Backbone Position Research Articles

C-H Functionalization of Poly(ethylene oxide) - Embracing Functionality, Degradability, and Molecular Delivery.

This study presents an organocatalytic C-H functionalization approach for postpolymerization modification (PPM) of poly(ethylene oxide) (PEO). Most of PEO PPM is previously processed at the end hydroxy group, but recent advances in C-H functionalization open a way to modify the backbone position. Structurally diverse carboxylic acids are attached to PEO through a cascade process of radical generation by peroxide and oxidation to oxocarbenium by tertiary butylammonium iodide. Attaching carboxylic acids yields a series of functionalize PEO with acetal units (2-5 mol%) in a backbone, which is not accessible via conventional copolymerization of epoxides. The optimized conditions minimizes the uncontrolled degradation or crosslinking from the highly reactive radical and oxocarbenium intermediate. The newly introduced acetal units bring degradability of PEO as well as delivery of carboxylic acid molecules. Hydrolysis studies with high molecular weight functionalization PEO (Mn = 13.0kgmol-1) confirm the steady release of fragmented PEO (Mn ∼ 2.0kgmol-1) and carboxylic acid over days and the process rate is not sensitive to pH variation between pH 5 and 9. The presented method offers a versatile and efficient way to modify PEO with potential energy and medical applications.

Triglycerides Stabilize Water/Organic Interfaces of Changing Area via Conformational Flexibility.

The role of triglycerides (TGs) in both natural and synthetic biological membranes has long been the subject of study, involving metabolism, disease, and colloidal synthesis. TGs have been found to be critical components for successful liposomal encapsulation via a water/oil/water double emulsion, which this work endeavors to explain. TGs can occupy multiple positions in biological membranes. The glycerol backbone can reside at the water/organic interface, adjacent to phospholipid headgroups ("m" conformation), typically with relatively low (<3%) solubility. The glycerol backbone can also occupy hydrophobic regions, where it is isolated from water ("h" or "oil" conformation). This can occur in either midmembrane positions or phospholipid-coated lipid droplets (LDs). These conformations can be distinguished using 13C-nuclear magnetic resonance spectroscopy (NMR), which determines the degree of hydration of the TG backbone. Using this method, it was revealed that TGs transition from "m" to "h" conformation as the organic solvent is removed via evaporation. A new transitional TG backbone position has been identified with a level of hydration between "m" and "h". These results suggest that TGs can temporarily coat and stabilize the large water/organic interfaces present after emulsification. As the organic solvent is removed and interfaces shrink, the TGs recede into midmembrane spaces or bud off into LDs, which are confirmed via transmission electron microscopy (TEM) and can be removed via centrifugation. Encapsulation efficiency is found to be inversely related to both the saturation and length of the TG acyl chains, indicating that membrane fluidization is a key property arising from the presence of TGs. Beyond clarification of a mechanism for high-efficiency liposomal encapsulation, these results implicate TGs as components that are able to stabilize biological membrane transitions involving a changing interfacial area and curvature. This role for TGs may be of use in the formulation of drug delivery systems as well as in the investigation of membrane transitions in life sciences.

Using single molecule polarization-sweep spectroscopy to monitor site-specific fluctuations of internal (iCy3)2 dimer-labeled DNA constructs at ss-ds DNA junctions.

Local fluctuations of the sugar-phosphate backbones of DNA (a form of DNA ‘breathing’) play key roles in protein-DNA assembly and enzymatic function. In this work, we monitored spectroscopic signals from single-molecules of DNA fork constructs labeled with two cyanine optical probes [(iCy3)2], which were rigidly inserted into the sugar-phosphate backbones at opposite positions of complementary single-strands. We thus studied the local conformational fluctuations of the DNA sugar-phosphate backbones at specific (iCy3)2 dimer-labeled positions relative to a single-stranded (ss) double-stranded (ds) DNA junction. These experiments are based on a newly-developed single-molecule spectroscopic method that uses a linearly polarized continuous wave laser in which the polarization direction is continuously rotated at radio frequencies. The emitted fluorescence from the single-molecule sample contains information about conformational changes of the exciton-coupled (iCy3)2 dimer probe, which monitor conformational fluctuations of the vicinal DNA sugar-phosphate backbones. Our results indicate that the local conformation of the DNA sugar-phosphate backbones at positions near ss-dsDNA junctions adopts four topologically-relevant macrostates. The probability that a particular macrostate is occupied depends on backbone position. We apply a kinetic network approach to interpret our observations of DNA backbone fluctuations at and near ss-dsDNA junctions, and we propose conformational assignments based on exciton-coupling models for the macrostates that we observe. This polarization-sweep single-molecule fluorescence method and analysis can be applied to study protein binding and macromolecular function at and near ss-dsDNA junctions, thus providing site-specific information about the free energy landscapes at various functionally relevant positions within such macromolecular complexes.

Via conformational flexibility, triglycerides stabilize organic-water interfaces of changing area.

The role of triglycerides (TGs) in both synthetic and biological membranes has long been the subject of study, involving metabolism, disease, and colloidal synthesis. TGs have been found to be critical components for successful liposomal encapsulation via double emulsion (Water/Oil/Water), which this work attempts to explain. TGs can occupy multiple positions in a biological membranes. The glycerol backbone can sit at the membrane's interface with water, adjacent to phospholipid headgroups (“surface” or “M” conformation), typically with relatively low (∼3%) solubility. TGs can also occupy “oil” phases, where the glycerol backbone is isolated from water, in either mid-membrane positions or lipoprotein-style phospholipid-coated TG droplets. Using 13C-Nuclear magnetic resonance spectroscopy (NMR) to determine the degree of hydration of the TG backbone, it was revealed that TGs transition from surface to oil phases as the organic solvent is removed via evaporation. A new, transitional TG backbone position has been identified, with a level of hydration between surface and oil. These results suggest that TGs are able to temporarily coat and stabilize the large water/organic interfaces present just after emulsification. As the chloroform evaporates and interfaces shrink, the TGs recede into mid-membrane spaces or to bud off into separate coated oil droplets, which are confirmed via transmission electron microscopy. These TG-rich droplets can be removed via high-speed centrifugation. Encapsulation efficiency is found to be inversely related to both chain saturation and length, indicating that membrane fluidization is a key property arising from the presence of TGs. Beyond clarification of a mechanism for high-efficiency liposomal encapsulation, these results implicate TGs as components that are able to stabilize biological membrane transitions involving changing interfacial area. This role for TGs may be of use in designing drug delivery systems and investigation of membrane transitions in life sciences.

Synthesis of Polysubstituted 2-Oxabicyclo[2.1.1]hexanes via Visible-Light-Induced Energy Transfer.

Synthesis of bicyclic scaffolds has attracted growing interest because they are of high importance in modern pharmaceutical development. Here we report a strategy to access polysubstituted 2-oxabicyclo[2.1.1]hexanes in a single operation from readily accessible benzoylformate esters and bicyclo[1.1.0]butanes via visible-light-induced triplet energy transfer catalysis. The process is proposed to involve a formal [2π + 2σ] photocycloaddition/backbone C-H abstraction/aryl group migration sequence. A diverse range of (hetero)aryl groups successfully underwent migration to the backbone (C2) position to provide previously inaccessible bicyclic molecules, and the ester group of the product can serve as a handle for downstream manipulation, thus offering opportunities to rapidly build up molecular complexity and access new sp3-rich chemical space.

A Sensitive Aptamer Fluorescence Anisotropy Sensor for Cd2+ Using Affinity-Enhanced Aptamers with Phosphorothioate Modification.

Rapid and sensitive detection of heavy metal cadmium ions (Cd2+) is of great significance to food safety and environmental monitoring, as Cd2+ contamination and exposure cause serious health risk. In this study we demonstrated an aptamer-based fluorescence anisotropy (FA) sensor for Cd2+ with a single tetramethylrhodamine (TMR)-labeled 15-mer Cd2+ binding aptamer (CBA15), integrating the strengths of aptamers as affinity recognition elements for preparation, stability, and modification, and the advantages of FA for signaling in terms of sensitivity, simplicity, reproducibility, and high throughput. In this sensor, the Cd2+-binding-induced aptamer structure change provoked significant alteration of FA responses. To acquire better sensing performance, we further introduced single phosphorothioate (PS) modification of CBA15 at a specific phosphate backbone position, to enhance aptamer affinity by possible strong interaction between sulfur and Cd2+. The aptamer with PS modification at the third guanine (G) nucleotide (CBA15-G3S) had four times higher affinity than CBA15. Using as an aptamer probe CBA15-G3S with a TMR label at the 12th T, we achieved sensitive selective FA detection of Cd2+, with a detection limit of 6.1 nM Cd2+. This aptamer-based FA sensor works in a direct format for detection without need for labeling Cd2+, overcoming the limitations of traditional competitive immuno-FA assay using antibodies and fluorescently labeled Cd2+. This FA method enabled the detection of Cd2+ in real water samples, showing broad application potential.

Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid.

Xeno-nucleic acids (XNAs) are synthetic genetic polymers with backbone structures composed of non-ribose or non-deoxyribose sugars. Phosphonomethylthreosyl nucleic acid (pTNA), a type of XNA that does not base pair with DNA or RNA, has been suggested as a possible genetic material for storing synthetic biology information in cells. A critical step in this process is the synthesis of XNA episomes using laboratory-evolved polymerases to copy DNA information into XNA. Here, we investigate the polymerase recognition of pTNA nucleotides using X-ray crystallography to capture the post-catalytic complex of engineered polymerases following the sequential addition of two pTNA nucleotides onto the 3′-end of a DNA primer. High-resolution crystal structures reveal that the polymerase mediates Watson–Crick base pairing between the extended pTNA adducts and the DNA template. Comparative analysis studies demonstrate that the sugar conformation and backbone position of pTNA are structurally more similar to threose nucleic acid than DNA even though pTNA and DNA share the same six-atom backbone repeat length. Collectively, these findings provide new insight into the structural determinants that guide the enzymatic synthesis of an orthogonal genetic polymer, and may lead to the discovery of new variants that function with enhanced activity.

Coasting zebrafish adjust to pursue

If you were asked to come up with a list of top predators, which would you put first: lions, hawks, sharks, zebrafish? Despite their diminutive size, tiny zebrafish are voracious hunters, pursuing larvae of their own and other species before feasting on them mercilessly. The question was, which strategy do the ravenous mini-predators use when in hot pursuit? Alberto Soto and Matthew McHenry, from the University of California, Irvine, USA, explain that some fish simply overwhelm their prey by pursuing them at top speed in one continuous deadly swoop, while other predators predict where their victim is heading and then aim to intercept them there directly. Yet zebrafish coast between propulsive bursts from their tails when going about their routine business, which is more analogous to the sporadic advances of ants than the relentless attack of a hawk. Curious to find out how predatory zebrafish home in on fleeing larvae, Soto and McHenry pitted adult zebrafish against individual larvae, filming 31 pursuits at 500 frames s–1, to discover which strategy the unlikely top predators favour.Analysing over 150,000 movie frames, the duo monitored the backbone position of each predatory adult to track their manoeuvres as they closed in for the kill. However, instead of turning into decisive assassins approaching in a single high-speed pursuit, the fish continued their hesitant approach, coasting between each flick of the tail. Yet, when the duo plotted the fish's paths, they realised that the zebrafish were using the same strategy as species that adjust their approach during a pursuit, instead of plotting a single linear interception course. And when they compared the sweep of each tail beat against the zebrafish's change in direction, it was clear that the fish were able to fine-tune each twist and turn to match the manoeuvres of their quarry during each deadly duet.‘Pure pursuit – where a predator orients its direction of travel directly toward prey – may be the best strategy for animals that move intermittently’, the duo says, explaining that the movements of escaping larvae are simply too random for their adversaries to set an accurate intercept path. And Soto and McHenry suggest that the zebrafish's sporadic strategy could buy them time to plot their next move, before propelling themselves in the correct direction with the next flick of the tail.

Binding of Benzanthrone Dye ABM to Insulin Amyloid Fibrils: Molecular Docking and Molecular Dynamics Simulation Studies

The binding of the benzanthrone dye ABM to the model amyloid fibrils of human insulin, referred to here as vealyl (12-VEALYL-17, insulin B-chain)), lyqlen (13-LYQLEN-18, insulin A-chain) and Insf ( 11-LVEALYL-17, B-chain) + 12-SLYQLENY-19, A-chain) was studied by the molecular docking and molecular dynamics simulations. To obtain the relaxed structures with the enhanced conformational stability, the model fibril structures were solvated and equilibrated in water at 300-310 K using the Gromacs simulation package, with backbone position restraints being applied to prevent the beta-sheet disruption. It appeared that the vealyl fibril relaxation resulted in the twisting of the two β-sheets, and only the vealyl fibril remained stable during 20 ns MD simulations of the relaxed structures. Next, Insf, vealyl, lyqlen, and vealyl (relaxed) fibrils were used for the molecular docking studies (by SwissDock), revealing the binding modes of ABM and standard amyloid marker Thioflavin T (ThT) to the examined fibril structures. Specifically, in the most energetically stable complex the vealyl (relaxed) fibril binding site for ABM was located on the dry steric zipper interface, although the dye was associated with only one twisted β-sheet. During the 20 ns MD simulation the ABM fibril location was changed to a deeper position in the dry interface between the two β-sheets, with the dye-interacting residues being represented by 6 LEU, 3 VAL, 2 ALA, 1 TYR and 1 GLU. The binging free energy Δ(Gbinding) for ABM complexation with vealyl (relaxed) fibril evaluated with the GMXPBSA GROMACS tool was found to be –31.4±1.8 kJ/mol, that is in accordance with our estimates derived from the fluorescence studies for ABM binding to the bovine insulin amyloid fibrils Δ(Gbinding)= –30.2 kJ/mol. The Lennard-Jones component appeared to dominate the dye-fibril interactions, with much smaller contributions of Coulombic and nonpolar solvation terms to the total Δ(Gbinding) value, and unfavorable effect of the polar solvation term. These findings indicate that a high specificity of ABM to the insulin amyloid fibrils may arise predominantly from the dye-protein hydrophobic interactions, followed by the formation of van der Waals contacts, thus providing additional evidence for sensitivity of the dye spectral properties to environmental polarity, suggested in our previous studies. Overall, the obtained results provided further insights into the atomistic mechanism of the ABM binding to insulin amyloid fibrils and can be used for development of the novel fluorescent reporters possessing high sensitivity to the amyloid assemblies.

Toward Complete Structure Elucidation of Glycerophospholipids in the Gas Phase through Charge Inversion Ion/Ion Chemistry.

Shotgun lipidomics has recently gained popularity for lipid analysis. Conventionally, shotgun analysis of glycerophospholipids via direct electrospray ionization tandem mass spectrometry (ESI-MS/MS) provides glycerophospholipid (GPL) class (i.e., headgroup composition) and fatty acyl composition. Reliant on low-energy collision-induced dissociation (CID), traditional ESI-MS/MS fails to define fatty acyl regiochemistry along the glycerol backbone or carbon-carbon double bond position(s) in unsaturated fatty acyl substituents. Therefore, isomeric GPLs are often unresolved, representing a significant challenge for shotgun-MS approaches. We developed a top-down shotgun-MS method utilizing gas-phase ion/ion charge inversion chemistry that provides near-complete GPL structural identification. First, in negative ion mode, CID of mass-selected GPL anions generates fatty acyl carboxylate anions via fragmentation of ester bonds linking the fatty acyl substituents at the sn-1 and sn-2 positions of the glycerol backbone. Product anions, including fatty acyl carboxylate ions, were then derivatized in the mass spectrometer via an ion/ion charge inversion reaction with tris-phenanthroline magnesium dications. Subsequent CID of charge-inverted fatty acyl complex cations yielded isomer-specific product ion spectra that permit (i) unambiguous assignment of carbon-carbon double bond position(s) and (ii) relative quantitation of isomeric fatty acyl substituents. The outlined strategy was applied to the analysis of targeted GPLs extracted from human plasma, including several proposed plasma biomarkers. A single experiment thus facilitates assignment of the GPL headgroup, fatty acyl composition, carbon-carbon double bond position(s) in unsaturated fatty acyl chains, and, in some cases, fatty acyl sn-position and relative abundances for isomeric fatty acyl substituents. Ultimately, this MSn platform paired with ion/ion chemistry permitted identification of major, and some minor, isomeric contributors that are unresolved using conventional ESI-MS/MS.

Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures.

Small molecule spectrophotometric probes for DNA/RNA and proteins are of the utmost importance for diagnostics in biochemical and biomedical research. Both, naturally occurring and synthetic probes, often include peptide sequence responsible for the selectivity toward the particular target; however, commercially available dyes are restricted to single point attachment to the peptide (having one reactive group). Here presented are our recent advances in the development of novel amino acidfluorophore probes, with the unique characteristic of free N- and C-terminus available for incorporation at any peptide backbone position. Intriguingly, already monomeric amino acid-fluorophores showed recognition among various DNA/RNA, whereby steric impact and contribution of halogens is systematically studied. Moreover, some dyes revealed intracellular mitochondria specificity. Further, several hetero-dimeric chromophore systems were prepared, demonstrating that synergistic effect can lead to simultaneous DNA, RNA and protein fluorimetric recognition, combined with enzyme inhibition. Also, homodimeric cyanines equipped with chlorine revealed intriguing DNA/RNA selectivity in respect to well-known parent TOTO and YOYO dyes.

A sensitive thrombin-linked sandwich immunoassay for protein targets using high affinity phosphorodithioate modified aptamer for thrombin labeling

Thrombin and its aptamers have been well studied and widely used as models in aptamer based assays and sensors. Here we reported a thrombin-linked sandwich immunoassay for proteins to demonstrate new applications of thrombin and the aptamers, converting protein detection to analysis of thrombin label. In this assay, target protein was sandwiched by the capture antibody on a microplate and the biotinylated detection antibody. Thrombin bound to one biotinylated aptamer, and then the thrombin-labeled aptamer was attached on the sandwich complex through streptavidin-biotin interaction by using streptavidin as a linker. Thrombin catalyzed cleavage of fluorogenic peptide substrates, generating fluorescence signals for target detection. Among a few different anti-thrombin aptamers, the use of one nuclease resistant RNA aptamer having phosphorodithioate (PS2) modification on a specific backbone position enabled higher assay sensitivity due to its much higher affinity. This thrombin-linked sandwich immunoassay allowed detection of prostate-specific antigen (PSA) at 2 pM, an important protein related cancer disease, with high sensitivity and specificity. The strategy was general, and also enabled sensitive detection of botulinum neurotoxin type A (BoNTA) light chain, one toxin protein causing risk to human health. This assay combines advantages of antibody recognition, aptamer affinity labeling, high affinity of aptamers, and enzyme activity of thrombin. Labeling thrombin on the immunosandwich complex through simple affinity binding overcomes limitations of covalent conjugating enzyme on antibody in conventional immunoassay. This assay is promising in applications for protein detection.

Automatic Inference of Sequence from Low-Resolution Crystallographic Data

At resolutions worse than 3.5Å, the electron density is weak or nonexistent at the locations of the side chains. Consequently, the assignment of the protein sequences to their correct positions along the backbone is a difficult problem. In this work, we propose a fully automated computational approach to assign sequence at low resolution. It is based on our surprising observation that standard reciprocal-space indicators, such as the initial unrefined R value, are sensitive enough to detect an erroneous sequence assignment of even a single backbone position. Our approach correctly determines the amino acid type for 15%, 13%, and 9% of the backbone positions in crystallographic datasets with resolutions of 4.0Å, 4.5Å, and 5.0Å, respectively. We implement these findings in an application for threading a sequence onto a backbone structure. For the three resolution ranges, the application threads 83%, 81%, and 64% of the sequences exactly as in the deposited PDB structures.

Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device.

Two A/C incompatibility group (IncA/C family) plasmids from the 1960s have been sequenced and classified into the A/C2 type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 genomic island not previously found in the family. In the 173.1-kb R16a, the 29.9-kb antibiotic resistance island (ARI) is located in a unique backbone position not utilized by ARIs. ARIR16a consists of Tn1, Tn6020, and Tn6333, harboring the resistance genes blaTEM-1D and aphA1b and a mer module, respectively; a truncated Tn5393 copy; and a gene cluster with unknown function. Plasmid IP40a is 170.4 kb in size and contains a 5.6-kb ARI inserted into the kfrA gene. ARIIP40a carrying blaTEM-1D and aphA1b genes is composed of Tn1 with a Tn6023 insertion. Additionally, IP40a harbors single IS2, IS186, and Tn1000 insertions scattered in the backbone; an IS150 copy in GIsul2; and a complete Tn6333 carrying a mer module at the position of ARIR16a Loss of resistance markers in R16a, IP40a, and R55 was observed during stability tests. Every phenotypic change proved to be the result of recombination events involving mobile elements. Intramolecular transposition of IS copies that generated IP40a derivatives lacking large parts of the backbone could account for the formation of other family members, too. The MinION platform proved to be a valuable tool in bacterial genome sequencing since it generates long reads that span repetitive elements and facilitates full-length plasmid or chromosome assembly. Nanopore technology enables rapid characterization of large, low-copy-number plasmids and their rearrangement products.

Bound cleavage at carboxyl group-glycerol backbone position in thermal cracking of the triglycerides in sunflower oil

Bound cleavage at carboxyl group-glycerol backbone position of triglyceride of sunflower oil during the thermal cracking reaction was studied. Required experiments were performed in a continuous tubular reactor at atmospheric pressure. Experimental results showed that cracking at each bond of OCOC depends on the temperature. At low process temperatures, decarboxylation was enhanced, while at high temperature more fatty acids were formed. When liquid products were fractionated into some light to heavy cuts, the distribution of fatty acids was observed. Concentration of COOH group in the cuts showed that at the cracking conditions, carboxylic acid head of fatty acids was more stable than their hydrocarbon chain, so the second bound cleavage step had been taken place along the hydrocarbon chain and lighter fatty acids were formed. As a result, a more accurate mechanism for thermal cracking of triglycerides is recommended. The presented mechanism would help the experimentalists to have an ccurate prediction of the products for thermal cracking process of triglycerides.

Anisotropic surface functionalization of Au nanorods driven by molecular architecture and curvature effects.

This work suggests a novel strategy to coat the caps and body of Au-nanorods (Au-NRs) with end-grafted polymer layers of different compositions by taking advantage of the different curvature of these two regions. A molecular theory was used to theoretically investigate the effect of local curvature and molecular architecture (intramolecular connectivity of the monomers) on the adsorption of polymer mixtures on cylindrical (Au-NR body) and spherical (Au-NR caps) surfaces. The adsorption process was systematically studied as a function of the backbone length, number and position of branches, quality of the solvent and total number of monomers of the polymer molecules in the mixture. The balance between repulsive forces and polymer-surface and polymer-polymer attractions governs the amount and composition of the adsorbed layer. This balance is in turn modulated by the architecture of the polymers, the curvature of the surface and the competition between the different polymers in the mixture for the available area. As a result, the equilibrium composition of the polymer layer on spheres and cylinders of the same radius differs, and in turn departs from that of the bulk solution. Curvature plays a major role: the available volume at a given distance from the surface is larger for spherical surfaces than for cylindrical ones, therefore the surface density of the bulkier (more branched) polymer in the mixture is larger on the Au-NR caps than on the Au-NR body. These results suggest that the combination of curvature at the nanoscale and tailored molecular architecture can confer anisotropic nanoparticles with spatially enriched domains and, therefore, lead to nanoconstructs with directional chemical interactions.

Triacylglycerol synthesis during nitrogen stress involves the prokaryotic lipid synthesis pathway and acyl chain remodeling in the microalgae Coccomyxa subellipsoidea

Triglyceride (TAG) synthesis during nitrogen starvation and recovery was addressed using Coccomyxa subellipsoidea by analyzing acyl-chain composition and redistribution using a bioreactor-controlled time course. Galactolipids, phospholipids and TAGs were profiled using liquid chromatography tandem mass spectroscopy (LC–MS/MS). TAG levels increased linearly through 10days of N starvation to a final concentration of 12.6% dry weight (DW), while chloroplast membrane lipids decreased from 5% to 1.5% DW. The relative quantities of TAG molecular species, differing in acyl chain length and glycerol backbone position, remained unchanged from 3 to 10days of N starvation. Six TAG species comprised approximately half the TAG pool. An average of 16.5% of the acyl chains had two or more double bonds consistent with their specific transfer from membrane lipids to TAGs during N starvation. The addition of nitrate following 10days of N starvation resulted in a dramatic shift from chloroplast-derived to endoplasmic reticulum-derived galactolipids (from <12% to >40%). A model for TAG synthesis in C. subellipsoidea was developed based on the acquired data and known plant pathways and data presented.

Cross-linked poly(arylene ether ketone) membranes sulfonated on both backbone and pendant position for high proton conduction and low water uptake

A series of cross-linkable poly(arylene ether ketone)s (PAEKs) with sulfonic acid groups on both the backbone and pendant positions are synthesized through direct condensation polymerization. The degree of sulfonation (DS) of the polymer backbone is controlled by changing the feed ratios of sulfonated to unsulfonated monomers. Post-polymerization reactions are successfully employed to prepare polymer electrolyte membranes for fuel cell applications. The chemical structures of the synthesized polymers are confirmed by 1H nuclear magnetic resonance (NMR) and Fourier transform infrared (FT-IR) spectroscopy. The thermal and mechanical properties of the membranes are characterized by thermogravimetric analysis and stress–strain test. The dependence of water uptake, methanol permeability, proton conductivity, and selectivity on DS is studied. The cross-linked sulfonated PAEK (CSPAEK) membranes with DS higher than 120% exhibit higher proton conductivity than those of Nafion® 117. The CSPAEK membranes maintain very low methanol permeability and water uptake. The properties of all the membrane are correlated with ionic cluster dimension measured by small angle X-ray scattering (SAXS).

Cross-Linked poly(arylene Ether Ketone) Membranes Sulfonated on both Backbone and Pendant Position for High Proton Conducting and Low Water Uptake

not Available.

Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).

We present the Molecular Software Library (MSL), a C++ library for molecular modeling. MSL is a set of tools that supports a large variety of algorithms for the design, modeling, and analysis of macromolecules. Among the main features supported by the library are methods for applying geometric transformations and alignments, the implementation of a rich set of energy functions, side chain optimization, backbone manipulation, calculation of solvent accessible surface area, and other tools. MSL has a number of unique features, such as the ability of storing alternative atomic coordinates (for modeling) and multiple amino acid identities at the same backbone position (for design). It has a straightforward mechanism for extending its energy functions and can work with any type of molecules. Although the code base is large, MSL was created with ease of developing in mind. It allows the rapid implementation of simple tasks while fully supporting the creation of complex applications. Some of the potentialities of the software are demonstrated here with examples that show how to program complex and essential modeling tasks with few lines of code. MSL is an ongoing and evolving project, with new features and improvements being introduced regularly, but it is mature and suitable for production and has been used in numerous protein modeling and design projects. MSL is open-source software, freely downloadable at http://msl-libraries.org. We propose it as a common platform for the development of new molecular algorithms and to promote the distribution, sharing, and reutilization of computational methods.