Visualizing the Adenylation Activities and Protein–Protein Interactions of Aryl Acid Adenylating Enzymes

Structural and activity studies have revealed the dynamic and transient actions of carrier protein (CP) activity in primary and secondary metabolic pathways. CP-mediated interactions play a central role in nonribosomal peptide biosynthesis, as they serve as covalent tethers for amino acid and aryl acid substrates and enable the growth of peptide intermediates. Strategies are therefore required to study protein–protein interactions efficiently. Herein, we describe activity-based probes used to demonstrate the protein–protein interactions between aryl CP (ArCP) and aryl acid adenylation (A) domains as well as the substrate specificities of the aryl acid A domains. If coupled with in-gel fluorescence imaging, this strategy allows visualization of the protein–protein interactions required to recognize and transfer the substrate to the partner ArCP. This technique has potential for the analysis of protein–protein interactions within these biosynthetic enzymes at the molecular level and for use in the combinatorial biosynthesis of new nonribosomal peptides.     

Targeted Nanoswitchable Inhibitors of Protein–Protein Interactions Involved in Apoptosis

Progress in drug delivery is hampered by a lack of efficient strategies to target drugs with high specificity and precise spatiotemporal regulation. The remote control of nanoparticles and drugs with light allows regulation of their action site and dosage. Peptide-based drugs are highly specific, non-immunogenic, and can be designed to cross the plasma membrane. In order to combine target specificity and remote control of drug action, here we describe a versatile strategy based on a generalized template to design nanoswitchable peptides that modulate protein–protein interactions upon light activation. This approach is demonstrated to promote photomodulation of two important targets involved in apoptosis (the interactions Bcl-xL–Bak and MDM2–p53), but can be also applied to a large pool of therapeutically relevant protein–protein interactions mediated by α-helical motifs. The template can be adjusted using readily available information about hot spots (residues contributing most to the binding energy) at the protein–protein interface of interest.     

Quantitation of Multiple Sphingolipid Classes Using Normal and Reversed-Phase LC–ESI–MS/MS: Comparative Profiling of Two Cell Lines

Sphingolipids are an important class of compounds that regulate signal transduction and other vital cellular processes. Herein, we report sensitive normal and reversed phase LC–MS/MS methods for quantitation of multiple sphingolipid classes. In the normal-phase ESI/MS/MS method, a high content of organic solvents was utilized, which, although it included hexane, ethyl acetate, acetonitrile containing 2% methanol, 1–2% acetic acid, and 5 mM ammonium acetate, resulted in a very efficient electrospray ionization of the ceramides (Cers) and hexosylceramides (MHCers). Three normal-phase LC–MS/MS methods using segmented phases were developed to specifically target Cers, MHCers, or sphingomyelins (SMs). This segmentation scheme increases the number of data points acquired for a given analyte and enhances the sensitivity and specificity of the measurements. Nine separate reversed phase chromatography methods were developed for the three classes of compounds. These assays were used for comparing the levels of Cers, SMs, and MHCers from mouse embryonic fibroblast (pMEF) and human embryonic kidney (HEK293) cells. These findings were then compared with the reported data from RAW264.7 mouse macrophage cells, BHK21 hamster cells, and human plasma and serum samples. The analysis of cell lines, using both normal and reversed phase chromatography, revealed discrimination based on the type of chromatography chosen, while sphingolipid assays of samples containing different amounts of protein showed different results, even after normalizing for protein content. Also, LC/MS/MS profiles were provided for the classes and individual compounds so that they could be used as “molecular profiles” for class or individual sample analysis.     

Stress-Responsive Expression,Subcellular Localization and Protein–Protein Interactions of the Rice Metacaspase Family

Metacaspases, a class of cysteine-dependent proteases like caspases in animals, are important regulators of programmed cell death (PCD) during development and stress responses in plants. The present study was focused on comprehensive analyses of expression patterns of the rice metacaspase (OsMC) genes in response to abiotic and biotic stresses and stress-related hormones. Results indicate that members of the OsMC family displayed differential expression patterns in response to abiotic (e.g., drought, salt, cold, and heat) and biotic (e.g., infection by Magnaporthe oryzae, Xanthomonas oryzae pv. oryzae and Rhizoctonia solani) stresses and stress-related hormones such as abscisic acid, salicylic acid, jasmonic acid, and 1-amino cyclopropane-1-carboxylic acid (a precursor of ethylene), although the responsiveness to these stresses or hormones varies to some extent. Subcellular localization analyses revealed that OsMC1 was solely localized and OsMC2 was mainly localized in the nucleus. Whereas OsMC3, OsMC4, and OsMC7 were evenly distributed in the cells, OsMC5, OsMC6, and OsMC8 were localized in cytoplasm. OsMC1 interacted with OsLSD1 and OsLSD3 while OsMC3 only interacted with OsLSD1 and that the zinc finger domain in OsMC1 is responsible for the interaction activity. The systematic expression and biochemical analyses of the OsMC family provide valuable information for further functional studies on the biological roles of OsMCs in PCD that is related to abiotic and biotic stress responses.     

Structure-Guided Synthesis and Evaluation of Small-Molecule Inhibitors Targeting Protein–Protein Interactions of BRCA1 tBRCT Domain

The tandem BRCT domains (tBRCT) of BRCA1 engage phosphoserine-containing motifs in target proteins to propagate intracellular signals initiated by DNA damage, thereby controlling cell cycle arrest and DNA repair. Recently, we identified Bractoppin, the first small-molecule inhibitor of the BRCA1 tBRCT domain, which selectively interrupts BRCA1-mediated cellular responses evoked by DNA damage. Here, we combine structure-guided chemical elaboration, protein mutagenesis and cellular assays to define the structural features responsible for Bractoppin's activity. Bractoppin fails to bind mutant forms of BRCA1 tBRCT bearing K1702A, a key residue mediating phosphopeptide recognition, or F1662R or L1701K that adjoin the pSer-recognition site. However, the M1775R mutation, which engages the Phe residue in the consensus phosphopeptide motif pSer-X-X-Phe, does not affect Bractoppin binding, confirming a binding mode distinct from the substrate phosphopeptide binding. We explored these structural features through structure-guided chemical elaboration and characterized structure–activity relationships (SARs) in biochemical assays. Two analogues, CCBT2088 and CCBT2103 were effective in abrogating BRCA1 foci formation and inhibiting G2 arrest induced by irradiation of cells. Collectively, our findings reveal structural features underlying the activity of a novel inhibitor of phosphopeptide recognition by the BRCA1 tBRCT domain, providing fresh insights to guide the development of inhibitors that target protein–protein interactions.     

Diacylglycerol Kinase η Activity in Cells Using Protein Myristoylation and Cellular Phosphatidic Acid Sensor

Diacylglycerol kinase (DGK) phosphorylates diacylglycerol to produce phosphatidic acid (PtdOH) and regulates the balance between two lipid second messengers: diacylglycerol and PtdOH. Several lines of evidence suggest that the η isozyme of DGK is involved in the pathogenesis of bipolar disorder. However, the detailed molecular mechanisms regulating the pathophysiological functions remain unclear. One reason is that it is difficult to detect the cellular activity of DGKη. To overcome this difficulty, we utilized protein myristoylation and a cellular PtdOH sensor, the N-terminal region of α-synuclein (α-Syn-N). Although DGKη expressed in COS-7 cells was broadly distributed in the cytoplasm, myristoylated (Myr)-AcGFP-DGKη and Myr-AcGFP-DGKη-KD (inactive (kinase-dead) mutant) were substantially localized in the plasma membrane. Moreover, DsRed monomer-α-Syn-N significantly colocalized with Myr-AcGFP-DGKη but not Myr-AcGFP-DGKη-KD at the plasma membrane. When COS-7 cells were osmotically shocked, all DGKη constructs were exclusively translocated to osmotic shock-responsive granules (OSRG). DsRed monomer-α-Syn-N markedly colocalized with only Myr-AcGFP-DGKη at OSRG and exhibited a higher signal/background ratio (3.4) than Myr-AcGFP-DGKη at the plasma membrane in unstimulated COS-7 cells (2.5), indicating that α-Syn-N more effectively detects Myr-AcGFP-DGKη activity in OSRG. Therefore, these results demonstrated that the combination of myristoylation and the PtdOH sensor effectively detects DGKη activity in cells and that this method is convenient to examine the molecular functions of DGKη. Moreover, this method will be useful for the development of drugs targeting DGKη. Furthermore, the combination of myristoylation (intensive accumulation in membranes) and α-Syn-N can be applicable to assays for various cytosolic PtdOH-generating enzymes.     

Novel Dextran-Supported Biological Probes Decorated with Disaccharide Entities for Investigating the Carbohydrate–Protein Interactions of Gal-3

The quest for novel natural-like biomolecular probes that can be used to gain information on biological recognition events is of topical interest to several scientific areas. In particular, the recognition of carbohydrates by proteins modulates a number of important biological processes. These molecular recognition events are, however, difficult to study by the use of naturally occurring oligosaccharides and polysaccharides owing to their intrinsic structural heterogeneity and to the many technical difficulties encountered during the isolation of sufficient quantities of pure material for detailed structural and biological studies. Therefore, the construction of homogenous biomolecular probes that can mimic both the biophysical properties of polysaccharide backbones and the properties of bioactive oligosaccharide fragments are highly sought after. Herein, synthetic methodology for the construction of well-defined bioconjugates consisting of biologically relevant disaccharide fragments grafted onto a dextran backbone is presented, and a preliminary NMR spectroscopy study of their interactions with galectin-3 as a model lectin is conducted.     

Chemical Space Overlap with Critical Protein–Protein Interface Residues in Commercial and Specialized Small-Molecule Libraries

There is growing interest in the use of structure-based virtual screening to identify small molecules that inhibit challenging protein–protein interactions (PPIs). In this study, we investigated how effectively chemical library members docked at the PPI interface mimic the position of critical side-chain residues known as “hot spots”. Three compound collections were considered, a commercially available screening collection (ChemDiv), a collection of diversity-oriented synthesis (DOS) compounds that contains natural-product-like small molecules, and a library constructed using established reactions (the “screenable chemical universe based on intuitive data organization”, SCUBIDOO). Three different tight PPIs for which hot-spot residues have been identified were selected for analysis: uPAR⋅uPA, TEAD4⋅Yap1, and Ca_Vα⋅Ca_Vβ. Analysis of library physicochemical properties was followed by docking to the PPI receptors. A pharmacophore method was used to measure overlap between small-molecule substituents and hot-spot side chains. Fragment-like conformationally restricted small molecules showed better hot-spot overlap for interfaces with well-defined pockets such as uPAR⋅uPA, whereas better overlap was observed for more complex DOS compounds in interfaces lacking a well-defined binding site such as TEAD4⋅Yap1. Virtual screening of conformationally restricted compounds targeting uPAR⋅uPA and TEAD4⋅Yap1 followed by experimental validation reinforce these findings, as the best hits were fragment-like and had few rotatable bonds for the former, while no hits were identified for the latter. Overall, such studies provide a framework for understanding PPIs in the context of additional chemical matter and new PPI definitions.     

Role of Chemical Mediators in Aquatic Interactions across the Prokaryote–Eukaryote Boundary

There is worldwide growing interest in the occurrence and diversity of metabolites used as chemical mediators in cross-kingdom interactions within aquatic systems. Bacteria produce metabolites to protect and influence the growth and life cycle of their eukaryotic hosts. In turn, the host provides a nutrient-enriched environment for the bacteria. Here, we discuss the role of waterborne chemical mediators that are responsible for such interactions in aquatic multi-partner systems, including algae or invertebrates and their associated bacteria. In particular, this review highlights recent advances in the chemical ecology of aquatic systems that support the overall ecological significance of signaling molecules across the prokaryote–eukaryote boundary (cross-kingdom interactions) for growth, development and morphogenesis of the host. We emphasize the value of establishing well-characterized model systems that provide the basis for the development of ecological principles that represent the natural lifestyle and dynamics of aquatic microbial communities and enable a better understanding of the consequences of environmental change and the most effective means of managing community interactions.     

Analysis of Phospholipids in Rat Brain Using Liquid Chromatography–Mass Spectrometry

The brain is a lipid-rich organ containing complex polar lipids including phospholipids (PLs) and sphingolipids. These lipids are involved in the structure and function of cell membranes in the brain. We developed a fast and efficient liquid chromatography–tandem mass spectrometry (LC–MS/MS) method to quantify five different classes of PLs [Choline glycerophospholipid (consists of phosphatidyl choline and plasmenyl choline in these samples), ethanolamine glycerophospholipid (consist of phosphatidyl ethanolamine and plasmenyl ethanolamine in these samples), phosphatidyl serine, phosphatidyl inositol, and sphingomyelin] in the brain tissues of 80-day-old Wistar rats. The PLs were extracted from rat brain using chloroform/methanol/water. After separation using a hydrophilic high performance liquid chromatography column, PL-class-specific fragmentation (head group identification) with a tandem mass spectrometer in positive ion mode was utilized to measure changes in the relative concentration of the five PL classes. The advantage of this approach was its improved specificity over previously reported LC–MS methods. The method had good repeatability (coefficient of variation 3–9%, excluding phosphatidyl inositol) and recovery (92–103%) and compared well with more laborious traditional methods.     

Synergism of α-Linolenic Acid, Conjugated Linoleic Acid and Calcium in Decreasing Adipocyte and Increasing Osteoblast Cell Growth

Whole fat milk and dairy products (although providing more energy compared to low- or non-fat products), are good sources of α-linolenic acid (ALA), conjugated linoleic acid (CLA) and calcium, which may be favorable in modulating bone and adipose tissue metabolism. We examined individual and/or synergistic effects of ALA, CLA and calcium (at levels similar to those in whole milk/dairy products) in regulating bone and adipose cell growth. ST2 stromal, MC3T3-L1 adipocyte-like and MC3T3-E1 osteoblast-like cells were treated with: (a) linoleic acid (LNA):ALA ratios = 1–5:1; (b) individual/combined 80–90 % c9, t11 (9,11) and 5–10 % t10, c12 (10,12) CLA isomers; (c) 0.5–3.0 mM calcium; (d) combinations of (a), (b), (c); and (e) control. Local mediators, including eicosanoids and growth factors, were measured. (a) The optimal effect was found at the 4:1 LNA:ALA ratio where insulin-like growth factor-1 (IGF-1) and IGF binding protein-3 (IGFBP-3) production was the lowest in MC3T3-L1 cells. (b) All CLA isomer blends decreased MC3T3-L1 and increased MC3T3-E1 cell differentiation. (c) 1.5–2.5 mM calcium increased ST2 and MC3T3-E1, and decreased MC3T3-L1 cell proliferation. (d) Combination of 4:1 LNA:ALA + 90:10 % CLA + 2.0 mM calcium lowered MC3T3-L1 and increased MC3T3-E1 cell differentiation. Overall, the optimal LNA:ALA ratio to enhance osteoblastogenesis and inhibit adipogenesis was 4:1. This effect was enhanced by 90:10 % CLA + 2.0 mM calcium, indicating possible synergism of these dietary factors in promoting osteoblast and inhibiting adipocyte differentiation in cell cultures.     

Investigation of Enantioselective Membrane Permeability of α-Lipoic Acid in Caco-2 and MDCKII Cell

α-Lipoic acid (LA) contains a chiral carbon and exists as two enantiomers (R-α-lipoic acid (RLA) and S-α-lipoic acid (SLA)). We previously demonstrated that oral bioavailability of RLA is better than that of SLA. This difference arose from the fraction absorbed multiplied by gastrointestinal availability (F_a × F_g) and hepatic availability (F_h) in the absorption phase. However, it remains unclear whether F_a and/or F_g are involved in enantioselectivity. In this study, Caco-2 cells and Madin–Darby canine kidney strain II cells were used to assess the enantioselectivity of membrane permeability. LA was actively transported from the apical side to basal side, regardless of the differences in its steric structure. Permeability rates were proportionally increased in the range of 10–250 µg LA/mL, and the permeability coefficient did not differ significantly between enantiomers. Hence, we conclude that enantioselective pharmacokinetics arose from the metabolism (F_h or F_g × F_h), and definitely not from the membrane permeation (F_a) in the absorption phase.     

Lipase-Catalyzed Synthesis of Saccharide–Fatty Acid Esters Using Suspensions of Saccharide Crystals in Solvent-Free Media

Saccharide–fatty acid esters, important biobased and biodegradable emulsifiers in foods, cosmetics, and pharmaceuticals, were produced with high yields and productivity via immobilized Rhizomucor miehei lipase-catalyzed esterification in solvent-free systems at 65 °C. Preliminary experiments demonstrated high rates of reaction occurred in the presence of acetone near or above its boiling point, due to the formation of 10–200 μm suspensions of saccharide particles. Subsequently, a two-step process was developed to produce a solvent-free supersaturated solution of 1.5–2.0 wt% saccharide that remained stable for ≥10–12 h. The solvent-free suspensions were used in a bioreactor system at 65 °C, consisting of a reservoir open to the atmosphere that contained molecular sieves, a peristaltic pump, and a packed bed bioreactor, operated under continuous recirculation. At 10 h intervals, suspensions were re-formed by treating the substrate/product mixture with additional acyl acceptor and applying strong agitation. Using this system and approach, a product mixture containing 88% fructose oleate was formed, of which 92% was monoester, within 6 days. This equates to a productivity of 0.2 mmol h⁻¹ g⁻¹, which is similar to values reported for synthesis in the presence of solvent.     

Liquid–Liquid Extraction of Isovaleric Acid Using Alamine 308/Diluent and Conventional Solvent Systems: Effect of Diluent and Acid Structure

Abstract

Distribution of isovaleric (3‐methyl butanoic) acid between water and Alamine 308 (triisooctylamine) dissolved in C₅ and C₆‐ring included diluents of proton‐donating and ‐accepting (cyclopentanol, cyclohexanone), polar (chlorobenzene) and inert (toluene) types, as well as a comparison with the extraction equilibria of pure diluent alone (chloroform) have been studied at 298 K. Among the tested C₆ ring‐containing and aliphatic diluents, cyclic alcohol/amine system yields the highest synergistic extraction efficiency. The strength of the complex solvation was found to be reasonably large for halogenated aromatics favoring mainly the formation of acid₁‐amine₂ structure. The influence of the acid structure over distribution has been interpreted through comparing the extractabilities of seven acids containing different functional groups, i.e., isovaleric, formic, levulinic, acetic, propanoic, pyruvic and nicotinic acids. The results were correlated using a modified linear solvation energy relation (METLER) and versions of the mass action law, i.e., a chemodel approach and a modified Langmuir equilibrium model comprising the formation of one or two acid‐multiple amines complex formation.     

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction

MicroRNA(miRNA)–mRNA interactions are important for understanding many biological processes, including development, differentiation and disease progression, but their identification is highly context-dependent. When computationally derived from sequence information alone, the identification should be verified by integrated analyses of mRNA and miRNA expression. The drawback of this strategy is the vast number of identified interactions, which prevents an experimental or detailed investigation of each pair. In this paper, we overcome this difficulty by the recently proposed principal component analysis (PCA)-based unsupervised feature extraction (FE), which reduces the number of identified miRNA–mRNA interactions that properly discriminate between patients and healthy controls without losing biological feasibility. The approach is applied to six cancers: hepatocellular carcinoma, non-small cell lung cancer, esophageal squamous cell carcinoma, prostate cancer, colorectal/colon cancer and breast cancer. In PCA-based unsupervised FE, the significance does not depend on the number of samples (as in the standard case) but on the number of features, which approximates the number of miRNAs/mRNAs. To our knowledge, we have newly identified miRNA–mRNA interactions in multiple cancers based on a single common (universal) criterion. Moreover, the number of identified interactions was sufficiently small to be sequentially curated by literature searches.     

Analysis of Particle Transport and Deposition of Micron-Sized Particles in a 90° Bend Using a Two-Fluid Eulerian–Eulerian Approach

Two-phase flows involving dispersed particle and droplet phases are common in a variety of natural and industrial processes, such as aerosols, blood flow, emulsions, and gas-catalyst systems. For sufficiently dilute particle/aerosol phases, a simplified one-way coupling is often assumed, in which the continuous primary phase is unaffected by the presence of the dispersed secondary phase and standard CFD methods can be applied. To predict the transport and deposition of the particle phase, typically a Lagrangian particle-tracking or Eulerian one-fluid/two-phase drift-flux approach is used. Here, a full two-fluid Eulerian modeling approach is presented for coarse particles (>1 μm), in which transport equations are numerically solved for both particle-phase continuity and particle-phase momentum. Simulation results were obtained for a laminar flow regime (Re 100 and 1000) in a 90° elbow, and the effects of grid topology and resolution were investigated. Additionally, gravity effects were considered for both Re cases. Results using this full two-fluid Eulerian approach were validated against experimental data and other computational studies. One key novel contribution of this work is presentation of a simple algorithm for stabilizing the Eulerian particle-phase equation. To the authors' knowledge, this is the first study documenting a full two-fluid Eulerian approach for dilute particle phases in laminar flow on unstructured (prism/tetrahedral) meshes. The results show the potential of the two-fluid approach for providing a useful alternative to the more typical Lagrangian approach for prediction of coarse-particle transport and wall deposition.

Copyright 2015 American Association for Aerosol Research     

Analysis of Data on Vapor–Liquid Equilibrium in Multicomponent Systems Using Artificial Neural Networks

Theoretical Foundations of Chemical Engineering - A brief analysis of the possibilities of using the method of artificial neural networks (ANNs) for assessing and correlating data on...     

Quantitative Analysis of Phytosterols in Edible Oils Using APCI Liquid Chromatography–Tandem Mass Spectrometry

Previous methods for the quantitative analysis of phytosterols have usually used GC–MS and require elaborate sample preparation including chemical derivatization. Other common methods such as HPLC with absorbance detection do not provide information regarding the identity of the analytes. To address the need for an assay that utilizes mass selectivity while avoiding derivatization, a quantitative method based on LC–tandem mass spectrometry (LC–MS–MS) was developed and validated for the measurement of six abundant dietary phytosterols and structurally related triterpene alcohols including brassicasterol, campesterol, cycloartenol, β-sitosterol, stigmasterol, and lupeol in edible oils. Samples were saponified, extracted with hexane and then analyzed using reversed phase HPLC with positive ion atmospheric pressure chemical ionization tandem mass spectrometry and selected reaction monitoring. The utility of the LC–MS–MS method was demonstrated by analyzing 14 edible oils. All six compounds were present in at least some of the edible oils. The most abundant phytosterol in all samples was β-sitosterol, which was highest in corn oil at 4.35 ± 0.03 mg/g, followed by campesterol in canola oil at 1.84 ± 0.01 mg/g. The new LC–MS–MS method for the quantitative analysis of phytosterols provides a combination of speed, selectivity and sensitivity that exceed those of previous assays.     

Synthesis and Sulfonation of an Aluminum-Based Metal–Organic Framework with Microwave Method and Using for the Esterification of Oleic Acid

Journal of Inorganic and Organometallic Polymers and Materials - In this study, the synthesis of MIL-53(Al) (Material Institute Lavoisier, MIL) material, which is an aluminum-containing...