Mixed Chain Research Articles

Apolipoprotein A-II-mediated Conformational Changes of Apolipoprotein A-I in Discoidal High Density Lipoproteins

It is well accepted that HDL has the ability to reduce risks for several chronic diseases. To gain insights into the functional properties of HDL, it is critical to understand the HDL structure in detail. To understand interactions between the two major apolipoproteins (apos), apoA-I and apoA-II in HDL, we generated highly defined benchmark discoidal HDL particles. These particles were reconstituted using a physiologically relevant phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) incorporating two molecules of apoA-I and one homodimer of apoA-II per particle. We utilized two independent mass spectrometry techniques to study these particles. The techniques are both sensitive to protein conformation and interactions and are namely: 1) hydrogen deuterium exchange combined with mass spectrometry and 2) partial acetylation of lysine residues combined with MS. Comparison of mixed particles with apoA-I only particles of similar diameter revealed that the changes in apoA-I conformation in the presence of apoA-II are confined to apoA-I helices 3-4 and 7-9. We discuss these findings with respect to the relative reactivity of these two particle types toward a major plasma enzyme, lecithin:cholesterol acyltransferase responsible for the HDL maturation process.

Nonclassical Odd–even Alternation in Mixed-Chain Diacylethanolamines: Implications of Polymorphism

N,O-Diacylethanolamines (DAEs), derived by the O-acylation of bioactive N-acylethanolamines (NAEs), are most likely present in biological membranes. In the present study, a homologous series of mixed chain DAEs with an N-palmitoyl chain and varying O-acyl chains (n = 6–16) have been synthesized and characterized. Differential scanning calorimetry (DSC) studies revealed a nonclassical type of odd–even alternation in the enthalpy and entropy of melting, with the odd–even effect becoming more prominent with increase in the O-acyl chain length. This was rationalized by analyzing the 3-dimensional structures of several DAEs. In most cases, two types of packing polymorphs (α and β) were observed; while the α polymorph is characterized by a mixed type of chain packing, in the β polymorph the chain packing is symmetric. Analysis of the crystal structures revealed that the odd–even effect is manifested through differences in the packing of acyl chains, with the packing being closer when both chains are even. A possible role of polymorphism in the odd–even effect has also been considered, and it was suggested that the nonclassical behavior observed in the alternation could be attributed to the presence of different fractions of the α and β forms in the bulk mixture. Similar nonclassical odd–even effects and polymorphism may exist in other mixed chain systems, which adopt an “L” shape.

Enzymatic measurement of phosphatidylserine in cultured cells

Phosphatidylserine (PS) is a quantitatively minor membrane phospholipid involved in diverse cellular functions. In this study, we developed a new fluorometric method for measuring PS using combinations of specific enzymes and Amplex Red. The calibration curve for PS measurement was linear and hyperbolic at low (0-50 µM) and high (50-1000 µM) concentrations, respectively, and the detection limit was 5 µM (50 pmol in the reaction mixture). This assay quantified PS regardless of the chain length and the number of double bonds. We applied this new method to the determination of PS content in HEK293 cells, which was validated by a recovery study and comparison with TLC-phosphorus assay. We showed that the PS content was high in sparse cells. The overexpression of PS synthase 1 elevated not only the cellular PS content but also the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) contents, suggesting the conversion of PS into PE and the enhancement of PC production. This new assay for PS measurement is simple, specific, sensitive, and high throughput, and it will be useful to clarify the metabolism and biological functions of PS.

TR-FRET-Based High-Throughput Screening Assay for Identification of UBC13 Inhibitors

UBC13 is a noncanonical ubiquitin conjugating enzyme (E2) that has been implicated in a variety of cellular signaling processes due to its ability to catalyze formation of lysine 63–linked polyubiquitin chains on various substrates. In particular, UBC13 is required for signaling by a variety of receptors important in immune regulation, making it a candidate target for inflammatory diseases. UBC13 is also critical for double-strand DNA repair and thus a potential radiosensitizer and chemosensitizer target for oncology. The authors developed a high-throughput screening (HTS) assay for UBC13 based on the method of time-resolved fluorescence resonance energy transfer (TR-FRET). The TR-FRET assay combines fluorochrome (Fl)–conjugated ubiquitin (fluorescence acceptor) with terbium (Tb)–conjugated ubiquitin (fluorescence donor), such that the assembly of mixed chains of Fl- and Tb-ubiquitin creates a robust TR-FRET signal. The authors defined conditions for optimized performance of the TR-FRET assay in both 384- and 1536-well formats. Chemical library screens (total 456 865 compounds) were conducted in high-throughput mode using various compound collections, affording superb Z′ scores (typically >0.7) and thus validating the performance of the assays. Altogether, the HTS assays described here are suitable for large-scale, automated screening of chemical libraries in search of compounds with inhibitory activity against UBC13.

Non-canonical ubiquitin-based signals for proteasomal degradation

Regulated cellular proteolysis is mediated largely by the ubiquitin-proteasome system (UPS). It is a highly specific process that is time- (e.g. cell cycle), compartment- (e.g. nucleus or endoplasmic reticulum) and substrate quality- (e.g. denatured or misfolded proteins) dependent, and allows fast adaptation to changing conditions. Degradation by the UPS is carried out through two successive steps: the substrate is covalently tagged with ubiquitin and subsequently degraded by the 26S proteasome. The accepted 'canonical' signal for proteasomal recognition is a polyubiquitin chain that is anchored to a lysine residue in the target substrate, and is assembled through isopeptide bonds involving lysine 48 of ubiquitin. However, several 'non-canonical' ubiquitin-based signals for proteasomal targeting have also been identified. These include chains anchored to residues other than internal lysine in the substrates, chains assembled through linking residues other than lysine 48 in ubiquitin, and mixed chains made of both ubiquitin and a ubiquitin-like protein. Furthermore, some proteins can be degraded following modification by a single ubiquitin (monoubiquitylation) or multiple single ubiquitins (multiple monoubiquitylation). Finally, some proteins can be proteasomally degraded without prior ubiquitylation (the process is also often referred to as ubiquitination). In this Commentary, we describe these recent findings and discuss the possible physiological roles of these diverse signals. Furthermore, we discuss the possible impact of this signal diversity on drug development.

Versatile lanthanide-azide complexes with azide/carboxylate/hydroxy mixed bridged chain exhibiting magnetic and luminescent properties

Two new lanthanide-azide complexes, [Ln2(N3)(isonic)2(OH)3(Hisonic)(H2O)]n (Ln=Yb for 1 and Tb for 2, isonic=isonicotinate), were obtained in hydrothermal condition. X-ray diffraction analysis indicated the two complexes are isomorphic chain structure in which the LnIII ions are mixed bridged by the azide anions, hydroxyl anions and carboxylate groups of the isonicotinate ligands. Further studies indicated weak antiferromagnetic interactions between the LnIII ions in 1 and 2, and complex 2 exhibit green sensitized Luminescent character of TbIII ion.

Synthesis of new linear poly(phenylpyridyl) chains

This paper describes for the first time an efficient approach of Suzuki Miyaura cross-coupling reaction leading to new mixed linear unsymmetric phenylpyridyl chains (garlands). We have studied the synthesis of new phenylpyridyl boronic species and their reactivity with a dihalogenated bipyridine to obtain four and six unit phenylpyridines.

Interface cross-linked polymeric micelles with mixed coronal chains prepared by RAFT polymerization at the interface

Poly(ethylene glycol-block-2-hydroxyethyl methacrylate-block-tert-butyl acrylate) (PEG-b-PHEMA-b-PtBA) triblock copolymer was synthesized by the sequential atom transfer radical polymerization (ATRP) of HEMA and tBA using an ATRP initiator terminated PEG (PEG-Br) as the macroinitiator. Azide groups were introduced to the short mid-blocks by reactions of the triblock copolymer with 2-bromoisobutyryl bromide and sodium azide. In aqueous solution, the triblock copolymer self-assembled into micelles with azide groups at the interfaces. Reactive polymeric micelles with reversible addition–fragmentation chain transfer agents (RAFT CTAs) at the interfaces were prepared by a click cross-linking reaction between dialkynetrithiocarbonate and the azide groups. FT-IR, 1H NMR, dynamic light scattering (DLS) and transmission electron microscopy (TEM) were used to characterize the interface cross-linked (ICL) micelles and the grafting of the RAFT CTAs to the interfaces. Polymeric micelles with PEG–poly(N-isopropylacrylamide) (PNIPAM) mixed coronal chains were prepared by the in situ RAFT polymerization of NIPAM at the interfaces. The TEM results demonstrate that the mixed coronal chains have nano-sized phase separation on the surfaces of the micelles. The use of the polymeric micelles as particulate emulsifiers was also investigated in this research. These ICL micelles with mixed coronal chains produce relatively fine 1-undecanol-in-water (o/w) emulsions compared to emulsions stabilized by the PEG homopolymer under the same conditions.

A kind of ferromagnetic-antiferromagnetic alternating spin chain equivalent to the mixed spin Heisenberg chain

By using the method of exact diagonalization, the properties of the spin-1/2 ferromagnetic-antiferromagnetic alternating Heisenberg chain are investigated. The spin-spin correlation, the sublattice magnetizations, the spin excitation spectrum and the magnetization curve of the model are calculated and compared with the corresponding properties of the mixed spin chain. The results show that the behaviors of the alternating Heisenberg chain are equivalent to those of the mixed spin chain when the ratio of antiferromagnetic to ferromagnetic coupling strength is very small. So, the properties of the mixed spin chain can be analyzed by using the spin-1/2 ferromagnetic-antiferromagnetic-antiferromagnetic alternating Heisenberg chain.

Ab Initio Study on the Structural and Magnetic Properties of Co-Pd and Co-Pt Linear and Zigzag Nanowires

Based on the projector augmented-wave method, the self-consistent electronic structure calculations were carried out on pure Co and mixed Co-Pd and Co-Pt free-standing linear and zigzag nanowires. The calculations reveal that the bond lengths for all these systems are generally increased as their structures change from the linear to the zigzag chain. The bond lengths for Co-Pd and Co-Pt wires are in between the values of corresponding pure system and the bond angles around 60° suggesting the possible formation of Co-Pd and Co-Pt bimetallic materials. In mixed Co-Pd and Co-Pt chains, the Co, Pd and Pt atoms have quite high local magnetic moments. The calculations suggest that the magnetic moments in linear nanowires are generally larger than the ones of corresponding zigzag nanowires. It is found that there is hybridization between Co 3d and Pd 4d, Co 3d and Pt 5d states, which may significantly affect structural stability and magnetism of Co-Pd and Co-Pt nanowires.

One pot synthesis of heterometallic 3d–3d azido architectures: assembling strategy and magnetic properties

The Cu(II) ions usually have different coordinated geometry to other 3d ions, especially Ni(II) and Co(II) ions, in azido-carboxylate mixed ligand systems. That provides a potential way to synthesize rare heterometallic 3d-3d azido complexes with peculiar magnetic properties. Assembling Cu(II), M(II) (M = Ni and Co), azido and nicotinic acid in hydrothermal condition, two novel isomorphic 3D heterometallic 3d-3d azido complexes, [CuM(N(3))(2)(nicotinate)(2)](∞) (M = Ni(II) for 1 and Co(II) for 2) were obtained. The structure of the complexes can be described as EO azido and syn,syn carboxylate mixed bridged spin sequence chains (-1/2-J(1)-1-J(2)-1/2- for 1 and -1/2-J(1)-3/2-J(2)-1/2- for 2) linked by the pyridyl groups. Dominant ferromagnetic interactions were observed between the Cu(II) and M(II) ions in the chains despite the largest M-N-M angle of about 129° in the 3d metal azido-carboxylate mixed coordinated systems and weak antiferromagnetic interactions between the chains. At low temperature, a spin-flop phase transition was present in the Co(II) involved complex 2.

Comparisons of Three Approaches for Discrete Conditional Models

This article describes three methods for computing a discrete joint density from full conditional densities. They are the Gibbs sampler, a hybrid method, and an interaction-based method. The hybrid method uses the iterative proportional fitting algorithm, and it is derived from the mixed parameterization of a contingency table. The interaction-based approach is derived from the canonical parameters, while the Gibbs sampler can be regarded as based on the mean parameters. In short, different approaches are motivated by different parameterizations. The setting of a bivariate conditionally specified distribution is used as the premise for comparing the numerical accuracy of the three methods. Detailed comparisons of marginal distributions, odds ratios and expected values are reported. We give theoretical justifications as to why the hybrid method produces better approximation than the Gibbs sampler. Generalizations to more than two variables are discussed. In practice, Gibbs sampler has certain advantages: it is conceptually easy to understand and there are many software tools available. Nevertheless, the hybrid method and the interaction-based method are accurate and simple alternatives when the Gibbs sampler results in a slowly mixing chain and requires substantial simulation efforts.

Protein monoubiquitination and polyubiquitination generate structural diversity to control distinct biological processes

Ubiquitination involves the attachment of ubiquitin (Ub) to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Polyubiquitination through different lysines (seven) or the N-terminus of Ub can generate different protein-Ub structures. These include monoubiquitinated proteins, polyubiqutinated proteins with homotypic chains through a particular lysine on Ub or mixed polyubiquitin chains generated by polymerization through different Ub lysines. The ability of the ubiquitination pathway to generate different protein-Ub structures provides versatility of this pathway to target proteins to different fates. Protein ubiquitination is catalyzed by Ub-conjugating and Ub-ligase enzymes, with different combinations of these enzymes specifying the type of Ub modification on protein substrates. How Ub-conjugating and Ub-ligase enzymes generate this structural diversity is not clearly understood. In the current review, we discuss mechanisms utilized by the Ub-conjugating and Ub-ligase enzymes to generate structural diversity during protein ubiquitination, with a focus on recent mechanistic insights into protein monoubiquitination and polyubiquitination.

Monitoring Policy and Organizational Forms in Franchised Chains

Franchising is nowadays a prominent way to organize the distribution sector. While previous literature suggests that monitoring issues are a critical determinant of organizational choices, it is rather silent on the optimal monitoring strategy once the organization of the chain is set. In this article, we analyze the monitoring policy of chains with both franchised and company-owned units. We develop a model in which a chain monitors its outlets under asymmetric information on local demands and managers’ efforts. We show that partial monitoring (i.e., when the franchisor monitors only a subset of its outlets) represents an optimal monitoring policy. Second, we identify the units that should be monitored. Finally, we discuss the impact of information technologies and outlet location on monitoring policy and how it may affect the proportion of franchised and company-owned units within the mixed chains.

Tubular chains in the structures of natural and synthetic silicates

Tubular chains in the structures of natural and synthetic silicates have been described and systematized using the theory of graphs and by unfolding the tube topology onto a plane. Eight types of tubular chains have been considered: seven silicon-oxygen chains and one mixed titanosilicate chain; their topological and geometric characteristics are analyzed. It is shown that the presence of large cavities in tubes is generally related to their occupation by large low-valence cations (K+, Cs+, Ba2+, Sr2+, etc.) and water molecules. The overwhelming majority of minerals containing tubular silicate fragments were found in hydrothermal veins of alkaline massifs in Russia and abroad.

Synthetic biology: building the language for a new science brick by metaphorical brick

Changes in the biosciences and their relations to society over the last decades provide a unique opportunity to examine whether or not such changes leave traces in the language we use to talk about them. In this article we examine metaphors used in English-speaking press coverage to conceptualize a new type of (interdisciplinary) bioscience: synthetic biology. Findings show that three central metaphors were used between 2008 and May 2010. They exploit social and cultural knowledge about books, computers and engines and are linked to knowledge of three revolutions in science and society (the printing, information and industrial revolutions). These three central metaphors are connected to each other through the concepts of reading/writing, designing and mass production and they focus on science as a revolutionary process rather than on the end results or products of science. Overall, we observed the use of a complex bricolage of mixed metaphors and chains of metaphors that root synthetic biology in historical events and achievements, while at the same time extolling its promises for the future.

Effects of Single-site Anisotropy on Mixed Diamond Chains with Spins 1 and 1/2

Effects of single-site anisotropy on mixed diamond chains with spins 1 and 1/2 are investigated in the ground states and at finite temperatures. There are phases where the ground state is a spin cluster solid, i.e., an array of uncorrelated spin-1 clusters separated by singlet dimers. The ground state is nonmagnetic for the easy-plane anisotropy, while it is paramagnetic for the easy-axis anisotropy. Also, there are the Néel, Haldane, and large- D phases, where the ground state is a single spin cluster of infinite size and the system is equivalent to the spin-1 Heisenberg chain with alternating anisotropy. The longitudinal and transverse susceptibilities and entropy are calculated at finite temperatures in the spin-cluster-solid phases. Their low-temperature behaviors are sensitive to anisotropy.

String formation and demixing in monolayers of dipolar colloidal mixtures

Employing hypernetted chain (HNC) integral equations and a stability analysis we investigate the structure and phase behavior of bidisperse mixtures of dipolar hard spheres with different size ratios s=σ(S)/σ(L) confined to a plane. The dipole moments of the particles are perfectly ordered along an in-plane direction, yielding anisotropic interactions favoring chain formation. Exploring a range of size ratios and compositions, our study predicts a complex interplay between aggregation phenomena, on the one hand, and volume phase transitions, on the other hand. In dilute, strongly asymmetric systems (s = 0.5), our HNC analysis indicates chain formation of the large particles, while the small particles act as a weakly correlated background. According to our fluctuation analysis, this aggregation behavior results in combined condensation-demixing transitions, with a trend towards pure demixing when the concentration of the large particles, c(L), becomes small. In dense systems, the most interesting results are found for intermediate size ratios, s ~ 0.7-0.8. Here we find signatures of a concentration-driven transition from pure chains of large particles (large c(L)) to mixed chains with alternating order of large and small particles (small c(L)). The two regimes are separated by a characteristic "jump" in the HNC non-solution line.

Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature

The structural parameters of fluid phase bilayers composed of phosphatidylcholines with fully saturated, mixed, and branched fatty acid chains, at several temperatures, have been determined by simultaneously analyzing small-angle neutron and X-ray scattering data. Bilayer parameters, such as area per lipid and overall bilayer thickness have been obtained in conjunction with intrabilayer structural parameters (e.g. hydrocarbon region thickness). The results have allowed us to assess the effect of temperature and hydrocarbon chain composition on bilayer structure. For example, we found that for all lipids there is, not surprisingly, an increase in fatty acid chain trans–gauche isomerization with increasing temperature. Moreover, this increase in trans–gauche isomerization scales with fatty acid chain length in mixed chain lipids. However, in the case of lipids with saturated fatty acid chains, trans–gauche isomerization is increasingly tempered by attractive chain–chain van der Waals interactions with increasing chain length. Finally, our results confirm a strong dependence of lipid chain dynamics as a function of double bond position along fatty acid chains.

Caracterização Estrutural e Ótica do Poli(3-metiltiofeno) (P3MT) Sintetizado Eletroquimicamente

In this work was synthesized electrochemically the poly(3-methylthiophene) (P3MT) on transparent conductive substrates of F-doped tin oxide (FTO), using as supporting electrolyte Et 4 NBF 4 or LiClO 4 in acetonitrile. To dedope the material, the samples were reduced electrochemically and chemically (in NH 4 OH solution). The films were characterized by electron paramagnetic resonance spectroscopy (EPR) and infrared spectroscopy (FTIR) and their optical properties examined by ultraviolet-visible absorption spectroscopy (UV-Vis) and photoluminescence (PL). Scanning electron microscopy (SEM) images of the first synthesized samples were performed to verify the degree of homogeneity of them. The FTIR spectra show the characteristic features of P3MT and, together with the results of EPR, allowed to evaluate the charge carriers and to identify benzoid and quinoid structures in the formation of chains. The UV-Vis absorption spectra helped to obtain the average gap energy of P3MT presenting the ?-?* transition band and a bipolaron band. In the PL spectra, with variation of excitation power, studies were performed through the fit with Gaussian functions, given the strong probability of the existence of two distinct contributions in the formation of the emission spectra. These two contributions were assigned to the emission of mixed chains (Gaussian centered at higher energy) and emission of benzoid chains (Gaussian of lower energy) in the formed polymeric material.