Dominant form of cationic peroxidase from sorghum roots

A dominant form of cationic peroxidase (PO-2) was isolated from sorghum (Sorghum bicolor L. Moench) roots and purified to electrophoretically homogeneous state. The enzyme is a monomer with mol wt of 49.7 kD. The optimum pH and the main catalytic constants (K_M, V_max, k_cat) were determined for oxidation of the main substrates including Н₂О₂, 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonate) (ABTS), 2,7-diaminofluorene, syringaldazine, 2,6-dimethoxyphenol, and o-dianisidine. The K_M values increased in the sequence: H₂O₂ < 2,7-diaminofluorene < ABTS < o-dianisidine, whereas the maximum turnover number (93.9 s^–1) was found for 2,7-diaminofluorene. Based on the analysis of molecular and catalytic properties of the enzyme, it was proven that PO-2 is a typical cationic plant peroxidase. Polycyclic aromatic hydrocarbons (phenanthrene, anthracene, fluorene), 2,2'-diphenic acid, and Ni ions had no significant influence on the activity of PO-2. The enzyme was inhibited by p-aminobenzoic acid, NaN₃, 1-naphthol, 9,10-anthraquinone, and 9,10-phenanthrenequinone. In the presence of NaN₃, 1-naphthol, and 9,10-phenanthrenequinone, a mixed competitive/noncompetitive type of inhibition was noted. The peroxidase PO-2 was found to oxidize synthetic anthraquinone dyes, phenanthrene, and some oxygenated derivatives of polycyclic aromatic hydrocarbons (9-phenanthrol; 1-naphthol; and 1-hydroxy-2-naphthoic, salicylic, and 2,2'-diphenic acids), which indirectly confirms the coupled plant–microbial metabolism of these compounds in the root zone of sorghum. The results indicate that 9,10-phenanthrenequinone and 2,2'-diphenic acid are the products of peroxidase-catalyzed oxidation of 9-phenanthrol.     

Analysis of Expression of the Amyloid-Degrading Enzyme Neprilysin in Brain Structures of 5xFAD Transgenic Mice

Journal of Evolutionary Biochemistry and Physiology - Neprilysin (NEP) is a neuropeptidase participating in transmission of various neuronal stimuli. It is also a major amyloid (Aβ)-degrading...     

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.     

Dynamics of antibody nuclease activity in blood of women during pregnancy and lactation

In human milk we previously found catalytic antibodies (abzymes) catalyzing hydrolysis of DNA, RNA, NMP, NDP, and NTP and also phosphorylation of proteins and lipids. In the present study we have analyzed nuclease activities of antibodies in blood of women during pregnancy and lactation. Blood of healthy male and female volunteers lacked catalytically active antibodies, whereas antibodies from blood of pregnant women hydrolyzed DNA and RNA and their relative activity varied over a wide range. Relative blood abzyme activities significantly increased after delivery and at the beginning of lactation. The highest abzyme activity was observed in blood of parturient women. Although the dynamics of changes in antibody DNase activity during pregnancy was rather individual for each woman, there was a common trend in the increase in antibody activity in the first and/or third trimester of the pregnancy. The DNase activity of IgG and IgM from blood of healthy pregnant women was 4-5 times less than that from pregnant women with pronounced autoimmune thyroiditis.     

Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization

Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 μg/ml (IC₅₀). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a β-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184–186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.     

Formation of striatum structural and ultrastructural organization in rat postnatal ontogenesis at changes of conditions of their embryonic development

Using light microscopy (Nissl and Golgi techniques), electron microscopy and immunohistochemistry, formation of structure of the brain striatum dorsolateral part from birth to three month of age was studied in rats submitted to acute hypoxia at the period of embryogenesis. Hypoxia at the 13.5th day of pregnancy (E 13.5) was found to lead to a delay of neuronogenesis for the first two weeks of postnatal development as compared with control animals, and the majority of large neurons for this period were degenerated by the type of chromatolysis with swelling of the cell body and processes and lysis of cytoplasmic organelles. By the end of the third week, shrunken hyperchromic or pycnomorphic neurons with the electron-dense cytoplasm and enlarged tubules of endoplasmic reticulum and Golgi complex were also observed. An increased number of swollen processes of glial cells was found in neuropil around the degenerating neurons. By the 30th day as well as in adult animals, destruction of mitochondrial apparatus, an increased number of lysosomes, and blade-shaped nuclei, which are characteristics of the apoptotic cell death, were observed. This is also confirmed by an increased expression of proapoptotic protein (p53) and its co-localization with caspase-3 in a part of neurons. Morphometric analysis showed a decrease of the cell distribution density in striatum and a change of ratio of different cell types in hypoxia-exposed rats as compared with control group. The most pronounced decrease (42.3% at the 5th day, 14.2% at the 10th day, p < 0.01) of the number of large neurons (larger than 80 μm²) was revealed at early stages of postnatal ontogenesis. After 3 postnatal weeks, the number of middle-sized neurons (30–95 μm²) decreased (by 11.8–19.2% as compared with control, p < 0.05). The obtained data have shown that changes of embryogenesis conditions (hypoxia) at the period of the most intensive proliferation of telencephalon neuroblasts lead to impairment of the process of striatal nervous tissue formation. This might be the cause of delay of development and disturbances of behavior and learning, which are observed in rats exposed to prenatal hypoxia.     

Mapping the amino acid properties of constituent nucleoporins onto the yeast nuclear pore complex

Visualization of molecular structures aids in the understanding of structural and functional roles of biological macromolecules. Macromolecular transport between the cell nucleus and cytoplasm is facilitated by the nuclear pore complex (NPC). The ring structure of the NPC is large and contains several distinct proteins (nucleoporins) which function as a selective gate for the passage of certain molecules into and out of the nucleus. In this note we demonstrate the utility of a python code that allows direct mapping of the physiochemical properties of the constituent nucleoporins on the scaffold of the yeast NPC׳s cytoplasmic view. We expect this tool to be useful for researchers to visualize the NPC based on their physiochemical properties and how it alters when specific mutations are introduced in one or more of the nucleoporins. The code developed using Python is available freely from the authors.