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At least 793 records · Page 44

The intermediate scattering function for lipid bilayer membranes: From nanometers to microns

A numerical scheme based upon established hydrodynamic and elastic considerations is introduced and used to predict the intermediate scattering function for lipid bilayer membranes. The predictions span multiple wavelength regimes, including those studied by dynamic light scattering (DLS; microns) and neutron spin-echo (NSE) spectroscopy (10-100 nm). The results validate a recent theory specific to the NSE regime and expose slight inaccuracies associated with the theoretical results available in the DLS regime. The assumptions that underlie both our numerical methods and the related theoretical predictions are reviewed in detail to explain when certain results can be applied to experiment and where caution must be exercised.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Correlation between length and tilt of lipid tails

It is becoming recognized from simulations, and to a lesser extent from experiment, that the classical Helfrich-Canham membrane continuum mechanics model can be fruitfully enriched by the inclusion of molecular tilt, even in the fluid, chain disordered, biologically relevant phase of lipid bilayers. Enriched continuum theories then add a tilt modulus κ{sub θ} to accompany the well recognized bending modulus κ. Different enrichment theories largely agree for many properties, but it has been noticed that there is considerable disagreement in one prediction; one theory postulates that the average length of the hydrocarbon chain tails increases strongly with increasing tilt and another predicts no increase. Our analysis of an all-atom simulation favors the latter theory, but it also shows that the overall tail length decreases slightly with increasing tilt. We show that this deviation from continuum theory can be reconciled by consideration of the average shape of the tails, which is a descriptor not obviously includable in continuum theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Correlated lateral phase separations in stacks of lipid membranes

Motivated by the experimental study of Tayebi et al. [Nat. Mater. 11, 1074 (2012)] on phase separation of stacked multi-component lipid bilayers, we propose a model composed of stacked two-dimensional Ising spins. We study both its static and dynamical features using Monte Carlo simulations with Kawasaki spin exchange dynamics that conserves the order parameter. We show that at thermodynamical equilibrium, due to strong inter-layer correlations, the system forms a continuous columnar structure for any finite interaction across adjacent layers. Furthermore, the phase separation shows a faster dynamics as the inter-layer interaction is increased. This temporal behavior is mainly due to an effective deeper temperature quench because of the larger value of the critical temperature, T{sub c}, for larger inter-layer interaction. When the temperature ratio, T/T{sub c}, is kept fixed, the temporal growth exponent does not increase and even slightly decreases as a function of the increased inter-layer interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evidence that Criegee intermediates drive autoxidation in unsaturated lipids

Significance Autoxidation leads to the slow persistent destruction of organic molecules causing oxidative stress and associated disease. The prevailing autoxidation mechanism of unsaturated lipids involves chain reactions initiated and propagated by H-atom abstraction, mediated by peroxy radicals and other reactive oxygen species. Here we report experimental evidence for an autoxidation mechanism initiated by OH, which is unanticipated and proceeds by OH addition followed by pathways involving Criegee intermediates (CIs). Although CIs are routinely encountered in atmospheric and synthetic organic chemistry, their role in autoxidation is unexpected. Our results suggest that in all likelihood these exotic species play a much more prominent and general role in the chemistry of cells, food, petrochemicals, and the environment beyond what is currently believed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein

Diverse extracellular proteins negatively regulate WNT signaling. One such regulator is adenomatosis polyposis coli down-regulated 1 (APCDD1), a conserved single-span transmembrane protein. In response to WNT signaling in a variety of tissues, APCDD1 transcripts are highly up-regulated. We have determined the three-dimensional structure of the extracellular domain of APCDD1, and this structure reveals an unusual architecture consisting of two closely apposed β-barrel domains (ABD1 and ABD2). ABD2, but not ABD1, has a large hydrophobic pocket that accommodates a bound lipid. The APCDD1 ECD can also bind to WNT7A, presumably via its covalently bound palmitoleate, a modification that is common to all WNTs and is essential for signaling. This work suggests that APCDD1 functions as a negative feedback regulator by titrating WNT ligands at the surface of responding cells.

59 BASIC BIOLOGICAL SCIENCES↗

Thermal Fluctuation and Elasticity of Lipid Vesicles Interacting with Pore-Forming Peptides

The thermal fluctuation and elasticity of dioleoyl-phosphocholine large unilamellar vesicle interacting with pore-forming peptide, melittin, were investigated by neutron spin-echo measurements. The relaxation behavior of the membrane fluctuation with different peptide to lipid molar ratio P/L can be divided into three regions, resulting from characteristic changes of the effective bending modulus {kappa}-tilde of the membrane which includes the effects of internal dissipation within the membrane. At low P/L, melittin is adsorbed parallel to the surface of membrane and {kappa}-tilde decreases significantly due to perturbation of hydrocarbon chain packing. At a critical P/L, melittin forms pores in the membrane and {kappa}-tilde starts to increase slightly due to high pore rigidity. At higher P/L where the repulsive interpore interaction becomes significant, {kappa}-tilde increases rapidly.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A 2A receptor (A 2A AR) at 2.0 Å resolution is determined and compared with previous A 2A AR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Finding new friends and revisiting old ones – how plant lipid droplets connect with other subcellular structures

Summary The number of described contact sites between different subcellular compartments and structures in eukaryotic cells has increased dramatically in recent years and, as such, has substantially reinforced the well‐known premise that these kinds of connections are essential for overall cellular organization and the proper functioning of cellular metabolic and signaling pathways. Here, we discuss contact sites involving plant lipid droplets (LDs), including LD‐endoplasmic reticulum (ER) connections that mediate the biogenesis of new LDs at the ER, LD‐peroxisome connections, that facilitate the degradation of LD‐stored triacylglycerols (TAGs), and the more recently discovered LD‐plasma membrane connections, which involve at least three novel proteins, but have a yet unknown physiological function(s).

60 APPLIED LIFE SCIENCES↗

Acoustic Methods to Monitor Protein Crystallization and to Detect Protein Crystals in Suspensions of Agarose and Lipidic Cubic Phase

Improvements needed for automated crystallography include crystal detection and crystal harvesting. A technique that uses acoustic droplet ejection to harvest crystals was previously reported. Here a method is described for using the same acoustic instrument to detect protein crystals and to monitor crystal growth. Acoustic pulses were used to monitor the progress of crystallization trials and to detect the presence and location of protein crystals. Crystals were detected, and crystallization was monitored in aqueous solutions and in lipidic cubic phase. Using a commercially available acoustic instrument, crystals measuring ~150 µm or larger were readily detected. Simple laboratory techniques were used to increase the sensitivity to 50 µm by suspending the crystals away from the plastic surface of the crystallization plate. This increased the sensitivity by separating the strong signal generated by the plate bottom that can mask the signal from small protein crystals. It is possible to further boost the acoustic reflection from small crystals by reducing the wavelength of the incident sound pulse, but our current instrumentation does not allow this option. In the future, commercially available sound-emitting transducers with a characteristic frequency near 300 MHz should detect and monitor the growth of individual 3 µm crystals.

59 BASIC BIOLOGICAL SCIENCES↗

Cation-containing lipid membranes – experiment and md simulations

Here, using small angle neutron diffraction and molecular dynamics simulations we studied the interactions between calcium (Ca 2+ ) or zinc (Zn 2+ ) cations, and oriented gel phase dipalmitoyl-phosphatidylcholine (DPPC) bilayers. For both cations studied at ~1:7 divalent metal ion to lipid molar ratio (Me2+:DPPC), bilayer thickness increased. Simulation results helped reveal subtle differences in the effects of the two cations on gel phase membranes.

59 BASIC BIOLOGICAL SCIENCES↗

Radiotracers For Lipid Signaling Pathways In Biological Systems

The primary focus of this project continues to be the development of radiotracers and radiotracer methodology for studying physiology and biochemistry. The compounds that have been labeled areacylethanolamines and acylglycerols that are, as classes, represented in both in plants and in animals. In the latter, some of these act as ligands for cannabinoid receptors and they are therefore known as endocannabinoids. Cannabinoid receptors are not found in plant genomes so that plants must contain other receptors and signaling systems that use acylethanolamines. Relatively little work has been done on that issue, though acylethanolamines do modulate plant growth and stress resistance, thus possessing obvious relevance to agriculture and energy production. Progress has been described in five peer-reviewed papers and seven meeting abstracts. Preparation of 2-acylglycerol lipid messengers in high purity. A novel enzymatic synthesis was developedthat gave pure 2-acylglycerols free of any rearrrangement to the thermodynamically more stable 1(3)-acylglycerol byproducts. The method utilized 1,3-dibutyryl-2-acylglycerol substrate ethanolysis by a resinimobilized lipase. Thus, pure radiolabeled 2-acylglycerols can now be conveniently prepared just prior to their utilization. These synthetic studies were published in the Journal of Medicinal Chemistry, 2011. Diacylglycerol lipase assay methodology. Diacylglycerol lipases (DAGLs) generate 2- acylglycerols, and are thus potential targets for disease- or growth-modifying agents, by means of reducing formation of 2-acylglycerols. A radioTLC assay of the hydrolysis of radiolabeled diglyceride substrate [1''-carbon-14]2-arachidonoyl-1-stearoyl-sn-glycerol has been implemented, and used to validate a novel, potentially highthroughput fluorescence resonance energy transfer (FRET) based assay. A number of new DAGL inhibitors that have selectivity for DAGLs were synthesized and screened. This work was very recently published in Bioorganic and Medicinal Chemistry Letters.Acylethanolamines. The work initially focused on myristoylethanolamine (MEA) labeled in the acyl moiety with tritium and with carbon-14. Standard coupling conditions were used and gave the desired radiotracers in decent yields. Tritiated product was needed for the search for binding sites of this signaling messenger, and C-14 labeled product for imaging using phosphorimaging screens. Additionally, C-14 MEA was prepared labeled in the ethanolamine moiety. Fluorine-18 labeled acylethanolamines. A multi-step synthesis was performed to obtain unlabeled N-(16- fluorohexadecanoyl)ethanolamide for an HPLC standard via the precursor 16-bromo-N- [2[(tetrahydro-2Hpyran-2-yl)oxy]ethyl]hexadecanoylamide. Near-anhydrous F-18 and the bromo precursor (approximately 2-3 mg) in acetonitrile (0.5 ml) were heated with a PETWave microwave reactor for 10 min at 80 °C. F-18 incorporation was checked using silica-gel TLC (8:92 methanol/chloroform). Deprotection was carried out using TFA. The crude product was purified by semi-preparative ODS HPLC (80:20 AcN/ H2O). The product peak was diluted in water, concentrated on an SPE column, and eluted in 1 mL EtOH. F-18 incorporation to form the THP protected product was >90% with negligible side products observed. Deprotection and HPLC purification proceeded successfully with >99% radiochemical l purity. Brain distribution studies were done in mice. This work was presented at the Society of Nuclear Medicine meeting in June 2012. Subsequent more detailed studies including whole body tissue distribution studies, microPET experiments and radiochromatographic studies were published in ACS Chemical Neurosciences in 2014. Iodine-125 labeled acylethanolamines. The precursor 12-bromo-N-[2[(tetrahydro-2H-pyran-2-yl)oxy]ethyl]dodecanoylamide was prepared and a 1 mg sample was subject to exchange labeling withradioiodide in refluxing acetonitrile for 1 hour. HPLC analysis as above indicated incorporation of about10% of the radioactivity into a compound with the expected retention time of the corresponding iodocompound. Treatment with TFA converted the radioactivity into a compound with the expected retentiontime of 12-iodododenanoyl ethanolamine. Radiotracer studies in plants. One of the aims of this funding was to follow up the studies of Tripathy et al. (Plant Physiol., 2003) who first reported high affinity binding sites for tritiated myristoylethanolamine in plants, and also reported blockage of these sites by the cannabinoid receptor antagonist AM281. Because plant genomes do not contain genes for cannabinoid receptors, this was an intriguing report. I-125 labeled AM281 was therefore prepared, to facilitate identification of binding sites for this compound in Arabodopsis thaliana plants. However, such sites could not be found, the binding studies were repeated in tobacco plants. Again, binding sites for AM281 were not found. Additionally, it has become evident that clear demonstration of binding sites for tritiated MEA is obscured by metabolic incorporation of radioactivity into plant tissues. Studies on this issue are being aggressively pursued. Binding methodologies used in experiments with animal tissues require modification for their optimal use with plant tissues. Detailed studies of [14C]myristoylethanolamine isotopomers and of [14C]arachidonoylethanolamine isotopomers Since the labeled compounds being prepared for experiments with plants may have utility in Nuclear Medicine, studies were conducted with some of these compounds in mice. The brain uptake of C-14 MEA labeled in either acyl or ethanolamine moiety was 3-4 fold higher than uptake of C-14 myristic acid or C-14 ethanolamine. Carrier MEA increased brain uptake. Autoradiographs of MEA showed regionally specific uptake, with somewhat different patterns for acyl and ethanolamine isotopomers. It is hypothesized that these labeled compounds might form the basis of autoradiographic imaging of regional activity of enzymes such as fatty acid amide hydrolase, which may regulate endocannabinoid tone in animals. Early results were presented at the 2011 ICRS meeting, and at the 2012 Society for Neurosciences. Narachidonoylethanolamine is an endocannabinoid signaling messenger in animals and is known as “anandamide”. It is one of several families of signaling molecules derived from arachidonic acid, the principal omega-6 polyunsaturated fatty acids (PUFA’s) in animal species. Other derivatives of arachidonic acid include thromboxanes and prostaglandins. Full details of the studies with the ethanolamide isotopomers were a part of the PhD dissertation of Kun Hu (nee Qian), and were submitted for publication to Nuclear Medicine and Biology in August 2016. Syntheses of [14C]docosahexanoylethanolamine isotopomers and preliminary biological investigations Docosahexaenoic acid (DHA) is the omega-3 PUFA that can be regarded in some respects as the counterpart of arachidonic acid in the omega-6 series. While arachidonic acid is proinflammatory, DHA is anti-inflammatory, and foods high in DHA (or artificially enriched in DHA) are commonly regarded as promoting health. In contrast to the large literature on the Nethanolamide of arachidonic acid (i.e. the endocannabinoid anandamide) as of now (9/25/2016) there are only six papers on the corresponding ethanolamide of DHA, and when our studies under this grant began there were none. Beneficial actions of endogenously produced DHAethanolamine (“synaptamide”) have been indicated, and to help elucidate the possible roles of synaptamide, we have synthesized this molecule for the first time labeled with C-14 in either the ethanolamine moiety or the fatty acid moiety. Studies of the disposition of endogenously administered isotopomers of DHA-ethanolamine are in progress, to complement tissue culture experiments evaluation hypothesized protective effects of this DHA derivative.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Simple Scattering: Lipid nanoparticle structural data repository

Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.

59 BASIC BIOLOGICAL SCIENCES↗

Catabolism and Deactivation of the Lipid-Derived Hormone Jasmonoyl-Isoleucine

The oxylipin hormone jasmonate controls myriad processes involved in plant growth, development, and immune function. The discovery of jasmonoyl-L-isoleucine (JA-Ile) as the major bioactive form of the hormone highlights the need to understand biochemical and cell biological processes underlying JA-Ile homeostasis. Among the major metabolic control points governing the accumulation of JA-Ile in plant tissues are the availability of jasmonic acid, the immediate precursor of JA-Ile, and oxidative enzymes involved in catabolism and deactivation of the hormone. Recent studies indicate that JA-Ile turnover is mediated by a ω-oxidation pathway involving members of the CYP94 family of cytochromes P450. This discovery opens new opportunities to genetically manipulate JA-Ile levels for enhanced resistance to environmental stress, and further highlights ω-oxidation as a conserved pathway for catabolism of lipid-derived signals in plants and animals. Functional characterization of the full complement of CYP94 P450s promises to reveal new pathways for jasmonate metabolism and provide insight into the evolution of oxylipin signaling in land plants.

54 ENVIRONMENTAL SCIENCES↗

Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry

Lipid mediators (LMs) are broadly defined as a class of bioactive lipophilic molecules that regulate cell-to-cell communication events with many having a strong correlation with various human diseases and conditions. LMs are usually analyzed with liquid chromatography and mass spectrometry (LC-MS), but their numerous isomers greatly complicate the measurements with essentially identical fragmentation spectra and LC separations not always sufficient for distinguishing the features. Herein, we characterized LMs having specific categories using ion mobility spectrometry coupled with mass spectrometry (IMS-MS). The collision cross-sections and m/z values from the IMS and MS analyses displayed distinct trend lines. Specifically, the structural trend lines for sodiated LMs originating from docosahexaenoic acid had the smallest collision cross-section values in relation to m/z, while those from linoleic acid had the largest. LC–IMS–MS analyses were also performed on LMs in flu infected mouse tissue samples. These multidimensional studies were able to assess known LMs while also detecting new species. Adding IMS separations to conventional LC–MS analyses show great utility for enabling better identification and characterization of LMs in complex biological samples.

59 BASIC BIOLOGICAL SCIENCES↗

Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.

Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.

ANN↗