The Electrostatic Basis of Diacylglycerol Pyrophosphate—Protein Interaction

Diacylglycerol pyrophosphate (DGPP) is an anionic phospholipid formed in plants, yeast, and parasites under multiple stress stimuli. It is synthesized by the phosphorylation action of phosphatidic acid (PA) kinase on phosphatidic acid, a signaling lipid with multifunctional properties. PA functions in the membrane through the interaction of its negatively charged phosphomonoester headgroup with positively charged proteins and ions. DGPP, like PA, can interact electrostatically via the electrostatic-hydrogen bond switch mechanism but differs from PA in its overall charge and shape. The formation of DGPP from PA alters the physicochemical properties as well as the structural dynamics of the membrane. This potentially impacts the molecular and ionic binding of cationic proteins and ions with the DGPP enriched membrane. However, the results of these important interactions in the stress response and in DGPP’s overall intracellular function is unknown. Here, using 31P MAS NMR, we analyze the effect of the interaction of low DGPP concentrations in model membranes with the peptides KALP23 and WALP23, which are flanked by positively charged Lysine and neutral Tryptophan residues, respectively. Our results show a significant effect of KALP23 on the charge of DGPP as compared to WALP23. There was, however, no significant effect on the charge of the phosphomonoester of DGPP due to the interaction with positively charged lipids, dioleoyl trimethylammonium propane (DOTAP) and dioleoyl ethyl-phosphatidylcholine (EtPC). Divalent calcium and magnesium cations induce deprotonation of the DGPP headgroup but showed no noticeable differences on DGPP’s charge. Our results lead to a novel model for DGPP—protein interaction.

Kinetic, Catalytic and Thermodynamic Properties of Immobilized Milk Clotting Enzyme on Activated Chitosan Polymer and its Application in Cheese Making

Milk clotting enzyme (MCE) from Bacillus circulans 25 was immobilized by covalent binding, ionic binding and entrapment methods using various carriers. MCE covalently immobilized on activated chitosan polymer with the bifunctional agent glutaraldehyde (Ch-MCE) exhibited highest immobilization yield (74.6 %). Comparing to the native MCE, Ch-MCE exhibited higher optimum pH, higher optimum reaction temperature, lower activation energy, higher half-life time, lower deactivation rate constant and higher energy for denaturation. After immobilization, maximum reaction rate, Michaelis-Menten constant, specificity constant, turnover number, and catalytic efficiency of the enzyme were significantly changed. Calculated thermodynamic parameters for denaturation (enthalpy, entropy and Gibbs free energy) confirmed that the catalytic properties of MCE were significantly improved after immobilization. Reusability tests showed that after 7 catalytic cycles, the Ch-MCE retained about 71 % of its activity confirming its suitability for industrial applications.

New Code for DNA Nucleotide Sequences

DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics.

New Code for DNA Nucleotide Sequences

DNA nucleotides consist of the complementary base pairs of Adenine-Thymine (A-T) and Cytosine-Guanine (C-G) that encode as a sequence for genes, and encode for an upstream initiation site that enables transcription. Recently, this lab has shown that steroid hormones are structurally symmetric with each of the four DNA nucleotide pairs and through an ionic binding process may enable gene transcription. Here, a new code is developed for DNA nucleotide sequences that relates to the initiation site for gene transcription. The structural code consists of the orientation of steroid molecules in binding to DNA nucleotides and the class of steroid molecules that form an intermolecular hydrogen bond with an available functional group of Thymine. This later class thereby describes a steroid hormone-DNA nucleotide-ion complex with three hydrogen bonds for A-T and T-A, which thereby matches the three internal hydrogen bonds associated with C-G and G-C. The code consists of two binary vectors to characterize the four configurations of DNA nucleotides and is shown to be consistent with known regulatory elements of DNA sequences associated with gene transcription, including the TATA box and the E-Box, along with other promoters. In addition, the code, which is bijective, is applied to analyze the DNA sequence associated with SARS-CoV-2 to identify regions with relevant structural characteristics.

Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore

Biological nanopores are capable of resolving small analytes down to a monoatomic ion. In this research, tetrachloroaurate(III), a polyatomic ion, is discovered to bind to the methionine residue (M113) of a wild-type α-hemolysin by reversible Au(III)-thioether coordination. However, the cylindrical pore geometry of α-hemolysin generates shallow ionic binding events (~5–6 pA) and may have introduced other undesired interactions. Inspired by nanopore sequencing, a Mycobacterium smegmatis porin A (MspA) nanopore, which possesses a conical pore geometry, is mutated to bind tetrachloroaurate(III). Subsequently, further amplified blockage events (up to ~55 pA) are observed, which report the largest single ion binding event from a nanopore measurement. By taking the embedded Au(III) as an atomic bridge, the MspA nanopore is enabled to discriminate between different biothiols from single molecule readouts. These phenomena suggest that MspA is advantageous for single molecule chemistry investigations and has applications as a hybrid biological nanopore with atomic adaptors.

Liver-on-a-Chip‒Magnetic Nanoparticle Bound Synthetic Metalloporphyrin-Catalyzed Biomimetic Oxidation of a Drug in a Magnechip Reactor

Biomimetic oxidation of drugs catalyzed by metalloporphyrins can be a novel and promising way for the effective and sustainable synthesis of drug metabolites. The immobilization of 5,10,15,20-tetrakis(2,3,4,5,6-pentafluorophenyl)iron(II) porphyrin (FeTPFP) and 5,10,15,20-tetrakis-(4-sulfonatophenyl)iron(II) porphyrin (FeTSPP) via stable covalent or rapid ionic binding on aminopropyl-functionalized magnetic nanoparticles (MNPs-NH2) were developed. These immobilized catalysts could be efficiently applied for the synthesis of new pharmaceutically active derivatives and liver related phase I oxidative major metabolite of an antiarrhythmic drug, amiodarone integrated in a continuous-flow magnetic chip reactor (Magnechip).

A Facile Nanodelivery Platform Based on Functionalized Hyperbranched Poly(ether-ester) for Individualized Antitumor Drugs: Pingyangmycin as a Model

Nanodelivery of antitumor drugs is a new treatment mode for cancer. The aim of this investigation was to construct and evaluate a facile nanodelivery platform for individualized antitumor drugs based on functionalized hyperbranched poly(ether-ester)s. Poly(ether-ester)s, as a kind of hyperbranched polymers, have received extensive attention. Three terminal-functionalized (OH–, NH2– and COOH–) hyperbranched poly(ether-ester)s were prepared and characterized by dynamic light scattering and attenuated total reflectance Fourier transform infrared spectroscopy. The relationship between chemical terminal variation and physical surface charges was investigated. Biocompatibility of these polymers was confirmed by methyl tetrazolium assays and scanning electron microscopy. As a model drug, pingyangmycin has antitumor and antiangiogenic effects. In the paper, pingyangmycin was mixed with carboxyl-modified hyperbranched poly(ether-ester) through ionic binding. Polymer-mixed pingyangmycin exhibited significant inhibition of HN-6 head and neck cancer human cellsin vitro. These studies demonstrate that functionalized hyperbranched (ether-ester)s can be exploited as a facile nanodelivery platform for antitumor therapy.