Native Polyacrylamide Gel Research Articles

DNA Ring-Opening Polymerization Driven by Base Stacking.

Supramolecular polymers, relying on reversible intermolecular interactions, promise a wide range of applications, including optoelectronic materials, self-healing materials, and biomedical delivery materials. Among potential molecular candidates, DNA strands act as an excellent platform. DNA has a well-established secondary structure (double helix), and its intermolecular interactions can be readily thermodynamically engineered and kinetically controlled. Extensive studies have demonstrated that various DNA motifs can polymerize/assemble into large polymers with different topology, geometry, and dimensionalities. Most of the reported polymerization is driven by hybridization of DNA strands. Herein, we report a novel system of DNA supramolecular polymerization that is driven by DNA base stacking. The polymerization has been confirmed by native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM). We believe that this work will expand the toolbox for DNA supramolecular polymerization and would, with further development, increase further control of DNA supramolecular polymerization.

Purification of a Thermostable β-mannanase from Paenibacillus Thiaminolyticus - characterization and its Potential Use as a Detergent Additive

Endo-1, 4- β- D-mannanase (EC 3.2.1.78) is a glycoside hydrolase involved in random cleavage of β-1, 4- D-manno-pyranosyl linkages within mannans and heteromannans and generates branched and linear oligosaccharides. A β-mannanase was purified from a thermotolerant bacterium Paenibacillus thiaminolyticus isolated from a soil sample. Enzyme was purified to homogeneity with specific activity of 8812 U/mg protein. Sodium dodecyl sulfate (SDS) and native poly-acryl amide gel electrophoresis indicated that the purified mannanase is a monomeric protein with a molecular mass of 38 kDa. The purified enzyme was found to be maximally active at temperature and pH of 60°C and 7.0, respectively. It was stable at 55°C for 24 h and maintained more than 50 % activity up to 3 h at 60°C. The enzyme was very stable in the pH range of 5.0-9.0. Purified β-mannanase demonstrated high stability after 1 h of pre-incubation with most of the tested organic solvents. Enzyme retained significant stability in the presence of various detergent additives, commercially available detergents and dish washing liquids. The high compatibility and substantial stability in the presence of nonionic detergents and dishwashing liquids confirmed its utility as an additive to dish washing liquids and laundry detergents. Enzyme exhibited efficacious de-staining of heteromannan based stains of chocolate ice cream and salad dressing in the wash performance test for detergent application. It also exhibited anti-soil redeposition effect on cotton swatches treated with tennis court clay and heteromannans.

Co-purification of nitrate reductase 1 with components of the cytochrome bcc-aa3 oxidase supercomplex from spores of Streptomyces coelicolor A3(2).

In order to reduce nitrate in vivo, the spore‐specific respiratory nitrate reductase, Nar1, of Streptomyces coelicolor relies on an active cytochrome bcc‐aa3 oxidase supercomplex (bcc‐aa3 supercomplex). This suggests that membrane‐associated Nar1, comprising NarG1, NarH1, and NarI1 subunits, might not act as a classical menaquinol oxidase but could either receive electrons from the bcc‐aa3 supercomplex, or require the supercomplex to stabilize the reductase in the membrane to allow it to function. To address the biochemical basis for this dependence on the bcc‐aa3 supercomplex, we purified two different Strep‐tagged variants of Nar1 and enriched the native enzyme complex from spore extracts using different chromatographic and electrophoretic procedures. Polypeptides associated with the isolated Nar1 complexes were identified using mass spectrometry and included components of the bcc‐aa3 supercomplex, along with an alternative, spore‐specific cytochrome b component, QcrB3. Surprisingly, we also co‐enriched the Nar3 enzyme with Nar1 from the wild‐type strain of S. coelicolor. Two differentially migrating active Nar1 complexes could be identified after clear native polyacrylamide gel electrophoresis; these had masses of approximately 450 and 250 kDa. The distribution of active Nar1 in these complexes was influenced by the presence of cytochrome bd oxidase and by QcrB3; the presence of the latter shifted Nar1 into the larger complex. Together, these data suggest that several respiratory complexes can associate in the spore membrane, including Nar1, Nar3, and the bcc‐aa3 supercomplex. Moreover, these findings provide initial support for the hypothesis that Nar1 and the bcc‐aa3 supercomplex physically associate.

ASSESSMENT OF GENETIC STRUCTURE VARIABILITY OF RAINBOW TROUT Oncorhynchus mykiss (WALBAUM, 1792) OF UKRAINIAN LOCAL STOCKS USING POLYMORPHIC BLOOD PLASMA PROTEINS

Rainbow trout is a valuable species of aquaculture, which is characterized by a high level of variability. Aim. The goal was to study the peculiarities of genetic variability of rainbow trout based on polymorphism of transferrin (TF), posttransferrin (PTF), esterase (EST) (EC 3.1.1.1.) and albumin (ALB) loci. Methods. Electrophoretic separation of plasma proteins of rainbow trout from three local stocks (Chernivtsi, Kharkiv and Transcarpathian) was carried out in the native polyacrylamide gel. Results. Peculiarities of the distribution and relative electrophoretic mobility of allelic variants of the studied loci of rainbow trout of Ukrainian local stocks were established.The results demonstrated the effectiveness of the analysis using methods of biochemical genetics to establish the characteristics of the genetic structure, the level of heterozygosity of local stocks and to carry out their differentiation. Conclusion. The use of selected markers would allow monitoring the dynamics of changes in the state of local stocks under the established conditions of cultivation in the future. Key words: rainbow trout, polymorphic blood plasma proteins, transferrin, posttransferrin, esterase, albumin.

Serum protein complex profiling reveals heterogeneity of Balanced constitutional population in traditional Chinese medicine through blue native polyacrylamide gel electrophoresis.

Pulse-taking is widely used for diagnosis and treatment in traditional Chinese medicine (TCM), and protein complexes in serum perform various biological functions. The Balanced constitution is one of the major constitutions in TCM, people with Balanced constitution can also share some common characteristics with unbalanced constitution types. Blue native polyacrylamide gel electrophoresis (BN-PAGE) was applied to the serum of 25 people with balanced constitutions. The patterns of the protein complexes could be recognized according to the number, molecular weight, and intensity of the gel bands. All of the individual bands from these patterns were cut and in-gel-digested with trypsin, followed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis for protein identification and biological function analysis. The protein complex patterns were roughly categorized as type A and B with high stability and reproducibility, and there were 15 and 16 gel bands in type A and type B, respectively. Among the 25 serum samples, 14 belonged to type A, and 11 belonged to type B. High-abundance proteins significantly decreased from 99% to 44% after BN-PAGE separation. The unique proteins in type A were mainly related to lipid metabolism, while the unique proteins in type B were involved in biological processes related to immune response and inflammatory regulation. The Qi-deficiency constitution converted score of type A was higher than that of type B, while the Damp-heat constitution converted score of type A was lower than that of type B. Our study provided an objective reference for diagnosis and prognosis, which might lay a foundation for establishing the characteristic protein complex spectra of all of the TCM constitutions.

Mitoapocynin, a mitochondria targeted derivative of apocynin induces mitochondrial ROS generation and apoptosis in multiple cell types including cardiac myoblasts: a potential constraint to its therapeutic use.

Mitoapocynin is a triphenylphosphonium conjugated derivative of apocynin that specifically locates to the mitochondria. It has been developed as a mitochondrially targeted therapeutic antioxidant. We attempted to attenuate the mitochondrial ROS induced in H9c2 cardiac myoblast cells treated with norepinephrine. Mitoapocynin was a poor quencher of total ROS as detected by the fluoroprobe DCFH-DA. Using mitochondrial superoxide specific probe MitoSoxRed, we found that 5-10µM mitoapocynin itself induces superoxide over and above that is generated by the norepinephrine treatment. A supposedly control molecule to mitoapocynin, the synthetic compound PhC11TPP, having the triphenylphosphonium group and a benzene moiety with C11 aliphatic chain spacer was also found to be a robust inducer of mitochondrial ROS. Subsequent assays with several cell lines viz., NIH3T3, HEK293, Neuro2A, MCF-7 and H9c2, showed that prolonged exposure to mitoapocynin induces cell death by apoptosis that can be partially prevented by the general antioxidant N-acetyl cysteine. Analyses of mitochondrial electron transport complexes by Blue Native Polyacrylamide gel electrophoresis showed that both mitoapocynin and PhC11TPP disrupt the mitochondrial Complex I and V, and in addition, PhC11TPP also damages the Complex IV. Our data thus highlights the limitations of the therapeutic use of mitoapocynin as an antioxidant.

Characterization of Homogeneous and Heterogeneous Amyloid-β42 Oligomer Preparations with Biochemical Methods and Infrared Spectroscopy Reveals a Correlation between Infrared Spectrum and Oligomer Size.

Soluble oligomers of the amyloid-β(1-42) (Aβ42) peptide, widely considered to be among the relevant neurotoxic species involved in Alzheimer’s disease, were characterized with a combination of biochemical and biophysical methods. Homogeneous and stable Aβ42 oligomers were prepared by treating monomeric solutions of the peptide with detergents. The prepared oligomeric solutions were analyzed with blue native and sodium dodecyl sulfate polyacrylamide gel electrophoresis, as well as with infrared (IR) spectroscopy. The IR spectra indicated a well-defined β-sheet structure of the prepared oligomers. We also found a relationship between the size/molecular weight of the Aβ42 oligomers and their IR spectra: The position of the main amide I′ band of the peptide backbone correlated with oligomer size, with larger oligomers being associated with lower wavenumbers. This relationship explained the time-dependent band shift observed in time-resolved IR studies of Aβ42 aggregation in the absence of detergents, during which the oligomer size increased. In addition, the bandwidth of the main IR band in the amide I′ region was found to become narrower with time in our time-resolved aggregation experiments, indicating a more homogeneous absorption of the β-sheets of the oligomers after several hours of aggregation. This is predominantly due to the consumption of smaller oligomers in the aggregation process.

Carbon and Nitrogen Sources Have No Impact on the Organization and Composition of Ustilago maydis Respiratory Supercomplexes

Respiratory supercomplexes are found in mitochondria of eukaryotic cells and some bacteria. A hypothetical role of these supercomplexes is electron channeling, which in principle should increase the respiratory chain efficiency and ATP synthesis. In addition to the four classic respiratory complexes and the ATP synthase, U. maydis mitochondria contain three type II NADH dehydrogenases (NADH for reduced nicotinamide adenine dinucleotide) and the alternative oxidase. Changes in the composition of the respiratory supercomplexes due to energy requirements have been reported in certain organisms. In this study, we addressed the organization of the mitochondrial respiratory complexes in U. maydis under diverse energy conditions. Supercomplexes were obtained by solubilization of U. maydis mitochondria with digitonin and separated by blue native polyacrylamide gel electrophoresis (BN-PAGE). The molecular mass of supercomplexes and their probable stoichiometries were 1200 kDa (I1:IV1), 1400 kDa (I1:III2), 1600 kDa (I1:III2:IV1), and 1800 kDa (I1:III2:IV2). Concerning the ATP synthase, approximately half of the protein is present as a dimer and half as a monomer. The distribution of respiratory supercomplexes was the same in all growth conditions. We did not find evidence for the association of complex II and the alternative NADH dehydrogenases with other respiratory complexes.

Substitution of Deoxycholate with the Amphiphilic Polymer Amphipol A8-35 Improves the Stability of Large Protein Complexes during Native Electrophoresis.

Native polyacrylamide gel electrophoresis (PAGE) is a powerful technique for protein complex separation that retains both their activity and structure. In photosynthetic research, native-PAGE is particularly useful given that photosynthetic complexes are generally large in size, ranging from 200 kD to 1 MD or more. Recently, it has been reported that the addition of amphipol A8-35 to solubilized protein samples improved protein complex stability. In a previous study, we found that amphipol A8-35 could substitute sodium deoxycholate (DOC), a conventional electrophoretic carrier, in clear-native (CN)-PAGE. In this study, we present the optimization of amphipol-based CN-PAGE. We found that the ratio of amphipol A8-35 to α-dodecyl maltoside, a detergent commonly used to solubilize photosynthetic complexes, was critical for resolving photosynthetic machinery in CN-PAGE. In addition, LHCII dissociation from PSII-LHCII was effectively prevented by amphipol-based CN-PAGE compared with that of DOC-based CN-PAGE. Our data strongly suggest that majority of the PSII-LHCII in vivo forms C2S2M2 at least in Arabidopsis and Physcomitrella. The other forms might appear owing to the dissociation of LHCII from PSII during sample preparation and electrophoresis, which could be prevented by the addition of amphipol A8-35 after solubilization from thylakoid membranes. These results suggest that amphipol-based CN-PAGE may be a better alternative to DOC-based CN-PAGE for the study of labile protein complexes.

Lanthanum: A novel inducer for enhancement of fungal laccase production by Shiraia bambusicola

Fungal laccases are industrially important inducible enzymes extensively used in the delignification of lignocellulosics, detoxification of environmental wastes and decolorization of textile dyes. The discovery of new inducers is crucial for laccase productivity by filamentous fungi. In this study, a novel laccase-producing strain S8 from a bambusicolous fungus Shiraia bambusicola was identified by using 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) as laccase secretion indicator and native polyacrylamide gel electrophoresis. The corresponding full-length cDNA of laccase was cloned and characterized. The effect of lanthanum (LaCl3) on extracellular laccase activity was tested at the concentration from 0.2 to 2.0 g/L and at different addition time (day 1–4) in the mycelium culture. In the presence of 1.0 g/L La3+ at the beginning of the mycelium cultures, the highest laccase activity (2.7 × 104 U/L) is reached after 10 days of cultivation, about tenfold higher compared with non-induced cultures. La3+ is shown to be a very strong inducer for fungal laccase activity with no inhibitory effect on fungal growth at the optimized concentration. In vivo, La3+ added to the mycelium culture not only promotes a continuous and high expression of laccase gene (lcc1), but also induces a rapid generation of signaling molecules including reactive oxygen species (ROS) and nitric oxygen (NO). Both the NO donor sodium nitroprusside (SNP) and exogenous hydrogen peroxide (H2O2) potentiate La3+-induced laccase activity and increase membrane permeability of hyphal cells. Moreover, the scavengers such as 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) for NO and vitamin C for ROS suppress the induction. These results suggest that these signals can mediate La3+-induced laccase biosynthesis and its secretion. Our study provides a basis for understanding the induction mechanism of La3+ on laccase and a practical strategy for enhanced fungal laccase production.

Solubilization and Stabilization of Native Membrane Proteins for Drug Discovery.

Membrane proteins (MPs) are stable in their native lipid environment. To enable structural and functional investigations, MPs need to be extracted from the membrane. This is a critical step that represents the main obstacle for MP biochemistry and structural biology. Here we describe detergent solubilization screening of MPs using dot-blot and Western-blot analyses. Good solubilization conditions are ranked for their best capacity to stabilize MPs using thermal shift assay. The protein functionality is evaluated by radioligand binding (for G-protein-coupled receptor) and ATPase activity (ABC Transporter) and finally the aggregation status as well as protein homogeneity are assessed by Native-polyacrylamide gel, chemical cross-linking, and size exclusion chromatography.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures.

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

Abstract 16602: Mitolamban is a Novel Cardiac-Enriched Mitochondrial Microprotein That Regulates Respiratory Complex III

Introduction: Emerging evidence suggests that many RNA molecules currently annotated as noncoding contain short open reading frames that code for functional small proteins called microproteins. Microproteins play critical roles in a diverse range of essential biological processes. To identify novel cardiac-expressed microproteins, we used a comparative genomics approach and identified mitolamban (Mtlbn) as a highly conserved 47-amino acid transmembrane protein that is abundantly expressed in the heart. Methods and Results: Subcellular localization studies showed that Mtlbn localized specifically to the inner mitochondrial membrane. Immunoprecipitations and mass spectrometry analysis indicated that Mtlbn interacted with subunits of complex III of the electron transport chain (ETC) and we observed the presence of Mtlbn in complex III respiratory supercomplexes (SCs) by blue native polyacrylamide gel electrophoresis (BN-PAGE). Cardiac-specific Mtlbn overexpressing transgenic (TG) mice and Mtlbn gene-deleted (knockout, KO) mice were generated to dissect the molecular function of this protein in the heart. Mtlbn TG mice developed cardiomyopathy and died prematurely with histological, biochemical and ultrastructural pathologic features. Metabolomic analysis indicated that hearts from TG mice had signs of increased oxidative stress and mitochondrial dysfunction. While Mtlbn KO mice had normal cardiac function and histological appearance, BN-PAGE analysis of purified mitochondria from KO hearts showed altered complex III composition. Functional assessment of purified heart mitochondria from Mtlbn KO mice revealed a reduction in complex III activity and metabolomic analysis of KO heart tissue indicated an altered metabolite profile consistent with deficiencies in complex III activity. Conclusions: Mtlbn is a novel heart-enriched microprotein that localizes to the inner mitochondrial membrane where it interacts with complex III of the ETC. Our data indicate that Mtlbn serves as a critical regulator of mitochondrial ETC activity through a direct role in affecting complex III function.

Study of Blood Cells and Serum Proteins of Three Different Varieties of Fowls

Background: In the present study attempts have been made to study the blood cells and serum proteins comparatively among three different varieties of fowls, namely Turkey, RIR and Kadaknath. Total RBC and WBC count and serum protein analysis were performed. Methods: The total RBC and WBC were counted with the help of Neubauer’s Haemocytometer. The serum proteins were separated and analysed by native polyacrylamide gel electrophoresis (PAGE). Result: The results showed that, among all the fowl varieties tested, the RBC counts were ranged from 3.01 to 4.46 millions/mm3 and the WBC counts were ranged from 18.26 to 21.78 thousands/mm3. The serum protein analysis revealed that some proteins are present in specific species and specific sex. Hence, these proteins may be counted as markers to determine the species and sex of the species.

유산소운동이 당뇨쥐 해마의 신경세포 LDH 동위효소, MCT2 및 GLUT3 단백질 발현에 미치는 영향

In the present study, the effects of aerobic exercise on expression of Lactate dehydrogenase (LDH) isozymes, Monocarboxylate transporter2 (MCT2) and Glucose transporter3 (GLUT3) in hippocampal neuron of Streptozotocin (STZ)-induced diabetic rats. The experimental animals were divided into three groups (n=10 in each group): the normal control group (CON), the diabetes mellitus group (DM), the diabetes and exercise group(DM-Ex). Animals in the exercise group were submitted to daily exercise in the water pool during 4weeks. Native polyacrylamide gel electrophoresis analysis for the purification of LDH isozyme was performed. Western blotting and immunohistochemistry analysis for the expression of MCT2 and GLUT3 was performed. Here in this study, LDH A4 and LDH A3B in DM were predominantly expressed compared to DM-Ex (p<.05), and LDH AB3 and LDH B4 in DM-Ex were predominantly expressed compared to DM (p<.05). MCT2 activity of DM and DM-Ex were significantly lower than that of CON (p<.05). MCT2 activity of DM-Ex was significantly higher than that of DM (p<.05). GLUT3 activity of DM and DM-Ex were significantly lower than that of CON (p<.05). GLUT3 activity of DM-Ex was significantly higher than that of DM (p<.05). The results of the present study indicate that aerobic exercise affects the production of ATP using lactic acid and the activity of neurons by adapting to the energy metabolic demands of diabetes in the hippocampal neurons.

Simple isolation for two forms of malic enzyme from crustacean abdomen muscle

Abstract Two forms of NADP-dependent malic enzyme (ME, EC 1.1.1.40) were purified from the abdomen muscle of the crayfish Orconectes limosus (Rafinesque, 1817) and the shrimp Crangon crangon L., 1758 by affinity chromatography on 2′,5′-ADP-Sepharose 4B, with good qualitative recovery in a single step, using a substrate activation method with a malate–manganese chloride pair. The enzymes were identified by native polyacrylamide gel electrophoresis stained for protein and enzyme activity. The faster migrating mitochondrial enzyme from crayfish is inhibited by sulfhydryl reagent and loses its activity. Ellman’s Reagent, 5,5′-Dithiobis-(2-nitrobenzoic acid) (DTNB), can be used for the differentiation and measurement of cytoplasmic and mitochondrial malic enzyme in decapod crustacean tissue.

The effective transfection of a low dose of negatively charged drug-loaded DNA-nanocarriers into cancer cells via scavenger receptors

DNA-nanotechnology-based nano-architecture scaffolds based on circular strands were designed in the form of DNA-nanowires (DNA-NWs) as a polymer of DNA-triangles. Circularizing a scaffold strand (84-NT) was the critical step followed by annealing with various staple strands to make stiff DNA-triangles. Atomic force microcopy (AFM), native polyacrylamide gel electrophoresis (PAGE), UV-analysis, MTT-assay, flow cytometry, and confocal imaging were performed to assess the formulated DNA-NWs and cisplatin (CPT) loading. The AFM and confocal microscopy images revealed a uniform shape and size distribution of the DNA-NWs, with lengths ranging from 2 to 4 μm and diameters ranging from 150 to 300 nm. One sharp band at the top of the lane (500 bp level) with the loss of electrophoretic mobility during the PAGE (native) gel analysis revealed the successful fabrication of DNA-NWs. The loading efficiency of CPT ranged from 66.85% to 97.35%. MTT and flow cytometry results showed biocompatibility of the blank DNA-NWs even at 95% concentration compared with the CPT-loaded DNA-NWs. The CPT-loaded DNA-NWs exhibited enhanced apoptosis (22%) compared to the apoptosis (7%) induced by the blank DNA-NWs. The release of CPT from the DNA-NWs was sustained at < 75% for 6 h in the presence of serum, demonstrating suitability for systemic applications. The IC50 of CPT@DNA-NWs was reduced to 12.8 nM CPT, as compared with the free CPT solution exhibiting an IC50 of 51.2 nM. Confocal imaging revealed the targetability, surface binding, and slow internalization of the DNA-NWs in the scavenger-receptor-rich cancer cell line (HepG2) compared with the control cell line.

Molecular basis of the interaction of Hsp90 with its co-chaperone Hop.

The heat shock protein (Hsp) Hsp90 is one of the most abundant proteins in the cell. It controls the functional turnover of proteins being involved in protein folding, refolding, transport as well as protein degradation. Co‐chaperones influence Hsp90's activity in different ways, among which the Hsp organizing protein (Hop) was found to inhibit its ATP hydrolysis upon binding. Despite the availability of a number of studies investigating the Hsp90:Hop complex, several aspects of the Hsp90:Hop interaction have remained unresolved. Here, we employed a combinatory approach comprising native polyacrylamide gel electrophoresis, isothermal titration calorimetry, multiangle light scattering, isothermal titration calorimetry, small‐angle X‐ray scattering, dynamic light scattering, and nuclear magnetic resonance, spectroscopy to obtain a comprehensive picture about the human Hsp90β:Hop association in solution. Our data show that only one Hop molecule binds the Hsp90β dimer, Hop can interact with the open and closed state of Hsp90β, and Hop's TPR2A‐2B domains determine the affinity for Hsp90's C‐terminal and middle domain, whereby the interaction with the C‐terminal domain of Hsp90β is sufficient to induce an allosteric conformational change between the two Hsp90β monomers in the Hsp902:Hop1 complex. Together, this study highlights the important role of the co‐chaperone Hop in reorganizing Hsp90 for efficient client loading.

The Important Roles Played in Substrate Binding of Aromatic Amino Acids in Exo-Inulinase From Kluyveromyces cicerisporus CBS 4857.

Inulinase is a member of the glycoside hydrolase family 32 (GH32). It catalyzes the randomly hydrolyzation of 2,1-β-D-fructosidic linkages in inulin and plays a role in the production of high-fructose syrup. In this study, detailed roles of the conserved residues W79, F113, M117, R181, C239, and W334 of the exo-inulinase from Kluyveromyces cicerisporus CBS4857 (KcINU1) in substrate binding and stabilization were evaluated by in silico analysis and site-directed mutagenesis. These residues belong to the conserved WG, FSGSMV, RDP, ECP, and WQY regions of the GH32 and are located around the catalytic pocket of KcINU1. Zymogram assay showed relatively weaker band for F113W and similar band for M117A compared to the wild-type enzyme toward inulin and sucrose, whereas all other variants showed no observable stain on the native polyacrylamide gel electrophoresis. These results were further confirmed with the dinitrosalicylic acid colorimetric method. It showed that the residual activities of F113W toward inulin and sucrose were 33.8 ± 3.3% and 96.2 ± 5.5%, respectively, and that of M117A were 103.8 ± 1.3% and 166.5 ± 12%, respectively. Results from fluorescence spectra indicated that there is a significant conformational change that happened in F113W compared to the wild-type enzyme, while M117A exhibited limited impact although the quenching effect was increased.

Identification of the natural product berberine as an antiviral drug

Drugs targeting the fusion process of viral entry into host cells have been approved for clinical use in the treatment of AIDS. There remains a great need to improve the use of existing drugs for HIV therapy. Berberine is traditionally used to treat diarrhea, bacillary dysentery, and gastroenteritis in clinics, here our research shows that berberine is effective in inhibiting HIV-1 entry. Native polyacrylamide gel electrophoresis studies reveal that berberine can directly bind to both N36 and C34 to form a novel N36-berberine-C34 complex and effectively block the six-helix bundle formation between the N-terminal heptad repeat peptide N36 and the C-terminal heptad repeat peptide C34. Circular dichroism experiments show that binding of berberine produces conformational changes that damages the secondary structures of 6-HB. Computer-aided molecular docking studies suggest a hydrogen bond with T-639 and two polar bonds with Q-563 and T-639 are established, involving the oxygen atom and the C=O group of the indole ring. Berberine completely inhibits six HIV-1 clade B isolates and exhibits antiviral activities in a concentration-dependent manner with IC50 values varying from 5.5 to 10.25 µg/ml. This compound-peptide interaction may represent a mechanism of action of antiviral activities of berberine. As a summary, these studies successfully identify compound berberine as a potential candidate drug for HIV-1 treatment. As a summary, antiviral activity of berberine in combination with its use in clinical practice, this medicine can be used as a potential clinically anti-HIV drug.