNA via the polymerase chain reaction.

    PubMed

    Giordano, B C; Copeland, E R; Landers, J P

    2001-01-01

    As microchip technology evolves to allow for the integration of more complex processes, particularly the polymerase chain reaction (PCR), it will become necessary to define simple approaches for minimizing the effects of surfaces on the chemistry/processes to be performed. We have explored alternatives to silanization of the glass surface with the use of additives that either dynamically coat or adsorb to the glass surface. Polyethylene glycol, polyvinylpyrrolidone (PVP), and hydroxyethylcellulose (HEC) have been explored as potential dynamic coatings and epoxy (poly)dimethylacrylamide (EPDMA) evaluated as an adsorbed coating. By carrying out analysis of the PCR products generated under different conditions via microchip electrophoresis, we demonstrate that these coating agents adequately passivate the glass surface in a manner that prevents interference with the subsequent PCR process. While several of the agents tested allowed for PCR amplification of DNA in glass, the EPDMA was clearly superior with respect to ease of preparation. However, more efficient PCR (larger mass of amplified product) could be obtained by silanizing the glass surface.

  18. Path-integral Monte Carlo simulations for electronic dynamics on molecular chains. II. Transport across impurities

    NASA Astrophysics Data System (ADS)

    Mühlbacher, Lothar; Ankerhold, Joachim

    2005-05-01

    Electron transfer (ET) across molecular chains including an impurity is studied based on a recently improved real-time path-integral Monte Carlo (PIMC) approach [L. Mühlbacher, J. Ankerhold, and C. Escher, J. Chem. Phys. 121 12696 (2004)]. The reduced electronic dynamics is studied for various bridge lengths and defect site energies. By determining intersite hopping rates from PIMC simulations up to moderate times, the relaxation process in the extreme long-time limit is captured within a sequential transfer model. The total transfer rate is extracted and shown to be enhanced for certain defect site energies. Superexchange turns out to be relevant for extreme gap energies only and then gives rise to different dynamical signatures for high- and low-lying defects. Further, it is revealed that the entire bridge compound approaches a steady state on a much shorter time scale than that related to the total transfer. This allows for a simplified description of ET along donor-bridge-acceptor systems in the long-time range.

  19. Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.

    PubMed

    Feldman, Jessica L; Dittenhafer-Reed, Kristin E; Kudo, Norio; Thelen, Julie N; Ito, Akihiro; Yoshida, Minoru; Denu, John M

    2015-05-19

    Acylation of lysine is an important protein modification regulating diverse biological processes. It was recently demonstrated that members of the human Sirtuin family are capable of catalyzing long chain deacylation, in addition to the well-known NAD(+)-dependent deacetylation activity [Feldman, J. L., Baeza, J., and Denu, J. M. (2013) J. Biol. Chem. 288, 31350-31356]. Here we provide a detailed kinetic and structural analysis that describes the interdependence of NAD(+)-binding and acyl-group selectivity for a diverse series of human Sirtuins, SIRT1-SIRT3 and SIRT6. Steady-state and rapid-quench kinetic analyses indicated that differences in NAD(+) saturation and susceptibility to nicotinamide inhibition reflect unique kinetic behavior displayed by each Sirtuin and depend on acyl substrate chain length. Though the rate of nucleophilic attack of the 2'-hydroxyl on the C1'-O-alkylimidate intermediate varies with acyl substrate chain length, this step remains rate-determining for SIRT2 and SIRT3; however, for SIRT6, this step is no longer rate-limiting for long chain substrates. Cocrystallization of SIRT2 with myristoylated peptide and NAD(+) yielded a co-complex structure with reaction product 2'-O-myristoyl-ADP-ribose, revealing a latent hydrophobic cavity to accommodate the long chain acyl group, and suggesting a general mechanism for long chain deacylation. Comparing two separately determined co-complex structures containing either a myristoylated peptide or 2'-O-myristoyl-ADP-ribose indicates there are conformational changes at the myristoyl-ribose linkage with minimal structural differences in the enzyme active site. During the deacylation reaction, the fatty acyl group is held in a relatively fixed position. We describe a kinetic and structural model to explain how various Sirtuins display unique acyl substrate preferences and how different reaction kinetics influence NAD(+) dependence. The biological implications are discussed.

  20. Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions

    NASA Astrophysics Data System (ADS)

    Adhikari, Ramesh; Bhattacharya, Aniket

    2013-05-01

    We study translocation dynamics of a semi-flexible polymer chain through a nanoscopic pore in two dimensions using Langevin dynamics simulation in presence of an external bias F inside the pore. For chain length N and stiffness parameter κb considered in this paper, we observe that the mean first passage time ⟨τ⟩ increases as < τ (kappa _b) > ˜ < τ (kappa _b=0) > l_p^{a_N}, where κb and lp are the stiffness parameter and persistence length, respectively, and aN is a constant that has a weak N dependence. We monitor the time dependence of the last monomer xN(t) at the cis compartment and calculate the tension propagation time (TP) ttp directly from simulation data for ⟨xN(t)⟩ ˜ t as alluded in recent nonequlibrium TP theory [T. Sakaue, Phys. Rev. E 76, 021803 (2007), 10.1103/PhysRevE.76.021803] and its modifications to Brownian dynamics tension propagation theory [T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012), 10.1103/PhysRevE.85.051803; T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, J. Chem. Phys. 137, 085101 (2012), 10.1063/1.4742188] originally developed to study translocation of a fully flexible chain. We also measure ttp from peak position of the waiting time distribution W(s) of the translocation coordinate s (i.e., the monomer inside the pore), and explicitly demonstrate the underlying TP picture along the chain backbone of a translocating chain to be valid for semi-flexible chains as well. From the simulation data, we determine the dependence of ttp on chain persistence length lp and show that the ratio ttp/⟨τ⟩ is independent of the bias F.

  1. Tuning the presence of dynamical phase transitions in a generalized X Y spin chain

    NASA Astrophysics Data System (ADS)

    Divakaran, Uma; Sharma, Shraddha; Dutta, Amit

    2016-05-01

    We study an integrable spin chain with three spin interactions and the staggered field (λ ) while the latter is quenched either slowly [in a linear fashion in time (t ) as t /τ , where t goes from a large negative value to a large positive value and τ is the inverse rate of quenching] or suddenly. In the process, the system crosses quantum critical points and gapless phases. We address the question whether there exist nonanalyticities [known as dynamical phase transitions (DPTs)] in the subsequent real-time evolution of the state (reached following the quench) governed by the final time-independent Hamiltonian. In the case of sufficiently slow quenching (when τ exceeds a critical value τ1), we show that DPTs, of the form similar to those occurring for quenching across an isolated critical point, can occur even when the system is slowly driven across more than one critical point and gapless phases. More interestingly, in the anisotropic situation we show that DPTs can completely disappear for some values of the anisotropy term (γ ) and τ , thereby establishing the existence of boundaries in the (γ -τ ) plane between the DPT and no-DPT regions in both isotropic and anisotropic cases. Our study therefore leads to a unique situation when DPTs may not occur even when an integrable model is slowly ramped across a QCP. On the other hand, considering sudden quenches from an initial value λi to a final value λf, we show that the condition for the presence of DPTs is governed by relations involving λi,λf, and γ , and the spin chain must be swept across λ =0 for DPTs to occur.

  2. Who Is the Dynamic Duo? How Infants Learn about the Identity of Objects in a Causal Chain

    ERIC Educational Resources Information Center

    Rakison, David H.; Smith, Gabriel Tobin; Ali, Areej

    2016-01-01

    Four experiments investigated infants' and adults' knowledge of the identity of objects in a causal sequence of events. In Experiments 1 and 2, 18- and 22-month-olds in the visual habituation procedure were shown a 3-step causal chain event in which the relation between an object's part (dynamic or static) and its causal role was either consistent…

  3. Effects of higher dietary protein intake on energy balance and metabolic control in children with long-chain 3-hydroxy acyl-CoA dehydrogenase (LCHAD) or trifunctional protein (TFP) deWciency

    PubMed Central

    Gillingham, Melanie B.; Purnell, Jonathan Q.; Jordan, Julia; Stadler, Diane; Haqq, Andrea M.; Harding, Cary O.

    2009-01-01

    The incidence of overweight and obesity is increasing among children with long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) or mitochondrial trifunctional (TFP) deficiency. Traditional treatment includes fasting avoidance and consumption of a low-fat, high-carbohydrate diet. A diet higher in protein and lower in carbohydrate may help to lower total energy intake while maintaining good metabolic control. To determine the short-term safety and eYcacy of a high protein diet, subjects were admitted to the General Clinical Research Center and fed an ad-libitum high-protein diet and a high-carbohydrate diet for 6 days each using a randomized, crossover design. Nine subjects with LCHAD or TFP deficiency, age 7–14 were enrolled. Body composition was determined by DEXA. Total energy intake was evaluated daily. Resting energy expenditure and substrate utilization were determined by indirect calorimetry. Post-prandial metabolic responses of plasma glucose, insulin, leptin, ghrelin, acylcarnitines, and triglyceride were determined in response to a liquid meal. Subjects had a higher fat mass, lower lean mass and higher plasma leptin levels compared to reference values. While on the high protein diet energy consumption was an average of 50 kcals/day lower (p=0.02) and resting energy expenditure was an average of 170 kcals/day higher (p=0.05) compared to the high carbohydrate diet. Short-term higher protein diets were safe, well tolerated, and resulted in lowered energy intake and increased energy expenditure than the standard high-carbohydrate diet. Long-term studies are needed to determine whether higher protein diets will reduce the risk of overweight and obesity in children with LCHAD or TFP deficiency. PMID:16996288

  4. Adaptive changes in individual acyl-CoA esters from hamster BAT during cold acclimation.

    PubMed

    Donatello, S; Spennetta, T; Strieleman, P; Woldegiorgis, G; Shrago, E

    1988-02-01

    Long-chain fatty acyl-CoA esters (LCFACoAE) were extracted from freeze-clamped powdered brown adipose tissue (BAT) obtained from thermoneutral control and cold-acclimated hamsters and the CoA esters individually separated by high-performance liquid chromatography. LCFACoAE of carbon chain length C12 to C20 were identified by increasing column retention time in the following order: C12:0, C14:1, C14:0, C16:1, C18:2, C16:0, C18:1, C18:0, and C20:4. The mean total LCFACoAE concentrations were 235 +/- 40 nmol/g protein for the control hamsters and 648 +/- 105 nmol/g protein for the 22-day cold-acclimated hamsters. A rapid fourfold increase in the levels of C16:0, C18:0, and C18:1 occurred within hours after initiation of the cold temperature, whereas the concentrations of the other six LCFACoAE either increased only slightly or remained unchanged. Almost 50% of the total LCFACoAE in the BAT of cold-acclimated hamsters was made up of C16:0, C18:0, and C18:1. These results, which demonstrate some dynamic changes in adipose tissue LCFACoAE, are consistent with their proposed role in the initiation and maintenance of BAT thermogenesis.

  5. Mean-field calculations of chain packing and conformational statistics in lipid bilayers: comparison with experiments and molecular dynamics studies.

    PubMed Central

    Fattal, D R; Ben-Shaul, A

    1994-01-01

    A molecular, mean-field theory of chain packing statistics in aggregates of amphiphilic molecules is applied to calculate the conformational properties of the lipid chains comprising the hydrophobic cores of dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers in their fluid state. The central quantity in this theory, the probability distribution of chain conformations, is evaluated by minimizing the free energy of the bilayer assuming only that the segment density within the hydrophobic region is uniform (liquidlike). Using this distribution we calculate chain conformational properties such as bond orientational order parameters and spatial distributions of the various chain segments. The lipid chains, both the saturated palmitoyl (-(CH2)14-CH3) and the unsaturated oleoyl (-(CH2)7-CH = CH-(CH2)7-CH3) chains are modeled using rotational isomeric state schemes. All possible chain conformations are enumerated and their statistical weights are determined by the self-consistency equations expressing the condition of uniform density. The hydrophobic core of the DPPC bilayer is treated as composed of single (palmitoyl) chain amphiphiles, i.e., the interactions between chains originating from the same lipid headgroup are assumed to be the same as those between chains belonging to different molecules. Similarly, the DOPC system is treated as a bilayer of oleoyl chains. The POPC bilayer is modeled as an equimolar mixture of palmitoyl and oleoyl chains. Bond orientational order parameter profiles, and segment spatial distributions are calculated for the three systems above, for several values of the bilayer thickness (or, equivalently, average area/headgroup) chosen, where possible, so as to allow for comparisons with available experimental data and/or molecular dynamics simulations. In most cases the agreement between the mean-field calculations, which are relatively easy to perform, and the

  6. Dynamic optimization of on-chip polymerase chain reaction by monitoring intracycle fluorescence using fast synchronous detection

    NASA Astrophysics Data System (ADS)

    Mondal, Sudip; Paul, Debjani; Venkataraman, V.

    2007-01-01

    The authors report on-chip dynamic optimization of polymerase chain reaction (PCR) based on a feedback technique utilizing synchronous detection of intracycle fluorescence every 500ms. From a direct measurement of polymerase activity, the authors determine the optimum extension temperature. The authors dynamically optimize PCR in an inductively heated microchip by sensing the saturation of extension in each cycle and applying the feedback. They demonstrate that, even with fast ramp rates, dynamic optimization leads to faster reactions compared to fixed-duration extension protocols for long DNA (>500bp). This optimization scheme uses a fairly universal dye Sybr Green I and can be applied to most PCRs.

  7. The dynamic excitation of a granular chain for biomedical ultrasound applications: contact mechanics finite element analysis and validation

    NASA Astrophysics Data System (ADS)

    Gélat, P.; Yang, J.; Thomas, P. J.; Hutchins, D. A.; Akanji, O.; Davis, L. A. J.; Freear, S.; Harput, S.; Saffari, N.

    2016-01-01

    There has been recent interest in the transmission of acoustic signals along granular chains of spherical beads to produce waveforms of relevance to biomedical ultrasound applications. Hertzian contact between adjacent beads can introduce different harmonic content into the signal as it propagates. This transduction mechanism has the potential to be of use in both diagnostic and therapeutic ultrasound applications, and is the object of the study presented here. Although discrete dynamics models of this behaviour exist, a more comprehensive solution must be sought if changes in shape and deformation of individual beads are to be considered. Thus, the finite element method was used to investigate the dynamics of a granular chain of six, 1 mm diameter chrome steel spherical beads excited at one end using a sinusoidal displacement signal at 73 kHz. Output from this model was compared with the solution provided by the discrete dynamics model, and good overall agreement obtained. In addition, it was able to resolve the complex dynamics of the granular chain, including the multiple collisions which occur. It was demonstrated that under dynamic excitation conditions, the inability of discrete mechanics models to account for elastic deformation of the beads when these lose contact, could lead to discrepancies with experimental observations.

  8. Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors

    PubMed Central

    Kougias, Panagiotis G.; Treu, Laura; Campanaro, Stefano; Zhu, Xinyu; Angelidaki, Irini

    2016-01-01

    The process stability of biogas plants is often deteriorated by the accumulation of Long Chain Fatty Acids (LCFA). The microbial community shifts due to LCFA disturbances have been poorly understood as the molecular techniques used were not able to identify the genome characteristics of uncultured microorganisms, and additionally, the presence of limited number of reference genomes in public databases prevented the comprehension of specific functional roles characterizing these microorganisms. The present study is the first research which deciphers by means of high throughput shotgun sequencing the dynamics of the microbial community during an inhibitory shock load induced by single pulses of unsaturated LCFA at two different concentrations (i.e. 2 g/L-reactor and 3 g/L-reactor). The metagenomic analysis showed that only the microbes associated with LCFA degradation could encode proteins related to “chemotaxis” and “flagellar assembly”, which promoted the ability to move towards the LCFA sources so as to degrade them. Moreover, the syntrophic interactions found between Syntrophomonas sp. together with Methanosarcina sp. were possibly assigned to the menaquinone-electron transfer. Finally, it was proven that a previously exposed to LCFA inoculum is more efficient in the degradation process of LCFA due to the specialization of the microbial consortium. PMID:27353502

  9. The cytotoxic effect of 2-acylated-1,4-naphthohydroquinones on leukemia/lymphoma cells.

    PubMed

    Pedroza, Diego A; De Leon, Fernando; Varela-Ramirez, Armando; Lema, Carolina; Aguilera, Renato J; Mito, Shizue

    2014-01-15

    Here, we tested seven 2-acylated-1,4-hydronaphthoquinones for their cytotoxic effects on a panel of cancer lymphoma/leukemia cells and compared to a non-cancer origin cell line. Several naphthohydroquinones exhibited selective cytotoxic effects on lymphoma/leukemia cells with lowest activity on non-cancer cells. The mode of cell death induced by an acylated naphthohydroquinone, which has a long alkyl chain, was found to be via apoptosis. Furthermore, the naphthohydroquinone provoked mitochondria depolarization and activation of its downstream effector, caspase-3, thus implicating the intrinsic apoptotic pathway as its mechanism to exert cell death.

  10. Localization of acyl coenzyme A:cholesterol acyltransferase gene to human chromosome 1q25

    SciTech Connect

    Chang, C.C.Y.; Chang, W.; Chang, T.Y. ); Noll, W.W.; Nutile-McMenemy, N. ); Lindsay, E.A.; Baldini, A. )

    1994-01-01

    Acyl coenzyme A:cholesterol acyltransferase (ACAT) is an intracellular enzyme that catalyzes the formation of cholesterol esters from cholesterol and long-chain fatty acyl-coenzyme A. It is believed that ACAT plays a key role in lipoprotein metabolism and atherogenesis. Recently the authors' laboratory succeeded in molecular cloning and functional expression of human macrophage ACAT cDNA. They have now mapped the ACAT gene to chromosome 1, band q25 by using fluorescence in situ hybridization to metaphase chromosomes, and by Southern blotting analysis of human-hamster somatic cell hybrid panels.

  11. The cytotoxic effect of 2-acylated-1,4-naphthohydroquinones on leukemia/lymphoma cells

    PubMed Central

    Pedroza, Diego A.; De Leon, Fernando; Varela-Ramirez, Armando; Lema, Carolina; Aguilera, Renato J.; Mito, Shizue

    2014-01-01

    Here, we tested seven 2-acylated-1,4-hydronaphthoquinones for their cytotoxic effects on a panel of cancer lymphoma/leukemia cells and compared to a non-cancer origin cell line. Several naphthohydroquinones exhibited selective cytotoxic effects on lymphoma/leukemia cells with lowest activity on non-cancer cells. The mode of cell death induced by an acylated naphthohydroquinone, which has a long alkyl chain, was found to be via apoptosis. Furthermore, the naphthohydroquinone provoked mitochondria depolarization and activation of its downstream effector, caspase-3, thus implicating the intrinsic apoptotic pathway as its mechanism to exert cell death. PMID:24368029

  12. Thermally activated magnetization reversal in monatomic magnetic chains on surfaces studied by classical atomistic spin-dynamics simulations.

    PubMed

    Bauer, David S G; Mavropoulos, Phivos; Lounis, Samir; Blügel, Stefan

    2011-10-05

    We analyse the spontaneous magnetization reversal of supported monatomic chains of finite length due to thermal fluctuations via atomistic spin-dynamics simulations. Our approach is based on the integration of the Landau-Lifshitz equation of motion of a classical spin Hamiltonian in the presence of stochastic forces. The associated magnetization lifetime is found to obey an Arrhenius law with an activation barrier equal to the domain wall energy in the chain. For chains longer than one domain wall width, the reversal is initiated by nucleation of a reversed magnetization domain primarily at the chain edge followed by a subsequent propagation of the domain wall to the other edge in a random-walk fashion. This results in a linear dependence of the lifetime on the chain length, if the magnetization correlation length is not exceeded. We studied chains of uniaxial and triaxial anisotropy and found that a triaxial anisotropy leads to a reduction of the magnetization lifetime due to a higher reversal attempt rate, even though the activation barrier is not changed.

  13. Real-time dynamics of a spin chain with Dzyaloshinskii-Moriya interactions: Spiral formation and quantum spin oscillations

    NASA Astrophysics Data System (ADS)

    Solano-Carrillo, E.; Franco, R.; Silva-Valencia, J.

    2011-08-01

    We studied the nonequilibrium short-time dynamics of a spin-1/2 chain with Dzyaloshinskii-Moriya interactions after a sudden quench by a transverse field. We found that inhomogeneous spin spirals with opposite chiralities propagate from the edges toward the center of the chain. This propagation is accompanied by quantum spin oscillations which decay asymptotically with time. A theoretical description of this phenomenon is given to a good accuracy with the help of numerical calculations with the adaptive time-dependent density matrix renormalization group algorithm.

  14. Dynamical light scattering for DNA-CTMA:DR1 chains: wormlike semi-flexible model, coil size and persistence length

    NASA Astrophysics Data System (ADS)

    Mitus, A. C.; Radosz, W.; Pawlik, G.; Lazar, C. A.; Kajzar, F.; Rau, I.

    2016-09-01

    Recent experimental Dynamic Light Scattering (DLS) studies of the coil sizes of DNA-CTMA:Rh solutions have lead to numerical discrepancies with theoretical predictions amounting to one-two orders of magnitude.1 In this paper, which has partially character of a tutorial, we present the basic theoretical concepts underlying an analysis of the polymer coil sizes from DLS experiments. In particular, we discuss the limitations of those methods. We present a wormlike model of a polymer chain which is a promising candidate for inferring information about the spatial structure of the DNA chain from experimental data.

  15. Low frequency dynamics of disordered XY spin chains and pinned density waves: from localized spin waves to soliton tunneling.

    PubMed

    Fogler, Michael M

    2002-05-06

    A long-standing problem of the low-energy dynamics of a disordered XY spin chain is reexamined. The case of a rigid chain is studied, where the quantum effects can be treated quasiclassically. It is shown that, as the frequency decreases, the relevant excitations change from localized spin waves to two-level systems to soliton-antisoliton pairs. The linear-response correlation functions are calculated. The results apply to other periodic glassy systems such as pinned density waves, planar vortex lattices, stripes, and disordered Luttinger liquids.

  16. Dynamics of the chemical master equation, a strip of chains of equations in d-dimensional space.

    PubMed

    Galstyan, Vahe; Saakian, David B

    2012-07-01

    We investigate the multichain version of the chemical master equation, when there are transitions between different states inside the long chains, as well as transitions between (a few) different chains. In the discrete version, such a model can describe the connected diffusion processes with jumps between different types. We apply the Hamilton-Jacobi equation to solve some aspects of the model. We derive exact (in the limit of infinite number of particles) results for the dynamic of the maximum of the distribution and the variance of distribution.

  17. Rheological behavior of acylated pepsin-solubilized collagen solutions: Effects of concentration

    NASA Astrophysics Data System (ADS)

    Li, Conghu; Duan, Lian; Tian, Zhenhua; Liu, Wentao; Li, Guoying; Huang, Xiaoping

    2015-11-01

    Effects of concentration on the rheological behavior of acylated pepsin-solubilized collagen solutions were investigated by steady shear tests, dynamic frequency sweep, creep tests and thixotropic loop measurements in this paper. The results showed that both acylated collagen and native collagen solutions exhibited the typical pseudoplastic behavior and displayed shear thinned behavior with the increase of shear rate. With the increase of acylated collagen concentrations from 5 to 10 mg/mL, shear viscosity, elasticity modulus ( G'), viscous modulus ( G″), complex viscosity ( η*), and the ability to resist deformation increased due to the physical entanglement, whilst loss tangent (tan δ) decreased. Additionally, with the increase of acylated collagen concentrations, the area of thixotropic loop increased from 6.94 to 44.40 watts/m3, indicating that the thixotropy of acylated collagen increased. Compared with native collagen solution, acylated collagen solution had stronger shear viscosity, η*, thixotropy, and ability to resist deformation. Furthermore, Power law model, Carreau model, Cross model, Leonov model and Burger model, were suitable for the fitting of the experimental data.

  18. The significance of clean and dirty animals for bacterial dynamics along the beef chain.

    PubMed

    Hauge, Sigrun J; Nesbakken, Truls; Moen, Birgitte; Røtterud, Ole-Johan; Dommersnes, Sissel; Nesteng, Ole; Østensvik, Øyvin; Alvseike, Ole

    2015-12-02

    This study investigated the bacterial dynamics along the beef chain for clean and dirty cattle in the slaughter and processing lines, using classic quantitative methods and molecular analyses. In addition, the Norwegian national guidelines for Good Hygiene Practices in Norway were evaluated. In these guidelines, cattle presented for slaughter are categorised according to hide cleanliness, resulting in separate processing lines for meat from very dirty animals and reduced prices to farmers. The study was conducted in two commercial abattoirs in Norway. Two groups were compared; 40 visually clean cattle and 40 visually dirty cattle presented for slaughter, with 20 from each group at each abattoir. The same animals were sampled at five sampling sites: hides, carcass surfaces after dehiding, just before chilling, after chilling, and meat trimmings. Meat trimmings were sampled in only one abattoir. Three hundred and sixty samples were collected by swabbing 100 cm(2) of the brisket area at the first four sampling sites, and sampling 200 g of meat trimmings at the fifth site. The results showed that the hides of dirty cattle had more Enterobacteriaceae and higher Aerobic Plate Counts (APC) than visually clean cattle (P<0.05), however there was no significant difference for Escherichia coli. For the other sampling sites, there were no differences between the dirty and the clean group. An effect of chilling/drying of the carcass surfaces was demonstrated by the significant reduction in the number of carcasses on which E. coli and Enterobacteriaceae were detected; from 11% and 39% before chilling to 1% and 16% after chilling, respectively. Enterobacteriaceae and E. coli were detected in only three and one of the meat trimming samples, respectively. Amplification and sequencing of the 16S rRNA gene from 643 Enterobacteriaceae colonies derived from 107 samples demonstrated that Escherichia/Shigella were dominant within this family on the hides. However, after dehiding, after

  19. Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Sacramento, P. D.; Machado, J. D. P.; Campbell, D. K.

    2015-10-01

    We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the ‘pseudofermion dynamical theory’ (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents {{\\zeta}τ}(k) controlling the singularities for both the longitudinal ≤ft(τ =l\\right) and transverse ≤ft(τ =t\\right) dynamical structure factors for the whole momentum range k\\in ]0,π[ , in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

  20. Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field.

    PubMed

    Carmelo, J M P; Sacramento, P D; Machado, J D P; Campbell, D K

    2015-10-14

    We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the 'pseudofermion dynamical theory' (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents ζ(τ)(k) controlling the singularities for both the longitudinal (τ = l) and transverse (τ = t) dynamical structure factors for the whole momentum range k ∈ ]0,π[, in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

  1. Long chain acyl-CoA synthetases and other acyl activating enzymes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proper synthesis and breakdown of molecules containing carboxylic acids is a vital part of metabolism in all living organisms. Given the relatively inert chemical nature of many carboxylic acids, activation is a necessary step prior to use in the various anabolic and catabolic pathways that utilize...

  2. Molecular dynamics studies of side chain effect on the beta-1,3-D-glucan triple helix in aqueous solution.

    PubMed

    Okobira, Tadashi; Miyoshi, Kentaro; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji

    2008-03-01

    beta-1,3-D-glucans have been isolated from fungi as right-handed 6(1) triple helices. They are categorized by the side chains bound to the main triple helix through beta-(1-->6)-D-glycosyl linkage. Indeed, since a glucose-based side chain is water soluble, the presence and frequency of glucose-based side chains give rise to significant variation in the physical properties of the glucan family. Curdlan has no side chains and self-assembles to form an water-insoluble triple helical structure, while schizophyllan, which has a 1,6-D-glucose side chain on every third glucose unit along the main chain, is completely water soluble. A thermal fluctuation in the optical rotatory dispersion is observed for the side chain, indicating probable co-operative interaction between the side chains and water molecules. This paper documents molecular dynamics simulations in aqueous solution for three models of the beta-1,3-D-glucan series: curdlan (no side chain), schizophyllan (a beta-(1-->6)-D-glycosyl side-chain at every third position), and a hypothetical triple helix with a side chain at every sixth main-chain glucose unit. A decrease was observed in the helical pitch as the population of the side chain increased. Two types of hydrogen bonding via water molecules, the side chain/main chain and the side chain/side chain hydrogen bonding, play an important role in determination of the triple helix conformation. The formation of a one-dimensional cavity of diameter about 3.5 A was observed in the schizophyllan triple helix, while curdlan showed no such cavity. The side chain/side chain hydrogen bonding in schizophyllan and the hypothetical beta-1,3-D-glucan triple helix could cause the tilt of the main-chain glucose residues to the helix.

  3. Synthesis, Surface Active Properties and Cytotoxicity of Sodium N-Acyl Prolines.

    PubMed

    Sreenu, Madhumanchi; Narayana Prasad, Rachapudi Badari; Sujitha, Pombala; Kumar, Chityal Ganesh

    2015-01-01

    Sodium N-acyl prolines (NaNAPro) were synthesized using mixture of fatty acids obtained from coconut, palm, karanja, Sterculia foetida and high oleic sunflower oils via Schotten-Baumann reaction in 58-75% yields to study the synergetic effect of mixture of hydrophobic fatty acyl functionalities like saturation, unsaturation and cyclopropene fatty acids with different chain lengths and aliphatic hetero cyclic proline head group on their surface and cytotoxicity activities. The products were characterized by chromatographic and spectral techniques. The synthesized products were evaluated for their surface active properties such as surface tension, wetting power, foaming characteristics, emulsion stability, calcium tolerance, critical micelle concentration (CMC) and thermodynamic properties. The results revealed that all the products exhibited superior surface active properties like CMC, calcium tolerance and emulsion stability as compared to the standard surfactant, sodium lauryl sulphate (SLS). In addition, palm, Sterculia foetida and high oleic sunflower fatty N-acyl prolines exhibited promising cytotoxicity against different tumor cell lines.

  4. Study of Triheptanoin for Treatment of Long-Chain Fatty Acid Oxidation Disorder

    ClinicalTrials.gov

    2017-03-21

    Very Long-chain acylCoA Dehydrogenase (VLCAD) Deficiency; Carnitine Palmitoyltransferase 2 (CPT2) Deficiency; Mitochondrial Trifunctional Protein (TFP) Deficiency; Long-chain 3 hydroxyacylCoA Dehydrogenase (LCHAD) Deficiency

  5. Quantifying chain reptation in entangled polymer melts: topological and dynamical mapping of atomistic simulation results onto the tube model.

    PubMed

    Stephanou, Pavlos S; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G; Kröger, Martin

    2010-03-28

    The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability psi(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed psi(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic

  6. Dynamical Models for NGC 6503 Using a Markov Chain Monte Carlo Technique

    NASA Astrophysics Data System (ADS)

    Puglielli, David; Widrow, Lawrence M.; Courteau, Stéphane

    2010-06-01

    We use Bayesian statistics and Markov chain Monte Carlo (MCMC) techniques to construct dynamical models for the spiral galaxy NGC 6503. The constraints include surface brightness (SB) profiles which display a Freeman Type II structure; H I and ionized gas rotation curves; the stellar rotation, which is nearly coincident with the ionized gas curve; and the line of sight stellar dispersion, which displays a σ-drop at the center. The galaxy models consist of a Sérsic bulge, an exponential disk with an optional inner truncation and a cosmologically motivated dark halo. The Bayesian/MCMC technique yields the joint posterior probability distribution function for the input parameters, allowing constraints on model parameters such as the halo cusp strength, structural parameters for the disk and bulge, and mass-to-light ratios. We examine several interpretations of the data: the Type II SB profile may be due to dust extinction, to an inner truncated disk, or to a ring of bright stars, and we test separate fits to the gas and stellar rotation curves to determine if the gas traces the gravitational potential. We test each of these scenarios for bar stability, ruling out dust extinction. We also find that the gas likely does not trace the gravitational potential, since the predicted stellar rotation curve, which includes asymmetric drift, is then inconsistent with the observed stellar rotation curve. The disk is well fit by an inner-truncated profile, but the possibility of ring formation by a bar to reproduce the Type II profile is also a realistic model. We further find that the halo must have a cuspy profile with γ >~ 1; the bulge has a lower M/L than the disk, suggesting a star-forming component in the center of the galaxy; and the bulge, as expected for this late-type galaxy, has a low Sérsic index with nb ~ 1-2, suggesting a formation history dominated by secular evolution.

  7. Residual structure and dynamics in DMSO-d6 denatured dynein light chain protein.

    PubMed

    Chakraborty, Swagata; Mohan, P M Krishna; Hosur, Ramakrishna V

    2012-01-01

    Structural and motional features in the denatured state of a protein dictate the early folding events starting from that state and these features vary depending upon the nature of the denaturant used. Here, we have attempted to decipher the early events in the folding of Dynein Light Chain protein (DLC8), starting from DMSO-d6 denatured state. Multinuclear NMR experiments were used to obtain the full spectral assignment. The HSQC spectrum shows the presence of two sets of peaks for the residues Met 1, Ser 2, Arg 4, Ala 11, Met 17, Thr 26, Lys 44, Tyr 50, Asn 51, Trp 54, His 55, Val 58, Gly 59, Ser 64, Tyr 65, His 68, Phe 86, Lys 87 indicating the presence of slow conformational transition in the heterogeneous ensemble. Analysis of residual structural propensities with secondary (13)C chemical shifts, (3)J(H(N)(-)H(α)) coupling constants and (1)H-(1)H NOE revealed the presence of local preferences which encompass both native and non-native like structures. The spectral density calculations, as obtained from measured R(1), R(2) and (1)H-(15)N steady state NOE values provide insights into the backbone dynamics on the milli to picosecond timescale. The segment Ser 14 - His 55 exhibits slow motions on the milli- to microsecond timescale arising from conformational exchange. The presence of native like structural preference, as well as conformational exchange classifies the above segment as the nucleation site of folding. Based on the observations, we propose here, the probable hierarchy of folding of DLC8 on dilution of denaturant: the two helices are formed first followed by the formation of β2 and β5.

  8. Dissipative particle dynamics study of translational diffusion of rigid-chain rodlike polymer in nematic phase

    NASA Astrophysics Data System (ADS)

    Zhao, Tongyang; Wang, Xiaogong

    2013-09-01

    In this study, dissipative particle dynamics (DPD) method was employed to investigate the translational diffusion of rodlike polymer in its nematic phase. The polymer chain was modeled by a rigid rod composed of consecutive DPD particles and solvent was represented by independent DPD particles. To fully understand the translational motion of the rods in the anisotropic phase, four diffusion coefficients, D_{||}u, D_ bot u, D_{||}n, D_ bot n were obtained from the DPD simulation. By definition, D_{||}n and D_ bot n denote the diffusion coefficients parallel and perpendicular to the nematic director, while D_{||}u and D_ bot u denote the diffusion coefficients parallel and perpendicular to the long axis of a rigid rod u. In the simulation, the velocity auto-correlation functions were used to calculate the corresponding diffusion coefficients from the simulated velocity of the rods. Simulation results show that the variation of orientational order caused by concentration and temperature changes has substantial influences on D_{||}u and D_ bot u. In the nematic phase, the changes of concentration and temperature will result in a change of local environment of rods, which directly influence D_{||}u and D_ bot u. Both D_{||}n and D_ bot n can be represented as averages of D_{||}u and D_ bot u, and the weighted factors are functions of the orientational order parameter S2. The effect of concentration and temperature on D_{||}n and D_ bot n demonstrated by the DPD simulation can be rationally interpreted by considering their influences on D_{||}u, D_ bot u and the order parameter S2.

  9. Interactions of acyl-coenzyme A with phosphatidylcholine bilayers and serum albumin

    SciTech Connect

    Boylan, J.G.; Hamilton, J.A. )

    1992-01-21

    Interactions of oleoyl- and octanoyl-coenzyme A (CoA) with phosphatidylcholine (PC) vesicles and bovine serum albumin (BSA) were investigated by NMR spectroscopy. Binding of acyl-CoA to small unilamellar PC vesicles and to BSA was detected by changes in {sup 13}C and {sup 31}P chemical shifts relative to the chemical shifts for aqueous acyl-CoA. PC vesicles remained intact with {le} 15 mol % oleoyl-CoA, while higher oleoyl-CoA proportions produced mixed micelles. In contrast, {sup 13}C spectra revealed rapid exchange (ms) of octanoyl-CoA between the aqueous phase and PC vesicles and a low affinity for the bilayer. Thus, the binding affinity of acyl-CoA for PC bilayers is dependent on the acyl chain length. Addition of ({sup 13}C)carboxyl-enriched oleic acid to oleoyl-CoA/BSA mixtures revealed simultaneous binding of oleic acid and oleoyl-CoA to BSA, with some perturbation of binding interactions. Thus, BSA contains multiple binding sites for oleoyl-CoA and can bind fatty acid and acyl-CoA simultaneously.

  10. Generation of fatty acids by an acyl esterase in the bioluminescent system of Photobacterium phosphoreum

    SciTech Connect

    Carey, L.M.; Rodriguez, A.; Meighen, E.

    1984-08-25

    The fatty acid reductase complex from Photobacterium phosphoreum has been discovered to have a long chain ester hydrolase activity associated with the 34K protein component of the complex. This protein has been resolved from the other components (50K and 58K) of the fatty acid reductase complex with a purity of > 95% and found to catalyze the transfer of acyl groups from acyl-CoA primarily to thiol acceptors with a low level of transfer to glycerol and water. Addition of the 50K protein of the complex caused a dramatic change in specificity increasing the transfer to oxygen acceptors. The acyl-CoA hydrolase activity increased almost 10-fold, and hence free fatty acids can be generated by the 34K protein when it is present in the fatty acid reductase complex. Hydrolysis of acyl-S-mercaptoethanol and acyl-1-glycerol and the ATP-dependent reduction of the released fatty acids to aldehyde for the luminescent reaction were also demonstrated for the reconstituted fatty acid reductase complex, raising the possibility that the immediate source of fatty acids for this reaction in vivo could be the membrane lipids and/or the fatty acid synthetase system.

  11. Exploring the Dynamics of Globalization: Supply Chain Vulnerability to Natural Disasters

    ERIC Educational Resources Information Center

    Kalafsky, Ronald V.; Conner, Neil

    2015-01-01

    Global supply chains play an increasingly important role in the economy and should therefore be addressed within geography coursework, especially given concerns that geographers have not fully explored various angles of globalization. This article explores the use of an online case study on supply chains and their vulnerability to natural…

  12. Fatty acyl-CoA reductase

    SciTech Connect

    Reiser, Steven E.; Somerville, Chris R.

    1998-12-01

    The present invention relates to bacterial enzymes, in particular to an acyl-CoA reductase and a gene encoding an acyl-CoA reductase, the amino acid and nucleic acid sequences corresponding to the reductase polypeptide and gene, respectively, and to methods of obtaining such enzymes, amino acid sequences and nucleic acid sequences. The invention also relates to the use of such sequences to provide transgenic host cells capable of producing fatty alcohols and fatty aldehydes.

  13. Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics

    SciTech Connect

    Plašienka, Dušan Martoňák, Roman; Cifra, Peter

    2015-04-21

    We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.

  14. Acyl-CoA oxidase complexes control the chemical message produced by Caenorhabditis elegans.

    PubMed

    Zhang, Xinxing; Feng, Likui; Chinta, Satya; Singh, Prashant; Wang, Yuting; Nunnery, Joshawna K; Butcher, Rebecca A

    2015-03-31

    Caenorhabditis elegans uses ascaroside pheromones to induce development of the stress-resistant dauer larval stage and to coordinate various behaviors. Peroxisomal β-oxidation cycles are required for the biosynthesis of the fatty acid-derived side chains of the ascarosides. Here we show that three acyl-CoA oxidases, which catalyze the first step in these β-oxidation cycles, form different protein homo- and heterodimers with distinct substrate preferences. Mutations in the acyl-CoA oxidase genes acox-1, -2, and -3 led to specific defects in ascaroside production. When the acyl-CoA oxidases were expressed alone or in pairs and purified, the resulting acyl-CoA oxidase homo- and heterodimers displayed different side-chain length preferences in an in vitro activity assay. Specifically, an ACOX-1 homodimer controls the production of ascarosides with side chains with nine or fewer carbons, an ACOX-1/ACOX-3 heterodimer controls the production of those with side chains with seven or fewer carbons, and an ACOX-2 homodimer controls the production of those with ω-side chains with less than five carbons. Our results support a biosynthetic model in which β-oxidation enzymes act directly on the CoA-thioesters of ascaroside biosynthetic precursors. Furthermore, we identify environmental conditions, including high temperature and low food availability, that induce the expression of acox-2 and/or acox-3 and lead to corresponding changes in ascaroside production. Thus, our work uncovers an important mechanism by which C. elegans increases the production of the most potent dauer pheromones, those with the shortest side chains, under specific environmental conditions.

  15. Acyl-CoA oxidase complexes control the chemical message produced by Caenorhabditis elegans

    PubMed Central

    Zhang, Xinxing; Feng, Likui; Chinta, Satya; Singh, Prashant; Wang, Yuting; Nunnery, Joshawna K.; Butcher, Rebecca A.

    2015-01-01

    Caenorhabditis elegans uses ascaroside pheromones to induce development of the stress-resistant dauer larval stage and to coordinate various behaviors. Peroxisomal β-oxidation cycles are required for the biosynthesis of the fatty acid-derived side chains of the ascarosides. Here we show that three acyl-CoA oxidases, which catalyze the first step in these β-oxidation cycles, form different protein homo- and heterodimers with distinct substrate preferences. Mutations in the acyl-CoA oxidase genes acox-1, -2, and -3 led to specific defects in ascaroside production. When the acyl-CoA oxidases were expressed alone or in pairs and purified, the resulting acyl-CoA oxidase homo- and heterodimers displayed different side-chain length preferences in an in vitro activity assay. Specifically, an ACOX-1 homodimer controls the production of ascarosides with side chains with nine or fewer carbons, an ACOX-1/ACOX-3 heterodimer controls the production of those with side chains with seven or fewer carbons, and an ACOX-2 homodimer controls the production of those with ω-side chains with less than five carbons. Our results support a biosynthetic model in which β-oxidation enzymes act directly on the CoA-thioesters of ascaroside biosynthetic precursors. Furthermore, we identify environmental conditions, including high temperature and low food availability, that induce the expression of acox-2 and/or acox-3 and lead to corresponding changes in ascaroside production. Thus, our work uncovers an important mechanism by which C. elegans increases the production of the most potent dauer pheromones, those with the shortest side chains, under specific environmental conditions. PMID:25775534

  16. Snow cover dynamic in the Atlas Chain (Morocco) using daily MODIS products over the last decade

    NASA Astrophysics Data System (ADS)

    Marchane, Ahmed; Jarlan, Lionel; Hanich, Lahoucine; Boudhar, Abdelghani; Gascoin, Simon; Le page, Michel; Tavernier, Adrien; Filali, Nourredine; Berjamy, Brahim; Khabba, Said; Chehbouni, Ghani

    2014-05-01

    Over semi-arid areas, snow cover in the mountains represents an important source of water for many people living downstream. This study evaluates the daily MODIS snow covered area products over the 7 catchments with a rain-snow functioning covering the Atlas chain in Morocco. To this objective, more than 4600 daily MODIS images from September 2000 to June 2013 have been processed based on a spatio-temporal filtering algorithm aiming at reducing the cloud coverage and the problem of discrimination between snow and cloud. The number of pixel identified as cloud is reduced by 96% from 22.6% to 0.8%. In a second step, the ability of the product to detect snow is tested against 5 stations of automatic snow depth measurements covering 22 complete seasons. The overall accuracy is equal to 90%. Although slightly lower than previously published validation studies, this is fairly good considering the highly varying dynamic of the snow cover in the region characterized by period of complete ablation even during the core of the winter due to high incoming radiation. The timing of the seasonal snow is also correctly detected with 11.4 days and 9.4 days of average errors with almost no bias for the onset date and the ablation date, respectively and 18.2 days on the snow cover duration. The processed fractional snow cover is also tested against a series of 19 clear images acquired by the FORMOSAT sensor at 8-m resolution from February to June 2009 in the Tensift catchment (Marrakech). The comparison of the two datasets results in a correlation coefficient of r=0.94 and an average low bias of 3.96 km² but some differences are observed during the very end of the ablation phase. Finally, the processed snow cover products provide insights into spatio-temporal variability of snow cover in the region which is analyzed through seasonal indicators including onset and melt-out date, the snow cover duration (SCD) and the maximum snow cover extent: (1) the dynamic is characterized by a

  17. Unique acyl-carnitine profiles are potential biomarkers for acquired mitochondrial disease in autism spectrum disorder

    PubMed Central

    Frye, R E; Melnyk, S; MacFabe, D F

    2013-01-01

    Autism spectrum disorder (ASD) has been associated with mitochondrial disease (MD). Interestingly, most individuals with ASD and MD do not have a specific genetic mutation to explain the MD, raising the possibility of that MD may be acquired, at least in a subgroup of children with ASD. Acquired MD has been demonstrated in a rodent ASD model in which propionic acid (PPA), an enteric bacterial fermentation product of ASD-associated gut bacteria, is infused intracerebroventricularly. This animal model shows validity as it demonstrates many behavioral, metabolic, neuropathologic and neurophysiologic abnormalities associated with ASD. This animal model also demonstrates a unique pattern of elevations in short-chain and long-chain acyl-carnitines suggesting abnormalities in fatty-acid metabolism. To determine if the same pattern of biomarkers of abnormal fatty-acid metabolism are present in children with ASD, the laboratory results from a large cohort of children with ASD (n=213) who underwent screening for metabolic disorders, including mitochondrial and fatty-acid oxidation disorders, in a medically based autism clinic were reviewed. Acyl-carnitine panels were determined to be abnormal if three or more individual acyl-carnitine species were abnormal in the panel and these abnormalities were verified by repeated testing. Overall, 17% of individuals with ASD demonstrated consistently abnormal acyl-carnitine panels. Next, it was determined if specific acyl-carnitine species were consistently elevated across the individuals with consistently abnormal acyl-carnitine panels. Significant elevations in short-chain and long-chain, but not medium-chain, acyl-carnitines were found in the ASD individuals with consistently abnormal acyl-carnitine panels—a pattern consistent with the PPA rodent ASD model. Examination of electron transport chain function in muscle and fibroblast culture, histological and electron microscopy examination of muscle and other biomarkers of

  18. Molecular Dynamics of Polycarbonate Chains at the Interface of Polycarbonate/Polystyrene Heterogeneous Blends

    DTIC Science & Technology

    1991-11-14

    DNP-selected; spin-echo 13C NI4R; interfacial-PC; PC/ PS blends; motion. 19. ABSTRACT (Continue on reverse if necessary and identify by block number...As monitored by DNP-selected dipolar rotational, spin-echo 13C NMR, interfacial-PC chains in thin-film PC/ PS blends have less motion than PC chains in...Ii l ’ f I i ABSTRACT As monitored by DNP-selected dipolar rotational, spin-echo 13C NMR, interfacial-PC chains in thin-film PC/ PS blends (see

  19. Unacylated ghrelin promotes adipogenesis in rodent bone marrow via ghrelin O-acyl transferase and GHS-R1a activity: evidence for target cell-induced acylation

    PubMed Central

    Hopkins, Anna L.; Nelson, Timothy A. S.; Guschina, Irina A.; Parsons, Lydia C.; Lewis, Charlotte L.; Brown, Richard C.; Christian, Helen C.; Davies, Jeffrey S.; Wells, Timothy

    2017-01-01

    Despite being unable to activate the cognate ghrelin receptor (GHS-R), unacylated ghrelin (UAG) possesses a unique activity spectrum that includes promoting bone marrow adipogenesis. Since a receptor mediating this action has not been identified, we re-appraised the potential interaction of UAG with GHS-R in the regulation of bone marrow adiposity. Surprisingly, the adipogenic effects of intra-bone marrow (ibm)-infused acylated ghrelin (AG) and UAG were abolished in male GHS-R-null mice. Gas chromatography showed that isolated tibial marrow adipocytes contain the medium-chain fatty acids utilised in the acylation of UAG, including octanoic acid. Additionally, immunohistochemistry and immunogold electron microscopy revealed that tibial marrow adipocytes show prominent expression of the UAG-activating enzyme ghrelin O-acyl transferase (GOAT), which is located in the membranes of lipid trafficking vesicles and in the plasma membrane. Finally, the adipogenic effect of ibm-infused UAG was completely abolished in GOAT-KO mice. Thus, the adipogenic action of exogenous UAG in tibial marrow is dependent upon acylation by GOAT and activation of GHS-R. This suggests that UAG is subject to target cell-mediated activation – a novel mechanism for manipulating hormone activity. PMID:28361877

  20. Insight into Coenzyme A cofactor binding and the mechanism of acyl-transfer in an acylating aldehyde dehydrogenase from Clostridium phytofermentans

    PubMed Central

    Tuck, Laura R.; Altenbach, Kirsten; Ang, Thiau Fu; Crawshaw, Adam D.; Campopiano, Dominic J.; Clarke, David J.; Marles-Wright, Jon

    2016-01-01

    The breakdown of fucose and rhamnose released from plant cell walls by the cellulolytic soil bacterium Clostridium phytofermentans produces toxic aldehyde intermediates. To enable growth on these carbon sources, the pathway for the breakdown of fucose and rhamnose is encapsulated within a bacterial microcompartment (BMC). These proteinaceous organelles sequester the toxic aldehyde intermediates and allow the efficient action of acylating aldehyde dehydrogenase enzymes to produce an acyl-CoA that is ultimately used in substrate-level phosphorylation to produce ATP. Here we analyse the kinetics of the aldehyde dehydrogenase enzyme from the fucose/rhamnose utilisation BMC with different short-chain fatty aldehydes and show that it has activity against substrates with up to six carbon atoms, with optimal activity against propionaldehyde. We have also determined the X-ray crystal structure of this enzyme in complex with CoA and show that the adenine nucleotide of this cofactor is bound in a distinct pocket to the same group in NAD+. This work is the first report of the structure of CoA bound to an aldehyde dehydrogenase enzyme and our crystallographic model provides important insight into the differences within the active site that distinguish the acylating from non-acylating aldehyde dehydrogenase enzymes. PMID:26899032

  1. Edge-mediated skyrmion chain and its collective dynamics in a confined geometry

    PubMed Central

    Du, Haifeng; Che, Renchao; Kong, Lingyao; Zhao, Xuebing; Jin, Chiming; Wang, Chao; Yang, Jiyong; Ning, Wei; Li, Runwei; Jin, Changqing; Chen, Xianhui; Zang, Jiadong; Zhang, Yuheng; Tian, Mingliang

    2015-01-01

    The emergence of a topologically nontrivial vortex-like magnetic structure, the magnetic skyrmion, has launched new concepts for memory devices. Extensive studies have theoretically demonstrated the ability to encode information bits by using a chain of skyrmions in one-dimensional nanostripes. Here, we report experimental observation of the skyrmion chain in FeGe nanostripes by using high-resolution Lorentz transmission electron microscopy. Under an applied magnetic field, we observe that the helical ground states with distorted edge spins evolve into individual skyrmions, which assemble in the form of a chain at low field and move collectively into the interior of the nanostripes at elevated fields. Such a skyrmion chain survives even when the width of the nanostripe is much larger than the size of single skyrmion. This discovery demonstrates a way of skyrmion formation through the edge effect, and might, in the long term, shed light on potential applications. PMID:26446692

  2. The Acyl Desaturase CER17 Is Involved in Producing Wax Unsaturated Primary Alcohols and Cutin Monomers.

    PubMed

    Yang, Xianpeng; Zhao, Huayan; Kosma, Dylan K; Tomasi, Pernell; Dyer, John M; Li, Rongjun; Liu, Xiulin; Wang, Zhouya; Parsons, Eugene P; Jenks, Matthew A; Lü, Shiyou

    2017-02-01

    We report n-6 monounsaturated primary alcohols (C26:1, C28:1, and C30:1 homologs) in the cuticular waxes of Arabidopsis (Arabidopsis thaliana) inflorescence stem, a class of wax not previously reported in Arabidopsis. The Arabidopsis cer17 mutant was completely deficient in these monounsaturated alcohols, and CER17 was found to encode a predicted ACYL-COENZYME A DESATURASE LIKE4 (ADS4). Studies of the Arabidopsis cer4 mutant and yeast variously expressing CER4 (a predicted fatty acyl-CoA reductase) with CER17/ADS4, demonstrated CER4's principal role in synthesis of these monounsaturated alcohols. Besides unsaturated alcohol deficiency, cer17 mutants exhibited a thickened and irregular cuticle ultrastructure and increased amounts of cutin monomers. Although unsaturated alcohols were absent throughout the cer17 stem, the mutation's effects on cutin monomers and cuticle ultrastructure were much more severe in distal than basal stems, consistent with observations that the CER17/ADS4 transcript was much more abundant in distal than basal stems. Furthermore, distal but not basal stems of a double mutant deficient for both CER17/ADS4 and LONG-CHAIN ACYL-COA SYNTHETASE1 produced even more cutin monomers and a thicker and more disorganized cuticle ultrastructure and higher cuticle permeability than observed for wild type or either mutant parent, indicating a dramatic genetic interaction on conversion of very long chain acyl-CoA precursors. These results provide evidence that CER17/ADS4 performs n-6 desaturation of very long chain acyl-CoAs in both distal and basal stems and has a major function associated with governing cutin monomer amounts primarily in the distal segments of the inflorescence stem.

  3. Dynamics of Composite Haldane Spin Chains in IPA-CuCl3

    SciTech Connect

    Masuda, Takatsugu; Zheludev, Andrey I; Manaka, H.; Regnault, L.-P.; Chung, J.-H.; Qiu, Y.

    2006-01-01

    Magnetic excitations in the quasi-one-dimensional antiferromagnet IPA-CuCl{sub 3} are studied by cold neutron inelastic scattering. Strongly dispersive gap excitations are observed. Contrary to previously proposed models, the system is best described as an asymmetric quantum spin ladder. The observed spectrum is interpreted in terms of composite Haldane spin chains. The key difference from actual S = 1 chains is a sharp cutoff of the single-magnon spectrum at a certain critical wave vector.

  4. The properties of tests for spatial effects in discrete Markov chain models of regional income distribution dynamics

    NASA Astrophysics Data System (ADS)

    Rey, Sergio J.; Kang, Wei; Wolf, Levi

    2016-10-01

    Discrete Markov chain models (DMCs) have been widely applied to the study of regional income distribution dynamics and convergence. This popularity reflects the rich body of DMC theory on the one hand and the ability of this framework to provide insights on the internal and external properties of regional income distribution dynamics on the other. In this paper we examine the properties of tests for spatial effects in DMC models of regional distribution dynamics. We do so through a series of Monte Carlo simulations designed to examine the size, power and robustness of tests for spatial heterogeneity and spatial dependence in transitional dynamics. This requires that we specify a data generating process for not only the null, but also alternatives when spatial heterogeneity or spatial dependence is present in the transitional dynamics. We are not aware of any work which has examined these types of data generating processes in the spatial distribution dynamics literature. Results indicate that tests for spatial heterogeneity and spatial dependence display good power for the presence of spatial effects. However, tests for spatial heterogeneity are not robust to the presence of strong spatial dependence, while tests for spatial dependence are sensitive to the spatial configuration of heterogeneity. When the spatial configuration can be considered random, dependence tests are robust to the dynamic spatial heterogeneity, but not so to the process mean heterogeneity when the difference in process means is large relative to the variance of the time series.

  5. Short-chain ceramides decrease skin barrier properties.

    PubMed

    Novotný, J; Janůsová, B; Novotný, M; Hrabálek, A; Vávrová, K

    2009-01-01

    Stratum corneum ceramides are major determinants of skin barrier function. Although their physiological and pathological role has been widely investigated, to date no structure-activity relationships have been established. In this study, a series of short-chain ceramide analogues with polar head structure identical to ceramide NS, a sphingosine length of 12 carbons and an acyl chain length of 2-12 carbons was synthesized. Their effect on skin permeability was evaluated using porcine skin and two model drugs, theophylline and indomethacin, and compared to that of a physiological ceramide NS. The results showed that the ceramide chain length was crucial for their barrier properties. Ceramides with a 4- to 8-carbon acyl chain were able to increase skin permeability for both drugs up to 10.8 times with maximum effect at a 6-carbon acyl chain. No increase in permeability was found for ceramide analogues with 2- and 12-carbon acyl chains and ceramide NS. The same relationships were obtained for skin concentrations of the model drugs. The relationship between ceramide acyl chain length and its ability to perturb skin barrier showed striking similarity to the behavior of short-chain ceramides in sphingomyelin/phospholipid membranes and confirmed that short-chain ceramides do not act as natural ceramides and their use as experimental tools should be cautious.

  6. Characterization of complex, heterogeneous lipid A samples using HPLC-MS/MS technique I. Overall analysis with respect to acylation, phosphorylation and isobaric distribution.

    PubMed

    Sándor, Viktor; Dörnyei, Ágnes; Makszin, Lilla; Kilár, Ferenc; Péterfi, Zoltán; Kocsis, Béla; Kilár, Anikó

    2016-11-01

    We established a new reversed phase-high performance liquid chromatography method combined with electrospray ionization quadrupole time-of-flight tandem mass spectrometry for the simultaneous determination and structural characterization of different lipid A types in bacteria (Escherichia coli O111, Salmonella adelaide O35 and Proteus morganii O34) showing serological cross-reactivity. The complex lipid A mixtures (obtained by simple extraction and acid hydrolysis of the outer membrane lipopolysaccharides) were separated and detected without phosphate derivatization. Several previously unidentified ions were detected, which differed in the number and type of acyl chains and number of phosphate groups. In several cases, we observed the different retention of isobaric lipid A species, which had different secondary fatty acyl distribution at the C2' or the C3' sites. The fragmentation of the various, C4' monophosphorylated lipid A species in deprotonated forms provided structural assignment for each component. Fragmentation pathways of the tri-acylated, tetra-acylated, penta-acylated, hexa-acylated and hepta-acylated lipid A components and of the lipid A partial structures are suggested. As standards, the hexa-acylated ion at m/z 1716 with the E. coli-type acyl distribution and the hepta-acylated ion at m/z 1954 with the Salmonella-type acyl distribution were used. The results confirmed the presence of multiple forms of lipid A in all strains analyzed. In addition, the negative-ion mode MS permitted efficient detection for non-phosphorylated lipid A components, too. Copyright © 2016 John Wiley & Sons, Ltd.

  7. Derivation of a Markov state model of the dynamics of a protein-like chain immersed in an implicit solvent

    SciTech Connect

    Schofield, Jeremy Bayat, Hanif

    2014-09-07

    A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local structure and bonding in a coarse-grained sense. The model is based on the assumption that the implicit solvent interacts on a fast time scale with the monomers of the chain compared to the time scale for structural rearrangements of the chain and provides sufficient friction so that the motion of monomers is governed by the Smoluchowski equation. A microscopic theory for the dynamics of the system is developed that reduces to a Markovian model of the kinetics under well-defined conditions. Microscopic expressions for the rate constants that appear in the Markov state model are analyzed and expressed in terms of a temperature-dependent linear combination of escape rates that themselves are independent of temperature. Excellent agreement is demonstrated between the theoretical predictions of the escape rates and those obtained through simulation of a stochastic model of the dynamics of bond formation. Finally, the Markov model is studied by analyzing the eigenvalues and eigenvectors of the matrix of transition rates, and the equilibration process for a simple helix-forming system from an ensemble of initially extended configurations to mainly folded configurations is investigated as a function of temperature for a number of different chain lengths. For short chains, the relaxation is primarily single-exponential and becomes independent of temperature in the low-temperature regime. The profile is more complicated for longer chains, where multi-exponential relaxation behavior is seen at intermediate temperatures followed by a low temperature regime in which the folding becomes rapid and single exponential. It is demonstrated that the behavior of the equilibration profile as the temperature is lowered can be understood in terms of the

  8. Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

    PubMed

    Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

    2011-07-21

    In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

  9. Decision support for green supply chain operations by integrating dynamic simulation and LCA indicators: diaper case study.

    PubMed

    Adhitya, Arief; Halim, Iskandar; Srinivasan, Rajagopalan

    2011-12-01

    As the issue of environmental sustainability is becoming an important business factor, companies are now looking for decision support tools to assess the fuller picture of the environmental impacts associated with their manufacturing operations and supply chain (SC) activities. Lifecycle assessment (LCA) is widely used to measure the environmental consequences assignable to a product. However, it is usually limited to a high-level snapshot of the environmental implications over the product value chain without consideration of the dynamics arising from the multitiered structure and the interactions along the SC. This paper proposes a framework for green supply chain management by integrating a SC dynamic simulation and LCA indicators to evaluate both the economic and environmental impacts of various SC decisions such as inventories, distribution network configuration, and ordering policy. The advantages of this framework are demonstrated through an industrially motivated case study involving diaper production. Three distinct scenarios are evaluated to highlight how the proposed approach enables integrated decision support for green SC design and operation.

  10. Ethanol Distribution, Dispensing, and Use: Analysis of a Portion of the Biomass-to-Biofuels Supply Chain Using System Dynamics

    SciTech Connect

    Vimmerstedt, L. J.; Bush, B.; Peterson, S.

    2012-05-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  11. A Markov chain method to determine the dynamic properties of compound extremes and their near future climate change signal

    NASA Astrophysics Data System (ADS)

    Sedlmeier, Katrin; Mieruch, Sebastian; Schädler, Gerd

    2014-05-01

    Compound extremes are receiving more and more attention in the scientific world because of their great impact on society. It is therefore of great interest how well state-of-the-art regional climate models can represent the dynamics of multivariate extremes. Furthermore, the near future climate change signal of compound extremes is interesting especially on the regional scale because high resolution information is needed for impact studies and mitigation and adaptation strategies. We use a method based on Markov Chains to assess these two questions. It is based on the representation of multivariate climate anomalies by first order Markov Chains. We partition our dataset into extreme and non-extreme regimes and reduce the multivariate dataset to a univariate time series which can then be described as a discrete stochastic process, a Markov Chain. From the transition matrix several descriptors such as persistence, recurrence time and entropy are derived which characterize the dynamic properties of the multivariate system. By comparing these descriptors for model and observation data, the representation of the dynamics of the climate system by different models is evaluated. Near future shifts or changes of the dynamics of compound extremes are detected by using regional climate projections and comparing the descriptors for different time periods. In order to obtain reliable estimates of a climate change signal, we use an ensemble of simulations to assess the uncertainty which arise in climate projections. Our work is based on an ensemble of high resolution (7 km) regional climate simulations for Central Europe with the COSMO-CLM regional climate model using different global driving data. The time periods considered are a control period (1971-200) and the near future (2021-2050) and running windows within these time periods. For comparison, E-Obs and HYRAS gridded observational datasets are used. The presentation will mainly focus on bivariate temperature and

  12. Ethanol distribution, dispensing, and use: analysis of a portion of the biomass-to-biofuels supply chain using system dynamics.

    PubMed

    Vimmerstedt, Laura J; Bush, Brian; Peterson, Steve

    2012-01-01

    The Energy Independence and Security Act of 2007 targets use of 36 billion gallons of biofuels per year by 2022. Achieving this may require substantial changes to current transportation fuel systems for distribution, dispensing, and use in vehicles. The U.S. Department of Energy and the National Renewable Energy Laboratory designed a system dynamics approach to help focus government action by determining what supply chain changes would have the greatest potential to accelerate biofuels deployment. The National Renewable Energy Laboratory developed the Biomass Scenario Model, a system dynamics model which represents the primary system effects and dependencies in the biomass-to-biofuels supply chain. The model provides a framework for developing scenarios and conducting biofuels policy analysis. This paper focuses on the downstream portion of the supply chain-represented in the distribution logistics, dispensing station, and fuel utilization, and vehicle modules of the Biomass Scenario Model. This model initially focused on ethanol, but has since been expanded to include other biofuels. Some portions of this system are represented dynamically with major interactions and feedbacks, especially those related to a dispensing station owner's decision whether to offer ethanol fuel and a consumer's choice whether to purchase that fuel. Other portions of the system are modeled with little or no dynamics; the vehicle choices of consumers are represented as discrete scenarios. This paper explores conditions needed to sustain an ethanol fuel market and identifies implications of these findings for program and policy goals. A large, economically sustainable ethanol fuel market (or other biofuel market) requires low end-user fuel price relative to gasoline and sufficient producer payment, which are difficult to achieve simultaneously. Other requirements (different for ethanol vs. other biofuel markets) include the need for infrastructure for distribution and dispensing and

  13. Exploring the Dynamics and Modeling National Budget as a Supply Chain System: A Proposal for Reengineering the Budgeting Process and for Developing a Management Flight Simulator

    DTIC Science & Technology

    2012-09-01

    beer production and distribution. The whole system consists of four entities: Retailer , Wholesaler, Distributor, and Factory (R, W, D, and F). It is...EXPLORING THE DYNAMICS AND MODELING NATIONAL BUDGET AS A SUPPLY CHAIN SYSTEM : A PROPOSAL FOR...MODELING NATIONAL BUDGET AS A SUPPLY CHAIN SYSTEM : A PROPOSAL FOR REENGINEERING THE BUDGETING PROCESS AND FOR DEVELOPING A MANAGEMENT FLIGHT

  14. Rotational dynamics of coumarin-153 and 4-aminophthalimide in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: effect of alkyl chain length on the rotational dynamics.

    PubMed

    Das, Sudhir Kumar; Sarkar, Moloy

    2012-01-12

    Rotational dynamics of two neutral organic solutes, coumarin-153 (C-153) and 4-aminophthalimide (AP), with only the latter having hydrogen-bond-donating ability, has been investigated in a series of 1-ethyl-3-methylimidazolium alkyl sulfate ionic liquids as a function of temperature. The ionic liquids differ only in the length of the linear alkyl side chain (alkyl = ethyl, butyl, hexyl, and octyl) on the anionic moiety. The present study has been undertaken to examine the role of alkyl side chains on the rotational dynamics of the two solutes in these ionic liquids. Analysis of the results using Stokes-Einstein-Debye hydrodynamic theory indicates that the rotational dynamics of C-153 lies between the stick and slip boundary condition in the ethyl analogue and finally reaches subslip condition as in case of the octyl substituent. The observed rotational behavior of C-153 has been explained on the basis of an increase in the size of the solvent, which offers lower friction for solute rotation. On the other hand, AP shows superstick behavior in the ethyl system and exceeds the stick limit in the octyl derivative. Superstick behavior of AP has been attributed to the specific hydrogen-bonding interaction between AP and the sulfate moiety. Proton NMR investigation confirms the hydrogen-bonding interaction between the N-H hydrogen of AP and the ionic liquid. The decrease in rotational coupling constant values for AP with increasing length of alkyl side chains has been attributed to the decrease in the solute-solvent-specific interaction with an increase in the alkyl side chain length on the sulfate moiety.

  15. Chain Conformation and Dynamics in Spin-Assisted Weak Polyelectrolyte Multilayers

    DOE PAGES

    Zhuk, Aliaksandr; Selin, Victor; Zhuk, Iryna; ...

    2015-03-13

    In this paper, we report on the effect of the deposition technique on film layering, stability, and chain mobility in weak polyelectrolyte layer-by-layer (LbL) films. Ellipsometry and neutron reflectometry (NR) showed that shear forces arising during spin-assisted assembly lead to smaller amounts of adsorbed polyelectrolytes within LbL films, result in a higher degree of internal film order, and dramatically improve stability of assemblies in salt solutions as compared to dip-assisted LbL assemblies. The underlying flattening of polyelectrolyte chains in spin-assisted LbL films was also revealed as an increase in ionization degree of the assembled weak polyelectrolytes. As demonstrated by fluorescencemore » recovery after photobleaching (FRAP), strong binding between spin-deposited polyelectrolytes results in a significant slowdown of chain diffusion in salt solutions as compared to dip-deposited films. Moreover, salt-induced chain intermixing in the direction perpendicular to the substrate is largely inhibited in spin-deposited films, resulting in only subdiffusional (<2 Å) chain displacements even after 200 h exposure to 1 M NaCl solutions. Finally, this persistence of polyelectrolyte layering has important ramifications for multistage drug delivery and optical applications of LbL assemblies.« less

  16. Chain Conformation and Dynamics in Spin-Assisted Weak Polyelectrolyte Multilayers

    SciTech Connect

    Zhuk, Aliaksandr; Selin, Victor; Zhuk, Iryna; Belov, Benjamin; Ankner, John F.; Sukhishvili, Svetlana A.

    2015-03-13

    In this paper, we report on the effect of the deposition technique on film layering, stability, and chain mobility in weak polyelectrolyte layer-by-layer (LbL) films. Ellipsometry and neutron reflectometry (NR) showed that shear forces arising during spin-assisted assembly lead to smaller amounts of adsorbed polyelectrolytes within LbL films, result in a higher degree of internal film order, and dramatically improve stability of assemblies in salt solutions as compared to dip-assisted LbL assemblies. The underlying flattening of polyelectrolyte chains in spin-assisted LbL films was also revealed as an increase in ionization degree of the assembled weak polyelectrolytes. As demonstrated by fluorescence recovery after photobleaching (FRAP), strong binding between spin-deposited polyelectrolytes results in a significant slowdown of chain diffusion in salt solutions as compared to dip-deposited films. Moreover, salt-induced chain intermixing in the direction perpendicular to the substrate is largely inhibited in spin-deposited films, resulting in only subdiffusional (<2 Å) chain displacements even after 200 h exposure to 1 M NaCl solutions. Finally, this persistence of polyelectrolyte layering has important ramifications for multistage drug delivery and optical applications of LbL assemblies.

  17. Dynamics of particle chain formation in a liquid polymer under ac electric field: modeling and experiments

    NASA Astrophysics Data System (ADS)

    Belijar, G.; Valdez-Nava, Z.; Diaham, S.; Laudebat, L.; Jones, T. B.; Lebey, T.

    2017-01-01

    Polymer/ceramic composite materials are of great interest for their many potential applications because of their ability to combine at least two properties of the constitutive elements: particles and matrix. In most cases, such enhanced properties are required only in one direction. Orthotropic materials can be elaborated by applying an ac electric field to form particle chain structures in the direction of the electric field due to the dielectrophoretic interactions affecting the particles. However, there is still a lack in the understanding of the impact of the structures on the properties of the material. The aim of this study is to propose a predictive model for the evolution of the permittivity during the chain formation, by including micro- and macroscopic phenomena. The chaining model is based on dipole-dipole interactions and the dielectric permittivity is computed through a finite element method. In parallel, an experimental study is performed with online permittivity measurements of composites during chaining. The developed model is able to predict the experimental results from 1 vol% while taking into account parameters such as the resin viscosity and permittivity and the transient evolution of the applied electric field. The formation of particle chains inside a material has applications in many domains such as electrorheological fluids, anisotropic composites, self-recovery materials etc. Such a developed model is a valuable tool for the tailoring of materials.

  18. ROMPgel beads in IRORI format: acylations revisited.

    PubMed

    Roberts, Richard S

    2005-01-01

    Functionalized "designer" polymers derived from ring-opening metathesis polymerization (ROMPgels) are attractive for their high loading, high purity, and ease of synthesis. Their physical state may vary from liquid to gel to granular solid, making a general method of handling these polymers difficult. By incorporating a suitable norbornene-substituted linker on standard Wang beads, ROMPgels can be easily grafted onto the resin, adding the convenience of a bead format while still maintaining the high loading and excellent site accessibility. This advantage is demonstrated by the use of an N-hydroxysuccinimide ROMPgel (3.3 mmol g(-1), a 3-fold increase from the parent linker resin) in IRORI Kan format. Conditions for the acylation of these IRORI-formatted ROMPgels are reported, along with the scope and limitations of the choice of acylating reagents. Yields are greatly improved by the use of perfluorinated solvents as a nonparticipating cosolvent in the acylation process. A simple titration method for the quantification of the acylated ROMPgels is also reported. Spent Kans are regenerated after each use without apparent loss of activity or purity after several cycles. Due to the high loading and reduced swelling of the ROMPgel resin, up to 0.39 mmol acyl group has successfully been recovered from a single IRORI mini