Zundel-Type H-Bonding in Biomolecular Ions

Using quantum chemical calculations and infrared multiphoton dissociation (IRMPD) spectroscopy in the fingerprint and X-H stretching regions, we demonstrate here that the all-Ala b ₆ fragment ion features a macrocyclic structure with C₂ symmetry. For this structure, the ionizing proton is equally shared by the Ala(1) and Ala(4) amide oxygens in a Zundel-type symmetric (X…H⁺…X) H-bond. Figure

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Platinum Complexes Containing Pyramidalized Germanium and Tin Dihalide Ligands Bound through σ,σ ME Multiple Bonds

We present the isolation of the first mononuclear dihalogermylene, and mono‐ and dinuclear stannylene complexes of transition metals. These exhibit exceptionally pyramidalized Group 14 centers. Additionally, removal of the halide substituents from the Ge/Sn atom was successfully performed in two ways, halide abstraction and reduction, leading to a variety of unusual structural motifs.     

Boryl‐Functionalized σ‐Alkynyl and Vinylidene Rhodium Complexes: Synthesis and Electronic Properties

The synthesis, reactivity, and properties of boryl‐functionalized σ‐alkynyl and vinylidene rhodium complexes such as trans‐[RhCl(?C?CHBMes₂)(PiPr₃)₂] and trans‐[Rh(C?CBMes₂)(IMe)(PiPr₃)₂] are reported. An equilibrium was found to exist between rhodium vinylidene complexes and the corresponding hydrido σ‐alkynyl complexes in solution. The complex trans‐[Rh(C?CBMes₂)(IMe)(PiPr₃)₂] (IMe=1,3‐dimethylimidazol‐2‐ylidene) was found to exhibit solvatochromism and can be quasireversibly oxidized and reduced electrochemically. Density functional calculations were performed to determine the reaction mechanism and to help rationalize the photophysical properties of trans‐[Rh(C?CBMes₂)(IMe)(PiPr₃)₂].     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

Characterization of a New Bacteriocin from Lactobacillus plantarum LE5 and LE27 Isolated from Ensiled Corn

Bacteriocins are low molecular peptides with antimicrobial activity, which are of great interest as food bio-preservatives and for treating diseases caused by pathogenic bacteria. In this study, we present the characterization of bacteriocins produced by Lactobacillus plantarum LE5 and LE27 isolated from ensiled corn. Bacteriocins were purified through ammonium sulfate precipitation and double dialysis by using 12- and 1-kDa membranes. Bacteriocins showed activity against Listeria innocua, Listeria monocytogenes, and Enteroccocus faecalis. Molecular weight was estimated through Tricine-SDS-PAGE and overloading the gel onto Mueller-Hinton agar seeded with L. monocytogenes, showing an inhibition zone between 5 and 10 kDa. NanoLC-MS/MS analysis allowed the identification of UPF0291 protein (UniProtKB/Swiss-Prot Q88VI7), which is also presented in other lactic acid bacteria without assigned function. Ab initio modeling showed it has an α-helix-rich structure and a large positive-charged region. Bacteriocins were stable between 4 and 121 °C and pH 2 and 12, and the activity was inhibited by SDS and proteases. Mode of action assay suggests that the bacteriocin causes of target microorganism. Taken together, these results describe a possible new class IIa bacteriocin produced by L. plantarum, which has a wide stability to physicochemical conditions, and that could be used as an alternative for the control of foodborne diseases.     

Conformational and electronic study of dopamine interacting with the D2 dopamine receptor

We report an exhaustive conformational and electronic study on dopamine (DA) interacting with the D₂ dopamine receptor (D₂DR). For the first time, the complete surface of the conformational potential energy of the complex DA/D₂DR is reported. Such a surface was obtained through the use of QM/MM calculations. A detailed study of the molecular interactions that stabilize and destabilize the different molecular complexes was carried out using two techniques: Quantum Theory of Atoms in Molecules computations and nuclear magnetic shielding constants calculations. A comparative study of the behavior of DA in the gas phase, aqueous solution, and in the active site of D₂DR has allowed us to evaluate the degree of deformation suffered by the ligand and, therefore, analyze how rustic are the lock-key model and the induced fit theory in this case. Our results allow us to propose one of the conformations obtained as the “biologically relevant” conformation of DA when it is interacting with the D₂DR.     

Green Synthesis of Gold and Silver Nanoparticles Using Leaf Extract of Capsicum chinense Plant

So far, several studies have focused on the synthesis of metallic nanoparticles making use of extracts from the fruit of the plants from the genus Capsicum. However, as the fruit is the edible, and highly commercial, part of the plant, in this work we focused on the leaves, a part of the plant that is considered agro-industrial waste. The biological synthesis of gold (AuNPs) and silver (AgNPs) nanoparticles using aqueous extracts of root, stem and leaf of Capsicum chinense was evaluated, obtaining the best results with the leaf extract. Gold and silver nanoparticles synthesized using leaf extract (AuNPs-leaf and AgNPs-leaf, respectively) were characterized by UV-visible spectrophotometry (UV-Vis), Fourier Transform Infrared Spectroscopy with Attenuated Total Reflection (FTIR-ATR), X-ray Photoelectron Spectroscopy (XPS), Ultra Hight Resolution Scanning Electron Microscopy coupled to Energy-Dispersive X-ray spectroscopy (UHR-SEM-EDX) and Transmission Electron Microscopy (TEM), and tested for their antioxidant and antimicrobial activities. In addition, different metabolites involved in the synthesis of nanoparticles were analyzed. We found that by the use of extracts derived from the leaf, we could generate stable and easy to synthesize AuNPs and AgNPs. The AuNPs-leaf were synthesized using microwave radiation, while the AgNPs-leaf were synthesized using UV light radiation. The antioxidant activity of the extract, determined by ABTS, showed a decrease of 44.7% and 60.7% after the synthesis of the AuNPs-leaf and AgNPs-leaf, respectively. After the AgNPs-leaf synthesis, the concentration of polyphenols, reducing sugars and amino acids decreased by 15.4%, 38.7% and 46.8% in the leaf extract, respectively, while after the AuNPs-leaf synthesis only reducing sugars decreased by 67.7%. These results suggest that these groups of molecules are implicated in the reduction/stabilization of the nanoparticles. Although the contribution of these compounds in the synthesis of the AuNPs-leaf and the AgNPs-leaf was different. Finally, the AgNPs-leaf inhibited the growth of S. aureus, E. coli, S. marcescens and E. faecalis. All of them are bacterial strains of clinical importance due to their fast antibiotic resistance development.     

A Ferrofluid with Surface Modified Nanoparticles for Magnetic Hyperthermia and High ROS Production

A ferrofluid with 1,2-Benzenediol-coated iron oxide nanoparticles was synthesized and physicochemically analyzed. This colloidal system was prepared following the typical co-precipitation method, and superparamagnetic nanoparticles of 13.5 nm average diameter, 34 emu/g of magnetic saturation, and 285 K of blocking temperature were obtained. Additionally, the zeta potential showed a suitable colloidal stability for cancer therapy assays and the magneto-calorimetric trails determined a high power absorption density. In addition, the oxidative capability of the ferrofluid was corroborated by performing the Fenton reaction with methylene blue (MB) dissolved in water, where the ferrofluid was suitable for producing reactive oxygen species (ROS), and surprisingly a strong degradation of MB was also observed when it was combined with H₂O₂. The intracellular ROS production was qualitatively corroborated using the HT-29 human cell line, by detecting the fluorescent rise induced in 2,7-dichlorofluorescein diacetate. In other experiments, cell metabolic activity was measured, and no toxicity was observed, even with concentrations of up to 4 mg/mL of magnetic nanoparticles (MNPs). When the cells were treated with magnetic hyperthermia, 80% of cells were dead at 43 °C using 3 mg/mL of MNPs and applying a magnetic field of 530 kHz with 20 kA/m amplitude.     

Specific Recognition of β-Galactofuranose-Containing Glycans of Synthetic Neoglycoproteins by Sera of Chronic Chagas Disease Patients

Chagas disease (CD) can be accurately diagnosed by detecting Trypanosoma cruzi in patients’ blood using polymerase chain reaction (PCR). However, parasite-derived biomarkers are of great interest for the serological diagnosis and early evaluation of chemotherapeutic efficacy when PCR may fail, owing to a blood parasite load below the method’s limit of detection. Previously, we focused on the detection of specific anti-α-galactopyranosyl (α-Gal) antibodies in chronic CD (CCD) patients elicited by α-Gal glycotopes copiously expressed on insect-derived and mammal-dwelling infective parasite stages. Nevertheless, these stages also abundantly express cell surface glycosylphosphatidylinositol (GPI)-anchored glycoproteins and glycoinositolphospholipids (GIPLs) bearing nonreducing terminal β-galactofuranosyl (β-Galf) residues, which are equally foreign to humans and, therefore, highly immunogenic. Here we report that CCD patients’ sera react specifically with synthetic β-Galf-containing glycans. We took a reversed immunoglycomics approach that entailed: (a) Synthesis of T. cruzi GIPL-derived Galfβ1,3Manpα-(CH₂)₃SH (glycan G29_SH) and Galfβ1,3Manpα1,2-[Galfβ1,3]Manpα-(CH₂)₃SH (glycan G32_SH); and (b) preparation of neoglycoproteins NGP29b and NGP32b, and their evaluation in a chemiluminescent immunoassay. Receiver-operating characteristic analysis revealed that NGP32b can distinguish CCD sera from sera of healthy individuals with 85.3% sensitivity and 100% specificity. This suggests that Galfβ1,3Manpα1,2-[Galfβ1,3]Manpα is an immunodominant glycotope and that NGP32b could potentially be used as a novel CCD biomarker.